./CBFlib-0.9.2.2/ 0000755 0000765 0000765 00000000000 11603751102 011576 5 ustar yaya yaya ./CBFlib-0.9.2.2/m4/ 0000755 0000765 0000765 00000000000 11603703065 012123 5 ustar yaya yaya ./CBFlib-0.9.2.2/m4/fcb_exit_binary.m4 0000644 0000765 0000765 00000004762 11603702103 015515 0 ustar yaya yaya m4_include(`fcblib_defines.m4')m4_dnl
` INTEGER FUNCTION FCB_EXIT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
PADDING )
!-----------------------------------------------------------------------
! Skip to end of binary section that was just read
!-----------------------------------------------------------------------
IMPLICIT NONE
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER(FCB_BYTES_IN_REC)
INTEGER(8),INTENT(IN) :: PADDING
!External functions called'
fcb_interface_FCB_READ_BYTE
fcb_interface_FCB_READ_LINE
fcb_interface_FCB_CI_STRNCMPARR
`!-----------------------------------------------------------------------
INTEGER,PARAMETER :: LINESIZE=2048
INTEGER(1) LINE(LINESIZE) ! BUFFER FOR THE NEXT LINE
INTEGER LINELEN ! VALID CHARACTERS IN LINE
INTEGER ITEM ! 1 FOR MIME ITEM FOUND, 0 OTHERWISE
INTEGER QUOTE
INTEGER TEXT_BITS
INTEGER COUNT
INTEGER BOUND_FOUND
CHARACTER*31 BOUNDARY
DATA BOUNDARY/"--CIF-BINARY-FORMAT-SECTION----"/
!-----------------------------------------------------------------------
! -- Skip the trailing pad
BYTE_IN_FILE = BYTE_IN_FILE+PADDING
! -- Skip to MIME boundary
BOUND_FOUND = 0
DO
FCB_EXIT_BINARY = &
FCB_READ_LINE(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER,LINE,LINESIZE,LINELEN)
IF(FCB_EXIT_BINARY.NE.0 ) RETURN
! *** DEBUG *** PRINT *," LINELEN, LINE: ", LINELEN, LINE(1:LINELEN)
IF (BOUND_FOUND .EQ. 0) THEN
IF (FCB_CI_STRNCMPARR(BOUNDARY,LINE,LINELEN,31).EQ.0) THEN
BOUND_FOUND = 1
! *** DEBUG *** PRINT *, &
! "MIME BOUNDARY --CIF-BINARY-FORMAT-SECTION---- FOUND"
END IF
END IF
IF (LINE(1).EQ.IACHAR(''`;''`)) THEN
IF (LINELEN.EQ.1.OR.LINE(2).EQ.32.OR.LINE(2).EQ.9) THEN
IF (BOUND_FOUND.EQ.0) THEN
PRINT *, " END OF TEXT FOUND BEFORE MIME BOUNDARY"
ELSE
EXIT
END IF
END IF
END IF
END DO
FCB_EXIT_BINARY = 0
RETURN
END FUNCTION FCB_EXIT_BINARY'
./CBFlib-0.9.2.2/m4/fcb_open_cifin.m4 0000644 0000765 0000765 00000003114 11603702103 015277 0 ustar yaya yaya m4_include(`fcblib_defines.m4')m4_dnl
` INTEGER FUNCTION FCB_OPEN_CIFIN(FILNAM,TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER)
!-----------------------------------------------------------------------
! FILNAM - Name of the file countaining the image (GIVEN)
! TAPIN - Fortran device unit number assigned to image file (GIVEN)
! LAST_CHAR -
! Last character read (RESULT)
! FCB_BYTES_IN_REC -
! Number of bytes in a record (GIVEN)
! BYTE_IN_FILE -
! Byte (counting from 1) of the byte to read (RESULT)
! REC_IN_FILE -
! Record (counting from 1) of next record to read (RESULT)
! BUFFER - Array of length FCB_BYTES_IN_REC (GIVEN)
!-----------------------------------------------------------------------
IMPLICIT NONE
CHARACTER(len=*),INTENT(IN) :: FILNAM
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER(1), INTENT(OUT):: LAST_CHAR
INTEGER, INTENT(OUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1), INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER FCB_RECORD_SIZE
'
fcb_errcode_CBF_FORMAT
fcb_errcode_CBF_FILEOPEN
fcb_errcode_CBF_FILEREAD
fcb_interface_FCB_CI_STRNCMPARR
fcb_macro_FCB_OPEN_CIFIN(`IOSTAT=FCB_OPEN_CIFIN',
`IOSTAT=FCB_OPEN_CIFIN',
`THEN
FCB_OPEN_CIFIN = CBF_FILEREAD
ENDIF')`
RETURN
END FUNCTION FCB_OPEN_CIFIN'
./CBFlib-0.9.2.2/m4/setup_py.m4 0000644 0000765 0000765 00000001175 11603702103 014231 0 ustar yaya yaya #
# pycbf/setup.py generated from m4/setup_py.m4
#
`# Import the things to build python binary extensions
from distutils.core import setup, Extension
# Make our extension module
e = Extension(''`_pycbf''`,
sources = ["pycbf_wrap.c","../src/cbf_simple.c"],
extra_compile_args=["-g"],
'm4_ifelse(regexlibdir,`NOREGEXLIBDIR',`library_dirs=["../lib/"],',`library_dirs=["../lib/","'regexlibdir`"],')`
'm4_ifelse(regexlib,`NOREGEXLIB',`libraries=["cbf"],',`libraries=["cbf","'regexlib`"],')`
include_dirs = ["../include"] )
# Build it
setup(name="_pycbf",ext_modules=[e],)'
./CBFlib-0.9.2.2/m4/fcb_next_binary.m4 0000644 0000765 0000765 00000057236 11603702103 015526 0 ustar yaya yaya m4_include(`fcblib_defines.m4')m4_dnl
` INTEGER FUNCTION FCB_NEXT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
ENCODING,SIZE,ID,DIGEST, &
COMPRESSION,BITS,VORZEICHEN,REELL,&
BYTEORDER,DIMOVER,DIM1,DIM2,DIM3, &
PADDING )
!-----------------------------------------------------------------------
! Skip to the next binary and parse MIME header.
!-----------------------------------------------------------------------
IMPLICIT NONE
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER(FCB_BYTES_IN_REC)
INTEGER, INTENT(OUT) :: ENCODING
INTEGER, INTENT(OUT) :: SIZE !Binary size
INTEGER, INTENT(OUT) :: ID !Binary ID
CHARACTER(len=*),INTENT(OUT):: DIGEST !Message digest
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER, INTENT(OUT):: BITS,VORZEICHEN,REELL
CHARACTER(len=*),INTENT(OUT):: BYTEORDER
! Possible parameter values for BYTEORDER are:
! "LITTLE_ENDIAN" supported
! "BIG_ENDIAN" not supported
INTEGER(8), INTENT(OUT):: DIMOVER
INTEGER(8), INTENT(OUT):: DIM1
INTEGER(8), INTENT(OUT):: DIM2
INTEGER(8), INTENT(OUT):: DIM3
INTEGER(8), INTENT(OUT):: PADDING
'
fcb_param_ENC_LIST_ALL
fcb_param_CBF_LIST_ALL
`
!External functions called'
fcb_interface_FCB_SKIP_WHITESPACE
fcb_interface_FCB_CI_STRNCMPARR
fcb_interface_FCB_NBLEN_ARRAY
fcb_interface_FCB_READ_LINE
fcb_interface_FCB_ATOL_WCNT
`!-----------------------------------------------------------------------
' fcb_errcode_CBF_FORMAT
`
INTEGER,PARAMETER :: LINESIZE=2048
INTEGER CONTINUATION
INTEGER(1) LINE(LINESIZE) ! BUFFER FOR THE NEXT LINE
INTEGER LINELEN ! VALID CHARACTERS IN LINE
INTEGER IC ! CHARACTER WITHIN LINE
INTEGER STATE ! SELECTION FROM VALUE (0, ...)
INTEGER ITEM ! 1 FOR MIME ITEM FOUND, 0 OTHERWISE
INTEGER LINE_COUNT ! NUMBER OF LINES INTO HEADER
INTEGER FRESH_LINE
INTEGER QUOTE
INTEGER TEXT_BITS
INTEGER COUNT
INTEGER FAILURE
INTEGER I,INTEXT,J
INTEGER VALUELEN(12)
CHARACTER*29 BOUNDARY
CHARACTER*32 VALUE(12)
DATA BOUNDARY/"--CIF-BINARY-FORMAT-SECTION--"/
DATA VALUE/ &
"Content-Type:", & ! /* State 0 */
"Content-Transfer-Encoding:", & ! /* State 1 */
"Content-MD5:", & ! /* State 2 */
"X-Binary-Size:", & ! /* State 3 */
"X-Binary-ID:", & ! /* State 4 */
"X-Binary-Element-Type:", & ! /* State 5 */
"X-Binary-Element-Byte-Order:", & ! /* State 6 */
"X-Binary-Size-Fastest-Dimension:", & ! /* State 7 */
"X-Binary-Size-Second-Dimension:", & ! /* State 8 */
"X-Binary-Size-Third-Dimension:", & ! /* State 9 */
"X-Binary-Size-Padding:", & ! /* State 10 */
"X-Binary-Number-of-Elements:" & ! /* State 11 */
/
!-----------------------------------------------------------------------
DO I = 1,12
VALUELEN(I)=LEN(TRIM(VALUE(I)))
END DO
FAILURE = 0
! -- Repeat : Skip lines until the start of a text field is reached and
! -- then loop until a mime boundary or end of the text field is reached
INTEXT=0
DO
IF (FCB_READ_LINE(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,BYTE_IN_FILE,&
REC_IN_FILE,BUFFER,LINE,LINESIZE,LINELEN).NE.0 ) THEN
FCB_NEXT_BINARY=1
RETURN
END IF
! *** DEBUG *** PRINT *," LINELEN, LINE: ", LINELEN, LINE(1:LINELEN)
IF (LINELEN.GT.0)THEN
IF (INTEXT.EQ.0)THEN
IF (LINE(1).EQ.IACHAR(''`;''`))INTEXT=1 !start of a text field
! *** DEBUG *** PRINT *, "FOUND START OF TEXT FIELD"
ELSE
IF (LINE(1).EQ.IACHAR(''`;''`))THEN
IF (LINELEN.EQ.1.OR.LINE(2).EQ.32.OR.LINE(2).EQ.9) &
INTEXT=0 !end of the text field is reached
ENDIF
IF (FCB_CI_STRNCMPARR(BOUNDARY,LINE,LINELEN,29).EQ.0)EXIT
ENDIF
ENDIF
ENDDO
! *** DEBUG *** PRINT *, "MIME BOUNDARY --CIF-BINARY-FORMAT-SECTION-- FOUND"
!-----------------------------------------------------------------------
STATE = -1
LINE_COUNT = 0
FRESH_LINE = 0
ENCODING = 0
SIZE = 0
ID = 0
DIGEST = ""
COMPRESSION = CBF_NONE
BITS = 0
VORZEICHEN = -1
REELL = -1
BYTEORDER="LITTLE_ENDIAN"
DIMOVER = 0
DIM1 = 0
DIM2 = 0
DIM3 = 0
PADDING = 0
DO
IF (FRESH_LINE.EQ.0) THEN
IF (FCB_READ_LINE(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC, &
BYTE_IN_FILE,REC_IN_FILE,BUFFER,LINE,LINESIZE,LINELEN).NE.0)&
THEN
FCB_NEXT_BINARY=1
RETURN
ENDIF
IF (LINELEN.GT.0 .AND. LINE(1).EQ.IACHAR(''`;''`) .AND. &
(LINELEN.EQ.1 .OR. LINE(2).EQ.IACHAR(''` ''`) .OR. &
LINE(2).EQ.Z''`09''`) ) GO TO 100
IF (FCB_CI_STRNCMPARR(BOUNDARY,LINE,LINELEN,29).EQ.0) &
GO TO 100
END IF
FRESH_LINE = 0
LINE_COUNT = LINE_COUNT+1
CONTINUATION = 0
IF (LINELEN.GT.0.AND. &
(LINE(1).EQ.IACHAR(''` ''`).OR.LINE(1).EQ.Z''`09''`))CONTINUATION=1
ITEM = 0
IF (CONTINUATION .EQ. 0 ) THEN
DO IC = 1, LINELEN
IF ((LINE(IC).EQ.IACHAR(''`:''`)).AND.(IC.GT.1))ITEM=1
IF ((ITEM.NE.0).OR.(LINE(IC).LE.32.OR.LINE(IC).GE.127)) EXIT
END DO
END IF
! Check for the end of the header
IF (LINE_COUNT.GT.1.AND.FCB_NBLEN_ARRAY(LINE,LINELEN).EQ.0) THEN
FCB_NEXT_BINARY = 0
RETURN
END IF
! Check for valid header-ness of line
IF (ITEM.EQ.0.AND.(LINE_COUNT.EQ.1.OR.CONTINUATION.EQ.0)) GO TO 110
! Look for the entries we are interested in
IC = 1
IF (ITEM.NE.0) THEN
DO STATE = 11,0,-1
J=STATE+1
I=VALUELEN(J)
IF (FCB_CI_STRNCMPARR(VALUE(J)(1:I),LINE,LINELEN,I).EQ.0)THEN
IC = I+1
EXIT
END IF
END DO
END IF
! Skip past comments and whitespace
IF (FCB_SKIP_WHITESPACE(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC, &
BYTE_IN_FILE,REC_IN_FILE,BUFFER,LINE,LINESIZE,LINELEN,IC, &
FRESH_LINE).NE.0) GO TO 100
SELECT CASE (STATE) ! Get the value
CASE (0) !"Content-Type:"
I=LINELEN-IC+1
IF (FCB_CI_STRNCMPARR("application/",LINE(IC:LINELEN),I,12).NE.0.AND.&
FCB_CI_STRNCMPARR("image/", LINE(IC:LINELEN),I, 6).NE.0.AND.&
FCB_CI_STRNCMPARR("text/", LINE(IC:LINELEN),I, 5).NE.0.AND.&
FCB_CI_STRNCMPARR("audio/", LINE(IC:LINELEN),I, 6).NE.0.AND.&
FCB_CI_STRNCMPARR("video/", LINE(IC:LINELEN),I, 6).NE.0) &
GO TO 110
DO
IF (IC.GT.LINELEN)EXIT
! Skip to the end of the section (a semicolon)
DO
IF (IC.GT.LINELEN)EXIT
IF (LINE(IC).EQ.Z''`22''`) THEN ! double quote
IC = IC+1
DO
IF (IC.GT.LINELEN)EXIT
IF (LINE(IC).EQ.Z''`22''`) THEN !double quote
IC = IC+1
EXIT
ELSE
IF (LINE(IC).EQ.Z''`5C''`) THEN !backslash
IC = IC+1
END IF
IF (IC .LE. LINELEN) IC = IC+1
END IF
END DO
ELSE
IF (LINE(IC).EQ.IACHAR(''`(''`)) THEN
FCB_NEXT_BINARY = FCB_SKIP_WHITESPACE(TAPIN, &
LAST_CHAR,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER,LINE,LINESIZE,LINELEN,IC, &
FRESH_LINE)
IF (FCB_NEXT_BINARY.NE.0) RETURN
ELSE
IF (LINE(IC).EQ.IACHAR(''`;''`)) THEN
IC = IC+1
EXIT
ELSE
IC = IC+1
END IF
END IF
END IF
END DO
FCB_NEXT_BINARY = FCB_SKIP_WHITESPACE(TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
LINE,LINESIZE,LINELEN,IC,FRESH_LINE)
IF (FCB_NEXT_BINARY.NE.0) RETURN
IF (FCB_CI_STRNCMPARR("conversions", &
LINE(IC:LINELEN), LINELEN-IC+1, 11) .EQ.0 ) THEN
IC = IC+11
FCB_NEXT_BINARY = FCB_SKIP_WHITESPACE(TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
LINE,LINESIZE,LINELEN,IC,FRESH_LINE)
IF (FCB_NEXT_BINARY.NE.0) RETURN
IF (LINE(IC).EQ.IACHAR(''`=''`)) THEN
IC = IC+1
FCB_NEXT_BINARY = FCB_SKIP_WHITESPACE(TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
LINE,LINESIZE,LINELEN,IC,FRESH_LINE)
IF (FCB_NEXT_BINARY.NE.0) RETURN
QUOTE = 0
IF (LINE(IC).EQ.Z''`22''`) QUOTE=1 ! double quote
COMPRESSION = CBF_NONE
IF (FCB_CI_STRNCMPARR("x-CBF_PACKED", &
LINE(IC+QUOTE:LINELEN),LINELEN-IC-QUOTE+1,12).EQ.0) &
COMPRESSION=CBF_PACKED
IF (FCB_CI_STRNCMPARR("x-CBF_PACKED_V2", &
LINE(IC+QUOTE:LINELEN),LINELEN-IC-QUOTE+1,15).EQ.0) &
COMPRESSION=CBF_PACKED_V2
IF (FCB_CI_STRNCMPARR("x-CBF_CANONICAL", &
LINE(IC+QUOTE:LINELEN),LINELEN-IC-QUOTE+1,15).EQ.0) &
COMPRESSION=CBF_CANONICAL
IF (FCB_CI_STRNCMPARR("x-cbf_byte_offset", &
LINE(IC+QUOTE:LINELEN),LINELEN-IC-QUOTE+1,17).EQ.0) &
COMPRESSION=CBF_BYTE_OFFSET
IF (FCB_CI_STRNCMPARR("x-cbf_predictor", &
LINE(IC+QUOTE:LINELEN),LINELEN-IC-QUOTE+1,15).EQ.0) &
COMPRESSION=CBF_PREDICTOR
IF ( (COMPRESSION .EQ. CBF_PACKED) .OR. &
(COMPRESSION .EQ. CBF_PACKED_V2) ) THEN
DO
IF (IC.GT.LINELEN)EXIT
! Skip to the end of the section (a semicolon)
DO
IF (IC.GT.LINELEN)EXIT
IF (LINE(IC).EQ.Z''`22''`) THEN ! double quote
IC = IC+1
DO
IF (IC.GT.LINELEN)EXIT
IF (LINE(IC).EQ.Z''`22''`) THEN !double quote
IC = IC+1
EXIT
ELSE
IF (LINE(IC).EQ.Z''`5C''`) THEN !backslash
IC = IC+1
END IF
IF (IC .LE. LINELEN) IC = IC+1
END IF
END DO
ELSE
IF (LINE(IC).EQ.IACHAR(''`(''`)) THEN
FCB_NEXT_BINARY = FCB_SKIP_WHITESPACE(TAPIN, &
LAST_CHAR,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER,LINE,LINESIZE,LINELEN,IC, &
FRESH_LINE)
IF (FCB_NEXT_BINARY.NE.0) RETURN
ELSE
IF (LINE(IC).EQ.IACHAR(''`;''`)) THEN
IC = IC+1
EXIT
ELSE
IC = IC+1
END IF
END IF
END IF
FCB_NEXT_BINARY = FCB_SKIP_WHITESPACE(TAPIN, &
LAST_CHAR,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER,LINE,LINESIZE,LINELEN,IC, &
FRESH_LINE)
IF (FCB_NEXT_BINARY.NE.0) RETURN
QUOTE = 0
IF (LINE(IC).EQ.Z''`22''`) QUOTE=1 ! double quote
IF (FCB_CI_STRNCMPARR("uncorrelated_sections", &
LINE(IC+QUOTE:LINELEN),LINELEN-IC-QUOTE+1,21).EQ.0) &
COMPRESSION = IOR(COMPRESSION,CBF_UNCORRELATED_SECTIONS)
IF (FCB_CI_STRNCMPARR("flat", &
LINE(IC+QUOTE:LINELEN),LINELEN-IC-QUOTE+1,4).EQ.0) &
COMPRESSION = IOR(COMPRESSION,CBF_FLAT_IMAGE)
END DO
END DO
END IF
END IF
END IF
END DO
STATE = -1
! *** DEBUG *** PRINT *, "COMPRESSION: ", COMPRESSION
CASE (1) ! Binary encoding
FAILURE = 1
QUOTE = 0;
IF (LINE(IC) .EQ. Z''`22''`) QUOTE = 1 !double quote
IF (FCB_CI_STRNCMPARR("Quoted-Printable", &
LINE(IC+QUOTE:LINELEN), LINELEN-IC-QUOTE+1, 16) .EQ. 0)THEN
IF (IC+16.EQ.LINELEN+1 .OR. &
FCB_NBLEN_ARRAY(LINE(IC+16),1).EQ.0 .OR. &
LINE(IC+16).EQ.IACHAR(''`(''`).OR. &
(QUOTE.EQ.1.AND.LINE(IC+16).EQ.Z''`22''`)) THEN !double quote
FAILURE = 0
ENCODING = ENC_QP
END IF
END IF
IF (FCB_CI_STRNCMPARR("Base64", &
LINE(IC+QUOTE:LINELEN), LINELEN-IC-QUOTE+1, 6) .EQ. 0)THEN
IF (IC+6.EQ.LINELEN+1 .OR. &
FCB_NBLEN_ARRAY(LINE(IC+6),1).EQ.0 .OR. &
LINE(IC+6).EQ.IACHAR(''`(''`).OR. &
(QUOTE.EQ.1.AND.LINE(IC+6).EQ.Z''`22''`)) THEN ! double quote
FAILURE = 0
ENCODING = ENC_BASE64
END IF
END IF
IF (FCB_CI_STRNCMPARR("X-Base32k", &
LINE(IC+QUOTE:LINELEN), LINELEN-IC-QUOTE+1, 9) .EQ. 0)THEN
IF (IC+9.EQ.LINELEN+1 .OR. &
FCB_NBLEN_ARRAY(LINE(IC+9),1).EQ.0 .OR. &
LINE(IC+9).EQ.IACHAR(''`(''`).OR. &
(QUOTE.EQ.1.AND.LINE(IC+9).EQ.Z''`22''`)) THEN ! double quote
FAILURE = 0
ENCODING = ENC_BASE32K
END IF
END IF
IF (FCB_CI_STRNCMPARR("X-Base8", &
LINE(IC+QUOTE:LINELEN), LINELEN-IC-QUOTE+1, 7) .EQ. 0)THEN
IF (IC+7.EQ.LINELEN+1 .OR. &
FCB_NBLEN_ARRAY(LINE(IC+7),1).EQ.0 .OR. &
LINE(IC+7).EQ.IACHAR(''`(''`).OR. &
(QUOTE.EQ.1.AND.LINE(IC+7).EQ.Z''`22''`)) THEN ! double quote
FAILURE = 0
ENCODING = ENC_BASE8
END IF
END IF
IF (FCB_CI_STRNCMPARR("X-Base10", &
LINE(IC+QUOTE:LINELEN), LINELEN-IC-QUOTE+1, 8) .EQ. 0)THEN
IF (IC+8.EQ.LINELEN+1 .OR. &
FCB_NBLEN_ARRAY(LINE(IC+8),1).EQ.0 .OR. &
LINE(IC+8).EQ.IACHAR(''`(''`).OR. &
(QUOTE.EQ.1.AND.LINE(IC+8).EQ.Z''`22''`)) THEN ! double quote
FAILURE = 0
ENCODING = ENC_BASE10
END IF
END IF
IF (FCB_CI_STRNCMPARR("X-Base16", &
LINE(IC+QUOTE:LINELEN), LINELEN-IC-QUOTE+1, 8) .EQ. 0)THEN
IF (IC+8.EQ.LINELEN+1 .OR. &
FCB_NBLEN_ARRAY(LINE(IC+8),1).EQ.0 .OR. &
LINE(IC+8).EQ.IACHAR(''`(''`).OR. &
(QUOTE.EQ.1.AND.LINE(IC+8).EQ.Z''`22''`)) THEN !double quote
FAILURE = 0
ENCODING = ENC_BASE16
END IF
END IF
IF (FCB_CI_STRNCMPARR("7bit", &
LINE(IC+QUOTE:LINELEN), LINELEN-IC-QUOTE+1, 4) .EQ. 0 .OR. &
FCB_CI_STRNCMPARR("8bit", &
LINE(IC+QUOTE:LINELEN), LINELEN-IC-QUOTE+1, 4) .EQ. 0 ) THEN
IF (IC+4.EQ.LINELEN+1 .OR. &
FCB_NBLEN_ARRAY(LINE(IC+4),1).EQ.0 .OR. &
LINE(IC+4).EQ.IACHAR(''`(''`).OR. &
(QUOTE.EQ.1.AND.LINE(IC+4).EQ.Z''`22''`)) THEN !double quote
FAILURE = 0
ENCODING = ENC_NONE
END IF
END IF
IF (FCB_CI_STRNCMPARR("Binary", &
LINE(IC+QUOTE:LINELEN), LINELEN-IC-QUOTE+1, 6) .EQ. 0) THEN
IF (IC+6.EQ.LINELEN+1 .OR. &
FCB_NBLEN_ARRAY(LINE(IC+6),1).EQ.0 .OR. &
LINE(IC+6).EQ.IACHAR(''`(''`).OR. &
(QUOTE.EQ.1.AND.LINE(IC+6).EQ.Z''`22''`)) THEN ! double quote
FAILURE = 0
ENCODING = ENC_NONE
END IF
END IF
IF (FAILURE.NE.0)GO TO 110
! *** DEBUG *** PRINT *, "ENCODING: ", ENCODING
CASE (2) ! Message digest
IF (LINELEN.GE.IC+23) THEN
DO I = IC,IC+23
DIGEST(I-IC+1:I-IC+1)=ACHAR(LINE(I))
END DO
ELSE
DO I = IC,LINELEN
DIGEST(I-IC+1:I-IC+1)=ACHAR(LINE(I))
END DO
DIGEST(LINELEN-IC+1:24)=''` ''`
END IF
! *** DEBUG *** PRINT *, "DIGEST: ", DIGEST
CASE (3) ! Binary size
SIZE = FCB_ATOL_WCNT(LINE(IC:LINELEN),LINELEN-IC+1,COUNT)
! *** DEBUG *** PRINT *, "SIZE: ", SIZE
CASE (4) ! Binary ID */
ID = FCB_ATOL_WCNT(LINE(IC:LINELEN),LINELEN-IC+1,COUNT)
! *** DEBUG *** PRINT *, "ID: ", ID
CASE (5)
! Binary element type (signed/unsigned ?-bit integer)
! or (signed ?-bit real/complex IEEE)
FAILURE = 3
QUOTE = 0
DO
IF (IC.GT.LINELEN)EXIT
FCB_NEXT_BINARY = FCB_SKIP_WHITESPACE(TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
LINE,LINESIZE,LINELEN,IC,FRESH_LINE)
IF (FCB_NEXT_BINARY.NE.0) RETURN
IF (LINE(IC) .EQ. Z''`22''`) THEN ! double quote
IF (QUOTE.NE.0) EXIT
IC = IC+1
QUOTE = QUOTE+1
END IF
IF (FAILURE .EQ. 3) THEN
IF (FCB_CI_STRNCMPARR("signed", &
LINE(IC:LINELEN),LINELEN-IC+1, 6) .EQ. 0) THEN
IC = IC+6
VORZEICHEN = 1
FAILURE = FAILURE-1
END IF
IF (FCB_CI_STRNCMPARR("unsigned", &
LINE(IC:LINELEN),LINELEN-IC+1, 8) .EQ. 0) THEN
IC = IC+8
VORZEICHEN = 0
FAILURE = FAILURE-1
END IF
END IF
IF (FAILURE .EQ. 2) THEN
COUNT = 0
TEXT_BITS = FCB_ATOL_WCNT(LINE(IC:LINELEN),LINELEN-IC+1,COUNT)
IF (FCB_CI_STRNCMPARR("-bit", &
LINE(IC+COUNT:LINELEN),LINELEN-IC-COUNT+1,3).EQ.0)THEN
IF (COUNT.NE.0.AND.TEXT_BITS.GT.0.AND.TEXT_BITS.LE.64)THEN
IC = IC+COUNT+1
BITS = TEXT_BITS
IF (LINE(IC) .EQ. IACHAR(''` ''`)) IC = IC+1
FAILURE = FAILURE-1
END IF
END IF
END IF
IF (FAILURE .EQ. 1) THEN
IF (FCB_CI_STRNCMPARR("integer", &
LINE(IC:LINELEN),LINELEN-IC+1, 7 ) .EQ. 0) THEN
FAILURE=FAILURE-1
REELL=0
ELSE
IF (FCB_CI_STRNCMPARR("real", &
LINE(IC:LINELEN), LINELEN-IC+1, 4 ) .EQ. 0 ) THEN
IC = IC+4
IF (LINE(IC).EQ.IACHAR(''` ''`)) IC = IC+1
IF (FCB_CI_STRNCMPARR("ieee", &
LINE(IC:LINELEN),LINELEN-IC+1,4).EQ.0) THEN
FAILURE=FAILURE-1
REELL = 1
END IF
ELSE
IF (FCB_CI_STRNCMPARR("complex", &
LINE(IC:LINELEN),LINELEN-IC+1,7).EQ.0) THEN
IC = IC+7
IF (LINE(IC).EQ.IACHAR(''` ''`)) IC = IC+1
IF (FCB_CI_STRNCMPARR("ieee", &
LINE(IC:LINELEN),LINELEN-IC+1,4).EQ.0) THEN
FAILURE=FAILURE-1
REELL = 1
END IF
END IF
END IF
END IF
END IF
IF (IC .LE. LINELEN) IC = IC+1
END DO
IF (FAILURE .NE. 0)GO TO 110
! *** DEBUG *** PRINT *, "VORZEICHEN, BITS, REELL",VORZEICHEN,BITS,REELL
CASE (6) ! Byte order of elements (only endian-ness is supported)
IF (0.EQ.FCB_CI_STRNCMPARR("big_endian", &
LINE(IC:LINELEN),LINELEN-IC+1,10) ) THEN
BYTEORDER="BIG_ENDIAN"
ELSE
IF (0.EQ.FCB_CI_STRNCMPARR("little_endian", &
LINE(IC:LINELEN),LINELEN-IC+1,13)) THEN
BYTEORDER="LITTLE_ENDIAN"
ELSE
GO TO 110
END IF
END IF
! *** DEBUG *** PRINT *, "BYTEORDER: ", BYTEORDER
CASE(7) ! Size of fastest dimension (Number of "fast" pixels)
DIM1 = FCB_ATOL_WCNT(LINE(IC:LINELEN),LINELEN-IC+1,COUNT)
! *** DEBUG *** PRINT *,"DIM1: ",DIM1
CASE(8) ! Size of second fastest dimension (Number of "slow" pixels)
DIM2 = FCB_ATOL_WCNT(LINE(IC:LINELEN),LINELEN-IC+1,COUNT)
! *** DEBUG *** PRINT *,"DIM2: ",DIM2
CASE(9) ! Size of third dimension
DIM3 = FCB_ATOL_WCNT(LINE(IC:LINELEN),LINELEN-IC+1,COUNT)
! *** DEBUG *** PRINT *,"DIM3: ",DIM3
CASE(10) ! Size of padding after the data
PADDING = FCB_ATOL_WCNT(LINE(IC:LINELEN),LINELEN-IC+1,COUNT)
! *** DEBUG *** PRINT *,"PADDING: ",PADDING
CASE (11) ! Overall number of elements
DIMOVER = FCB_ATOL_WCNT(LINE(IC:LINELEN),LINELEN-IC+1,COUNT)
! *** DEBUG *** PRINT *,"DIMOVER: ",DIMOVER
END SELECT
ENDDO
100 FCB_NEXT_BINARY = -1
RETURN
110 FCB_NEXT_BINARY = CBF_FORMAT
RETURN
END FUNCTION FCB_NEXT_BINARY'
./CBFlib-0.9.2.2/m4/Makefile.m4 0000644 0000765 0000765 00000220055 11603702103 014076 0 ustar yaya yaya m4_define(`cbf_version',`0.9.2')m4_dnl
m4_define(`cbf_date',`12 Feb 2011')m4_dnl
m4_ifelse(cbf_system,`',`m4_define(`cbf_system',`LINUX')')
`######################################################################
# Makefile - command file for make to create CBFlib #
# #
# Version 'cbf_version cbf_date` #
# #
# Paul Ellis and #
# Herbert J. Bernstein (yaya@bernstein-plus-sons.com) #
# #
# (C) Copyright 2006 - 2011 Herbert J. Bernstein #
# #
######################################################################
######################################################################
# #
# YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL #
# #
# ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS #
# OF THE LGPL #
# #
######################################################################
########################### GPL NOTICES ##############################
# #
# This program is free software; you can redistribute it and/or #
# modify it under the terms of the GNU General Public License as #
# published by the Free Software Foundation; either version 2 of #
# (the License, or (at your option) any later version. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program; if not, write to the Free Software #
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA #
# 02111-1307 USA #
# #
######################################################################
######################### LGPL NOTICES ###############################
# #
# This library is free software; you can redistribute it and/or #
# modify it under the terms of the GNU Lesser General Public #
# License as published by the Free Software Foundation; either #
# version 2.1 of the License, or (at your option) any later version. #
# #
# This library is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU #
# Lesser General Public License for more details. #
# #
# You should have received a copy of the GNU Lesser General Public #
# License along with this library; if not, write to the Free #
# Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, #
# MA 02110-1301 USA #
# #
######################################################################
######################################################################
# #
# Stanford University Notices #
# for the CBFlib software package that incorporates SLAC software #
# on which copyright is disclaimed #
# #
# This software #
# ------------- #
# The term "this software", as used in these Notices, refers to #
# those portions of the software package CBFlib that were created by #
# employees of the Stanford Linear Accelerator Center, Stanford #
# University. #
# #
# Stanford disclaimer of copyright #
# -------------------------------- #
# Stanford University, owner of the copyright, hereby disclaims its #
# copyright and all other rights in this software. Hence, anyone #
# may freely use it for any purpose without restriction. #
# #
# Acknowledgement of sponsorship #
# ------------------------------ #
# This software was produced by the Stanford Linear Accelerator #
# Center, Stanford University, under Contract DE-AC03-76SFO0515 with #
# the Department of Energy. #
# #
# Government disclaimer of liability #
# ---------------------------------- #
# Neither the United States nor the United States Department of #
# Energy, nor any of their employees, makes any warranty, express or #
# implied, or assumes any legal liability or responsibility for the #
# accuracy, completeness, or usefulness of any data, apparatus, #
# product, or process disclosed, or represents that its use would #
# not infringe privately owned rights. #
# #
# Stanford disclaimer of liability #
# -------------------------------- #
# Stanford University makes no representations or warranties, #
# express or implied, nor assumes any liability for the use of this #
# software. #
# #
# Maintenance of notices #
# ---------------------- #
# In the interest of clarity regarding the origin and status of this #
# software, this and all the preceding Stanford University notices #
# are to remain affixed to any copy or derivative of this software #
# made or distributed by the recipient and are to be affixed to any #
# copy of software made or distributed by the recipient that #
# contains a copy or derivative of this software. #
# #
# Based on SLAC Software Notices, Set 4 #
# OTT.002a, 2004 FEB 03 #
######################################################################
######################################################################
# NOTICE #
# Creative endeavors depend on the lively exchange of ideas. There #
# are laws and customs which establish rights and responsibilities #
# for authors and the users of what authors create. This notice #
# is not intended to prevent you from using the software and #
# documents in this package, but to ensure that there are no #
# misunderstandings about terms and conditions of such use. #
# #
# Please read the following notice carefully. If you do not #
# understand any portion of this notice, please seek appropriate #
# professional legal advice before making use of the software and #
# documents included in this software package. In addition to #
# whatever other steps you may be obliged to take to respect the #
# intellectual property rights of the various parties involved, if #
# you do make use of the software and documents in this package, #
# please give credit where credit is due by citing this package, #
# its authors and the URL or other source from which you obtained #
# it, or equivalent primary references in the literature with the #
# same authors. #
# #
# Some of the software and documents included within this software #
# package are the intellectual property of various parties, and #
# placement in this package does not in any way imply that any #
# such rights have in any way been waived or diminished. #
# #
# With respect to any software or documents for which a copyright #
# exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT. #
# #
# Even though the authors of the various documents and software #
# found here have made a good faith effort to ensure that the #
# documents are correct and that the software performs according #
# to its documentation, and we would greatly appreciate hearing of #
# any problems you may encounter, the programs and documents any #
# files created by the programs are provided **AS IS** without any *
# warranty as to correctness, merchantability or fitness for any #
# particular or general use. #
# #
# THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF #
# PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE #
# PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS #
# OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE #
# PROGRAMS OR DOCUMENTS. #
######################################################################
######################################################################
# #
# The IUCr Policy #
# for the Protection and the Promotion of the STAR File and #
# CIF Standards for Exchanging and Archiving Electronic Data #
# #
# Overview #
# #
# The Crystallographic Information File (CIF)[1] is a standard for #
# information interchange promulgated by the International Union of #
# Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the #
# recommended method for submitting publications to Acta #
# Crystallographica Section C and reports of crystal structure #
# determinations to other sections of Acta Crystallographica #
# and many other journals. The syntax of a CIF is a subset of the #
# more general STAR File[2] format. The CIF and STAR File approaches #
# are used increasingly in the structural sciences for data exchange #
# and archiving, and are having a significant influence on these #
# activities in other fields. #
# #
# Statement of intent #
# #
# The IUCr''`s interest in the STAR File is as a general data #
# interchange standard for science, and its interest in the CIF, #
# a conformant derivative of the STAR File, is as a concise data #
# exchange and archival standard for crystallography and structural #
# science. #
# #
# Protection of the standards #
# #
# To protect the STAR File and the CIF as standards for #
# interchanging and archiving electronic data, the IUCr, on behalf #
# of the scientific community, #
# #
# # holds the copyrights on the standards themselves, *
# #
# # owns the associated trademarks and service marks, and *
# #
# # holds a patent on the STAR File. *
# #
# These intellectual property rights relate solely to the #
# interchange formats, not to the data contained therein, nor to #
# the software used in the generation, access or manipulation of #
# the data. #
# #
# Promotion of the standards #
# #
# The sole requirement that the IUCr, in its protective role, #
# imposes on software purporting to process STAR File or CIF data #
# is that the following conditions be met prior to sale or #
# distribution. #
# #
# # Software claiming to read files written to either the STAR *
# File or the CIF standard must be able to extract the pertinent #
# data from a file conformant to the STAR File syntax, or the CIF #
# syntax, respectively. #
# #
# # Software claiming to write files in either the STAR File, or *
# the CIF, standard must produce files that are conformant to the #
# STAR File syntax, or the CIF syntax, respectively. #
# #
# # Software claiming to read definitions from a specific data *
# dictionary approved by the IUCr must be able to extract any #
# pertinent definition which is conformant to the dictionary #
# definition language (DDL)[3] associated with that dictionary. #
# #
# The IUCr, through its Committee on CIF Standards, will assist #
# any developer to verify that software meets these conformance #
# conditions. #
# #
# Glossary of terms #
# #
# [1] CIF: is a data file conformant to the file syntax defined #
# at http://www.iucr.org/iucr-top/cif/spec/index.html #
# #
# [2] STAR File: is a data file conformant to the file syntax #
# defined at http://www.iucr.org/iucr-top/cif/spec/star/index.html #
# #
# [3] DDL: is a language used in a data dictionary to define data #
# items in terms of "attributes". Dictionaries currently approved #
# by the IUCr, and the DDL versions used to construct these #
# dictionaries, are listed at #
# http://www.iucr.org/iucr-top/cif/spec/ddl/index.html #
# #
# Last modified: 30 September 2000 #
# #
# IUCr Policy Copyright (C) 2000 International Union of #
# Crystallography #
######################################################################
# Version string
VERSION = 'cbf_version`
#
# Comment out the next line if scratch test files sould be retain
#
CLEANTESTS = yes
'm4_ifelse(cbf_use_pycifrw,`yes',`
#
# Definitions to get versions of PyCifRW and PLY
#
PYCIFRW = PyCifRW-3.3_6Dec09
PLY = ply-3.2
PYCIFRWFLAG = -DCBF_USE_PYCIFRW
')m4_dnl
`
#
# Definition to get a version of tifflib to support tiff2cbf
#
TIFF = tiff-3.9.4-rev-6Feb11
TIFFPREFIX = $(PWD)
#
# Definitions to get a stable version of regex
#
REGEX = regex-20090805
REGEXDIR = /usr/lib
REGEXDEP =
# Program to use to retrieve a URL
DOWNLOAD = wget
# Flag to control symlinks versus copying
SLFLAGS = --use_ln
#
# Program to use to pack shars
#
SHAR = /usr/bin/shar
#SHAR = /usr/local/bin/gshar
#
# Program to use to create archives
#
AR = /usr/bin/ar
#
# Program to use to add an index to an archive
#
RANLIB = /usr/bin/ranlib
#
# Program to use to decompress a data file
#
DECOMPRESS = /usr/bin/bunzip2
#
# Program to use to compress a data file
#
COMPRESS = /usr/bin/bzip2
#
# Program to use to generate a signature
#
SIGNATURE = /usr/bin/openssl dgst -md5
#
# Extension for compressed data file (with period)
#
CEXT = .bz2
#
# Extension for signatures of files
#
SEXT = .md5
# call to time a command
#TIME =
#TIME = time
#
# Program to display differences between files
#
DIFF = diff -u -b
#
# Program to generate wrapper classes for Python
#
PYSWIG = swig -python
#
# Program to generate wrapper classes for Java
#
JSWIG = swig -java
#
# Program to generate LaTex and HTML program documentation
#
NUWEB = nuweb
#
# Compiler for Java
#
JAVAC = javac
#
# Java archiver for compiled classes
#
JAR = jar
#
# Java SDK root directory
#
ifeq ($(JDKDIR),)
JDKDIR = /usr/lib/java
endif
ifneq ($(CBF_DONT_USE_LONG_LONG),)
NOLLFLAG = -DCBF_DONT_USE_LONG_LONG
else
NOLLFLAG =
endif
#
# PYCBF definitions
#
PYCBFEXT = so
PYCBFBOPT =
SETUP_PY = setup.py
#
# Set the compiler and flags
#
'm4_ifelse(cbf_system,`OSX',`
#########################################################
#
# Appropriate compiler definitions for MAC OS X
# Also change defintion of DOWNLOAD
#
#########################################################
CC = gcc
C++ = g++
CFLAGS = -g -O2 -Wall -ansi -pedantic
F90C = gfortran
F90FLAGS = -g -fno-range-check
F90LDFLAGS = -bind_at_load
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
DOWNLOAD = /sw/bin/wget',
cbf_system,`OSX_gcc42',`
#########################################################
#
# Appropriate compiler definitions for MAC OS X
# with gcc 4.2
# Also change defintion of DOWNLOAD
#
#########################################################
CC = gcc
C++ = g++
CFLAGS = -g -O2 -Wall -ansi -pedantic
F90C = gfortran
F90FLAGS = -g -fno-range-check
F90LDFLAGS = -bind_at_load
SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(INSTALLDIR)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB)
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
DOWNLOAD = /sw/bin/wget',
cbf_system,`OSX_gcc42_DMALLOC',`
#########################################################
#
# Appropriate compiler definitions for MAC OS X
# with gcc 4.2 and DMALLOC
# Also change defintion of DOWNLOAD
#
#########################################################
CC = gcc
C++ = g++
CFLAGS = -g -O2 -Wall -ansi -pedantic -DDMALLOC -DDMALLOC_FUNC_CHECK -I$(HOME)/include
F90C = gfortran
F90FLAGS = -g -fno-range-check
F90LDFLAGS = -bind_at_load
SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(INSTALLDIR)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB)
EXTRALIBS = -lm -L$(HOME)/lib -ldmalloc
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
DOWNLOAD = /sw/bin/wget',
cbf_system,`LINUX_64',`
#########################################################
#
# Appropriate compiler definitions for Linux x86_64
# with gcc version 4.2
#
#########################################################
CC = gcc -m64
C++ = g++ -m64
CFLAGS = -g -O2 -Wall -D_USE_XOPEN_EXTENDED -fno-strict-aliasing
F90C = gfortran -m64
F90FLAGS = -g -fno-range-check
F90LDFLAGS =
SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(INSTALLDIR)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB)
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
DOWNLOAD = /sw/bin/wget',
cbf_system,`LINUX_gcc42',`
#########################################################
#
# Appropriate compiler definitions for Linux
# with gcc version 4.2
#
#########################################################
CC = gcc
C++ = g++
CFLAGS = -g -O2 -Wall -D_USE_XOPEN_EXTENDED -fno-strict-aliasing
F90C = gfortran
F90FLAGS = -g -fno-range-check
F90LDFLAGS =
SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(INSTALLDIR)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB)
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time',
cbf_system,`LINUX',`
#########################################################
#
# Appropriate compiler definitions for Linux
#
#########################################################
CC = gcc
C++ = g++
CFLAGS = -g -O2 -Wall -D_USE_XOPEN_EXTENDED -fno-strict-aliasing
F90C = gfortran
F90FLAGS = -g
F90LDFLAGS =
SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(INSTALLDIR)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB)
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time',
cbf_system,`LINUX_gcc42_DMALLOC',`
#########################################################
#
# Appropriate compiler definitions for Linux
# with gcc version 4.2 and DMALLOC
#
#########################################################
CC = gcc
C++ = g++
CFLAGS = -g -O2 -Wall -D_USE_XOPEN_EXTENDED -fno-strict-aliasing -DDMALLOC -DDMALLOC_FUNC_CHECK -I$(HOME)/include
F90C = gfortran
F90FLAGS = -g -fno-range-check
F90LDFLAGS =
SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(INSTALLDIR)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB)
EXTRALIBS = -lm -L$(HOME)/lib -ldmalloc
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time',
cbf_system,`LINUX_DMALLOC',`
#########################################################
#
# Appropriate compiler definitions for Linux and DMALLOC
#
#########################################################
CC = gcc
C++ = g++
CFLAGS = -g -O2 -Wall -D_USE_XOPEN_EXTENDED -fno-strict-aliasing -DDMALLOC -DDMALLOC_FUNC_CHECK -I$(HOME)/include
F90C = gfortran
F90FLAGS = -g
F90LDFLAGS =
SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(INSTALLDIR)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB)
EXTRALIBS = -lm -L$(HOME)/lib -ldmalloc
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time',
cbf_system,`AIX',`
#########################################################
#
# Appropriate compiler definitions for AIX
#
#########################################################
CC = xlc
C++ = xlC
CFLAGS = -g -O2 -Wall
F90C = xlf90
F90FLAGS = -g -qsuffix=f=f90
F90LDFLAGS =
M4FLAGS = -Dfcb_bytes_in_rec=131072
EXTRALIBS = -lm
TIME = time',
cbf_system,`MINGW',`
#########################################################
#
# Appropriate compiler definitions for Mingw
# Also change from symlinks to copies and
# use default paths for utilities
#
#########################################################
CC = gcc
C++ = g++
CFLAGS = -g -O2 -Wall -static -I/usr/include -fno-strict-aliasing
F90C = g95
F90FLAGS = -g
F90LDFLAGS =
M4FLAGS = -Dfcb_bytes_in_rec=4096
SOCFLAGS = -D_JNI_IMPLEMENTATION_
SOLDFLAGS = -shared -Wl,--kill-at
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/win32
EXTRALIBS = -L$(REGEXDIR) -lregex -lm
REGEXDEP = $(REGEXDIR)/libregex.a
TIME =
PYCBFEXT = pyd
PYCBFBOPT = --compiler=mingw32
SETUP_PY = setup_MINGW.py
JDKDIR = /java
JSWIG = /swig/swig -java
PYSWIG = /swig/swig -python
SLFLAGS = --use_cp
SHAR = shar
AR = ar
RANLIB = ranlib
DECOMPRESS = bunzip2',
cbf_system,`IRIX_gcc',`
#########################################################
#
# Appropriate compiler definitions for IRIX w. gcc
# No f90
# use default paths for utilities
#
#########################################################
CC = gcc
C++ = g++
CFLAGS = -g -O2 -Wall
F90C =
F90FLAGS =
M4FLAGS = -Dfcb_bytes_in_rec=4096
EXTRALIBS = -lm
TIME =
SHAR = shar
AR = ar
RANLIB =
DECOMPRESS = bunzip2',
`
#########################################################
#
# Appropriate compiler definitions for default (Linux)
#
#########################################################
CC = gcc
C++ = g++
CFLAGS = -g -O2 -Wall -D_USE_XOPEN_EXTENDED -fno-strict-aliasing
F90C = gfortran
F90FLAGS = -g -fno-range-check
F90LDFLAGS =
SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(INSTALLDIR)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB)
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time')`
ifneq ($(NOFORTRAN),)
F90C =
endif
#
# Directories
#
ROOT = .
LIB = $(ROOT)/lib
SOLIB = $(ROOT)/solib
JCBF = $(ROOT)/jcbf
JAVADIR = $(ROOT)/java
BIN = $(ROOT)/bin
SRC = $(ROOT)/src
INCLUDE = $(ROOT)/include
M4 = $(ROOT)/m4
PYCBF = $(ROOT)/pycbf
EXAMPLES = $(ROOT)/examples
DECTRIS_EXAMPLES = $(EXAMPLES)/dectris_cbf_template_test
DOC = $(ROOT)/doc
GRAPHICS = $(ROOT)/html_graphics
DATADIRI = $(ROOT)/../CBFlib_$(VERSION)_Data_Files_Input
DATADIRO = $(ROOT)/../CBFlib_$(VERSION)_Data_Files_Output
DATADIRS = $(ROOT)/../CBFlib_$(VERSION)_Data_Files_Output_Sigs_Only
INSTALLDIR = $(HOME)
#
# URLs from which to retrieve the data directories
#
DATAURLBASE = http://downloads.sf.net/cbflib/
DATAURLI = $(DATAURLBASE)/CBFlib_$(VERSION)_Data_Files_Input.tar.gz
DATAURLO = $(DATAURLBASE)/CBFlib_$(VERSION)_Data_Files_Output.tar.gz
DATAURLS = $(DATAURLBASE)/CBFlib_$(VERSION)_Data_Files_Output_Sigs_Only.tar.gz
#
# URLs from which to retrieve needed external package snapshots
#
'm4_ifelse(cbf_use_pycifrw,`yes',`
PYCIFRWURL = http://downloads.sf.net/cbflib/$(PYCIFRW).tar.gz
PLYURL = http://www.dabeaz.com/ply/$(PLY).tar.gz
')m4_dnl
`REGEXURL = http://downloads.sf.net/cbflib/$(REGEX).tar.gz
TIFFURL = http://downloads.sf.net/cbflib/$(TIFF).tar.gz
#
# Include directories
#
INCLUDES = -I$(INCLUDE) -I$(SRC)
######################################################################
# You should not need to make modifications below this line #
######################################################################
#
# Suffixes of files to be used or built
#
.SUFFIXES: .c .o .f90 .m4
.m4.f90:
m4 -P $(M4FLAGS) $< > $@
ifneq ($(F90C),)
.f90.o:
$(F90C) $(F90FLAGS) -c $< -o $@
endif
#
# Common dependencies
#
COMMONDEP = Makefile
#
# Source files
#
SOURCE = $(SRC)/cbf.c \
$(SRC)/cbf_alloc.c \
$(SRC)/cbf_ascii.c \
$(SRC)/cbf_binary.c \
$(SRC)/cbf_byte_offset.c \
$(SRC)/cbf_canonical.c \
$(SRC)/cbf_codes.c \
$(SRC)/cbf_compress.c \
$(SRC)/cbf_context.c \
$(SRC)/cbf_copy.c \
$(SRC)/cbf_file.c \
$(SRC)/cbf_getopt.c \
$(SRC)/cbf_lex.c \
$(SRC)/cbf_packed.c \
$(SRC)/cbf_predictor.c \
$(SRC)/cbf_read_binary.c \
$(SRC)/cbf_read_mime.c \
$(SRC)/cbf_simple.c \
$(SRC)/cbf_string.c \
$(SRC)/cbf_stx.c \
$(SRC)/cbf_tree.c \
$(SRC)/cbf_uncompressed.c \
$(SRC)/cbf_write.c \
$(SRC)/cbf_write_binary.c \
$(SRC)/cbf_ws.c \
$(SRC)/md5c.c
'm4_ifelse(cbf_use_pycifrw,`yes',`
PYSOURCE = $(SRC)/drel_lex.py \
$(SRC)/drel_yacc.py \
$(SRC)/drelc.py \
$(SRC)/drel_prep.py
')m4_dnl
`
F90SOURCE = $(SRC)/fcb_atol_wcnt.f90 \
$(SRC)/fcb_ci_strncmparr.f90 \
$(SRC)/fcb_exit_binary.f90 \
$(SRC)/fcb_nblen_array.f90 \
$(SRC)/fcb_next_binary.f90 \
$(SRC)/fcb_open_cifin.f90 \
$(SRC)/fcb_packed.f90 \
$(SRC)/fcb_read_bits.f90 \
$(SRC)/fcb_read_byte.f90 \
$(SRC)/fcb_read_image.f90 \
$(SRC)/fcb_read_line.f90 \
$(SRC)/fcb_read_xds_i2.f90 \
$(SRC)/fcb_skip_whitespace.f90 \
$(EXAMPLES)/test_fcb_read_image.f90 \
$(EXAMPLES)/test_xds_binary.f90
#
# Header files
#
HEADERS = $(INCLUDE)/cbf.h \
$(INCLUDE)/cbf_alloc.h \
$(INCLUDE)/cbf_ascii.h \
$(INCLUDE)/cbf_binary.h \
$(INCLUDE)/cbf_byte_offset.h \
$(INCLUDE)/cbf_canonical.h \
$(INCLUDE)/cbf_codes.h \
$(INCLUDE)/cbf_compress.h \
$(INCLUDE)/cbf_context.h \
$(INCLUDE)/cbf_copy.h \
$(INCLUDE)/cbf_file.h \
$(INCLUDE)/cbf_getopt.h \
$(INCLUDE)/cbf_lex.h \
$(INCLUDE)/cbf_packed.h \
$(INCLUDE)/cbf_predictor.h \
$(INCLUDE)/cbf_read_binary.h \
$(INCLUDE)/cbf_read_mime.h \
$(INCLUDE)/cbf_simple.h \
$(INCLUDE)/cbf_string.h \
$(INCLUDE)/cbf_stx.h \
$(INCLUDE)/cbf_tree.h \
$(INCLUDE)/cbf_uncompressed.h \
$(INCLUDE)/cbf_write.h \
$(INCLUDE)/cbf_write_binary.h \
$(INCLUDE)/cbf_ws.h \
$(INCLUDE)/global.h \
$(INCLUDE)/cbff.h \
$(INCLUDE)/md5.h
#
# m4 macro files
#
M4FILES = $(M4)/fcblib_defines.m4 \
$(M4)/fcb_exit_binary.m4 \
$(M4)/fcb_next_binary.m4 \
$(M4)/fcb_open_cifin.m4 \
$(M4)/fcb_packed.m4 \
$(M4)/fcb_read_bits.m4 \
$(M4)/fcb_read_image.m4 \
$(M4)/fcb_read_xds_i2.m4 \
$(M4)/test_fcb_read_image.m4 \
$(M4)/test_xds_binary.m4
#
# Documentation files
#
DOCUMENTS = $(DOC)/CBFlib.html \
$(DOC)/CBFlib.txt \
$(DOC)/CBFlib_NOTICES.html \
$(DOC)/CBFlib_NOTICES.txt \
$(DOC)/ChangeLog \
$(DOC)/ChangeLog.html \
$(DOC)/MANIFEST \
$(DOC)/gpl.txt $(DOC)/lgpl.txt
#
# HTML Graphics files
#
JPEGS = $(GRAPHICS)/CBFbackground.jpg \
$(GRAPHICS)/CBFbig.jpg \
$(GRAPHICS)/CBFbutton.jpg \
$(GRAPHICS)/cbflibbackground.jpg \
$(GRAPHICS)/cbflibbig.jpg \
$(GRAPHICS)/cbflibbutton.jpg \
$(GRAPHICS)/cifhome.jpg \
$(GRAPHICS)/iucrhome.jpg \
$(GRAPHICS)/noticeButton.jpg
#
# Default: instructions
#
default:
@echo ''` ''`
@echo ''`***************************************************************''`
@echo ''` ''`
@echo ''` PLEASE READ README and doc/CBFlib_NOTICES.txt''`
@echo ''` ''`
@echo ''` Before making the CBF library and example programs, check''`
@echo ''` that the C compiler name and flags are correct:''`
@echo ''` ''`
@echo ''` The current values are:''`
@echo ''` ''`
@echo ''` $(CC) $(CFLAGS) $(NOLLFLAG) $(PYCIFRWFLAG)''`
@echo ''` ''`
@echo ''` Before installing the CBF library and example programs, check''`
@echo ''` that the install directory is correct:''`
@echo ''` ''`
@echo ''` The current value :''`
@echo ''` ''`
@echo ''` $(INSTALLDIR) ''`
@echo ''` ''`
@echo ''` To compile the CBF library and example programs type:''`
@echo ''` ''`
@echo ''` make clean''`
@echo ''` make all''`
@echo ''` ''`
@echo ''` To compile the CBF library as a shared object library, type:''`
@echo ''` ''`
@echo ''` make shared''`
@echo ''` ''`
@echo ''` To compile the Java wrapper classes for CBF library, type:''`
@echo ''` ''`
@echo ''` make javawrapper''`
@echo ''` ''`
@echo ''` To run a set of tests type:''`
@echo ''` ''`
@echo ''` make tests''`
@echo ''` ''`
@echo ''` To run some java tests type:''`
@echo ''` ''`
@echo ''` make javatests''`
@echo ''` ''`
@echo ''` The tests assume that several data files are in the directories''`
@echo ''` $(DATADIRI) and $(DATADIRO)''`
@echo ''` ''`
@echo ''` Alternatively tests can be run comparing MD5 signatures only by''`
@echo ''` ''`
@echo ''` make tests_sigs_only''`
@echo ''` ''`
@echo ''` These signature only tests save space and download time by''`
@echo ''` assuming that input data files and the output signatures''`
@echo ''` are in the directories''`
@echo ''` $(DATADIRI) and $(DATADIRS)''`
@echo ''` ''`
@echo ''` These directory can be obtained from''`
@echo ''` ''`
@echo ''` $(DATAURLI) ''`
@echo ''` $(DATAURLO) ''`
@echo ''` $(DATAURLS) ''`
@echo ''` ''`
@echo ''` To clean up the directories type:''`
@echo ''` ''`
@echo ''` make clean''`
@echo ''` ''`
@echo ''` To install the library and binaries type:''`
@echo ''` ''`
@echo ''` make install''`
@echo ''` ''`
@echo ''`***************************************************************''`
@echo ''` ''`
#
# Compile the library and examples
#
all:: $(BIN) $(SOURCE) $(F90SOURCE) $(HEADERS) \
'm4_ifelse(cbf_use_pycifrw,`yes',`
$(PYCIFRW) $(PLY) \
')m4_dnl
` symlinksdone $(REGEXDEP) \
$(LIB)/libcbf.a \
$(LIB)/libfcb.a \
$(LIB)/libimg.a \
$(BIN)/adscimg2cbf \
$(BIN)/cbf2adscimg \
$(BIN)/convert_image \
$(BIN)/convert_minicbf \
$(BIN)/sequence_match \
$(BIN)/arvai_test \
$(BIN)/makecbf \
$(BIN)/img2cif \
$(BIN)/adscimg2cbf \
$(BIN)/cif2cbf \
$(BIN)/testcell \
$(BIN)/cif2c \
$(BIN)/testreals \
$(BIN)/testflat \
$(BIN)/testflatpacked
ifneq ($(F90C),)
all:: $(BIN)/test_xds_binary \
$(BIN)/test_fcb_read_image
endif
shared: $(SOLIB)/libcbf.so $(SOLIB)/libfcb.so $(SOLIB)/libimg.so
javawrapper: shared $(JCBF) $(JCBF)/cbflib-$(VERSION).jar $(SOLIB)/libcbf_wrap.so
ifneq ($(CBFLIB_USE_PYCIFRW),)
PYCIFRWDEF = -Dcbf_use_pycifrw=yes
else
PYCIFRWDEF =
endif
Makefiles: Makefile \
Makefile_LINUX \
Makefile_LINUX_64 \
Makefile_LINUX_gcc42 \
Makefile_LINUX_DMALLOC \
Makefile_LINUX_gcc42_DMALLOC \
Makefile_OSX \
Makefile_OSX_gcc42 \
Makefile_OSX_gcc42_DMALLOC \
Makefile_AIX \
Makefile_MINGW \
Makefile_IRIX_gcc
Makefile_LINUX: $(M4)/Makefile.m4
-cp Makefile_LINUX Makefile_LINUX_old
m4 -P $(PYCIFRWDEF) -Dcbf_system=LINUX $(M4)/Makefile.m4 > Makefile_LINUX
Makefile_LINUX_DMALLOC: $(M4)/Makefile.m4
-cp Makefile_LINUX Makefile_LINUX_old
m4 -P $(PYCIFRWDEF) -Dcbf_system=LINUX_DMALLOC $(M4)/Makefile.m4 > Makefile_LINUX_DMALLOC
Makefile_LINUX_64: $(M4)/Makefile.m4
-cp Makefile_LINUX_64 Makefile_LINUX_64_old
m4 -P $(PYCIFRWDEF) -Dcbf_system=LINUX_64 $(M4)/Makefile.m4 > Makefile_LINUX_64
Makefile_LINUX_gcc42: $(M4)/Makefile.m4
-cp Makefile_LINUX_gcc42 Makefile_LINUX_gcc42_old
m4 -P $(PYCIFRWDEF) -Dcbf_system=LINUX_gcc42 $(M4)/Makefile.m4 > Makefile_LINUX_gcc42
Makefile_LINUX_gcc42_DMALLOC: $(M4)/Makefile.m4
-cp Makefile_LINUX_gcc42 Makefile_LINUX_gcc42_old
m4 -P $(PYCIFRWDEF) -Dcbf_system=LINUX_gcc42_DMALLOC $(M4)/Makefile.m4 > Makefile_LINUX_gcc42_DMALLOC
Makefile_OSX: $(M4)/Makefile.m4
-cp Makefile_OSX Makefile_OSX_old
m4 -P $(PYCIFRWDEF) -Dcbf_system=OSX $(M4)/Makefile.m4 > Makefile_OSX
Makefile_OSX_gcc42: $(M4)/Makefile.m4
-cp Makefile_OSX_gcc42 Makefile_OSX_gcc42_old
m4 -P $(PYCIFRWDEF) -Dcbf_system=OSX_gcc42 $(M4)/Makefile.m4 > Makefile_OSX_gcc42
Makefile_OSX_gcc42_DMALLOC: $(M4)/Makefile.m4
-cp Makefile_OSX_gcc42 Makefile_OSX_gcc42_old
m4 -P $(PYCIFRWDEF) -Dcbf_system=OSX_gcc42_DMALLOC $(M4)/Makefile.m4 > Makefile_OSX_gcc42_DMALLOC
Makefile_AIX: $(M4)/Makefile.m4
-cp Makefile_AIX Makefile_AIX_old
m4 -P $(PYCIFRWDEF) -Dcbf_system=AIX $(M4)/Makefile.m4 > Makefile_AIX
Makefile_MINGW: $(M4)/Makefile.m4
-cp Makefile_MINGW Makefile_MINGW_old
m4 -P $(PYCIFRWDEF) -Dcbf_system=MINGW $(M4)/Makefile.m4 > Makefile_MINGW
Makefile_IRIX_gcc: $(M4)/Makefile.m4
-cp Makefile_IRIX_gcc Makefile_IRIX_gcc_old
m4 -P $(PYCIFREDEF) -Dcbf_system=IRIX_gcc $(M4)/Makefile.m4 > Makefile_IRIX_gcc
Makefile: $(M4)/Makefile.m4
-cp Makefile Makefile_old
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
chmod a+x doc/.symlinks
chmod a+x doc/.undosymlinks
chmod a+x libtool/.symlinks
chmod a+x libtool/.undosymlinks
./.symlinks $(SLFLAGS)
touch symlinksdone
install: all $(INSTALLDIR) $(INSTALLDIR)/lib $(INSTALLDIR)/bin \
$(INSTALLDIR)/include $(INSTALLDIR)/include/cbflib \
$(PYSOURCE)
-chmod -R 755 $(INSTALLDIR)/include/cbflib
-chmod 755 $(INSTALLDIR)/lib/libcbf.a
-cp $(INSTALLDIR)/lib/libcbf.a $(INSTALLDIR)/lib/libcbf_old.a
cp $(LIB)/libcbf.a $(INSTALLDIR)/lib/libcbf.a
-cp $(INSTALLDIR)/lib/libimg.a $(INSTALLDIR)/lib/libimg_old.a
cp $(LIB)/libimg.a $(INSTALLDIR)/lib/libimg.a
-cp $(INSTALLDIR)/bin/adscimg2cbf $(INSTALLDIR)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(INSTALLDIR)/bin/adscimg2cbf
-cp $(INSTALLDIR)/bin/cbf2adscimg $(INSTALLDIR)/bin/cbf2adscimg_old
cp $(BIN)/cbf2adscimg $(INSTALLDIR)/bin/cbf2adscimg
-cp $(INSTALLDIR)/bin/convert_image $(INSTALLDIR)/bin/convert_image_old
cp $(BIN)/convert_image $(INSTALLDIR)/bin/convert_image
-cp $(INSTALLDIR)/bin/convert_minicbf $(INSTALLDIR)/bin/convert_minicbf_old
cp $(BIN)/convert_minicbf $(INSTALLDIR)/bin/convert_minicbf
-cp $(INSTALLDIR)/bin/makecbf $(INSTALLDIR)/bin/makecbf_old
cp $(BIN)/makecbf $(INSTALLDIR)/bin/makecbf
-cp $(INSTALLDIR)/bin/img2cif $(INSTALLDIR)/bin/img2cif_old
cp $(BIN)/img2cif $(INSTALLDIR)/bin/img2cif
-cp $(INSTALLDIR)/bin/cif2cbf $(INSTALLDIR)/bin/cif2cbf_old
cp $(BIN)/cif2cbf $(INSTALLDIR)/bin/cif2cbf
-cp $(INSTALLDIR)/bin/sequence_match $(INSTALLDIR)/bin/sequence_match_old
cp $(BIN)/sequence_match $(INSTALLDIR)/bin/sequence_match
-cp $(INSTALLDIR)/bin/arvai_test $(INSTALLDIR)/bin/arvai_test_old
cp $(BIN)/arvai_test $(INSTALLDIR)/bin/arvai_test
-cp $(INSTALLDIR)/bin/cif2c $(INSTALLDIR)/bin/cif2c_old
cp $(BIN)/cif2c $(INSTALLDIR)/bin/cif2c
-cp $(INSTALLDIR)/bin/testreals $(INSTALLDIR)/bin/testreals_old
cp $(BIN)/testreals $(INSTALLDIR)/bin/testreals
-cp $(INSTALLDIR)/bin/testflat $(INSTALLDIR)/bin/testflat_old
cp $(BIN)/testflat $(INSTALLDIR)/bin/testflat
-cp $(INSTALLDIR)/bin/testflatpacked $(INSTALLDIR)/bin/testflatpacked_old
cp $(BIN)/testflatpacked $(INSTALLDIR)/bin/testflatpacked
'm4_ifelse(cbf_use_pycifrw,`yes',`
cp $(SRC)/drel_lex.py $(INSTALLDIR)/bin/drel_lex.py
cp $(SRC)/drel_yacc.py $(INSTALLDIR)/bin/drel_yacc.py
cp $(SRC)/drelc.py $(INSTALLDIR)/bin/drelc.py
cp $(SRC)/drel_prep.py $(INSTALLDIR)/bin/drel_prep.py
')m4_dnl
` chmod -R 755 $(INSTALLDIR)/include/cbflib
-rm -rf $(INSTALLDIR)/include/cbflib_old
-cp -r $(INSTALLDIR)/include/cbflib $(INSTALLDIR)/include/cbflib_old
-rm -rf $(INSTALLDIR)/include/cbflib
cp -r $(INCLUDE) $(INSTALLDIR)/include/cbflib
chmod 644 $(INSTALLDIR)/lib/libcbf.a
chmod 755 $(INSTALLDIR)/bin/convert_image
chmod 755 $(INSTALLDIR)/bin/convert_minicbf
chmod 755 $(INSTALLDIR)/bin/makecbf
chmod 755 $(INSTALLDIR)/bin/img2cif
chmod 755 $(INSTALLDIR)/bin/cif2cbf
chmod 755 $(INSTALLDIR)/bin/sequence_match
chmod 755 $(INSTALLDIR)/bin/arvai_test
chmod 755 $(INSTALLDIR)/bin/cif2c
chmod 755 $(INSTALLDIR)/bin/testreals
chmod 755 $(INSTALLDIR)/bin/testflat
chmod 755 $(INSTALLDIR)/bin/testflatpacked
chmod 644 $(INSTALLDIR)/include/cbflib/*.h
'm4_ifelse(cbf_use_pycifrw,`yes',`
#
# PyCifRW
#
$(PYCIFRW):
$(DOWNLOAD) $(PYCIFRWURL)
tar -xvf $(PYCIFRW).tar.gz
-rm $(PYCIFRW).tar.gz
(cd $(PYCIFRW); python setup.py install )
#
# PLY
#
$(PLY):
$(DOWNLOAD) $(PLYURL)
tar -xvf $(PLY).tar.gz
-rm $(PLY).tar.gz
(cd $(PLY); python setup.py install )
')m4_dnl
`
#
# REGEX
#
ifneq ($(REGEXDEP),)
$(REGEXDEP): $(REGEX)
(cd $(REGEX); ./configure; make install)
endif
$(REGEX):
$(DOWNLOAD) $(REGEXURL)
tar -xvf $(REGEX).tar.gz
-rm $(REGEX).tar.gz
#
# TIFF
#
$(TIFF):
$(DOWNLOAD) $(TIFFURL)
tar -xvf $(TIFF).tar.gz
-rm $(TIFF).tar.gz
(cd $(TIFF); ./configure --prefix=$(TIFFPREFIX); make install)
#
# Directories
#
$(INSTALLDIR):
mkdir -p $(INSTALLDIR)
$(INSTALLDIR)/lib: $(INSTALLDIR)
mkdir -p $(INSTALLDIR)/lib
$(INSTALLDIR)/bin: $(INSTALLDIR)
mkdir -p $(INSTALLDIR)/bin
$(INSTALLDIR)/include: $(INSTALLDIR)
mkdir -p $(INSTALLDIR)/include
$(INSTALLDIR)/include/cbflib: $(INSTALLDIR)/include
mkdir -p $(INSTALLDIR)/include/cbflib
$(LIB):
mkdir $@
$(BIN):
mkdir $@
$(SOLIB):
mkdir $@
$(JCBF):
mkdir $@
#
# Parser
#
$(SRC)/cbf_stx.c: $(SRC)/cbf.stx.y
bison $(SRC)/cbf.stx.y -o $(SRC)/cbf.stx.tab.c -d
mv $(SRC)/cbf.stx.tab.c $(SRC)/cbf_stx.c
mv $(SRC)/cbf.stx.tab.h $(INCLUDE)/cbf_stx.h
#
# CBF library
#
$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB)
$(CC) $(CFLAGS) $(NOLLFLAG) $(PYCIFRWFLAG) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
$(AR) cr $@ *.o
mv *.o $(LIB)
ifneq ($(RANLIB),)
$(RANLIB) $@
endif
$(SOLIB)/libcbf.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
$(CC) $(CFLAGS) $(NOLLFLAG) $(PYCIFRWFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
$(CC) -o $@ *.o $(SOLDFLAGS) $(EXTRALIBS)
rm *.o
#
# IMG library
#
$(LIB)/libimg.a: $(EXAMPLES)/img.c $(HEADERS) $(COMMONDEP) $(LIB)
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
$(AR) cr $@ img.o
ifneq ($(RANLIB),)
$(RANLIB) $@
endif
rm img.o
$(SOLIB)/libimg.so: $(SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
$(CC) $(CFLAGS) $(NOLLFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(EXAMPLES)/img.c
$(CC) -o $@ img.o $(SOLDFLAGS)
rm img.o
#
# CBF and IMG libraries
#
CBF_IMG_LIBS: $(LIB)/libcbf.a $(LIB)/libimg.a
#
# FCB library
#
$(LIB)/libfcb.a: $(F90SOURCE) $(COMMONDEP) $(LIB)
ifneq ($(F90C),)
$(F90C) $(F90FLAGS) -c $(F90SOURCE)
$(AR) cr $@ *.o
ifneq ($(RANLIB),)
$(RANLIB) $@
endif
rm *.o
else
echo "Define F90C to build $(LIB)/libfcb.a"
endif
$(SOLIB)/libfcb.so: $(F90SOURCE) $(HEADERS) $(COMMONDEP) $(SOLIB)
ifneq ($(F90C),)
$(F90C) $(F90FLAGS) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) -c $(F90SOURCE)
$(F90C) $(F90FLAGS) -o $@ *.o $(SOLDFLAGS)
rm *.o
else
echo "Define F90C to build $(SOLIB)/libfcb.so"
endif
#
# Python bindings
#
$(PYCBF)/_pycbf.$(PYCBFEXT): $(PYCBF) $(LIB)/libcbf.a \
$(PYCBF)/$(SETUP_PY) \
$(LIB)/libfcb.a \
$(LIB)/libimg.a \
$(PYCBF)/pycbf.i \
$(PYCBF)/cbfhandlewrappers.i \
$(PYCBF)/cbfdetectorwrappers.i \
$(PYCBF)/cbfgenericwrappers.i \
$(PYCBF)/cbfgoniometerwrappers.i
(cd $(PYCBF); python $(SETUP_PY) build $(PYCBFBOPT); cp build/lib.*/_pycbf.$(PYCBFEXT) .)
$(PYCBF)/setup.py: $(M4)/setup_py.m4
(m4 -P -Dregexlib=NOREGEXLIB -Dregexlibdir=NOREGEXLIBDIR $(M4)/setup_py.m4 > $@)
$(PYCBF)/setup_MINGW.py: m4/setup_py.m4
(m4 -P -Dregexlib=regex -Dregexlibdir=$(REGEXDIR) $(M4)/setup_py.m4 > $@)
$(LIB)/_pycbf.$(PYCBFEXT): $(PYCBF)/_pycbf.$(PYCBFEXT)
cp $(PYCBF)/_pycbf.$(PYCBFEXT) $(LIB)/_pycbf.$(PYCBFEXT)
$(PYCBF)/pycbf.pdf: $(PYCBF)/pycbf.w
(cd $(PYCBF); \
$(NUWEB) pycbf; \
latex pycbf; \
$(NUWEB) pycbf; \
latex pycbf; \
dvipdfm pycbf )
$(PYCBF)/CBFlib.txt: $(DOC)/CBFlib.html
links -dump $(DOC)/CBFlib.html > $(PYCBF)/CBFlib.txt
$(PYCBF)/cbfhandlewrappers.i \
$(PYCBF)/cbfdetectorwrappers.i \
$(PYCBF)/cbfgenericwrappers.i \
$(PYCBF)/cbfgoniometerwrappers.i: $(PYCBF)/CBFlib.txt $(PYCBF)/make_pycbf.py
(cd $(PYCBF); python make_pycbf.py; $(PYSWIG) pycbf.i; python setup.py build)
#
# Java bindings
#
$(JCBF)/cbflib-$(VERSION).jar: $(JCBF) $(JCBF)/jcbf.i
$(JSWIG) -I$(INCLUDE) -package org.iucr.cbflib -outdir $(JCBF) $(JCBF)/jcbf.i
$(JAVAC) -d . $(JCBF)/*.java
$(JAR) cf $@ org
$(SOLIB)/libcbf_wrap.so: $(JCBF)/cbflib-$(VERSION).jar $(SOLIB)/libcbf.so
$(CC) $(CFLAGS) $(NOLLFLAG) $(SOCFLAGS) $(INCLUDES) $(WARNINGS) $(JAVAINCLUDES) -c $(JCBF)/jcbf_wrap.c
$(CC) -o $@ jcbf_wrap.o $(SOLDFLAGS) -L$(SOLIB) -lcbf
rm jcbf_wrap.o
#
# F90SOURCE
#
$(SRC)/fcb_exit_binary.f90: $(M4)/fcb_exit_binary.m4 $(M4)/fcblib_defines.m4
(cd $(M4); m4 -P $(M4FLAGS) fcb_exit_binary.m4) > $(SRC)/fcb_exit_binary.f90
$(SRC)/fcb_next_binary.f90: $(M4)/fcb_next_binary.m4 $(M4)/fcblib_defines.m4
(cd $(M4); m4 -P $(M4FLAGS) fcb_next_binary.m4) > $(SRC)/fcb_next_binary.f90
$(SRC)/fcb_open_cifin.f90: $(M4)/fcb_open_cifin.m4 $(M4)/fcblib_defines.m4
(cd $(M4); m4 -P $(M4FLAGS) fcb_open_cifin.m4) > $(SRC)/fcb_open_cifin.f90
$(SRC)/fcb_packed.f90: $(M4)/fcb_packed.m4 $(M4)/fcblib_defines.m4
(cd $(M4); m4 -P $(M4FLAGS) fcb_packed.m4) > $(SRC)/fcb_packed.f90
$(SRC)/fcb_read_bits.f90: $(M4)/fcb_read_bits.m4 $(M4)/fcblib_defines.m4
(cd $(M4); m4 -P $(M4FLAGS) fcb_read_bits.m4) > $(SRC)/fcb_read_bits.f90
$(SRC)/fcb_read_image.f90: $(M4)/fcb_read_image.m4 $(M4)/fcblib_defines.m4
(cd $(M4); m4 -P $(M4FLAGS) fcb_read_image.m4) > $(SRC)/fcb_read_image.f90
$(SRC)/fcb_read_xds_i2.f90: $(M4)/fcb_read_xds_i2.m4 $(M4)/fcblib_defines.m4
(cd $(M4); m4 -P $(M4FLAGS) fcb_read_xds_i2.m4) > $(SRC)/fcb_read_xds_i2.f90
$(EXAMPLES)/test_fcb_read_image.f90: $(M4)/test_fcb_read_image.m4 $(M4)/fcblib_defines.m4
(cd $(M4); m4 -P $(M4FLAGS) test_fcb_read_image.m4) > $(EXAMPLES)/test_fcb_read_image.f90
$(EXAMPLES)/test_xds_binary.f90: $(M4)/test_xds_binary.m4 $(M4)/fcblib_defines.m4
(cd $(M4); m4 -P $(M4FLAGS) test_xds_binary.m4) > $(EXAMPLES)/test_xds_binary.f90
#
# convert_image example program
#
$(BIN)/convert_image: $(LIB)/libcbf.a $(EXAMPLES)/convert_image.c $(EXAMPLES)/img.c \
$(GOPTLIB) $(GOPTINC)
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/convert_image.c $(EXAMPLES)/img.c $(GOPTLIB) -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
#
# convert_minicbf example program
#
$(BIN)/convert_minicbf: $(LIB)/libcbf.a $(EXAMPLES)/convert_minicbf.c \
$(GOPTLIB) $(GOPTINC)
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/convert_minicbf.c $(GOPTLIB) -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
#
# makecbf example program
#
$(BIN)/makecbf: $(LIB)/libcbf.a $(EXAMPLES)/makecbf.c $(LIB)/libimg.a
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/makecbf.c -L$(LIB) \
-lcbf $(EXTRALIBS) -limg -o $@
#
# adscimg2cbf example program
#
$(BIN)/adscimg2cbf: $(LIB)/libcbf.a $(EXAMPLES)/adscimg2cbf.c $(EXAMPLES)/adscimg2cbf_sub.c
$(CC) $(CFLAGS) $(NOLLFLAG) -D_SVID_SOURCE $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/adscimg2cbf.c $(EXAMPLES)/adscimg2cbf_sub.c -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
#
# cbf2adscimg example program
#
$(BIN)/cbf2adscimg: $(LIB)/libcbf.a $(EXAMPLES)/cbf2adscimg.c $(EXAMPLES)/cbf2adscimg_sub.c
$(CC) $(CFLAGS) $(NOLLFLAG) -D_SVID_SOURCE $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/cbf2adscimg.c $(EXAMPLES)/cbf2adscimg_sub.c -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
#
# changtestcompression example program
#
$(BIN)/changtestcompression: $(LIB)/libcbf.a $(EXAMPLES)/changtestcompression.c
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/changtestcompression.c -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
#
# img2cif example program
#
$(BIN)/img2cif: $(LIB)/libcbf.a $(EXAMPLES)/img2cif.c $(LIB)/libimg.a \
$(GOPTLIB) $(GOTPINC)
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/img2cif.c $(GOPTLIB) -L$(LIB) \
-lcbf $(EXTRALIBS) -limg -o $@
#
# cif2cbf example program
#
$(BIN)/cif2cbf: $(LIB)/libcbf.a $(EXAMPLES)/cif2cbf.c $(LIB)/libimg.a \
$(GOPTLIB) $(GOPTINC)
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/cif2cbf.c $(GOPTLIB) -L$(LIB) \
-lcbf $(EXTRALIBS) -limg -o $@
#
# dectris cbf_template_t program
#
$(BIN)/cbf_template_t: $(DECTRIS_EXAMPLES)/cbf_template_t.c \
$(DECTRIS_EXAMPLES)/mx_cbf_t_extras.h \
$(DECTRIS_EXAMPLES)/mx_parms.h
$(CC) $(CFLAGS) $(NOLLFLAG) -I $(DECTRIS_EXAMPLES) $(WARNINGS) \
$(DECTRIS_EXAMPLES)/cbf_template_t.c -o $@
#
# testcell example program
#
$(BIN)/testcell: $(LIB)/libcbf.a $(EXAMPLES)/testcell.C
$(C++) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/testcell.C -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
#
# cif2c example program
#
$(BIN)/cif2c: $(LIB)/libcbf.a $(EXAMPLES)/cif2c.c
$(C++) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/cif2c.c -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
#
# sauter_test example program
#
$(BIN)/sauter_test: $(LIB)/libcbf.a $(EXAMPLES)/sauter_test.C
$(C++) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/sauter_test.C -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
#
# sequence_match example program
#
$(BIN)/sequence_match: $(LIB)/libcbf.a $(EXAMPLES)/sequence_match.c $(LIB)/libimg.a \
$(GOPTLIB) $(GOPTINC)
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/sequence_match.c $(GOPTLIB) -L$(LIB) \
-lcbf $(EXTRALIBS) -limg -o $@
#
# tiff2cbf example program
#
$(BIN)/tiff2cbf: $(LIB)/libcbf.a $(EXAMPLES)/tiff2cbf.c \
$(GOPTLIB) $(GOPTINC) $(TIFF)
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
-I$(TIFFPREFIX)/include $(EXAMPLES)/tiff2cbf.c $(GOPTLIB) -L$(LIB) \
-lcbf -L$(TIFFPREFIX)/lib -ltiff $(EXTRALIBS) -limg -o $@
#
# Andy Arvai''`s buffered read test program
#
$(BIN)/arvai_test: $(LIB)/libcbf.a $(EXAMPLES)/arvai_test.c $(LIB)/libimg.a \
$(GOPTLIB) $(GOPTINC)
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/arvai_test.c $(GOPTLIB) -L$(LIB) \
-lcbf $(EXTRALIBS) -limg -o $@
#
# testreals example program
#
$(BIN)/testreals: $(LIB)/libcbf.a $(EXAMPLES)/testreals.c
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/testreals.c -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
#
# testflat example program
#
$(BIN)/testflat: $(LIB)/libcbf.a $(EXAMPLES)/testflat.c
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/testflat.c -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
#
# testflatpacked example program
#
$(BIN)/testflatpacked: $(LIB)/libcbf.a $(EXAMPLES)/testflatpacked.c
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/testflatpacked.c -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
ifneq ($(F90C),)
#
# test_xds_binary example program
#
$(BIN)/test_xds_binary: $(LIB)/libfcb.a $(EXAMPLES)/test_xds_binary.f90
$(F90C) $(F90FLAGS) $(F90LDFLAGS) $(EXAMPLES)/test_xds_binary.f90 \
-L$(LIB) -lfcb -o $@
#
# test_fcb_read_image example program
#
$(BIN)/test_fcb_read_image: $(LIB)/libfcb.a $(EXAMPLES)/test_fcb_read_image.f90
$(F90C) $(F90FLAGS) $(F90LDFLAGS) $(EXAMPLES)/test_fcb_read_image.f90 \
-L$(LIB) -lfcb -o $@
endif
#
# testcbf (C)
#
$(BIN)/ctestcbf: $(EXAMPLES)/testcbf.c $(LIB)/libcbf.a
$(CC) $(CFLAGS) $(NOLLFLAG) $(INCLUDES) $(WARNINGS) \
$(EXAMPLES)/testcbf.c -L$(LIB) \
-lcbf $(EXTRALIBS) -o $@
#
# testcbf (Java)
#
$(BIN)/testcbf.class: $(EXAMPLES)/testcbf.java $(JCBF)/cbflib-$(VERSION).jar $(SOLIB)/libcbf_wrap.so
$(JAVAC) -cp $(JCBF)/cbflib-$(VERSION).jar -d $(BIN) $(EXAMPLES)/testcbf.java
#
# Data files for tests
#
$(DATADIRI):
(cd ..; $(DOWNLOAD) $(DATAURLI))
(cd ..; tar -zxvf CBFlib_$(VERSION)_Data_Files_Input.tar.gz)
-(cd ..; rm CBFlib_$(VERSION)_Data_Files_Input.tar.gz)
$(DATADIRO):
(cd ..; $(DOWNLOAD) $(DATAURLO))
(cd ..; tar -zxvf CBFlib_$(VERSION)_Data_Files_Output.tar.gz)
-(cd ..; rm CBFlib_$(VERSION)_Data_Files_Output.tar.gz)
$(DATADIRS):
(cd ..; $(DOWNLOAD) $(DATAURLS))
(cd ..; tar -zxvf CBFlib_$(VERSION)_Data_Files_Output_Sigs_Only.tar.gz)
-(cd ..; rm CBFlib_$(VERSION)_Data_Files_Output_Sigs_Only.tar.gz)
# Input Data Files
TESTINPUT_BASIC = example.mar2300
DATADIRI_INPUT_BASIC = $(DATADIRI)/example.mar2300$(CEXT)
TESTINPUT_EXTRA = 9ins.cif mb_LP_1_001.img insulin_pilatus6m.cbf testrealin.cbf \
testflatin.cbf testflatpackedin.cbf XRD1621.tif
DATADIRI_INPUT_EXTRA = $(DATADIRI)/9ins.cif$(CEXT) $(DATADIRI)/mb_LP_1_001.img$(CEXT) \
$(DATADIRI)/insulin_pilatus6m.cbf$(CEXT) $(DATADIRI)/testrealin.cbf$(CEXT) \
$(DATADIRI)/testflatin.cbf$(CEXT) $(DATADIRI)/testflatpackedin.cbf$(CEXT) \
$(DATADIRI)/XRD1621.tif$(CEXT)
# Output Data Files
TESTOUTPUT = adscconverted_flat_orig.cbf \
adscconverted_orig.cbf converted_flat_orig.cbf converted_orig.cbf \
insulin_pilatus6mconverted_orig.cbf \
mb_LP_1_001_orig.cbf testcell_orig.prt \
test_xds_bin_testflatout_orig.out \
test_xds_bin_testflatpackedout_orig.out test_fcb_read_testflatout_orig.out \
test_fcb_read_testflatpackedout_orig.out \
XRD1621_orig.cbf XRD1621_I4encbC100_orig.cbf
NEWTESTOUTPUT = adscconverted_flat.cbf \
adscconverted.cbf converted_flat.cbf converted.cbf \
insulin_pilatus6mconverted.cbf \
mb_LP_1_001.cbf testcell.prt \
test_xds_bin_testflatout.out \
test_xds_bin_testflatpackedout.out test_fcb_read_testflatout.out \
test_fcb_read_testflatpackedout.out \
XRD1621.cbf XRD1621_I4encbC100.cbf
DATADIRO_OUTPUT = $(DATADIRO)/adscconverted_flat_orig.cbf$(CEXT) \
$(DATADIRO)/adscconverted_orig.cbf$(CEXT) \
$(DATADIRO)/converted_flat_orig.cbf$(CEXT) \
$(DATADIRO)/converted_orig.cbf$(CEXT) \
$(DATADIRO)/insulin_pilatus6mconverted_orig.cbf$(CEXT) \
$(DATADIRO)/mb_LP_1_001_orig.cbf$(CEXT) \
$(DATADIRO)/testcell_orig.prt$(CEXT) \
$(DATADIRO)/test_xds_bin_testflatout_orig.out$(CEXT) \
$(DATADIRO)/test_xds_bin_testflatpackedout_orig.out$(CEXT) \
$(DATADIRO)/test_fcb_read_testflatout_orig.out$(CEXT) \
$(DATADIRO)/test_fcb_read_testflatpackedout_orig.out$(CEXT) \
$(DATADIRO)/XRD1621_orig.cbf$(CEXT) \
$(DATADIRO)/XRD1621_I4encbC100_orig.cbf$(CEXT)
DATADIRO_OUTPUT_SIGNATURES = $(DATADIRO)/adscconverted_flat_orig.cbf$(SEXT) \
$(DATADIRO)/adscconverted_orig.cbf$(SEXT) \
$(DATADIRO)/converted_flat_orig.cbf$(SEXT) \
$(DATADIRO)/converted_orig.cbf$(SEXT) \
$(DATADIRO)/insulin_pilatus6mconverted_orig.cbf$(SEXT) \
$(DATADIRO)/mb_LP_1_001_orig.cbf$(SEXT) \
$(DATADIRO)/testcell_orig.prt$(SEXT) \
$(DATADIRO)/test_xds_bin_testflatout_orig.out$(SEXT) \
$(DATADIRO)/test_xds_bin_testflatpackedout_orig.out$(SEXT) \
$(DATADIRO)/test_fcb_read_testflatout_orig.out$(SEXT) \
$(DATADIRO)/test_fcb_read_testflatpackedout_orig.out$(SEXT) \
$(DATADIRO)/XRD1621_orig.cbf$(SEXT) \
$(DATADIRO)/XRD1621_I4encbC100_orig.cbf$(SEXT)
# Output Data File Signatures
TESTOUTPUTSIGS = adscconverted_flat_orig.cbf$(SEXT) \
adscconverted_orig.cbf$(SEXT) converted_flat_orig.cbf$(SEXT) converted_orig.cbf$(SEXT) \
insulin_pilatus6mconverted_orig.cbf$(SEXT) \
mb_LP_1_001_orig.cbf$(SEXT) testcell_orig.prt$(SEXT) \
test_xds_bin_testflatout_orig.out$(SEXT) \
test_xds_bin_testflatpackedout_orig.out$(SEXT) test_fcb_read_testflatout_orig.out$(SEXT) \
test_fcb_read_testflatpackedout_orig.out$(SEXT) \
XRD1621_orig.cbf$(SEXT)
DATADIRS_OUTPUT_SIGNATURES = $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT) \
$(DATADIRS)/adscconverted_orig.cbf$(SEXT) \
$(DATADIRS)/converted_flat_orig.cbf$(SEXT) \
$(DATADIRS)/converted_orig.cbf$(SEXT) \
$(DATADIRS)/insulin_pilatus6mconverted_orig.cbf$(SEXT) \
$(DATADIRS)/mb_LP_1_001_orig.cbf$(SEXT) \
$(DATADIRS)/testcell_orig.prt$(SEXT) \
$(DATADIRS)/test_xds_bin_testflatout_orig.out$(SEXT) \
$(DATADIRS)/test_xds_bin_testflatpackedout_orig.out$(SEXT) \
$(DATADIRS)/test_fcb_read_testflatout_orig.out$(SEXT) \
$(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT) \
$(DATADIRS)/XRD1621_orig.cbf$(SEXT) \
$(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
# Fetch Input Data Files
$(TESTINPUT_BASIC): $(DATADIRI) $(DATADIRI_INPUT_BASIC)
$(DECOMPRESS) < $(DATADIRI)/$@$(CEXT) > $@
cp $(DATADIRI)/$@$(SEXT) $@$(SEXT)
-$(SIGNATURE) < $@ | $(DIFF) - $@$(SEXT)
$(TESTINPUT_EXTRA): $(DATADIRI) $(DATADIRI_INPUT_EXTRA)
$(DECOMPRESS) < $(DATADIRI)/$@$(CEXT) > $@
cp $(DATADIRI)/$@$(SEXT) $@$(SEXT)
-$(SIGNATURE) < $@ | $(DIFF) - $@$(SEXT)
# Fetch Output Data Files and Signatures
$(TESTOUTPUT): $(DATADIRO) $(DATADIRO_OUTPUT) $(DATADIRO_OUTPUT_SIGNATURES)
$(DECOMPRESS) < $(DATADIRO)/$@$(CEXT) > $@
cp $(DATADIRO)/$@$(SEXT) $@$(SEXT)
-$(SIGNATURE) < $@ | $(DIFF) - $@$(SEXT)
# Fetch Output Data File Signatures
$(TESTOUTPUTSIGS): $(DATADIRS) $(DATADIRS_OUTPUT_SIGNATURES)
cp $(DATADIRS)/$@ $@
#
# Tests
#
tests: $(LIB) $(BIN) symlinksdone basic extra dectristests pycbftests
tests_sigs_only: $(LIB) $(BIN) symlinksdone basic extra_sigs_only
restore_output: $(NEWTESTOUTPUT) $(DATADIRO)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRO)/adscconverted_flat_orig.cbf$(SEXT)
$(SIGNATURE) < adscconverted.cbf > $(DATADIRO)/adscconverted_orig.cbf$(SEXT)
$(SIGNATURE) < converted_flat.cbf > $(DATADIRO)/converted_flat_orig.cbf$(SEXT)
$(SIGNATURE) < converted.cbf > $(DATADIRO)/converted_orig.cbf$(SEXT)
$(SIGNATURE) < insulin_pilatus6mconverted.cbf > $(DATADIRO)/insulin_pilatus6mconverted_orig.cbf$(SEXT)
$(SIGNATURE) < mb_LP_1_001.cbf$ > $(DATADIRO)/mb_LP_1_001_orig.cbf$(SEXT)
$(SIGNATURE) < testcell.prt > $(DATADIRO)/testcell_orig.prt$(SEXT)
$(SIGNATURE) < test_xds_bin_testflatout.out > $(DATADIRO)/test_xds_bin_testflatout_orig.out$(SEXT)
$(SIGNATURE) < test_xds_bin_testflatpackedout.out > $(DATADIRO)/test_xds_bin_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < test_fcb_read_testflatout.out > $(DATADIRO)/test_fcb_read_testflatout_orig.out$(SEXT)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRO)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRO)/XRD1621_I4encbC100_orig.cbf$(SEXT)
$(COMPRESS) < adscconverted_flat.cbf > $(DATADIRO)/adscconverted_flat_orig.cbf$(CEXT)
$(COMPRESS) < adscconverted.cbf > $(DATADIRO)/adscconverted_orig.cbf$(CEXT)
$(COMPRESS) < converted_flat.cbf > $(DATADIRO)/converted_flat_orig.cbf$(CEXT)
$(COMPRESS) < converted.cbf > $(DATADIRO)/converted_orig.cbf$(CEXT)
$(COMPRESS) < insulin_pilatus6mconverted.cbf > $(DATADIRO)/insulin_pilatus6mconverted_orig.cbf$(CEXT)
$(COMPRESS) < mb_LP_1_001.cbf$ > $(DATADIRO)/mb_LP_1_001_orig.cbf$(CEXT)
$(COMPRESS) < testcell.prt > $(DATADIRO)/testcell_orig.prt$(CEXT)
$(COMPRESS) < test_xds_bin_testflatout.out > $(DATADIRO)/test_xds_bin_testflatout_orig.out$(CEXT)
$(COMPRESS) < test_xds_bin_testflatpackedout.out > $(DATADIRO)/test_xds_bin_testflatpackedout_orig.out$(CEXT)
$(COMPRESS) < test_fcb_read_testflatout.out > $(DATADIRO)/test_fcb_read_testflatout_orig.out$(CEXT)
$(COMPRESS) < test_fcb_read_testflatpackedout.out > $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out$(CEXT)
$(COMPRESS) < XRD1621.cbf > $(DATADIRO)/XRD1621_orig.cbf$(CEXT)
$(COMPRESS) < XRD1621_I4encbC100.cbf > $(DATADIRO)/XRD1621_I4encbC100_orig.cbf$(CEXT)
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
$(SIGNATURE) < adscconverted.cbf > $(DATADIRS)/adscconverted_orig.cbf$(SEXT)
$(SIGNATURE) < converted_flat.cbf > $(DATADIRS)/converted_flat_orig.cbf$(SEXT)
$(SIGNATURE) < converted.cbf > $(DATADIRS)/converted_orig.cbf$(SEXT)
$(SIGNATURE) < insulin_pilatus6mconverted.cbf > $(DATADIRS)/insulin_pilatus6mconverted_orig.cbf$(SEXT)
$(SIGNATURE) < mb_LP_1_001.cbf$ > $(DATADIRS)/mb_LP_1_001_orig.cbf$(SEXT)
$(SIGNATURE) < testcell.prt > $(DATADIRS)/testcell_orig.prt$(SEXT)
$(SIGNATURE) < test_xds_bin_testflatout.out > $(DATADIRS)/test_xds_bin_testflatout_orig.out$(SEXT)
$(SIGNATURE) < test_xds_bin_testflatpackedout.out > $(DATADIRS)/test_xds_bin_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < test_fcb_read_testflatout.out > $(DATADIRS)/test_fcb_read_testflatout_orig.out$(SEXT)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
# Basic Tests
#
basic: $(BIN)/makecbf $(BIN)/img2cif $(BIN)/cif2cbf $(TESTINPUT_BASIC)
$(BIN)/makecbf example.mar2300 makecbf.cbf
$(BIN)/img2cif -c flatpacked -m headers -d digest \
-e base64 example.mar2300 img2cif_packed.cif
$(BIN)/img2cif -c canonical -m headers -d digest \
-e base64 example.mar2300 img2cif_canonical.cif
$(BIN)/img2cif -c flatpacked -m headers -d digest \
-e none example.mar2300 img2cif_packed.cbf
$(BIN)/img2cif -c canonical -m headers -d digest \
-e none example.mar2300 img2cif_canonical.cbf
$(BIN)/cif2cbf -e none -c flatpacked \
img2cif_canonical.cif cif2cbf_packed.cbf
$(BIN)/cif2cbf -e none -c canonical \
img2cif_packed.cif cif2cbf_canonical.cbf
-cmp cif2cbf_packed.cbf makecbf.cbf
-cmp cif2cbf_packed.cbf img2cif_packed.cbf
-cmp cif2cbf_canonical.cbf img2cif_canonical.cbf
#
# Extra Tests
#
ifneq ($(F90C),)
extra: $(BIN)/convert_image $(BIN)/convert_minicbf $(BIN)/cif2cbf $(BIN)/testcell \
$(BIN)/testreals $(BIN)/testflat $(BIN)/testflatpacked \
$(BIN)/test_xds_binary $(BIN)/test_fcb_read_image $(BIN)/convert_minicbf \
$(BIN)/sauter_test $(BIN)/adscimg2cbf $(BIN)/cbf2adscimg \
$(BIN)/changtestcompression $(BIN)/tiff2cbf \
basic $(TESTINPUT_EXTRA) $(TESTOUTPUT)
else
extra: $(BIN)/convert_image $(BIN)/convert_minicbf $(BIN)/cif2cbf $(BIN)/testcell \
$(BIN)/testreals $(BIN)/testflat $(BIN)/testflatpacked \
$(BIN)/convert_minicbf \
$(BIN)/sauter_test $(BIN)/adscimg2cbf $(BIN)/cbf2adscimg \
basic $(TESTINPUT_EXTRA) $(TESTOUTPUT)
endif
$(TIME) $(BIN)/cif2cbf -e hex -c none \
makecbf.cbf cif2cbf_ehcn.cif
$(TIME) $(BIN)/cif2cbf -e none -c flatpacked \
cif2cbf_ehcn.cif cif2cbf_encp.cbf; rm cif2cbf_ehcn.cif
-cmp makecbf.cbf cif2cbf_encp.cbf
$(TIME) $(BIN)/cif2cbf -i 9ins.cif -o 9ins.cbf
-cmp 9ins.cif 9ins.cbf
$(TIME) $(BIN)/convert_image -F example.mar2300 converted_flat.cbf
-cmp converted_flat.cbf converted_flat_orig.cbf
$(TIME) $(BIN)/convert_image example.mar2300 converted.cbf
-cmp converted.cbf converted_orig.cbf
-$(TIME) $(BIN)/testcell < testcell.dat > testcell.prt
-cmp testcell.prt testcell_orig.prt
$(TIME) $(BIN)/convert_image -F -d adscquantum315 mb_LP_1_001.img adscconverted_flat.cbf
-cmp adscconverted_flat.cbf adscconverted_flat_orig.cbf
$(TIME) $(BIN)/convert_image -d adscquantum315 mb_LP_1_001.img adscconverted.cbf
-cmp adscconverted.cbf adscconverted_orig.cbf
$(TIME) $(BIN)/adscimg2cbf --no_pad --cbf_packed,flat mb_LP_1_001.img
-cmp mb_LP_1_001.cbf mb_LP_1_001_orig.cbf
ifneq ($(CLEANTESTS),)
mv mb_LP_1_001.cbf nmb_LP_1_001.cbf
else
cp mb_LP_1_001.cbf nmb_LP_1_001.cbf
endif
$(TIME) $(BIN)/cbf2adscimg nmb_LP_1_001.cbf
-cmp nmb_LP_1_001.img mb_LP_1_001.img
rm nmb_LP_1_001.cbf
ifneq ($(CLEANTESTS),)
rm nmb_LP_1_001.img
endif
$(TIME) $(BIN)/convert_minicbf -d pilatus6m insulin_pilatus6m.cbf insulin_pilatus6mconverted.cbf
-cmp insulin_pilatus6mconverted.cbf insulin_pilatus6mconverted_orig.cbf
$(TIME) $(BIN)/testreals
-cmp testrealin.cbf testrealout.cbf
$(TIME) $(BIN)/testflat
-cmp testflatin.cbf testflatout.cbf
$(TIME) $(BIN)/testflatpacked
-cmp testflatpackedin.cbf testflatpackedout.cbf
ifneq ($(F90C),)
echo testflatout.cbf | $(TIME) $(BIN)/test_xds_binary > test_xds_bin_testflatout.out
-$(DIFF) test_xds_bin_testflatout.out test_xds_bin_testflatout_orig.out
echo testflatpackedout.cbf | $(TIME) $(BIN)/test_xds_binary > test_xds_bin_testflatpackedout.out
-$(DIFF) test_xds_bin_testflatpackedout.out test_xds_bin_testflatpackedout_orig.out
echo testflatout.cbf | $(TIME) $(BIN)/test_fcb_read_image > test_fcb_read_testflatout.out
-$(DIFF) test_fcb_read_testflatout.out test_fcb_read_testflatout_orig.out
echo testflatpackedout.cbf | $(TIME) $(BIN)/test_fcb_read_image > test_fcb_read_testflatpackedout.out
-$(DIFF) test_fcb_read_testflatpackedout.out test_fcb_read_testflatpackedout_orig.out
endif
$(TIME) $(BIN)/sauter_test
$(TIME) $(BIN)/changtestcompression
$(TIME) (export LD_LIBRARY_PATH=$(LIB);$(BIN)/tiff2cbf XRD1621.tif XRD1621.cbf)
-$(DIFF) XRD1621.cbf XRD1621_orig.cbf
$(TIME) $(BIN)/cif2cbf -I 4 -C 100. -L 0. -e n -c b -i XRD1621.cbf -o XRD1621_I4encbC100.cbf
-$(DIFF) XRD1621_I4encbC100.cbf XRD1621_I4encbC100_orig.cbf
ifneq ($(F90C),)
extra_sigs_only: $(BIN)/convert_image $(BIN)/convert_minicbf $(BIN)/cif2cbf $(BIN)/testcell \
$(BIN)/testreals $(BIN)/testflat $(BIN)/testflatpacked \
$(BIN)/test_xds_binary $(BIN)/test_fcb_read_image $(BIN)/convert_minicbf \
$(BIN)/sauter_test $(BIN)/adscimg2cbf $(BIN)/cbf2adscimg $(BIN)/tiff2cbf \
basic $(TESTINPUT_EXTRA) $(TESTOUTPUTSIGS)
else
extra_sigs_only: $(BIN)/convert_image $(BIN)/convert_minicbf $(BIN)/cif2cbf $(BIN)/testcell \
$(BIN)/testreals $(BIN)/testflat $(BIN)/testflatpacked \
$(BIN)/convert_minicbf \
$(BIN)/sauter_test $(BIN)/adscimg2cbf\
basic $(TESTINPUT_EXTRA) $(TESTOUTPUTSIGS)
endif
$(TIME) $(BIN)/cif2cbf -e hex -c none \
makecbf.cbf cif2cbf_ehcn.cif
$(TIME) $(BIN)/cif2cbf -e none -c packed \
cif2cbf_ehcn.cif cif2cbf_encp.cbf; rm cif2cbf_ehcn.cif
-cmp makecbf.cbf cif2cbf_encp.cbf
$(TIME) $(BIN)/cif2cbf -i 9ins.cif -o 9ins.cbf
-cmp 9ins.cif 9ins.cbf
$(TIME) $(BIN)/convert_image -F example.mar2300 converted_flat.cbf
-$(SIGNATURE) < converted_flat.cbf | $(DIFF) - converted_flat_orig.cbf$(SEXT); rm converted_flat.cbf
$(TIME) $(BIN)/convert_image example.mar2300 converted.cbf
-$(SIGNATURE) < converted.cbf | $(DIFF) - converted_orig.cbf$(SEXT); rm converted.cbf
-$(TIME) $(BIN)/testcell < testcell.dat | \
$(SIGNATURE) | $(DIFF) - testcell_orig.prt$(SEXT)
$(TIME) $(BIN)/convert_image -F -d adscquantum315 mb_LP_1_001.img adscconverted_flat.cbf
-$(SIGNATURE) < adscconverted_flat.cbf | $(DIFF) - adscconverted_flat_orig.cbf$(SEXT)
$(TIME) $(BIN)/convert_image -d adscquantum315 mb_LP_1_001.img adscconverted.cbf
-$(SIGNATURE) < adscconverted.cbf | $(DIFF) - adscconverted_orig.cbf$(SEXT); rm adscconverted.cbf
$(TIME) $(BIN)/adscimg2cbf --cbf_packed,flat mb_LP_1_001.img
-$(SIGNATURE) < mb_LP_1_001.cbf | $(DIFF) - mb_LP_1_001_orig.cbf$(SEXT)
mv mb_LP_1_001.cbf nmb_LP_1_001.cbf
$(TIME) $(BIN)/cbf2adscimg nmb_LP_1_001.cbf
-cmp nmb_LP_1_001.img mb_LP_1_001.img
rm nmb_LP_1_001.cbf
rm nmb_LP_1_001.img
$(TIME) $(BIN)/convert_minicbf -d pilatus6m insulin_pilatus6m.cbf insulin_pilatus6mconverted.cbf
-$(SIGNATURE) < insulin_pilatus6mconverted.cbf | $(DIFF) - insulin_pilatus6mconverted_orig.cbf$(SEXT); rm insulin_pilatus6mconverted.cbf
$(TIME) $(BIN)/testreals
-cmp testrealin.cbf testrealout.cbf
$(TIME) $(BIN)/testflat
-cmp testflatin.cbf testflatout.cbf
$(TIME) $(BIN)/testflatpacked
-cmp testflatpackedin.cbf testflatpackedout.cbf
ifneq ($(F90C),)
echo testflatout.cbf | $(TIME) $(BIN)/test_xds_binary | \
$(SIGNATURE) | $(DIFF) - test_xds_bin_testflatout_orig.out$(SEXT)
echo testflatpackedout.cbf | $(TIME) $(BIN)/test_xds_binary | \
$(SIGNATURE) | $(DIFF) - test_xds_bin_testflatpackedout_orig.out$(SEXT)
echo testflatout.cbf | $(TIME) $(BIN)/test_fcb_read_image | \
$(SIGNATURE) | $(DIFF) - test_fcb_read_testflatout_orig.out$(SEXT)
echo testflatpackedout.cbf | $(TIME) $(BIN)/test_fcb_read_image | \
$(SIGNATURE) | $(DIFF) - test_fcb_read_testflatpackedout_orig.out$(SEXT)
endif
$(TIME) $(BIN)/sauter_test
$(TIME) $(BIN)/tiff2cbf XRD1621.tif XRD1621.cbf
$(TIME) $(BIN)/cif2cbf -I 4 -C 100. -L 0. -e n -c b -i XRD1621.cbf -o XRD1621_I4encbC100.cbf
-$(SIGNATURE) < XRD1621.cbf | $(DIFF) - XRD1621_orig.cbf$(SEXT); rm XRD1621.cbf
-$(SIGNATURE) < XRD1621_I4encbC100.cbf | $(DIFF) - XRD1621_I4encbC100_orig.cbf$(SEXT); rm XRD1621_I4encbC100.cbf
@-rm -f adscconverted_flat.cbf
@-rm -f $(TESTINPUT_BASIC) $(TESTINPUT_EXTRA) $(TESTOUTPUTSIGS)
@-rm -f cif2cbf_packed.cbf makecbf.cbf \
cif2cbf_packed.cbf img2cif_packed.cbf \
cif2cbf_canonical.cbf img2cif_canonical.cbf
@-rm -f testrealout.cbf testflatout.cbf testflatpackedout.cbf \
cif2cbf_encp.cbf img2cif_canonical.cif img2cif_packed.cif 9ins.cbf
pycbftests: $(PYCBF)/_pycbf.$(PYCBFEXT)
(cd $(PYCBF); python pycbf_test1.py)
(cd $(PYCBF); python pycbf_test2.py)
(cd $(PYCBF); python pycbf_test3.py)
javatests: $(BIN)/ctestcbf $(BIN)/testcbf.class $(SOLIB)/libcbf_wrap.so
$(BIN)/ctestcbf > testcbfc.txt
$(LDPREFIX) java -cp $(JCBF)/cbflib-$(VERSION).jar:$(BIN) testcbf > testcbfj.txt
$(DIFF) testcbfc.txt testcbfj.txt
dectristests: $(BIN)/cbf_template_t $(DECTRIS_EXAMPLES)/cbf_test_orig.out
(cd $(DECTRIS_EXAMPLES); ../../bin/cbf_template_t; diff -a -u cbf_test_orig.out cbf_template_t.out)
#
# Remove all non-source files
#
empty:
@-rm -f $(LIB)/*.o
@-rm -f $(LIB)/libcbf.a
@-rm -f $(LIB)/libfcb.a
@-rm -f $(LIB)/libimg.a
@-rm -f $(LIB)/_pycbf.$(PYCBFEXT)
@-rm -f $(PYCBF)/_pycbf.$(PYCBFEXT)
@-rm -f $(PYCBF)/build/*/_pycbf.$(PYCBFEXT)
@-rm -f $(PYCBF)/build/src/cbf_simple.o
@-rm -f $(PYCBF)/build/*/pycbf_wrap.o
@-rm -rf $(BIN)/adscimg2cbf*
@-rm -rf $(BIN)/cbf2adscimg*
@-rm -rf $(BIN)/makecbf*
@-rm -rf $(BIN)/img2cif*
@-rm -rf $(BIN)/cif2cbf*
@-rm -rf $(BIN)/convert_image*
@-rm -rf $(BIN)/convert_minicbf*
@-rm -rf $(BIN)/test_fcb_read_image*
@-rm -rf $(BIN)/test_xds_binary*
@-rm -rf $(BIN)/testcell*
@-rm -rf $(BIN)/cif2c*
@-rm -rf $(BIN)/testreals*
@-rm -rf $(BIN)/testflat*
@-rm -rf $(BIN)/testflatpacked*
@-rm -rf $(BIN)/cbf_template_t*
@-rm -rf $(BIN)/sauter_test*
@-rm -rf $(BIN)/arvai_test*
@-rm -rf $(BIN)/changtestcompression*
@-rm -rf $(BIN)/tiff2cbf*
@-rm -f makecbf.cbf
@-rm -f img2cif_packed.cif
@-rm -f img2cif_canonical.cif
@-rm -f img2cif_packed.cbf
@-rm -f img2cif_canonical.cbf
@-rm -f img2cif_raw.cbf
@-rm -f cif2cbf_packed.cbf
@-rm -f cif2cbf_canonical.cbf
@-rm -f converted.cbf
@-rm -f adscconverted.cbf
@-rm -f converted_flat.cbf
@-rm -f adscconverted_flat.cbf
@-rm -f adscconverted_flat_rev.cbf
@-rm -f mb_LP_1_001.cbf
@-rm -f cif2cbf_ehcn.cif
@-rm -f cif2cbf_encp.cbf
@-rm -f 9ins.cbf
@-rm -f 9ins.cif
@-rm -f testcell.prt
@-rm -f example.mar2300
@-rm -f converted_orig.cbf
@-rm -f adscconverted_orig.cbf
@-rm -f converted_flat_orig.cbf
@-rm -f adscconverted_flat_orig.cbf
@-rm -f adscconverted_flat_rev_orig.cbf
@-rm -f mb_LP_1_001_orig.cbf
@-rm -f insulin_pilatus6mconverted_orig.cbf
@-rm -f insulin_pilatus6mconverted.cbf
@-rm -f insulin_pilatus6m.cbf
@-rm -f testrealin.cbf
@-rm -f testrealout.cbf
@-rm -f testflatin.cbf
@-rm -f testflatout.cbf
@-rm -f testflatpackedin.cbf
@-rm -f testflatpackedout.cbf
@-rm -f CTC.cbf
@-rm -f test_fcb_read_testflatout.out
@-rm -f test_fcb_read_testflatpackedout.out
@-rm -f test_xds_bin_testflatpackedout.out
@-rm -f test_xds_bin_testflatout.out
@-rm -f test_fcb_read_testflatout_orig.out
@-rm -f test_fcb_read_testflatpackedout_orig.out
@-rm -f test_xds_bin_testflatpackedout_orig.out
@-rm -f test_xds_bin_testflatout_orig.out
@-rm -f mb_LP_1_001.img
@-rm -f 9ins.cif
@-rm -f testcell_orig.prt
@-rm -f $(DECTRIS_EXAMPLES)/cbf_template_t.out
@-rm -f XRD1621.cbf
@-rm -f XRD1621_orig.cbf
@-rm -f XRD1621_orig.cbf
@-rm -f XRD1621_I4encbC100.cbf
@-rm -f $(SRC)/fcb_exit_binary.f90
@-rm -f $(SRC)/fcb_next_binary.f90
@-rm -f $(SRC)/fcb_open_cifin.f90
@-rm -f $(SRC)/fcb_packed.f90
@-rm -f $(SRC)/fcb_read_bits.f90
@-rm -f $(SRC)/fcb_read_image.f90
@-rm -f $(SRC)/fcb_read_xds_i2.f90
@-rm -f $(EXAMPLES)/test_fcb_read_image.f90
@-rm -f $(EXAMPLES)/test_xds_binary.f90
@-rm -f symlinksdone
@-rm -f $(TESTOUTPUT) *$(SEXT)
@-rm -f $(SOLIB)/*.o
@-rm -f $(SOLIB)/libcbf_wrap.so
@-rm -f $(SOLIB)/libjcbf.so
@-rm -f $(SOLIB)/libimg.so
@-rm -f $(SOLIB)/libfcb.so
@-rm -rf $(JCBF)/org
@-rm -f $(JCBF)/*.java
@-rm -f $(JCBF)/jcbf_wrap.c
@-rm -f $(SRC)/cbf_wrap.c
@-rm -f $(BIN)/ctestcbf $(BIN)/testcbf.class testcbfc.txt testcbfj.txt
@-rm -rf $(REGEX)
@-rm -rf $(TIFF)
./.undosymlinks
#
# Remove temporary files
#
clean:
@-rm -f core
@-rm -f *.o
@-rm -f *.u
#
# Restore to distribution state
#
distclean: clean empty
#
# Create a Tape Archive for distribution
#
tar: $(DOCUMENTS) $(SOURCE) $(SRC)/cbf.stx $(HEADERS) $(M4FILES)\
$(EXAMPLES) \
README.html README Makefile \
$(JPEGS)
-/bin/rm -f CBFlib.tar*
tar cvBf CBFlib.tar \
$(DOCUMENTS) $(SOURCE) $(SRC)/cbf.stx $(HEADERS) $(M4FILES)\
$(EXAMPLES) \
README.html README Makefile \
$(JPEGS)
gzip --best CBFlib.tar
'
./CBFlib-0.9.2.2/m4/test_xds_binary.m4 0000644 0000765 0000765 00000001260 11603702103 015555 0 ustar yaya yaya m4_include(`fcblib_defines.m4')` PROGRAM TEST
IMPLICIT NONE
CHARACTER(LEN=100) LINE
INTEGER(2) IFRAME(1000,1000), DPREV
INTEGER(4) JFRAME(1000,1000)
INTEGER IER, I, J, K'
fcb_interface_FCB_READ_XDS_I2
` PRINT *,''` NAME OF TEST CBF ''`
READ *, LINE
IER = FCB_READ_XDS_I2(LINE,9,1000,1000,IFRAME,JFRAME)
IF (IER.NE.0) THEN
PRINT *," ERROR: ", IER
ELSE
DPREV = 0
DO I = 1,1000
DO J = 1,1000
IF (IFRAME(I,J).NE.DPREV) THEN
PRINT *,"ROW ", I, ":"
PRINT *,(IFRAME(I,K),K=1,1000)
DPREV = IFRAME(I,1000)
GO TO 1000
ENDIF
END DO
1000 CONTINUE
END DO
END IF
STOP
END
' ./CBFlib-0.9.2.2/m4/fcb_read_xds_i2.m4 0000644 0000765 0000765 00000023035 11603702103 015355 0 ustar yaya yaya m4_include(`fcblib_defines.m4')
` INTEGER FUNCTION FCB_READ_XDS_I2(FILNAM,TAPIN,NX,NY,IFRAME,JFRAME)
!-----------------------------------------------------------------------
! Reads a 32 bit integer two''`s complement image compressed by a
! BYTE-OFFSET algorithm. W. Kabsch, Version 9-2006
!
! REVISED 1-2007, H. J. Bernstein to conform to CBFlib_0.7.7
! (http://www.bernstein-plus-sons.com/software/CBF)
!
! The BYTE-OFFSET algorithm is a slightly simplified version of
! that described in Andy Hammersley''`s web page
! (http://www.esrf.fr/computing/Forum/imgCIF/cbf_definition.html)
!
!-----------------------------------------------------------------------
! FILNAM - Name of the file countaining the image (GIVEN)
! TAPIN - Fortran device unit number assigned to image file (GIVEN)
! NX - Number of "fast" pixels of the image (GIVEN)
! NY - Number of "slow" pixels of the image (GIVEN)
! IFRAME - 16 bit coded image as needed by XDS (RESULT)
! Returns (as function value) (RESULT)
! CBF_FORMAT (=1):
! cannot handle this CBF format (not implemented)
! 0: No error
! -1: Cannot determine endian architecture of this machine
! -2: Cannot open image file
! -3: Wrong image format
! -4: Cannot read image
!-----------------------------------------------------------------------
IMPLICIT NONE
CHARACTER(len=*),INTENT(IN) :: FILNAM
INTEGER, INTENT(IN) :: TAPIN,NX,NY
INTEGER(2), INTENT(OUT):: IFRAME(NX*NY)
INTEGER(4), INTENT(OUT):: JFRAME(NX,NY)
INTEGER(8) NELEM,NELEM_READ
! -- Definition of CBF_FORMAT'
fcb_errcode_CBF_FORMAT
`! -- External functions called'
fcb_interface_FCB_READ_BYTE
fcb_interface_FCB_NEXT_BINARY
fcb_interface_FCB_CI_STRNCMPARR
fcb_interface_FCB_DECOMPRESS_PACKED_I4
INTEGER(2) CNT2PIX
`! -- Local variables
INTEGER,PARAMETER:: FCB_BYTES_IN_REC='m4_ifelse(`fcb_bytes_in_rec',`',4096,`fcb_bytes_in_rec')`
INTEGER FCB_RECORD_SIZE,BYTE_IN_FILE,REC_IN_FILE, &
STEP,FIRST2,LAST2,FIRST4,LAST4,I,J,IOS
INTEGER(4) DIFF,PIXVALUE,MARKER,IADR
INTEGER(2) SHORTINT
INTEGER(1) BUFFER(FCB_BYTES_IN_REC),LAST_CHAR,ONEBYTE, &
TWOBYTES(2),FOURBYTES(4),ENDIANORDER(4), &
MARKBYTES(4)
INTEGER ENCODING
'
fcb_param_ENC_LIST_ALL
` INTEGER SIZE
INTEGER ID
INTEGER COMPRESSION
'
fcb_param_CBF_LIST_ALL
`
INTEGER BITS,VORZEICHEN,REELL
CHARACTER(len=24) DIGEST
CHARACTER(len=14) BYTEORDER
!Possible parameter values for BYTEORDER are:
!"LITTLE_ENDIAN" supported
!"BIG_ENDIAN" not supported
INTEGER(8) DIMOVER
INTEGER(8) DIM1 !Number of "fast" pixels of the image
INTEGER(8) DIM2 !Number of "slow" pixels of the image
INTEGER(8) DIM3
INTEGER(8) PADDING
INTEGER(4) PREV_ELEMENT
DATA ENDIANORDER/Z''`12''`,Z''`34''`,Z''`56''`,Z''`78''`/
DATA MARKBYTES/Z''`0C''`,Z''`1A''`,Z''`04''`,Z''`D5''`/
!-----------------------------------------------------------------------
! -- Determine endian architecture of this machine
!-----------------------------------------------------------------------
! Definition: If the lowest memory address of multi-byte data is
! considered the starting address of the data, the least
! significant byte (LSB) is at the lowest memory address
! for a ''`little_endian''` cpu architecture.
!
! Example: The 32 bit hex value Z''`12345678''` is stored as follows:
! ENDIAN ORDER BYTE0 BYTE1 BYTE2 BYTE3
! Big Endian 12 34 56 78(LSB)
! Little Endian 78(LSB) 56 34 12
!-----------------------------------------------------------------------
PIXVALUE=TRANSFER(ENDIANORDER,PIXVALUE)
STEP=0
IF (PIXVALUE .EQ. Z''`78563412''`) THEN !Little Endian machine
STEP=1
FIRST2=1;LAST2=2
FIRST4=1;LAST4=4
ENDIF
IF (PIXVALUE .EQ. Z''`12345678''`) THEN ! Big Endian machine
STEP=-1
FIRST2=2;LAST2=1
FIRST4=4;LAST4=1
ENDIF
IF (STEP.EQ.0)GO TO 110
'fcb_macro_FCB_OPEN_CIFIN(`ERR=120',`IOSTAT=IOS',`GO TO 130') m4_dnl
`
IF (IOS.GT.0) GO TO 140
!-----------------------------------------------------------------------
! -- Skip to the next binary and parse the MIME header
!-----------------------------------------------------------------------
IF (FCB_NEXT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,BYTE_IN_FILE,&
REC_IN_FILE,BUFFER,ENCODING,SIZE,ID,DIGEST,COMPRESSION,BITS, &
VORZEICHEN,REELL,BYTEORDER,DIMOVER,DIM1,DIM2,DIM3,PADDING).NE.0)&
GO TO 130
IF ((DIM1.NE.NX).OR.(DIM2.NE.NY))GO TO 130
!-----------------------------------------------------------------------
! -- Advance to start of binary image data
!-----------------------------------------------------------------------
! In CBF the binary data begins immediately after the first occurence
! of the following 4 bytes (MARKBYTES) in the image file
! Octet Hex Decimal Purpose
! 1 0C 12 (ctrl-L) End the current page
! 2 1A 26 (ctrl-Z) Stop listings in MS-DOS
! 3 04 04 (Ctrl-D) Stop listings in UNIX
! 4 D5 213 Binary section begins
! 5..5+n-1 Binary data (n octets)
!-----------------------------------------------------------------------
MARKER=TRANSFER(MARKBYTES,MARKER)
FOURBYTES=0
DO
DO I=1,3
FOURBYTES(I)=FOURBYTES(I+1)
ENDDO
BYTE_IN_FILE=BYTE_IN_FILE+1
IF (FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,FOURBYTES(4)).NE.0) GO TO 140
PIXVALUE=TRANSFER(FOURBYTES,PIXVALUE)
IF (PIXVALUE.EQ.MARKER)EXIT
ENDDO
! *** DEBUG *** PRINT *, "fwa-1 address of IMAGE at: "
! *** DEBUG *** PRINT *, "BYTE_IN_FILE: ", BYTE_IN_FILE
! *** DEBUG *** PRINT *, "REC_IN_FILE: ", REC_IN_FILE
!-----------------------------------------------------------------------
! -- Read data image of 32 bit two''`s complement integers, compressed
! -- by the BYTE-OFFSET algorithm.
! -- After the expansion the original pixel values are coded by 16 bit
! -- in a special way suitable for XDS (see INTEGER*2 FUNCTION CNT2PIX).
!-----------------------------------------------------------------------
FCB_READ_XDS_I2=CBF_FORMAT !Cannot handle this CBF format
IF ((BYTEORDER.EQ."LITTLE_ENDIAN").AND.(ENCODING.EQ.ENC_NONE).AND.&
(IAND(COMPRESSION,CBF_COMPRESSION_MASK).EQ.CBF_BYTE_OFFSET))THEN
PIXVALUE=0
DO IADR=1,NX*NY
BYTE_IN_FILE=BYTE_IN_FILE+1
IF (FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,ONEBYTE).NE.0) GO TO 140
DIFF=ONEBYTE
IF (DIFF.EQ.-128)THEN
DO I=FIRST2,LAST2,STEP
BYTE_IN_FILE=BYTE_IN_FILE+1
IF (FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,TWOBYTES(I)).NE.0)GO TO 140
ENDDO
SHORTINT=TRANSFER(TWOBYTES,SHORTINT)
DIFF=SHORTINT
IF (DIFF.EQ.-32768)THEN
DO I=FIRST4,LAST4,STEP
BYTE_IN_FILE=BYTE_IN_FILE+1
IF (FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,FOURBYTES(I)).NE.0) &
GO TO 140
ENDDO
DIFF=TRANSFER(FOURBYTES,DIFF)
ENDIF
ENDIF
PIXVALUE=PIXVALUE+DIFF
IFRAME(IADR)=CNT2PIX(PIXVALUE) ! xds-specific 16 bit coding
ENDDO
FCB_READ_XDS_I2=0 !No error
ELSE
IF ((BYTEORDER.EQ."LITTLE_ENDIAN").AND.(ENCODING.EQ.ENC_NONE).AND.&
((IAND(COMPRESSION,CBF_COMPRESSION_MASK).EQ.CBF_PACKED) .OR. &
(IAND(COMPRESSION,CBF_COMPRESSION_MASK).EQ.CBF_PACKED_V2)))THEN
NELEM = NX*NY
FCB_READ_XDS_I2=FCB_DECOMPRESS_PACKED_I4 (JFRAME,NELEM,NELEM_READ, &
VORZEICHEN, COMPRESSION, DIM1, DIM2, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
IF (NELEM_READ.NE.NELEM) PRINT *, "EARLY TERMINATION AT ",NELEM_READ
PREV_ELEMENT = 0
DO J = 1,NY
DO I = 1,NX
IF (JFRAME(I,J).NE.PREV_ELEMENT) THEN
PREV_ELEMENT = JFRAME(I,J)
PRINT *,"ARRAY(",I+(J-1)*NX,") =",JFRAME(I,J)
ENDIF
IFRAME(I+(J-1)*NX) = CNT2PIX(JFRAME(I,J))
END DO
END DO
END IF
END IF
!-----------------------------------------------------------------------
100 CLOSE(TAPIN)
RETURN
110 FCB_READ_XDS_I2=-1 !Cannot determine endian architecture of this machine
RETURN
120 FCB_READ_XDS_I2=-2 !Cannot open image file
RETURN
130 FCB_READ_XDS_I2=-3 !Wrong image format
GO TO 100
140 FCB_READ_XDS_I2=-4 !Cannot read image
GO TO 100
END FUNCTION FCB_READ_XDS_I2
INTEGER(2) FUNCTION CNT2PIX(I32)
IMPLICIT NONE
INTEGER(4),INTENT(IN)::I32
INTEGER(4),PARAMETER ::RATIO=32 !compression ratio
INTEGER(4),PARAMETER ::OFLOW=RATIO*32768 !largest 32 bit INTEGER
INTEGER(4),PARAMETER ::UFLOW=1-32768/RATIO !smallest 32 bit INTEGER
REAL(4) R
! I16=CNT2PIX(I32) codes an integer I32 in the range UFLOW<=I32<=OFLOW
! by a 16 bit number I16.
! J32=PIX2CNT(I16) retrieves an approximation to the original value
! with a maximum absolute error of RATIO/2.
R=MIN(I32,OFLOW)
R=MAX(I32,UFLOW)
IF (I32.GT.32767)R=-R/RATIO
CNT2PIX=NINT(R)
RETURN
END FUNCTION CNT2PIX'
./CBFlib-0.9.2.2/m4/fcblib_defines.m4 0000644 0000765 0000765 00000126760 11603702103 015307 0 ustar yaya yaya m4_define(`fcb_not_first',`')m4_dnl
m4_define(`fcb_is_last',`is_last')m4_dnl
m4_dnl Error codes:
m4_define(`fcb_errcode_CBF_FORMAT',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_FORMAT = Z''`00000001''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 1')m4_dnl
m4_define(`fcb_errcode_CBF_ALLOC',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_ALLOC = Z''`00000002''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 2')m4_dnl
m4_define(`fcb_errcode_CBF_ARGUMENT',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_ARGUMENT = Z''`00000004''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 4')m4_dnl
m4_define(`fcb_errcode_CBF_ASCII',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_ASCII = Z''`00000008''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 8')m4_dnl
m4_define(`fcb_errcode_CBF_BINARY',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_BINARY = Z''`00000010''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 16')m4_dnl
m4_define(`fcb_errcode_CBF_BITCOUNT',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_BITCOUNT = Z''`00000020''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 32')m4_dnl
m4_define(`fcb_errcode_CBF_ENDOFDATA',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_ENDOFDATA = Z''`00000040''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 64')m4_dnl
m4_define(`fcb_errcode_CBF_FILECLOSE',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_FILECLOSE = Z''`00000080''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 128')m4_dnl
m4_define(`fcb_errcode_CBF_FILEOPEN',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_FILEOPEN = Z''`00000100''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 256')m4_dnl
m4_define(`fcb_errcode_CBF_FILEREAD',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_FILEREAD = Z''`00000200''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 512')m4_dnl
m4_define(`fcb_errcode_CBF_FILESEEK',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_FILESEEK = Z''`00000400''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 1024')m4_dnl
m4_define(`fcb_errcode_CBF_FILETELL',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_FILETELL = Z''`00000800''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 2048')m4_dnl
m4_define(`fcb_errcode_CBF_FILEWRITE',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_FILEWRITE = Z''`00001000''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 4096')m4_dnl
m4_define(`fcb_errcode_CBF_IDENTICAL',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_IDENTICAL = Z''`00002000''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 8192')m4_dnl
m4_define(`fcb_errcode_CBF_NOTFOUND',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_NOTFOUND = Z''`00004000''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 16384')m4_dnl
m4_define(`fcb_errcode_CBF_OVERFLOW',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_OVERFLOW = Z''`00008000''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 32768')m4_dnl
m4_define(`fcb_errcode_CBF_UNDEFINED',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_UNDEFINED = Z''`00010000''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 65536')m4_dnl
m4_define(`fcb_errcode_CBF_NOTIMPLEMENTED',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_NOTIMPLEMENTED = Z''`00020000''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` ! 131072')m4_dnl
m4_define(`fcb_errcode_LIST_ALL',
m4_define(`fcb_is_last',`')m4_dnl
!
! Definitions of CBF error code parameters
!
fcb_errcode_CBF_FORMAT
m4_define(`fcb_not_first',`not_first')m4_dnl
fcb_errcode_CBF_ALLOC
fcb_errcode_CBF_ARGUMENT
fcb_errcode_CBF_ASCII
fcb_errcode_CBF_BINARY
fcb_errcode_CBF_BITCOUNT
fcb_errcode_CBF_ENDOFDATA
fcb_errcode_CBF_FILECLOSE
fcb_errcode_CBF_FILEOPEN
fcb_errcode_CBF_FILEREAD
fcb_errcode_CBF_FILESEEK
fcb_errcode_CBF_FILETELL
fcb_errcode_CBF_FILEWRITE
fcb_errcode_CBF_IDENTICAL
fcb_errcode_CBF_NOTFOUND
fcb_errcode_CBF_OVERFLOW
fcb_errcode_CBF_UNDEFINED
m4_define(`fcb_is_last',`is_last')m4_dnl
fcb_errcode_CBF_NOTIMPLEMENTED
m4_define(`fcb_not_first',`')m4_dnl
)m4_dnl
m4_dnl
m4_dnl Possible parameter values for ENCODING are:
m4_define(`fcb_param_ENC_NONE',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')ENC_NONE = Z''`0001''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Use BINARY encoding')m4_dnl
m4_define(`fcb_param_ENC_BASE64',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')ENC_BASE64 = Z''`0002''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Use BASE64 encoding')m4_dnl
m4_define(`fcb_param_ENC_BASE32k',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')ENC_BASE32K = Z''`0004''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Use X-BASE32K encoding')m4_dnl
m4_define(`fcb_param_ENC_QP',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')ENC_QP = Z''`0008''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Use QUOTED-PRINTABLE encoding')m4_dnl
m4_define(`fcb_param_ENC_BASE10',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')ENC_BASE10 = Z''`0010''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Use BASE10 encoding')m4_dnl
m4_define(`fcb_param_ENC_BASE16',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')ENC_BASE16 = Z''`0020''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Use BASE16 encoding')m4_dnl
m4_define(`fcb_param_ENC_BASE8',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')ENC_BASE8 = Z''`0040''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Use BASE8 encoding')m4_dnl
m4_define(`fcb_param_ENC_LIST_ALL',
m4_define(`fcb_is_last',`')m4_dnl
!
! Definitions of CBF encodings parameters
!
fcb_param_ENC_NONE
m4_define(`fcb_not_first',`not_first')m4_dnl
fcb_param_ENC_BASE64
fcb_param_ENC_BASE32k
fcb_param_ENC_QP
fcb_param_ENC_BASE10
fcb_param_ENC_BASE16
m4_define(`fcb_is_last',`is_last')m4_dnl
fcb_param_ENC_BASE8
m4_define(`fcb_not_first',`')m4_dnl
)m4_dnl
m4_dnl
m4_dnl Possible parameter values for COMPRESSION are:
m4_dnl
m4_define(`fcb_param_CBF_INTEGER',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_INTEGER = Z''`0010''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Uncompressed integer')m4_dnl
m4_define(`fcb_param_CBF_FLOAT',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_FLOAT = Z''`0020''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Uncompressed IEEE floating point')m4_dnl
m4_define(`fcb_param_CBF_CANONICAL',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_CANONICAL = Z''`0050''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Canonical compression')m4_dnl
m4_define(`fcb_param_CBF_PACKED',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_PACKED = Z''`0060''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Packed compression')m4_dnl
m4_define(`fcb_param_CBF_PACKED_V2',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_PACKED_V2 = Z''`0090''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Packed compression')m4_dnl
m4_define(`fcb_param_CBF_BYTE_OFFSET',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_BYTE_OFFSET = Z''`0070''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Byte Offset Compression')m4_dnl
m4_define(`fcb_param_CBF_PREDICTOR',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_PREDICTOR = Z''`0080''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Predictor_Huffman Compression')m4_dnl
m4_define(`fcb_param_CBF_NONE',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_NONE = Z''`0040''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !No compression flag')m4_dnl
m4_define(`fcb_param_CBF_COMPRESSION_MASK',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_COMPRESSION_MASK = &
Z''`00FF''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Mask to sep compressiontype from flags')m4_dnl
m4_define(`fcb_param_CBF_FLAG_MASK',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_FLAG_MASK = Z''`0F00''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Mask to sep flags from compression type')m4_dnl
m4_define(`fcb_param_CBF_UNCORRELATED_SECTIONS',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_UNCORRELATED_SECTIONS =&
Z''`0100''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Flag for uncorrelated sections')m4_dnl
m4_define(`fcb_param_CBF_FLAT_IMAGE',
`m4_ifelse(fcb_not_first,`',``INTEGER,PARAMETER:: &
'',``'')CBF_FLAT_IMAGE = Z''`0200''`m4_ifelse(fcb_is_last,`is_last',` ',``, &'')'` !Flag for flat (linear) images')m4_dnl
m4_define(`fcb_param_CBF_LIST_ALL',
m4_define(`fcb_is_last',`')m4_dnl
!
! Definitions of CBF compression parameters
!
fcb_param_CBF_INTEGER
m4_define(`fcb_not_first',`not_first')m4_dnl
fcb_param_CBF_FLOAT
fcb_param_CBF_CANONICAL
fcb_param_CBF_PACKED
fcb_param_CBF_PACKED_V2
fcb_param_CBF_BYTE_OFFSET
fcb_param_CBF_PREDICTOR
fcb_param_CBF_NONE
fcb_param_CBF_COMPRESSION_MASK
fcb_param_CBF_FLAG_MASK
fcb_param_CBF_UNCORRELATED_SECTIONS
m4_define(`fcb_is_last',`is_last')m4_dnl
fcb_param_CBF_FLAT_IMAGE
m4_define(`fcb_not_first',`')m4_dnl
)m4_dnl
m4_dnl
m4_dnl fcblib function interfaces
m4_dnl
m4_define(`fcb_interface_FCB_ATOL_WCNT',
`INTERFACE
INTEGER(8) FUNCTION FCB_ATOL_WCNT(ARRAY,N,CNT)
!-----------------------------------------------------------------------
! Converts bytes in ARRAY to an INTEGER(8), consuming CNT bytes
!-----------------------------------------------------------------------
INTEGER, INTENT(OUT):: CNT
INTEGER, INTENT(IN):: N
INTEGER(1),INTENT(IN):: ARRAY(N)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_CI_STRNCMPARR',
`INTERFACE
INTEGER FUNCTION FCB_CI_STRNCMPARR(STRING, ARRAY, N, LIMIT)
!-----------------------------------------------------------------------
! Compares up to LIMIT characters of STRING and ARRAY case insensitive
!-----------------------------------------------------------------------
CHARACTER(LEN=*),INTENT(IN):: STRING
INTEGER, INTENT(IN):: N,LIMIT
INTEGER(1), INTENT(IN):: ARRAY(N)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_DECOMPRESS_PACKED_I2',
`INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_I2 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_DECOMPRESS_PACKED_I4',
`INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_I4 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_DECOMPRESS_PACKED_3D_I2',
`INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_3D_I2 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_DECOMPRESS_PACKED_3D_I4',
`INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_3D_I4 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_EXIT_BINARY',
`INTERFACE
INTEGER FUNCTION FCB_EXIT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
PADDING )
!-----------------------------------------------------------------------
! Skip to end of binary section that was just read
!-----------------------------------------------------------------------
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER(FCB_BYTES_IN_REC)
INTEGER(8),INTENT(IN) :: PADDING
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_NBLEN_ARRAY',
`INTERFACE
INTEGER FUNCTION FCB_NBLEN_ARRAY(ARRAY, ARRAYLEN)
!-----------------------------------------------------------------------
! Returns the non-blank length of an array
!-----------------------------------------------------------------------
INTEGER, INTENT(IN):: ARRAYLEN
INTEGER(1), INTENT(IN):: ARRAY(ARRAYLEN)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_NEXT_BINARY',
`INTERFACE
INTEGER FUNCTION FCB_NEXT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
ENCODING,SIZE,ID,DIGEST, &
COMPRESSION,BITS,VORZEICHEN,REELL,&
BYTEORDER,DIMOVER,DIM1,DIM2,DIM3, &
PADDING )
!-----------------------------------------------------------------------
! Skip to the next binary and parse MIME header.
!-----------------------------------------------------------------------
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER(FCB_BYTES_IN_REC)
INTEGER, INTENT(OUT) :: ENCODING,SIZE,ID,COMPRESSION,BITS, &
VORZEICHEN,REELL
CHARACTER(*), INTENT(OUT):: BYTEORDER,DIGEST
INTEGER(8), INTENT(OUT):: DIMOVER
INTEGER(8), INTENT(OUT):: DIM1
INTEGER(8), INTENT(OUT):: DIM2
INTEGER(8), INTENT(OUT):: DIM3
INTEGER(8), INTENT(OUT):: PADDING
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_OPEN_CIFIN',
`INTERFACE
INTEGER FUNCTION FCB_OPEN_CIFIN(FILNAM,TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER)
!-----------------------------------------------------------------------
! -- Open CBF file named FILNAM and connect to unit number TAPIN
!-----------------------------------------------------------------------
! We have chosen to use the direct access method to read the file
! with explicit buffer handling. This approach is general but
! clumpsy. Rather than putting the buffer and its control variables
! into COMMON these are passed as local arguments to make the routines
! inherently ''`threadsafe''` in a parallel programming environment.
! Note also, that a reading error could occur for the last record
! if it did not fill a full block. This could be avoided if the
! images were padded with a sufficient number of additional bytes
! (arbitrary values) after the end of the valid binary data.
!
! The more natural method would use byte stream I/O which is,
! unfortunately, only an extension of Fortran 90 that has been
! implemented in some compilers (like the Intel ifort) but
! not in all (like the SGI IRIX f90).
! For BSD style opens, there is a special variant on the direct
! access open with a recl of 1 to give byte-by-byte access.
!-----------------------------------------------------------------------
! FILNAM - Name of the file countaining the image (GIVEN)
! TAPIN - Fortran device unit number assigned to image file (GIVEN)
! LAST_CHAR -
! Last character read (RESULT)
! FCB_BYTES_IN_REC -
! Number of bytes in a record (GIVEN)
! BYTE_IN_FILE -
! Byte (counting from 1) of the byte to read (RESULT)
! REC_IN_FILE -
! Record (counting from 1) of next record to read (RESULT)
! BUFFER - Array of length FCB_BYTES_IN_REC (GIVEN)
!-----------------------------------------------------------------------
IMPLICIT NONE
CHARACTER(len=*),INTENT(IN) :: FILNAM
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER(1), INTENT(OUT):: LAST_CHAR
INTEGER, INTENT(OUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1), INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_READ_BITS',
`INTERFACE
INTEGER FUNCTION FCB_READ_BITS(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
BITCOUNT,IINT,LINT)
!-----------------------------------------------------------------------
! Get integer value starting at BYTE_IN_FILE from file TAPIN
! continuing through BITCOUNT bits, with sign extension.
! (first byte is BYTE_IN_FILE=1)
!-----------------------------------------------------------------------
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER, INTENT(INOUT):: BCOUNT
INTEGER(1),INTENT(INOUT):: BBYTE
INTEGER, INTENT(IN):: BITCOUNT
INTEGER, INTENT(IN):: LINT
INTEGER(4), INTENT(OUT):: IINT(LINT)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_READ_BYTE',
`INTERFACE
INTEGER FUNCTION FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,IBYTE)
!-----------------------------------------------------------------------
! Get byte number BYTE_IN_FILE from file (first byte is BYTE_IN_FILE=1)
!-----------------------------------------------------------------------
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER(1), INTENT(OUT):: IBYTE
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_READ_LINE',
`INTERFACE
INTEGER FUNCTION FCB_READ_LINE(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC, &
BYTE_IN_FILE,REC_IN_FILE,BUFFER,LINE,N,LINELEN)
!-----------------------------------------------------------------------
! Reads successive bytes into byte array LINE(N), stopping at N,
! error or first CR(Z''`0D''`) or LF(Z''`0A''`), discarding a LF after a CR.
!-----------------------------------------------------------------------
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC,N
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER, INTENT(OUT):: LINELEN
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER(FCB_BYTES_IN_REC)
INTEGER(1), INTENT(OUT):: LINE(N)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_READ_IMAGE_I2',
`INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_I2(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, PADDING, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
!-----------------------------------------------------------------------
! Reads a 16-bit integer twos complement 2D image
!
! compressed by a BYTE_OFFSET algorithm by W. Kabsch based
! on a proposal by A. Hammersley or
! compressed by a PACKED algorithm by J. P. Abrahams as
! used in CCP4, with modifications by P. Ellis and
! H. J. Bernstein.
!
! The BYTE-OFFSET algorithm is a slightly simplified version of
! that described in Andy Hammersley''`s web page
! (http://www.esrf.fr/computing/Forum/imgCIF/cbf_definition.html)
!
!-----------------------------------------------------------------------
! ARRAY - Image (RESULT)
! NELEM - The number of elements to be read (GIVEN)
! NELEM_READ
! - The number of elements actually read (RESULT)
! ELSIGN - Flag for signed (1) OR unsigned (0) data (GIVEN)
! COMPRESSION
! - The actual compression of the image (RESULT)
! DIM1 - The fastest dimension of ARRAY (GIVEN)
! DIM2 - The slowest dimension (GIVEN)
! TAPIN - Fortran device unit number assigned to image file (GIVEN)
! FCB_BYTES_IN_REC
! - The number of bytes in each bufferload to read (GIVEN)
! BYTE_IN_FILE
! - The position in the file of the next byte to read (GIVEN,
! RESULT)
! REC_IN_FILE
! - The record number from 1 of the block in BUFFER (GIVEN,
! RESULT)
! BUFFER - Buffer of bytes read from the file (GIVEN,
! RESULT)
! PADDING - Pad bytes after the binary (RESULT)
!
! Returns (as function value) (RESULT)
! CBF_FORMAT (=1):
! cannot handle this CBF format (not implemented)
! 0: No error
!-----------------------------------------------------------------------
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_READ_IMAGE_I4',
`INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_I4(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, PADDING, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
!-----------------------------------------------------------------------
! Reads a 32-bit integer twos complement 2D image
!
! compressed by a BYTE_OFFSET algorithm by W. Kabsch based
! on a proposal by A. Hammersley or
! compressed by a PACKED algorithm by J. P. Abrahams as
! used in CCP4, with modifications by P. Ellis and
! H. J. Bernstein.
!
! The BYTE-OFFSET algorithm is a slightly simplified version of
! that described in Andy Hammersley''`s web page
! (http://www.esrf.fr/computing/Forum/imgCIF/cbf_definition.html)
!
!-----------------------------------------------------------------------
! ARRAY - Image (RESULT)
! NELEM - The number of elements to be read (GIVEN)
! NELEM_READ
! - The number of elements actually read (RESULT)
! ELSIGN - Flag for signed (1) OR unsigned (0) data (GIVEN)
! COMPRESSION
! - The actual compression of the image (RESULT)
! DIM1 - The fastest dimension of ARRAY (GIVEN)
! DIM2 - The slowest dimension (GIVEN)
! TAPIN - Fortran device unit number assigned to image file (GIVEN)
! FCB_BYTES_IN_REC
! - The number of bytes in each bufferload to read (GIVEN)
! BYTE_IN_FILE
! - The position in the file of the next byte to read (GIVEN,
! RESULT)
! REC_IN_FILE
! - The record number from 1 of the block in BUFFER (GIVEN,
! RESULT)
! BUFFER - Buffer of bytes read from the file (GIVEN,
! RESULT)
! PADDING - Pad bytes after the binary (RESULT)
!
! Returns (as function value) (RESULT)
! CBF_FORMAT (=1):
! cannot handle this CBF format (not implemented)
! 0: No error
!-----------------------------------------------------------------------
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_READ_IMAGE_3D_I2',
`INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_3D_I2(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, PADDING, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
!-----------------------------------------------------------------------
! Reads a 16-bit integer twos complement 3D image
!
! compressed by a BYTE_OFFSET algorithm by W. Kabsch based
! on a proposal by A. Hammersley or
! compressed by a PACKED algorithm by J. P. Abrahams as
! used in CCP4, with modifications by P. Ellis and
! H. J. Bernstein.
!
! The BYTE-OFFSET algorithm is a slightly simplified version of
! that described in Andy Hammersley''`s web page
! (http://www.esrf.fr/computing/Forum/imgCIF/cbf_definition.html)
!
!-----------------------------------------------------------------------
! ARRAY - Image (RESULT)
! NELEM - The number of elements to be read (GIVEN)
! NELEM_READ
! - The number of elements actually read (RESULT)
! ELSIGN - Flag for signed (1) OR unsigned (0) data (GIVEN)
! COMPRESSION
! - The actual compression of the image (RESULT)
! DIM1 - The fastest dimension of ARRAY (GIVEN)
! DIM2 - The slowest dimension (GIVEN)
! TAPIN - Fortran device unit number assigned to image file (GIVEN)
! FCB_BYTES_IN_REC
! - The number of bytes in each bufferload to read (GIVEN)
! BYTE_IN_FILE
! - The position in the file of the next byte to read (GIVEN,
! RESULT)
! REC_IN_FILE
! - The record number from 1 of the block in BUFFER (GIVEN,
! RESULT)
! BUFFER - Buffer of bytes read from the file (GIVEN,
! RESULT)
! PADDING - Pad bytes after the binary (RESULT)
!
! Returns (as function value) (RESULT)
! CBF_FORMAT (=1):
! cannot handle this CBF format (not implemented)
! 0: No error
!-----------------------------------------------------------------------
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_READ_IMAGE_3D_I4',
`INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_3D_I4(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, PADDING, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
!-----------------------------------------------------------------------
! Reads a 32-bit integer twos complement 3D image
!
! compressed by a BYTE_OFFSET algorithm by W. Kabsch based
! on a proposal by A. Hammersley or
! compressed by a PACKED algorithm by J. P. Abrahams as
! used in CCP4, with modifications by P. Ellis and
! H. J. Bernstein.
!
! The BYTE-OFFSET algorithm is a slightly simplified version of
! that described in Andy Hammersley''`s web page
! (http://www.esrf.fr/computing/Forum/imgCIF/cbf_definition.html)
!
!-----------------------------------------------------------------------
! ARRAY - Image (RESULT)
! NELEM - The number of elements to be read (GIVEN)
! NELEM_READ
! - The number of elements actually read (RESULT)
! ELSIGN - Flag for signed (1) OR unsigned (0) data (GIVEN)
! COMPRESSION
! - The actual compression of the image (RESULT)
! DIM1 - The fastest dimension of ARRAY (GIVEN)
! DIM2 - The slowest dimension (GIVEN)
! TAPIN - Fortran device unit number assigned to image file (GIVEN)
! FCB_BYTES_IN_REC
! - The number of bytes in each bufferload to read (GIVEN)
! BYTE_IN_FILE
! - The position in the file of the next byte to read (GIVEN,
! RESULT)
! REC_IN_FILE
! - The record number from 1 of the block in BUFFER (GIVEN,
! RESULT)
! BUFFER - Buffer of bytes read from the file (GIVEN,
! RESULT)
! PADDING - Pad bytes after the binary (RESULT)
!
! Returns (as function value) (RESULT)
! CBF_FORMAT (=1):
! cannot handle this CBF format (not implemented)
! 0: No error
!-----------------------------------------------------------------------
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_READ_INTEGER',
`INTERFACE
INTEGER FUNCTION FCB_READ_INTEGER(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
VALSIGN,BITCOUNT,IINT,LINT)
!-----------------------------------------------------------------------
! Get integer value starting at BYTE_IN_FILE from file TAPIN
! continuing through BITCOUNT bits, with optional sign extension.
! (first byte is BYTE_IN_FILE=1)
!-----------------------------------------------------------------------
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER, INTENT(INOUT):: BCOUNT
INTEGER(1),INTENT(INOUT):: BBYTE
INTEGER, INTENT(IN):: VALSIGN,BITCOUNT
INTEGER, INTENT(IN):: LINT
INTEGER(4), INTENT(OUT):: IINT(LINT)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_READ_XDS_I2',
`INTERFACE
INTEGER FUNCTION FCB_READ_XDS_I2(FILNAM,TAPIN,NX,NY,IFRAME,JFRAME)
!-----------------------------------------------------------------------
! Reads a 32 bit integer two''`s complement image compressed by a
! BYTE-OFFSET algorithm. W. Kabsch, Version 9-2006
!
! REVISED 1-2007, H. J. Bernstein to conform to CBFlib_0.7.7
! (http://www.bernstein-plus-sons.com/software/CBF)
!
! The BYTE-OFFSET algorithm is a slightly simplified version of
! that described in Andy Hammersley''`s web page
! (http://www.esrf.fr/computing/Forum/imgCIF/cbf_definition.html)
!
!-----------------------------------------------------------------------
! FILNAM - Name of the file countaining the image (GIVEN)
! TAPIN - Fortran device unit number assigned to image file (GIVEN)
! NX - Number of "fast" pixels of the image (GIVEN)
! NY - Number of "slow" pixels of the image (GIVEN)
! IFRAME - 16 bit coded image as needed by XDS (RESULT)
! JFRAME - 32 bit scratch array (RESULT)
! Returns (as function value) (RESULT)
! 1: cannot handle this CBF format (not implemented)
! 0: No error
! -1: Cannot determine endian architecture of this machine
! -2: Cannot open image file
! -3: Wrong image format
! -4: Cannot read image
!-----------------------------------------------------------------------
IMPLICIT NONE
CHARACTER(len=*),INTENT(IN) :: FILNAM
INTEGER, INTENT(IN) :: TAPIN,NX,NY
INTEGER(2), INTENT(OUT):: IFRAME(NX*NY)
INTEGER(4), INTENT(OUT):: JFRAME(NX,NY)
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_SKIP_WHITESPACE',
`INTERFACE
INTEGER FUNCTION FCB_SKIP_WHITESPACE(TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER,&
LINE,N,LINELEN,ICUR,FRESH_LINE)
!-----------------------------------------------------------------------
! Skips forward on the current LINE of size N with data in
! LINE(1:LINELEN) from the current position ICUR moving over
! whitespace and comments, reading new lines into LINE if
! needed. The flag FRESH_LINE indicates that a fresh line
! should be read on entry.
!-----------------------------------------------------------------------
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC,N
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE,LINELEN,ICUR, &
FRESH_LINE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC),LINE(N), &
LAST_CHAR
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_UPDATE_JPA_POINTERS_I2',
`INTERFACE
INTEGER FUNCTION FCB_UPDATE_JPA_POINTERS_I2(TRAIL_INDEX_ARRAY,&
NDIM1, NDIM2, ARRAY, DIM1, DIM2, AVERAGE, COMPRESSION)
INTEGER(8),INTENT(INOUT):: TRAIL_INDEX_ARRAY(4), NDIM1, NDIM2
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER(2), INTENT(IN):: ARRAY(DIM1,DIM2)
INTEGER(4), INTENT(OUT):: AVERAGE
INTEGER, INTENT(IN):: COMPRESSION
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_UPDATE_JPA_POINTERS_I4',
`INTERFACE
INTEGER FUNCTION FCB_UPDATE_JPA_POINTERS_I4(TRAIL_INDEX_ARRAY,&
NDIM1, NDIM2, ARRAY, DIM1, DIM2, AVERAGE, COMPRESSION)
INTEGER(8),INTENT(INOUT):: TRAIL_INDEX_ARRAY(4), NDIM1, NDIM2
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER(4), INTENT(IN):: ARRAY(DIM1,DIM2)
INTEGER(4), INTENT(OUT):: AVERAGE
INTEGER, INTENT(IN):: COMPRESSION
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_UPDATE_JPA_POINTERS_3D_I2',
`INTERFACE
INTEGER FUNCTION FCB_UPDATE_JPA_POINTERS_3D_I2(TRAIL_INDEX_ARRAY,&
NDIM1, NDIM2, NDIM3, ARRAY, DIM1, DIM2, DIM3, AVERAGE, COMPRESSION)
INTEGER(8),INTENT(INOUT):: TRAIL_INDEX_ARRAY(8), NDIM1, NDIM2, NDIM3
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER(2), INTENT(IN):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(4), INTENT(OUT):: AVERAGE
INTEGER, INTENT(IN):: COMPRESSION
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_define(`fcb_interface_FCB_UPDATE_JPA_POINTERS_3D_I4',
`INTERFACE
INTEGER FUNCTION FCB_UPDATE_JPA_POINTERS_3D_I4(TRAIL_INDEX_ARRAY,&
NDIM1, NDIM2, NDIM3, ARRAY, DIM1, DIM2, DIM3, AVERAGE, COMPRESSION)
IMPLICIT NONE
INTEGER(8),INTENT(INOUT):: TRAIL_INDEX_ARRAY(8), NDIM1, NDIM2, NDIM3
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER(4), INTENT(IN):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(4), INTENT(OUT):: AVERAGE
INTEGER, INTENT(IN):: COMPRESSION
END FUNCTION
!-----------------------------------------------------------------------
END INTERFACE')m4_dnl
m4_dnl
m4_dnl macro version of cbf file open to be used both in the library
m4_dnl and in applications that wish to avoid the long argument list
m4_dnl
m4_dnl The macro should be called with 3 arguments
m4_dnl $1 should give any additional parameters to OPEN
m4_dnl such as ERR=120 or IOSTAT=IOS
m4_dnl $2 should give any additional parameters for the
m4_dnl first read such as ERR=140 or IOSTAT=IOS
m4_dnl $3 should give any the action to take if the file
m4_dnl does not begin with "###CBF: "
m4_define(`fcb_macro_FCB_OPEN_CIFIN',
``!-----------------------------------------------------------------------
! -- Open CBF file named FILNAM and connect to unit number TAPIN
!-----------------------------------------------------------------------
! We have chosen to use the direct access method to read the file
! with explicit buffer handling. This approach is general but
! clumpsy. Rather than putting the buffer and its control variables
! into COMMON these are passed as local arguments to make the routines
! inherently '''``threadsafe'''`` in a parallel programming environment.
! Note also, that a reading error could occur for the last record
! if it did not fill a full block. This could be avoided if the
! images were padded with a sufficient number of additional bytes
! (arbitrary values) after the end of the valid binary data.
!
! The more natural method would use byte stream I/O which is,
! unfortunately, only an extension of Fortran 90 that has been
! implemented in some compilers (like the Intel ifort) but
! not in all (like the SGI IRIX f90).
! For BSD style opens, there is a special variant on the direct
! access open with a recl of 1 to give byte-by-byte access.
!-----------------------------------------------------------------------
INQUIRE(IOLENGTH=FCB_RECORD_SIZE)BUFFER
OPEN(UNIT=TAPIN,FILE=TRIM(FILNAM),STATUS='''``OLD'''``,ACTION='''``READ'''``, &
ACCESS='''``DIRECT'''``,FORM='''``UNFORMATTED'''``,RECL=FCB_RECORD_SIZE, &
$1)
! *** DEBUG *** PRINT *, "RECL: ", FCB_RECORD_SIZE
DO BYTE_IN_FILE = 1, FCB_BYTES_IN_REC
BUFFER(BYTE_IN_FILE) = 0
END DO
READ(TAPIN,REC=1,$2)BUFFER !Read the first record'
m4_ifelse($3,`',`',` IF (FCB_CI_STRNCMPARR("###CBF: ",BUFFER,FCB_BYTES_IN_REC,8).NE.0) &
'$3` !Check for presence of the CBF-format keyword')`
REC_IN_FILE=1
BYTE_IN_FILE=0
LAST_CHAR=0
'')m4_dnl
m4_define(`fcb_interface_LIST_ALL',`
!
! Definitions of fcblib interfaces
!
fcb_interface_FCB_ATOL_WCNT
fcb_interface_FCB_CI_STRNCMPARR
fcb_interface_FCB_DECOMPRESS_PACKED_I2
fcb_interface_FCB_DECOMPRESS_PACKED_I4
fcb_interface_FCB_DECOMPRESS_PACKED_3D_I2
fcb_interface_FCB_DECOMPRESS_PACKED_3D_I4
fcb_interface_FCB_EXIT_BINARY
fcb_interface_FCB_NBLEN_ARRAY
fcb_interface_FCB_NEXT_BINARY
fcb_interface_FCB_OPEN_CIFIN
fcb_interface_FCB_READ_BITS
fcb_interface_FCB_READ_BYTE
fcb_interface_FCB_READ_INTEGER
fcb_interface_FCB_READ_LINE
fcb_interface_FCB_READ_XDS_I2
fcb_interface_FCB_SKIP_WHITESPACE
fcb_interface_FCB_UPDATE_JPA_POINTERS_I2
fcb_interface_FCB_UPDATE_JPA_POINTERS_I4
fcb_interface_FCB_UPDATE_JPA_POINTERS_3D_I2
fcb_interface_FCB_UPDATE_JPA_POINTERS_3D_I4
') ./CBFlib-0.9.2.2/m4/fcb_read_image.m4 0000644 0000765 0000765 00000026332 11603702103 015252 0 ustar yaya yaya m4_dnl fcb_read_image.m4 -- m4 macro file to generate I2, I4,
m4_dnl and 3D_I2 and 3D_I4 versions
m4_dnl of FCB_READ_IMAGE
m4_include(`fcblib_defines.m4')
m4_define(`fcb_macro_FCB_READ_IMAGE',
`! FCB_READ_IMAGE_$1.F90
!
! Derived from f90 test code by W. Kabsch
! H. J. Bernstein, 24 March 2007
!
! Reads the next binary image from a CIF files that
! has already been opened. Leaves the file open and
! positioned just after the binary and still within
! the text field
!
! This version is for
!
! m4_ifelse($1,`I2',`2-D INTEGER*2 arrays',
$1,`I4',`2-D INTEGER*4 arrays',
$1,`3D_I2',`3-D INTEGER*2 arrays',
$1,`3D_I4',`3-D INTEGER*4 arrays',`2-D INTEGER*2 arrays')
m4_define(`fcb_3d_flag',`2D')m4_dnl
m4_ifelse($1,`3D_I2',`m4_define(`fcb_3d_flag',`3D')',
$1,`3D_I4',`m4_define(`fcb_3d_flag',`3D')')m4_dnl
!
! with function
!
! FCB_READ_IMAGE_$1
INTEGER FUNCTION FCB_READ_IMAGE_$1(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, m4_ifelse(fcb_3d_flag,`3D',
`DIM3, ') &
PADDING,TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
!-----------------------------------------------------------------------
m4_ifelse($1,`I2',
`! Reads a 16-bit integer twos complement 2D image',
$1,`I4',
`! Reads a 32-bit integer twos complement 2D image',
$1,`3D_I2',
`! Reads a 16-bit integer twos complement 3D image',
$1,`3D_I4',
`! Reads a 32-bit integer twos complement 3D image')
!
! compressed by a BYTE_OFFSET algorithm by W. Kabsch based
! on a proposal by A. Hammersley or
! compressed by a PACKED algorithm by J. P. Abrahams as
! used in CCP4, with modifications by P. Ellis and
! H. J. Bernstein.
!
! The BYTE-OFFSET algorithm is a slightly simplified version of
! that described in Andy Hammersley''`s web page
! (http://www.esrf.fr/computing/Forum/imgCIF/cbf_definition.html)
!
!-----------------------------------------------------------------------
! ARRAY - Image (RESULT)
! NELEM - The number of elements to be read (GIVEN)
! NELEM_READ
! - The number of elements actually read (RESULT)
! ELSIGN - Flag for signed (1) OR unsigned (0) data (GIVEN)
! COMPRESSION
! - The actual compression of the image (RESULT)
! DIM1 - The fastest dimension of ARRAY (GIVEN)
m4_ifelse(`fcb_3d_flag',`3D',
`! DIM2 - The next slower dimension (GIVEN)
! DIM3 - The slowest dimension (GIVEN)',
`! DIM2 - The slowest dimension (GIVEN)')
! TAPIN - Fortran device unit number assigned to image file (GIVEN)
! FCB_BYTES_IN_REC
! - The number of bytes in each bufferload to read (GIVEN)
! BYTE_IN_FILE
! - The position in the file of the next byte to read (GIVEN,
! RESULT)
! REC_IN_FILE
! - The record number from 1 of the block in BUFFER (GIVEN,
! RESULT)
! BUFFER - Buffer of bytes read from the file (GIVEN,
! RESULT)
! PADDING - Pad bytes after the binary (RESULT)
!
! Returns (as function value) (RESULT)
! CBF_FORMAT (=1):
! cannot handle this CBF format (not implemented)
! 0: No error
!-----------------------------------------------------------------------
IMPLICIT NONE
INTEGER(8), INTENT(IN):: DIM1,DIM2`'m4_ifelse(fcb_3d_flag,`3D',
`,DIM3')
INTEGER(m4_ifelse($1,`I2',2,$1,`3D_I2',2,4)), INTENT(OUT):: ARRAY(DIM1,DIM2`'m4_ifelse(fcb_3d_flag,`3D',
`,DIM3'))
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
! -- Definition of CBF_FORMAT
fcb_errcode_CBF_FORMAT
! -- External functions called
fcb_interface_FCB_READ_BYTE
fcb_interface_FCB_NEXT_BINARY
fcb_interface_FCB_CI_STRNCMPARR
fcb_interface_FCB_DECOMPRESS_PACKED_$1
! -- Local variables
INTEGER STEP,FIRST2,LAST2,FIRST4,LAST4,II,I,J`'m4_ifelse(fcb_3d_flag,
`3D',`,K')
INTEGER(4) DIFF,PIXVALUE,MARKER,IADR
INTEGER(2) SHORTINT
INTEGER(1) LAST_CHAR,ONEBYTE, &
TWOBYTES(2),FOURBYTES(4),ENDIANORDER(4), &
MARKBYTES(4)
INTEGER ENCODING
fcb_param_ENC_LIST_ALL
INTEGER SIZE
INTEGER ID
fcb_param_CBF_LIST_ALL
INTEGER BITS,VORZEICHEN,REELL
CHARACTER(len=24) DIGEST
CHARACTER(len=14) BYTEORDER
!Possible parameter values for BYTEORDER are:
!"LITTLE_ENDIAN" supported
!"BIG_ENDIAN" not supported
INTEGER(8) DIMOVER
INTEGER(8) LDIM1 !Number of "fast" pixels of the image
INTEGER(8) LDIM2 !Number of "slow" pixels of the image
INTEGER(8) LDIM3
INTEGER(4) PREV_ELEMENT
DATA ENDIANORDER/Z''`12''`,Z''`34''`,Z''`56''`,Z''`78''`/
DATA MARKBYTES/Z''`0C''`,Z''`1A''`,Z''`04''`,Z''`D5''`/
!-----------------------------------------------------------------------
! -- Determine endian architecture of this machine
!-----------------------------------------------------------------------
! Definition: If the lowest memory address of multi-byte data is
! considered the starting address of the data, the least
! significant byte (LSB) is at the lowest memory address
! for a ''`little_endian''` cpu architecture.
!
! Example: The 32 bit hex value Z''`12345678''` is stored as follows:
! ENDIAN ORDER BYTE0 BYTE1 BYTE2 BYTE3
! Big Endian 12 34 56 78(LSB)
! Little Endian 78(LSB) 56 34 12
!-----------------------------------------------------------------------
PIXVALUE=TRANSFER(ENDIANORDER,PIXVALUE)
STEP=0
IF (PIXVALUE .EQ. Z''`78563412''`) THEN !Little Endian machine
STEP=1
FIRST2=1;LAST2=2
FIRST4=1;LAST4=4
ENDIF
IF (PIXVALUE .EQ. Z''`12345678''`) THEN ! Big Endian machine
STEP=-1
FIRST2=2;LAST2=1
FIRST4=4;LAST4=1
ENDIF
IF (STEP.EQ.0)GO TO 110
!-----------------------------------------------------------------------
! -- Skip to the next binary and parse the MIME header
!-----------------------------------------------------------------------
IF (FCB_NEXT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,BYTE_IN_FILE,&
REC_IN_FILE,BUFFER,ENCODING,SIZE,ID,DIGEST,COMPRESSION,BITS, &
VORZEICHEN,REELL,BYTEORDER,DIMOVER,LDIM1,LDIM2,LDIM3,PADDING).NE.0) &
GO TO 130
IF ((DIM1.NE.LDIM1).OR.(DIM2.NE.LDIM2)`'m4_ifelse(`fcb_3d_flag',
`3D',`.OR.(DIM3.NE.LDIM3)'))GO TO 130
!-----------------------------------------------------------------------
! -- Advance to start of binary image data
!-----------------------------------------------------------------------
! In CBF the binary data begins immediately after the first occurence
! of the following 4 bytes (MARKBYTES) in the image file
! Octet Hex Decimal Purpose
! 1 0C 12 (ctrl-L) End the current page
! 2 1A 26 (ctrl-Z) Stop listings in MS-DOS
! 3 04 04 (Ctrl-D) Stop listings in UNIX
! 4 D5 213 Binary section begins
! 5..5+n-1 Binary data (n octets)
!-----------------------------------------------------------------------
MARKER=TRANSFER(MARKBYTES,MARKER)
FOURBYTES=0
DO
DO I=1,3
FOURBYTES(I)=FOURBYTES(I+1)
ENDDO
BYTE_IN_FILE=BYTE_IN_FILE+1
IF (FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,FOURBYTES(4)).NE.0) GO TO 140
PIXVALUE=TRANSFER(FOURBYTES,PIXVALUE)
IF (PIXVALUE.EQ.MARKER)EXIT
ENDDO
! *** DEBUG *** PRINT *, "fwa-1 address of IMAGE at: "
! *** DEBUG *** PRINT *, "BYTE_IN_FILE: ", BYTE_IN_FILE
! *** DEBUG *** PRINT *, "REC_IN_FILE: ", REC_IN_FILE
!-----------------------------------------------------------------------
! -- Read data image of 32 bit two''`s complement integers, compressed
! -- by the BYTE-OFFSET algorithm.
! -- After the expansion the original pixel values are coded by 16 bit
! -- in a special way suitable for XDS (see INTEGER*2 FUNCTION CNT2PIX).
!-----------------------------------------------------------------------
FCB_READ_IMAGE_$1=CBF_FORMAT !Cannot handle this CBF format
IF ((BYTEORDER.EQ."LITTLE_ENDIAN").AND.(ENCODING.EQ.ENC_NONE).AND.&
(IAND(COMPRESSION,CBF_COMPRESSION_MASK).EQ.CBF_BYTE_OFFSET))THEN
PIXVALUE=0
NELEM_READ=0
m4_ifelse(fcb_3d_flag,
`3D',`DO K = 1, DIM3')
DO J = 1, DIM2
DO I = 1, DIM1
BYTE_IN_FILE=BYTE_IN_FILE+1
IF (FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,ONEBYTE).NE.0) GO TO 140
DIFF=ONEBYTE
IF (DIFF.EQ.-128)THEN
DO II=FIRST2,LAST2,STEP
BYTE_IN_FILE=BYTE_IN_FILE+1
IF (FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,TWOBYTES(II)).NE.0)GO TO 140
ENDDO
SHORTINT=TRANSFER(TWOBYTES,SHORTINT)
DIFF=SHORTINT
IF (DIFF.EQ.-32768)THEN
DO II=FIRST4,LAST4,STEP
BYTE_IN_FILE=BYTE_IN_FILE+1
IF (FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,FOURBYTES(II)).NE.0) &
GO TO 140
ENDDO
DIFF=TRANSFER(FOURBYTES,DIFF)
ENDIF
ENDIF
PIXVALUE=PIXVALUE+DIFF
ARRAY(I,J`'m4_ifelse(fcb_3d_flag,`3D',`,K')) = PIXVALUE
NELEM_READ=NELEM_READ+1
ENDDO
ENDDO`'m4_ifelse(fcb_3d_flag,`3D',`
ENDDO')
FCB_READ_IMAGE_$1=0 !No error
ELSE
IF ((BYTEORDER.EQ."LITTLE_ENDIAN").AND.(ENCODING.EQ.ENC_NONE).AND. &
((IAND(COMPRESSION,CBF_COMPRESSION_MASK).EQ.CBF_PACKED) .OR. &
(IAND(COMPRESSION,CBF_COMPRESSION_MASK).EQ.CBF_PACKED_V2)))THEN
FCB_READ_IMAGE_$1=FCB_DECOMPRESS_PACKED_$1 (ARRAY,NELEM,NELEM_READ, &
VORZEICHEN, COMPRESSION, DIM1, DIM2,`'m4_ifelse(fcb_3d_flag,`3D',`DIM3,') &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
IF (NELEM_READ.NE.NELEM) PRINT *, "EARLY TERMINATION AT ",NELEM_READ
PREV_ELEMENT = 0
END IF
END IF
!-----------------------------------------------------------------------
100 RETURN
110 FCB_READ_IMAGE_$1=-1 !Cannot determine endian architecture of this machine
RETURN
130 FCB_READ_IMAGE_$1=-3 !Wrong image format
GO TO 100
140 FCB_READ_IMAGE_$1=-4 !Cannot read image
GO TO 100
END FUNCTION FCB_READ_IMAGE_$1')
fcb_macro_FCB_READ_IMAGE(`I2')
fcb_macro_FCB_READ_IMAGE(`I4')
fcb_macro_FCB_READ_IMAGE(`3D_I2')
fcb_macro_FCB_READ_IMAGE(`3D_I4')
./CBFlib-0.9.2.2/m4/test_fcb_read_image.m4 0000644 0000765 0000765 00000015101 11603702103 016301 0 ustar yaya yaya m4_include(`fcblib_defines.m4')` PROGRAM TEST
IMPLICIT NONE
CHARACTER(LEN=100) LINE
INTEGER(2) IFRAME(1000,1000), DPREV
INTEGER(4) JFRAME(1000,1000)
INTEGER(4) KFRAME(50,60,70)
INTEGER,PARAMETER:: FCB_BYTES_IN_REC='m4_ifelse(`fcb_bytes_in_rec',`',4096,`fcb_bytes_in_rec')`
INTEGER IER, I, J, K, TAPIN, SIZE
INTEGER BYTE_IN_FILE, REC_IN_FILE, DTARG, ID
INTEGER(1) LAST_CHAR, BUFFER(FCB_BYTES_IN_REC)
INTEGER COMPRESSION, BITS, VORZEICHEN, REELL, ENCODING
INTEGER(8) DIM1, DIM2, DIM3, DIMOVER, PADDING
INTEGER(8) NELEM, NELEM_READ
CHARACTER(len=24) DIGEST
CHARACTER(len=14) BYTEORDER
'
fcb_interface_FCB_EXIT_BINARY
fcb_interface_FCB_OPEN_CIFIN
fcb_interface_FCB_NEXT_BINARY
fcb_interface_FCB_READ_IMAGE_I2
fcb_interface_FCB_READ_IMAGE_I4
fcb_interface_FCB_READ_IMAGE_3D_I2
fcb_interface_FCB_READ_IMAGE_3D_I4
TAPIN=9
` PRINT *,''` NAME OF TEST CBF ''`
READ *, LINE
IER = FCB_OPEN_CIFIN(LINE,TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER)
IF (IER.NE.0) THEN
PRINT *,"FILE OPEN ERROR: ", IER
STOP
END IF
! Read an array 1000 x 1000 INTEGER(4) in a flat field of 1000
PRINT *, " 1000 x 1000 I4 TEST "
NELEM = 1000*1000
DIM1 = 1000
DIM2 = 1000
IER = FCB_READ_IMAGE_I4(JFRAME,NELEM,NELEM_READ, &
1, COMPRESSION, DIM1, DIM2, PADDING, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
IF (IER.NE.0) THEN
PRINT *," FCB_READ_IMAGE_I4 ERROR: ", IER
STOP
ELSE
DPREV = 0
DO J = 1,1000
DO I = 1,1000
DTARG = 1000
IF (JFRAME(I,J).NE.DTARG) THEN
PRINT *, "IFRAME(",I,",",J,") = ", &
JFRAME(I,J), ", SHOULD BE ",DTARG
END IF
END DO
END DO
END IF
IER = FCB_EXIT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, PADDING )
IF (IER.NE.0) THEN
PRINT *," FCB_EXIT_BINARY ERROR: ", IER
STOP
END IF
! Read an array 1000 x 1000 INTEGER(2) in a flat field of 1000
PRINT *, " 1000 x 1000 I2 TEST "
IER = FCB_READ_IMAGE_I2(IFRAME,NELEM,NELEM_READ, &
1, COMPRESSION, DIM1, DIM2, PADDING, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
IF (IER.NE.0) THEN
PRINT *," FCB_READ_IMAGE_I2 ERROR: ", IER
STOP
ELSE
DPREV = 0
DO J = 1,1000
DO I = 1,1000
DTARG = 1000
IF (IFRAME(I,J).NE.DTARG) THEN
PRINT *, "IFRAME(",I,",",J,") = ", &
IFRAME(I,J), ", SHOULD BE ",DTARG
END IF
END DO
END DO
END IF
IER = FCB_EXIT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, PADDING )
IF (IER.NE.0) THEN
PRINT *," FCB_EXIT_BINARY ERROR: ", IER
STOP
END IF
! Read an array 1000 x 1000 INTEGER(4) in a flat field of 1000
! except for -3 along the main diagonal and its transpose
PRINT *, " 1000 x 1000 I4 TEST, WITH -3 on diag and transpose "
IER = FCB_READ_IMAGE_I4(JFRAME,NELEM,NELEM_READ, &
1, COMPRESSION, DIM1, DIM2, PADDING, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
IF (IER.NE.0) THEN
PRINT *," FCB_READ_IMAGE_I4 ERROR: ", IER
STOP
ELSE
DPREV = 0
DO J = 1,1000
DO I = 1,1000
DTARG = 1000
IF (I .EQ. J .OR. 1001-I .EQ. J) THEN
DTARG = -3
END IF
IF (JFRAME(I,J).NE.DTARG) THEN
PRINT *, "IFRAME(",I,",",J,") = ", &
JFRAME(I,J), ", SHOULD BE ",DTARG
END IF
END DO
END DO
END IF
IER = FCB_EXIT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, PADDING )
IF (IER.NE.0) THEN
PRINT *," FCB_EXIT_BINARY ERROR: ", IER
STOP
END IF
! Read an array 1000 x 1000 INTEGER(2) in a flat field of 1000
! except for -3 along the main diagonal and its transpose
PRINT *, " 1000 x 1000 I2 TEST, WITH -3 on diag and transpose "
IER = FCB_READ_IMAGE_I2(IFRAME,NELEM,NELEM_READ, &
1, COMPRESSION, DIM1, DIM2, PADDING, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
IF (IER.NE.0) THEN
PRINT *," FCB_READ_IMAGE_I2 ERROR: ", IER
STOP
ELSE
DPREV = 0
DO J = 1,1000
DO I = 1,1000
DTARG = 1000
IF (I .EQ. J .OR. 1001-I .EQ. J) THEN
DTARG = -3
END IF
IF (IFRAME(I,J).NE.DTARG) THEN
PRINT *, "IFRAME(",I,",",J,") = ", &
IFRAME(I,J), ", SHOULD BE ",DTARG
END IF
END DO
END DO
END IF
IER = FCB_EXIT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, PADDING )
IF (IER.NE.0) THEN
PRINT *," FCB_EXIT_BINARY ERROR: ", IER
STOP
END IF
! Read an array 50 x 60 x 70 INTEGER(4) in a flat field of 1000,
! except for -3 along the main diagonal and the values i+j+k-3
! every 1000th pixel
PRINT *, " 50 x 60 x 70 3D_I4 TEST "
DIM1 = 50
DIM2 = 60
DIM3 = 70
NELEM = DIM1*DIM2*DIM3
IER = FCB_READ_IMAGE_3D_I4(KFRAME,NELEM,NELEM_READ, &
1, COMPRESSION, DIM1, DIM2, DIM3, PADDING, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
IF (IER.NE.0) THEN
PRINT *," FCB_READ_IMAGE_3D_I4 ERROR: ", IER
STOP
ELSE
DPREV = 0
DO K = 1,70
DO J = 1,60
DO I = 1,50
DTARG = 1000
IF (I .EQ. J .OR. J .EQ. K) THEN
DTARG = -3
END IF
IF (MOD(I-1+(J-1)*50+(K-1)*50*60,1000).EQ.0) THEN
DTARG = I+J+K-3
END IF
IF (KFRAME(I,J,K).NE.DTARG) THEN
PRINT *, "KFRAME(",I,",",J,",",K,") = ", &
KFRAME(I,J,K), ", SHOULD BE ",DTARG
END IF
END DO
END DO
END DO
END IF
PRINT *, "TESTS COMPLETED"
STOP
END
' ./CBFlib-0.9.2.2/m4/fcb_read_bits.m4 0000644 0000765 0000765 00000013345 11603702103 015131 0 ustar yaya yaya m4_include(`fcblib_defines.m4')m4_dnl
` INTEGER FUNCTION FCB_READ_BITS(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
BITCOUNT,IINT,LINT)
!-----------------------------------------------------------------------
! Get integer value starting at BYTE_IN_FILE from file TAPIN
! continuing through BITCOUNT bits, with sign extension.
! (first byte is BYTE_IN_FILE=1)
!-----------------------------------------------------------------------
IMPLICIT NONE
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER, INTENT(INOUT):: BCOUNT
INTEGER(1),INTENT(INOUT):: BBYTE
INTEGER, INTENT(IN):: BITCOUNT
INTEGER, INTENT(IN):: LINT
INTEGER(4), INTENT(OUT):: IINT(LINT)
INTEGER I,J,LBITCOUNT,COUNT,KINTS
INTEGER(8) BITCODE,TBITCODE, M, MASK8
!-----------------------------------------------------------------------
INTEGER MAXBITS, NUMINTS
'
fcb_interface_FCB_READ_BYTE
`
MAXBITS = 32
NUMINTS = (BITCOUNT+MAXBITS-1)/MAXBITS
MASK8 = Z''`000000FF''`
DO KINTS = 1,NUMINTS
LBITCOUNT = MAXBITS
IF (KINTS.EQ.NUMINTS) LBITCOUNT = BITCOUNT-(NUMINTS-1)*32
COUNT = BCOUNT
BITCODE = BBYTE
BITCODE = IAND(BITCODE,MASK8)
DO
IF (COUNT .GE. LBITCOUNT) EXIT
BYTE_IN_FILE=BYTE_IN_FILE+1
FCB_READ_BITS = &
FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BBYTE)
IF (FCB_READ_BITS.NE.0) RETURN
BCOUNT=8
TBITCODE = BBYTE
TBITCODE = IAND(TBITCODE,MASK8)
CALL MVBITS(TBITCODE,0,MIN(8,32-COUNT),BITCODE,COUNT)
COUNT = COUNT+8
END DO
! SIGN EXTEND
IF (LBITCOUNT .LT. MAXBITS) THEN
M = 1
M = ISHFT(M,LBITCOUNT-1)
IF (IAND(BITCODE,M).NE.0) THEN
IINT(KINTS) = IOR(BITCODE,-M)
ELSE
IINT(KINTS) = IAND(BITCODE,NOT(-M))
ENDIF
ELSE
IINT(KINTS) = BITCODE
ENDIF
! SAVE THE REMAINING BITS FOR NEXT TIME
TBITCODE = BBYTE
TBITCODE = ISHFT(IAND(TBITCODE,MASK8),-(BCOUNT-(COUNT-LBITCOUNT)) )
BBYTE = TBITCODE
BCOUNT = COUNT-LBITCOUNT
END DO
FCB_READ_BITS = 0
RETURN
END FUNCTION FCB_READ_BITS
INTEGER FUNCTION FCB_READ_INTEGER(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
VALSIGN,BITCOUNT,IINT,LINT)
!-----------------------------------------------------------------------
! Get integer value starting at BYTE_IN_FILE from file TAPIN
! continuing through BITCOUNT bits, with optional sign extension.
! (first byte is BYTE_IN_FILE=1)
!-----------------------------------------------------------------------
IMPLICIT NONE
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER, INTENT(INOUT):: BCOUNT
INTEGER(1),INTENT(INOUT):: BBYTE
INTEGER, INTENT(IN):: VALSIGN,BITCOUNT
INTEGER, INTENT(IN):: LINT
INTEGER(4), INTENT(OUT):: IINT(LINT)
INTEGER SIGNBITS, VALBITS, NUMINTS, FRI
INTEGER I,J,LBITCOUNT,COUNT
INTEGER(4) TVAL(4), BITCODE,TBITCODE, M
INTEGER(4) XSIGN(1)
' fcb_errcode_CBF_OVERFLOW
fcb_interface_FCB_READ_BITS
`
!-----------------------------------------------------------------------
IF (BITCOUNT .LE. 0) THEN
IINT(1) = 0
FCB_READ_INTEGER = 0
RETURN
END IF
SIGNBITS = BITCOUNT-32
IF (SIGNBITS .GT. 0) THEN
VALBITS = BITCOUNT-SIGNBITS
ELSE
VALBITS = BITCOUNT
END IF
! READ THE VALUE
FRI = &
FCB_READ_BITS(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
VALBITS,IINT,LINT)
FCB_READ_INTEGER = FRI
IF (FCB_READ_INTEGER .NE. 0) RETURN
IF (VALBITS .LT. 32 .AND. VALSIGN .EQ. 0) THEN
IINT(1) = IAND(IINT(1),NOT(-ISHFT(1,VALBITS)) )
ENDIF
DO
IF (SIGNBITS .LE. 0) EXIT
IF (SIGNBITS .LT. 32) THEN
FRI = &
FCB_READ_BITS(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
SIGNBITS,XSIGN,1)
FCB_READ_INTEGER = FRI
IF (FCB_READ_INTEGER .NE. 0) RETURN
ELSE
FRI = &
FCB_READ_BITS(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
32,XSIGN,1)
FCB_READ_INTEGER = FRI
IF (FCB_READ_INTEGER .NE. 0) RETURN
END IF
SIGNBITS = SIGNBITS-32
IF ((IINT(1) .LT. 0 .AND. VALSIGN.NE.0 .AND. XSIGN(1).NE.-1) &
.OR. ((IINT(1) .GE. 0 .OR. VALSIGN.EQ.0) .AND. XSIGN(1).NE.0)&
) THEN
FCB_READ_INTEGER = CBF_OVERFLOW
IINT(1) = -1
IF (VALSIGN.NE.0) THEN
IF (XSIGN(1).GE. 0) THEN
IINT(1) = Z''`7FFFFFFF''`
ELSE
IINT(1) = Z''`80000000''`
END IF
END IF
RETURN
END IF
END DO
FCB_READ_INTEGER = 0
RETURN
END FUNCTION FCB_READ_INTEGER'
./CBFlib-0.9.2.2/m4/fcb_packed.m4 0000644 0000765 0000765 00000044450 11603702103 014425 0 ustar yaya yaya m4_dnl fcb_packed.m4 -- m4 macro file to generate I2, I4,
m4_dnl and 3D_I2 and 3D_I4 versions
m4_dnl of FCB_DECOMPRESS_PACKED
m4_include(`fcblib_defines.m4')m4_dnl
m4_define(`fcb_macro_FCB_PACKED',
`! FCB_PACKED_$1.f90
!
! Derived from CBFlib cbf_packed.c
! H. J. Bernstein, 25 February 2007
!
! Based on J. P. Abrahams pack_c.c
! incorporated under GPL and LGPL in
! CBFlib with permission from CCP4 and
! from J. P. Abramhams
!
! Also based in part on test_pack.f90
! translation of an earlier pack_c.c
! by W. Kabsch and K. Rohm
! Update pointers for averaging in J. P. Abrahams CCP4 compression
! algorithm. These f90 routines are derived from
! cbf_update_jpa_pointers, reworked as one routine
! for 2-dimensional arrays and one routine for 3-dimensional
! arrays, with I2 and I4 variants for each.
!
! This version is for
!
! m4_ifelse($1,`I2',`2-D INTEGER*2 arrays',
$1,`I4',`2-D INTEGER*4 arrays',
$1,`3D_I2',`3-D INTEGER*2 arrays',
$1,`3D_I4',`3-D INTEGER*4 arrays',`2-D INTEGER*2 arrays')
m4_define(`fcb_3d_flag',`2D')m4_dnl
m4_ifelse($1,`3D_I2',`m4_define(`fcb_3d_flag',`3D')',
$1,`3D_I4',`m4_define(`fcb_3d_flag',`3D')')m4_dnl
m4_define(`fcb_i2_flag',`I2')m4_dnl
m4_ifelse($1,`I4',`m4_define(`fcb_i2_flag',`I4')',
$1,`3D_I4',`m4_define(`fcb_i2_flag',`I4')')m4_dnl
!
! with functions
!
! FCB_UPDATE_JPA_POINTERS_$1
! FCB_DECOMPRESS_PACKED_$1
!
! In the f90 implementation TRAIL_INDEX_ARRAY(1..8) has been
! replaced by TRAIL_INDEX_ARRAY(1..4) for 2-dimensional
! arrays and TRAIL_INDEX_ARRAY(1..8) for 3-dimensional arrays
! containing array indices or 0, for the array as if it
! were a linear array.
!
! On entry, TRAIL_INDEX_ARRAY(1) should point to the data element
! immediately prior to the next data element to be processed, either
! in the same row (fastest index) or, at the end of the prior row
! if the next data element to be processed is at the end of a row
!
! ndim1, ndim2, ndim3 should point to the indices of the same
! data element as TRAIL_INDEX_ARRAY(1) points to. These values
! will be incremented to be the indices of the next data element
! to be processed before populating TRAIL_INDEX_ARRAY.
!
! On exit, TRAIL_INDEX_ARRAY(1..8) will have been populated with
! pointers to the data elements to be used in forming the average.
! Elements that will not be used will be set to NULL. Note
! that TRAIL_INDEX_ARRAY(1) may be set to NULL.
!
! If we mark the next element to be processed with a "*" and the
! entries in TRAIL_INDEX_ARRAY with their array indices 1 .. 8, the
! possible patterns of settings in the general case are:
!
! current section:
!
! - - - - 1 * - - - -
! - - - - 4 3 2 - - -
! - - - - - - - - - -
!
! prior section:
!
! - - - - - 5 - - - -
! - - - - 8 7 6 - - -
! - - - - - - - - - -
!
! If there is no prior section (i.e. ndim3 is 0, or
! the CBF_UNCORRELATED_SECTIONS flag is set
! to indicate discontinuous sections), the values
! for TRAIL_INDEX_ARRAY (5..8) will all be NULL. When
! there is a prior section, TRAIL_INDEX_ARRAY(6..8) are
! pointers to the elements immediately below the
! elements pointed to by TRAIL_INDEX_ARRAY(2..4), but
! TRAIL_INDEX_ARRAY(5) is one element further along
! its row to be directly below the next element to
! be processed.
!
! The first element of the first row of the first section
! is a special case, with no averaging. This function
! should not be called for that case.
!
! In the first row of the first section (ndim2 == 1,
! and ndim3 == 1), after the first element (ndim1 > 1),
! only TRAIL_INDEX_ARRAY(1) is used
!
! current section:
!
! - - - - 1 * - - - -
! For subsequent rows of the first section (ndim2 > 1,
! and ndim3 == 1), for the first element (ndim1 == 1),
! two elements from the prior row are used:
!
! current section:
!
! * - - - - - - - - -
! 3 2 - - - - - - - -
! - - - - - - - - - -
! while for element after the first element, but before
! the last element of the row, a full set of 4 elements
! is used:
!
! current section:
!
! - - - - 1 * - - - -
! - - - - 4 3 2 - - -
! - - - - - - - - - -
!
! For the last element of a row (ndim1 == dim1-1), two
! elements are used
!
! current section:
!
! - - - - - - - - 1 *
! - - - - - - - - - 3
! - - - - - - - - - -
!
! For sections after the first section, provided the
! CBF_UNCORRELATED_SECTIONS flag is not set in compression,
! for each non-NULL entry in TRAIL_INDEX_ARRAY (1..4) an entry
! is made in TRAIL_INDEX_ARRAY (5..8), except for the
! first element of the first row of a section. In that
! case an entry is made in TRAIL_INDEX_ARRAY(5).
INTEGER FUNCTION FCB_UPDATE_JPA_POINTERS_$1(TRAIL_INDEX_ARRAY,&
NDIM1, NDIM2, m4_ifelse(fcb_3d_flag,`3D',
`NDIM3, ')ARRAY, DIM1, DIM2, m4_ifelse(fcb_3d_flag,`3D',
`DIM3, ')AVERAGE, COMPRESSION)
IMPLICIT NONE
INTEGER(8), INTENT(IN):: DIM1,DIM2`'m4_ifelse(fcb_3d_flag,`3D',`,DIM3')
INTEGER(8),INTENT(INOUT):: TRAIL_INDEX_ARRAY(`'m4_ifelse(fcb_3d_flag,
`3D',`8',`4')), NDIM1, NDIM2`'m4_ifelse(fcb_3d_flag,`3D',`, NDIM3',` ')
INTEGER(m4_ifelse($1,`I2',2,$1,`3D_I2',2,4)), INTENT(IN):: ARRAY(DIM1,DIM2`'m4_ifelse(fcb_3d_flag,`3D',`,DIM3'))
INTEGER(4), INTENT(OUT):: AVERAGE
INTEGER, INTENT(IN):: COMPRESSION
INTEGER I, J, K, IFAST, m4_ifelse(fcb_3d_flag,`3D',`IMID, ')ISLOW
INTEGER LOGTWO(4)
m4_ifelse(fcb_i2_flag,`I2',
` INTEGER(4), PARAMETER:: SIGNMASK=Z'''``00008000'''``
INTEGER(4), PARAMETER:: LIMMASK=Z'''``0000FFFF'''``')
fcb_param_CBF_LIST_ALL
DATA LOGTWO / 1,2,0,3 /
AVERAGE = 0
NDIM1 = NDIM1+1
IF (NDIM1 .EQ. DIM1+1) THEN
NDIM1 = 1
NDIM2 = NDIM2+1
m4_ifelse(fcb_3d_flag,`3D',
`` IF (NDIM2 .EQ. DIM2+1) THEN
NDIM2 = 1
NDIM3 = NDIM3+1
END IF
'') END IF
DO I = 2,m4_ifelse(fcb_3d_flag,`3D',`8',`4')
TRAIL_INDEX_ARRAY(I) = 0
END DO
IF (NDIM2 > 1) THEN ! NOT IN THE FIRST ROW
TRAIL_INDEX_ARRAY(2) = TRAIL_INDEX_ARRAY(1)-(DIM1-2) ! DOWN 1 RIGHT 2
TRAIL_INDEX_ARRAY(3) = TRAIL_INDEX_ARRAY(1)-(DIM1-1) ! DOWN 1 RIGHT 1
IF (NDIM1 > 1) THEN ! NOT IN THE FIRST COLUMN
TRAIL_INDEX_ARRAY(4) = TRAIL_INDEX_ARRAY(1)-DIM1 ! DOWN 1
IF (NDIM1 .EQ. DIM1) THEN ! LAST COLUMN
TRAIL_INDEX_ARRAY(2) = 0
TRAIL_INDEX_ARRAY(4) = 0
END IF
ELSE ! FIRST COLUMN
TRAIL_INDEX_ARRAY(1) = 0
END IF
m4_ifelse(fcb_3d_flag,`3D',
`` IF (NDIM3 .GT. 1 .AND. &
IAND(COMPRESSION,CBF_UNCORRELATED_SECTIONS).EQ.0 ) THEN
IF (TRAIL_INDEX_ARRAY(1).NE.0) THEN
TRAIL_INDEX_ARRAY(5) = &
TRAIL_INDEX_ARRAY(1) - DIM1*DIM2 + 1
END IF
DO I = 2,4
IF (TRAIL_INDEX_ARRAY(I).NE.0) THEN
TRAIL_INDEX_ARRAY(I+4) = &
TRAIL_INDEX_ARRAY(I) - DIM1*DIM2
END IF
END DO
END IF
'') ELSE ! FIRST ROW OF A SECTION
IF (NDIM1 .EQ. 1 ) THEN
m4_ifelse(fcb_3d_flag,`3D',
`` TRAIL_INDEX_ARRAY(5) = TRAIL_INDEX_ARRAY(1) - (DIM1*DIM2-1)
'') TRAIL_INDEX_ARRAY(1) = 0
END IF
END IF
J = 0
m4_ifelse(fcb_3d_flag,`3D',
` DO I = 1,8
IF (TRAIL_INDEX_ARRAY(I).NE.0) THEN
J = J+1
ISLOW = 1+(TRAIL_INDEX_ARRAY(I)-1)/(DIM1*DIM2)
IMID = 1+MOD(TRAIL_INDEX_ARRAY(I)-1,DIM1*DIM2)
IMID = 1+(IMID-1)/DIM1
IFAST = 1+MOD(TRAIL_INDEX_ARRAY(I)-1,DIM1)
AVERAGE = AVERAGE+ARRAY(IFAST,IMID,ISLOW)
END IF
END DO
',
` DO I = 1,4
IF (TRAIL_INDEX_ARRAY(I).NE.0) THEN
J = J+1
ISLOW = 1+(TRAIL_INDEX_ARRAY(I)-1)/DIM1
IFAST = 1+MOD(TRAIL_INDEX_ARRAY(I)-1,DIM1)
AVERAGE = AVERAGE+ARRAY(IFAST,ISLOW)
END IF
END DO
')
K = ISHFT(J,-1)
IF ( K .GT. 0 ) THEN
m4_ifelse(fcb_i2_flag,`I2',
` AVERAGE = IAND(AVERAGE,LIMMASK)
IF (IAND(AVERAGE+K,SIGNMASK).NE.0) AVERAGE = IOR(AVERAGE,NOT(LIMMASK))')
IF (AVERAGE .GE.0) THEN
AVERAGE = ISHFT(AVERAGE+K,-LOGTWO(K))
ELSE
AVERAGE = NOT(ISHFT(NOT(AVERAGE+K),-LOGTWO(K)))
ENDIF
END IF
FCB_UPDATE_JPA_POINTERS_$1 = 0
RETURN
END FUNCTION FCB_UPDATE_JPA_POINTERS_$1
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_$1 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, m4_ifelse(fcb_3d_flag,`3D',
``DIM3, '') &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
IMPLICIT NONE
INTEGER(8), INTENT(IN):: DIM1,DIM2`'m4_ifelse(fcb_3d_flag,`3D',
`,DIM3')
INTEGER(m4_ifelse($1,`I2',2,$1,`3D_I2',2,4)), INTENT(OUT):: ARRAY(DIM1,DIM2`'m4_ifelse(fcb_3d_flag,`3D',
`,DIM3'))
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER(8) TRAIL_INDEX_ARRAY(m4_ifelse(fcb_3d_flag,`3D',8,4))
INTEGER I, V2FLAG, AVGFLAG, CLIPBITS, BITS
INTEGER(8) NDIM1, NDIM2, m4_ifelse(fcb_3d_flag,`3D',
`NDIM3,')LDIM1, LDIM2`'m4_ifelse(fcb_3d_flag,`3D',
`, LDIM3')
INTEGER COUNT, PIXEL, NEXT(1), IINT, IBITS
INTEGER BCOUNT
INTEGER(1) BBYTE
INTEGER ERRORCODE, KBITS, KSIGN, PIXELCOUNT
INTEGER(4) VORZEICHEN, UNSIGN, ELEMENT, LIMIT
INTEGER(4) LAST_ELEMENT
INTEGER(4) DISCARD(2), OFFSET(3)
! *** DEBUG *** INTEGER(4) PREV_ELEMENT, PREV_INDEX
fcb_interface_FCB_READ_INTEGER
fcb_interface_FCB_READ_BITS
fcb_interface_FCB_UPDATE_JPA_POINTERS_$1
fcb_param_CBF_LIST_ALL
fcb_errcode_LIST_ALL
! Version 1 bit lengths
INTEGER(4),PARAMETER:: &
CBF_PACKED_BITS1 = 4, &
CBF_PACKED_BITS2 = 5, &
CBF_PACKED_BITS3 = 6, &
CBF_PACKED_BITS4 = 7, &
CBF_PACKED_BITS5 = 8, &
CBF_PACKED_BITS6 = 16
! Version 2 bit lengths
INTEGER(4),PARAMETER:: &
CBF_PACKED_V2_BITS1 = 3, &
CBF_PACKED_V2_BITS2 = 4, &
CBF_PACKED_V2_BITS3 = 5, &
CBF_PACKED_V2_BITS4 = 6, &
CBF_PACKED_V2_BITS5 = 7, &
CBF_PACKED_V2_BITS6 = 8, &
CBF_PACKED_V2_BITS7 = 9, &
CBF_PACKED_V2_BITS8 = 10, &
CBF_PACKED_V2_BITS9 = 11, &
CBF_PACKED_V2_BITS10 = 12, &
CBF_PACKED_V2_BITS11 = 13, &
CBF_PACKED_V2_BITS12 = 14, &
CBF_PACKED_V2_BITS13 = 15, &
CBF_PACKED_V2_BITS14 = 16
INTEGER(4) CBF_PACKED_BITS(8), CBF_PACKEDV2_BITS(16)
DATA CBF_PACKED_BITS/ 0, CBF_PACKED_BITS1, &
CBF_PACKED_BITS2, CBF_PACKED_BITS3, CBF_PACKED_BITS4, &
CBF_PACKED_BITS5, CBF_PACKED_BITS6, 65 /
DATA CBF_PACKEDV2_BITS/ 0, CBF_PACKED_V2_BITS1, &
CBF_PACKED_V2_BITS2, CBF_PACKED_V2_BITS3, &
CBF_PACKED_V2_BITS4, CBF_PACKED_V2_BITS5, &
CBF_PACKED_V2_BITS6, CBF_PACKED_V2_BITS7, &
CBF_PACKED_V2_BITS8, CBF_PACKED_V2_BITS9, &
CBF_PACKED_V2_BITS10, CBF_PACKED_V2_BITS11, &
CBF_PACKED_V2_BITS12, CBF_PACKED_V2_BITS13, &
CBF_PACKED_V2_BITS14, 65 /
BCOUNT = 0
BBYTE = 0
! Discard the file_nelem entry (64 bits) */
FCB_DECOMPRESS_PACKED_$1 = &
FCB_READ_INTEGER(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
0,64,DISCARD,2)
IF (FCB_DECOMPRESS_PACKED_$1 .NE. 0) RETURN
! Discard the minimum element entry (64 bits) */
FCB_DECOMPRESS_PACKED_$1 = &
FCB_READ_INTEGER(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
0,64,DISCARD,2)
IF (FCB_DECOMPRESS_PACKED_$1 .NE. 0) RETURN
! Discard the maximum element entry (64 bits) */
FCB_DECOMPRESS_PACKED_$1 = &
FCB_READ_INTEGER(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
0,64,DISCARD,2)
IF (FCB_DECOMPRESS_PACKED_$1 .NE. 0) RETURN
! Discard the reserved entry (64 bits) */
FCB_DECOMPRESS_PACKED_$1 = &
FCB_READ_INTEGER(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
0,64,DISCARD,2)
IF (FCB_DECOMPRESS_PACKED_$1 .NE. 0) RETURN
V2FLAG = 0
IF (IAND(COMPRESSION,CBF_COMPRESSION_MASK).EQ.CBF_PACKED_V2) &
V2FLAG = 1
AVGFLAG = 1
IF (DIM1 .EQ. 0 .AND. DIM2 .EQ. 0 `'m4_ifelse(fcb_3d_flag,`3D',`.AND. DIM3 .EQ. 0')) AVGFLAG = 0
BITS = m4_ifelse($1,`I2',16,$1,`3D_I2',16,32)
CLIPBITS = 0
IF (AVGFLAG .NE. 0) CLIPBITS=BITS
DO I =1,m4_ifelse(fcb_3d_flag,`3D',8,4)
TRAIL_INDEX_ARRAY(I) = 0
END DO
VORZEICHEN = m4_ifelse($1,`I2',Z''`00008000''`,$1,`3D_I2',Z''`00008000''`,Z''`80000000''`)
UNSIGN = 0
IF (ELSIGN.NE.0) UNSIGN=VORZEICHEN
LIMIT = m4_ifelse($1,`I2',Z''`0000FFFF''`,$1,`3D_I2',Z''`0000FFFF''`,Z''`FFFFFFFF''`)
! Initialise the first element
LAST_ELEMENT = UNSIGN
! *** DEBUG *** PREV_ELEMENT = 0
! *** DEBUG *** PREV_INDEX = 0
m4_ifelse(fcb_3d_flag,`3D',` LDIM3 = DIM3
IF (DIM3.EQ.0) LDIM3 = 1')
LDIM2 = DIM2
IF (DIM2.EQ.0) LDIM2 = 1
LDIM1 = DIM1
m4_ifelse(fcb_3d_flag,`3D',` IF (DIM1.EQ.0) LDIM1 = NELEM/(LDIM2*LDIM3)
IF (LDIM1*LDIM2*LDIM3.NE.NELEM) THEN
',
` IF (DIM1.EQ.0) LDIM1 = NELEM/LDIM2
IF (LDIM1*LDIM2.NE.NELEM) THEN')
FCB_DECOMPRESS_PACKED_$1 = CBF_ARGUMENT
RETURN
END IF
! Read the elements
COUNT = 0
PIXEL = 0
NDIM1 = 1
NDIM2 = 1
m4_ifelse(fcb_3d_flag,`3D',` NDIM3 = 1')
DO
IF (COUNT .GE. NELEM) EXIT
! GET THE NEXT 6 BITS OF DATA
FCB_DECOMPRESS_PACKED_$1 = &
FCB_READ_INTEGER(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
0,6+V2FLAG,NEXT,1)
IF (FCB_DECOMPRESS_PACKED_$1 .NE. 0) THEN
NELEM_READ=COUNT+PIXEL
RETURN
END IF
PIXELCOUNT = ISHFT(1,IAND(NEXT(1),7))
IF (V2FLAG.NE.0) THEN
BITS = CBF_PACKEDV2_BITS(1+IAND(ISHFT(NEXT(1),-3),15) )
ELSE
BITS = CBF_PACKED_BITS(1+IAND(ISHFT(NEXT(1),-3),7) )
END IF
IF (AVGFLAG.NE.0 .AND. BITS.EQ. 65) BITS = CLIPBITS
! READ THE OFFSETS
IF ( PIXELCOUNT + COUNT .GT. NELEM ) &
PIXELCOUNT = NELEM - COUNT
DO PIXEL = 0, PIXELCOUNT-1
ELEMENT = LAST_ELEMENT
OFFSET(1) = 0
OFFSET(2) = 0
OFFSET(3) = 0
ERRORCODE = 0
IF (BITS .NE. 0) THEN
IF (BITS .GT. 32 ) THEN
IINT = 1
DO IBITS=0,BITS-1,32
KSIGN = 1
IF (IBITS .LT. BITS-32) KSIGN = 0
KBITS = BITS-32*(IINT-1)
IF (IBITS .LT. BITS-32) KBITS = 32
ERRORCODE=IOR(ERRORCODE, &
FCB_READ_INTEGER(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
KSIGN,KBITS,OFFSET(IINT:IINT),1) )
IINT = IINT+1
END DO
ELSE
ERRORCODE = FCB_READ_BITS(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
BITS,OFFSET(1:1),1)
END IF
END IF
IF (ERRORCODE.NE.0) THEN
NELEM_READ = COUNT+PIXEL
FCB_DECOMPRESS_PACKED_$1 = ERRORCODE
RETURN
END IF
ELEMENT = ELEMENT+OFFSET(1)
ELEMENT = IAND(ELEMENT,LIMIT)
ELEMENT = ELEMENT-UNSIGN
TRAIL_INDEX_ARRAY(1) = NDIM1+(NDIM2-1)*LDIM1`'m4_ifelse(fcb_3d_flag,`3D',` &
+(NDIM3-1)*LDIM1*LDIM2')
ARRAY(NDIM1,NDIM2`'m4_ifelse(fcb_3d_flag,`3D',`,NDIM3')) = ELEMENT
! *** DEBUG *** IF (PREV_ELEMENT.NE.ELEMENT.OR.PREV_INDEX.NE.TRAIL_INDEX_ARRAY(1)-1) THEN
! *** DEBUG *** PREV_ELEMENT = ELEMENT
! *** DEBUG *** PRINT *, "ARRAY(",TRAIL_INDEX_ARRAY(1),") = ", ELEMENT
! *** DEBUG *** END IF
! *** DEBUG *** PREV_INDEX= TRAIL_INDEX_ARRAY(1)
IF (AVGFLAG.NE.0) THEN
FCB_DECOMPRESS_PACKED_$1 = &
FCB_UPDATE_JPA_POINTERS_$1(TRAIL_INDEX_ARRAY,&
NDIM1, NDIM2, m4_ifelse(fcb_3d_flag,`3D',
`NDIM3,')ARRAY, LDIM1, LDIM2, m4_ifelse(fcb_3d_flag,`3D',
`LDIM3,')LAST_ELEMENT, COMPRESSION)
LAST_ELEMENT = LAST_ELEMENT + UNSIGN
LAST_ELEMENT = IAND(LAST_ELEMENT,LIMIT)
ELSE
LAST_ELEMENT = ELEMENT+UNSIGN
NDIM1 = NDIM1+1
IF (NDIM1 .GT. LDIM1) THEN
NDIM1 = 1
NDIM2 = NDIM2+1
m4_ifelse(fcb_3d_flag,`3D',
` IF(NDIM2 .GT. LDIM2) THEN
NDIM2 = 1
NDIM3 = NDIM3+1
END IF')
END IF
ENDIF
END DO
COUNT = COUNT+PIXELCOUNT
END DO
NELEM_READ = COUNT
FCB_DECOMPRESS_PACKED_$1 = 0
RETURN
END FUNCTION FCB_DECOMPRESS_PACKED_$1')
fcb_macro_FCB_PACKED(`I2')
fcb_macro_FCB_PACKED(`I4')
fcb_macro_FCB_PACKED(`3D_I2')
fcb_macro_FCB_PACKED(`3D_I4')
./CBFlib-0.9.2.2/bin/ 0000755 0000765 0000765 00000000000 11603703065 012353 5 ustar yaya yaya ./CBFlib-0.9.2.2/bin/.keepme 0000644 0000765 0000765 00000000000 11603702115 013603 0 ustar yaya yaya ./CBFlib-0.9.2.2/doc/ 0000755 0000765 0000765 00000000000 11603751102 012343 5 ustar yaya yaya ./CBFlib-0.9.2.2/doc/Iarray_intensities.gain.html 0000644 0000765 0000765 00000005403 11603702115 020015 0 ustar yaya yaya
(IUCr) CIF Definition save__array_intensities.gain
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The value of this data item is the identifier of one of
the axes in the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to _axis.id in the
AXIS category.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Data items in the ARRAY_DATA category are the containers for
the array data items described in the category ARRAY_STRUCTURE.
It is recognized that the data in this category needs to be used in
two distinct ways. During a data collection the lack of ancillary
data and timing constraints in processing data may dictate the
need to make a 'miniCBF' nothing more than an essential minimum
of information to record the results of the data collection. In that
case it is proper to use the ARRAY_DATA category as a
container for just a single image and a compacted, beam-line
dependent list of data collection parameter values. In such
a case, only the tags '_array_data.header_convention',
'_array_data.header_contents' and '_array_data.data' need be
populated.
For full processing and archiving, most of the tags in this
dictionary will need to be populated.
Examples:
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and is
presented as hexadecimal data. The first character 'H' on the
data lines means hexadecimal. It could have been 'O' for octal
or 'D' for decimal. The second character on the line shows
the number of bytes in each word (in this case '4'), which then
requires eight hexadecimal digits per word. The third character
gives the order of octets within a word, in this case '<'
for the ordering 4321 (i.e. 'big-endian'). Alternatively, the
character '>' could have been used for the ordering 1234
(i.e. 'little-endian'). The block has a 'message digest'
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
Example 2 -
This example shows a single image in a miniCBF, provided by
E. Eikenberry. The entire CBF consists of one data block
containing one category and three tags. The CBFlib
program convert_miniCBF and a suitable template file
can be used to convert this miniCBF to a full imgCIF
file.
###CBF: VERSION 1.5
# CBF file written by CBFlib v0.7.8
data_insulin_pilatus6m
_array_data.header_convention SLS_1.0
_array_data.header_contents
;
# Detector: PILATUS 6M SN: 60-0001
# 2007/Jun/17 15:12:36.928
# Pixel_size 172e-6 m x 172e-6 m
# Silicon sensor, thickness 0.000320 m
# Exposure_time 0.995000 s
# Exposure_period 1.000000 s
# Tau = 194.0e-09 s
# Count_cutoff 1048575 counts
# Threshold_setting 5000 eV
# Wavelength 1.2398 A
# Energy_range (0, 0) eV
# Detector_distance 0.15500 m
# Detector_Voffset -0.01003 m
# Beam_xy (1231.00, 1277.00) pixels
# Flux 22487563295 ph/s
# Filter_transmission 0.0008
# Start_angle 13.0000 deg.
# Angle_increment 1.0000 deg.
# Detector_2theta 0.0000 deg.
# Polarization 0.990
# Alpha 0.0000 deg.
# Kappa 0.0000 deg.
# Phi 0.0000 deg.
# Chi 0.0000 deg.
# Oscillation_axis X, CW
# N_oscillations 1
;
_array_data.data
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_BYTE_OFFSET"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 6247567
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
X-Binary-Element-Byte-Order: LITTLE_ENDIAN
Content-MD5: 8wO6i2+899lf5iO8QPdgrw==
X-Binary-Number-of-Elements: 6224001
X-Binary-Size-Fastest-Dimension: 2463
X-Binary-Size-Second-Dimension: 2527
X-Binary-Size-Padding: 4095
...
--CIF-BINARY-FORMAT-SECTION----
;
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
./CBFlib-0.9.2.2/doc/map_edit.html 0000644 0000765 0000765 00000026416 11603702115 015024 0 ustar yaya yaya #######
# MAP #
#######
save_MAP
_category.description
; Data items in the MAP category record
the details of a maps. Maps record values of parameters,
such as density, that are functions of position within
a cell or are functions of orthogonal coordinates in
three space.
A map may is composed of one or more map segments
specified in the MAP_SEGMENT category.
Maps are optionally keyed to a particular _diffrn.id
or to a particular _entry.id, so that multiple maps
for different data collections or entries may be
collected in one data block.
Examples are given in the MAP_SEGMENT category.
;
_category.id map
_category.mandatory_code no
loop_
_category_key.name '_map.id'
'_map.diffrn_id'
'_map.entry_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.details
_item_description.description
; The value of _map.details should give a
description of special aspects of each map.
;
_item.name '_map.details'
_item.category_id map
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.diffrn_id
_item_description.description
; This item is a pointer to _diffrn.id in the
DIFFRN category.
;
_item.name '_map.diffrn_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.entry_id
_item_description.description
; This item is a pointer to _entry.id in the
ENTRY category.
;
_item.name '_map.entry_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.id
_item_description.description
; The value of _map.id must uniquely identify
each map for the given diffrn.id or entry.id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map.id' map yes
'_map_segment.id' map_segment yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_segment.id' '_map.id'
save_
###########################
# MAP_SEGMENT #
###########################
save_MAP_SEGMENT
_category.description
; Data items in the MAP_SEGMENT category record
the details about each segment (section or brick) of a map.
;
_category.id map_segment
_category.mandatory_code no
loop_
_category_key.name '_map_segment.id'
'_map_segment.map_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map, each consisting of one
segment, both using the same array structure
and mask.
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
loop_
_map_segment.map_id
_map_segment.id
_map_segment.array_id
_map_segment.binary_id
_map_segment.mask_array_id
_map_segment.mask_binary_id
rho_calc rho_calc map_structure 1 mask_structure 1
rho_obs rho_obs map_structure 2 mask_structure 1
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map_segment.array_id
_item_description.description
; The value of _map_segment.array_id identifies the array structure
into which the map is organized.
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.array_id'
_item.category_id map_segment
_item.mandatory_code yes
_item_type.code code
save_
save__map_segment.binary_id
_item_description.description
; The value of _map_segment.binary_id distinguishes the particular set
of data organized according to _map_segment.array_id in which
the data values of the map are stored.
This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.mask_array_id
_item_description.description
; The value of _map_segment.mask_array_id, if given, the array structure
into which the mask for the map is organized. If no value is given,
then all elements of the map are valid. If a value is given, then
only elements of the map for which the corresponding element of
the mask is non-zero are valid. The value of
_map_segment.mask_array_id differ from the value of
_map_segment.array_id in order to permit the mask to be given
as, say, unsigned 8-bit integers, while the map is given as
a data type with more range. However, the two array structures
must be aligned, using the same axes in the same order with the
same displacements and increments
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.mask_array_id'
_item.category_id map_segment
_item.mandatory_code no
_item_type.code code
save_
save__map_segment.mask_binary_id
_item_description.description
; The value of _map_segment.mask_binary_id identifies the particular set
of data organized according to _map_segment.mask_array_id specifying
the mask for the map.
This item is a pointer to _array_data.mask_binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.mask_binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.id
_item_description.description
; The value of _map_segment.id must uniquely
identify each segment of a map.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map_segment.id'
map_segment
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_data_frame.map_segment_id'
'_map_segment.id'
save_
save__map_segment.map_id
_item_description.description
; This item is a pointer to _map.id
in the MAP category.
;
_item.name '_map_segment.map_id'
_item.category_id map_segment
_item.mandatory_code yes
_item_type.code code
save_
save__map_segment.details
_item_description.description
; The value of _map_segment.details should give a
description of special aspects of each segment of a map.
;
_item.name '_map_segment.details'
_item.category_id map_segment
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
; Example to be provided
;
;
;
save_
./CBFlib-0.9.2.2/doc/Idiffrn_frame_data.details.html 0000644 0000765 0000765 00000005205 11603702115 020403 0 ustar yaya yaya
(IUCr) CIF Definition save__diffrn_frame_data.details
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Polarization ratio of the diffraction beam incident on the
crystal. This is the ratio of the perpendicularly polarized to
the parallel polarized component of the radiation. The
perpendicular component forms an angle of
_diffrn_radiation.polarisn_norm to the normal to the
diffraction plane of the sample (i.e. the plane containing
the incident and reflected beams).
Type: float
Mandatory item: no
Alias: _diffrn_radiation_polarisn_ratio
(cif_core.dic
version 2.0.1)
The permitted range is [0.0, infinity)
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
./CBFlib-0.9.2.2/doc/CBFlib_NOTICES.txt 0000644 0000765 0000765 00000170507 11603702115 015363 0 ustar yaya yaya CBFlib Notices
COPYING
All of the CBFlib 0.7.7 package may be distributed under the terms of the
GNU General Public License (the GPL), see
http://www.gnu.org/licenses/gpl.txt
Alternatively most of the CBFlib 0.7.7 package may be distributed under
the terms of the GNU Lesser General Public License (the LGPL), see
http://www.gnu.org/licenses/lgpl.txt
The portions that may be distributed under the LGPL indentified as such in
the comments of the relevant files, and include the portions constituting
the API, but do not include the documentation nor does it include the
example programs. The documentation and examples may only be distributed
under the GPL.
----------------------------------------------------------------------
----------------------------------------------------------------------
THE FIRST ALTERNATIVE LICENSE FOR ALL OF CBFLIB (GPL)
(Valid for versions of CBFlib starting with release 0.7.5)
========================== GPL STARTS HERE =================================
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
License is intended to guarantee your freedom to share and change free
software--to make sure the software is free for all its users. This
General Public License applies to most of the Free Software
Foundation's software and to any other program whose authors commit to
using it. (Some other Free Software Foundation software is covered by
the GNU Library General Public License instead.) You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
this service if you wish), that you receive source code or can get it
if you want it, that you can change the software or use pieces of it
in new free programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid
anyone to deny you these rights or to ask you to surrender the rights.
These restrictions translate to certain responsibilities for you if you
distribute copies of the software, or if you modify it.
For example, if you distribute copies of such a program, whether
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you have. You must make sure that they, too, receive or can get the
source code. And you must show them these terms so they know their
rights.
We protect your rights with two steps: (1) copyright the software, and
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Also, for each author's protection and ours, we want to make certain
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Finally, any free program is threatened constantly by software
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patent must be licensed for everyone's free use or not licensed at all.
The precise terms and conditions for copying, distribution and
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GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains
a notice placed by the copyright holder saying it may be distributed
under the terms of this General Public License. The "Program", below,
refers to any such program or work, and a "work based on the Program"
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that is to say, a work containing the Program or a portion of it,
either verbatim or with modifications and/or translated into another
language. (Hereinafter, translation is included without limitation in
the term "modification".) Each licensee is addressed as "you".
Activities other than copying, distribution and modification are not
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is covered only if its contents constitute a work based on the
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Whether that is true depends on what the Program does.
1. You may copy and distribute verbatim copies of the Program's
source code as you receive it, in any medium, provided that you
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notices that refer to this License and to the absence of any warranty;
and give any other recipients of the Program a copy of this License
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You may charge a fee for the physical act of transferring a copy, and
you may at your option offer warranty protection in exchange for a fee.
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when run, you must cause it, when started running for such
interactive use in the most ordinary way, to print or display an
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notice that there is no warranty (or else, saying that you provide
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the Program is not required to print an announcement.)
These requirements apply to the modified work as a whole. If
identifiable sections of that work are not derived from the Program,
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entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest
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In addition, mere aggregation of another work not based on the Program
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END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
Copyright (C)
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Library General
Public License instead of this License.
=========================== GPL ENDS HERE ==================================
----------------------------------------------------------------------
----------------------------------------------------------------------
THE SECOND ALTERNATIVE LICENSE FOR CERTAIN PORTIONS OF CBFLIB
INCLUDING THE API ITSELF,
BUT NOT THE DOCUMENTATION AND NOT THE EXAMPLES (LGPL)
(Valid for versions of CBFlib starting with release 0.7.5)
========================== LGPL STARTS HERE ================================
GNU LESSER GENERAL PUBLIC LICENSE
Version 2.1, February 1999
Copyright (C) 1991, 1999 Free Software Foundation, Inc.
51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
[This is the first released version of the Lesser GPL. It also counts
as the successor of the GNU Library Public License, version 2, hence
the version number 2.1.]
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----------------------------------------------------------------------
Stanford University Notices
for the CBFlib software package that incorporates SLAC software on which
copyright is disclaimed
This software
The term 'this software', as used in these Notices, refers to those
portions of the software package CBFlib that were created by employees of
the Stanford Linear Accelerator Center, Stanford University.
Stanford disclaimer of copyright
Stanford University, owner of the copyright, hereby disclaims its
copyright and all other rights in this software. Hence, anyone may freely
use it for any purpose without restriction.
Acknowledgement of sponsorship
This software was produced by the Stanford Linear Accelerator Center,
Stanford University, under Contract DE-AC03-76SFO0515 with the Department
of Energy.
Government disclaimer of liability
Neither the United States nor the United States Department of Energy, nor
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Stanford disclaimer of liability
Stanford University makes no representations or warranties, express or
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Maintenance of notices
In the interest of clarity regarding the origin and status of this
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remain affixed to any copy or derivative of this software made or
distributed by the recipient and are to be affixed to any copy of software
made or distributed by the recipient that contains a copy or derivative of
this software.
Based on SLAC Software Notices, Set 4 OTT.002a, 2004 FEB 03
----------------------------------------------------------------------
----------------------------------------------------------------------
The IUCr Policy
for the Protection and the Promotion of the STAR File and
CIF Standards for Exchanging and Archiving Electronic Data
Overview
The Crystallographic Information File (CIF)[1] is a standard for
information interchange promulgated by the International Union of
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method for submitting publications to Acta Crystallographica Section C and
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Statement of intent
The IUCr's interest in the STAR File is as a general data interchange
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Protection of the standards
To protect the STAR File and the CIF as standards for interchanging and
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Glossary of terms
[1] CIF:
is a data file conformant to the file syntax defined at
http://www.iucr.org/iucr-top/cif/spec/index.html
[2] STAR File:
is a data file conformant to the file syntax defined at
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[3] DDL:
is a language used in a data dictionary to define data items in terms of
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http://www.iucr.org/iucr-top/cif/spec/ddl/index.html
Last modified: 30 September 2000
IUCr Policy Copyright (C) 2000 International Union of Crystallography
----------------------------------------------------------------------
----------------------------------------------------------------------
CBFlib V0.1 Notice
The following Diclaimer Notice applies to CBFlib V0.1, from which this
version is derived.
* The items furnished herewith were developed under the sponsorship of
the U.S. Government. Neither the U.S., nor the U.S. D.O.E., nor the
Leland Stanford Junior University, nor their employees, makes any
warranty, express or implied, or assumes any liability or
responsibility for accuracy, completeness or usefulness of any
information, apparatus, product or process disclosed, or represents
that its use will not infringe privately-owned rights. Mention of any
product, its manufacturer, or suppliers shall not, nor is it intended
to, imply approval, disapproval, or fitness for any particular use.
The U.S. and the University at all times retain the right to use and
disseminate the furnished items for any purpose whatsoever.
* Notice 91 02 01
----------------------------------------------------------------------
----------------------------------------------------------------------
CIFPARSE notice
Portions of this software are loosely based on the CIFPARSE software
package from the NDB at Rutgers university (see
http://ndbserver.rutgers.edu/NDB/mmcif/software). CIFPARSE is part of the
NDBQUERY application, a program component of the Nucleic Acid Database
Project [ H. M. Berman, W. K. Olson, D. L. Beveridge, J. K. Westbrook, A.
Gelbin, T. Demeny, S. H. Shieh, A. R. Srinivasan, and B. Schneider.
(1992). The Nucleic Acid Database: A Comprehensive Relational Database of
Three-Dimensional Structures of Nucleic Acids. Biophys J., 63, 751-759.],
whose cooperation is gratefully acknowledged, especially in the form of
design concepts created by J. Westbrook.
Please be aware of the following notice in the CIFPARSE API:
* This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR
IMPLIED. RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE
WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT.
----------------------------------------------------------------------
----------------------------------------------------------------------
MPACK notice
Portions of this library are adapted from the "mpack/munpack version 1.5"
routines, written by John G. Myers. Mpack and munpack are utilities for
encoding and decoding (respectively) binary files in MIME (Multipurpose
Internet Mail Extensions) format mail messages. The mpack software used is
(C) Copyright 1993,1994 by Carnegie Mellon University, All Rights
Reserved, and is subject to the following notice:
* Permission to use, copy, modify, distribute, and sell this software
and its documentation for any purpose is hereby granted without fee,
provided that the above copyright notice appear in all copies and that
both that copyright notice and this permission notice appear in
supporting documentation, and that the name of Carnegie Mellon
University not be used in advertising or publicity pertaining to
distribution of the software without specific, written prior
permission. Carnegie Mellon University makes no representations about
the suitability of this software for any purpose. It is provided "as
is" without express or implied warranty.
* CARNEGIE MELLON UNIVERSITY DISCLAIMS ALL WARRANTIES WITH REGARD TO
THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
FITNESS, IN NO EVENT SHALL CARNEGIE MELLON UNIVERSITY BE LIABLE FOR
ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT
OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
----------------------------------------------------------------------
----------------------------------------------------------------------
MD5 Notice
The following notice applies to the message digest software in md5.h and
md5.c which are optionally used by this library. To that extent, this
library is a work "derived from the RSA Data Security, Inc. MD5
Message-Digest Algorithm".
The software in md5.h and md5.c is Copyright (C) 1991-2, RSA Data
Security, Inc. Created 1991. All rights reserved, and is subject to the
following notice:
* License to copy and use this software is granted provided that it is
identified as the "RSA Data Security, Inc. MD5 Message-Digest
Algorithm" in all material mentioning or referencing this software or
this function.
* License is also granted to make and use derivative works provided that
such works are identified as "derived from the RSA Data Security, Inc.
MD5 Message-Digest Algorithm" in all material mentioning or
referencing the derived work.
* RSA Data Security, Inc. makes no representations concerning either the
merchantability of this software or the suitability of this software
for any particular purpose. It is provided "as is" without express or
implied warranty of any kind.
* These notices must be retained in any copies of any part of this
documentation and/or software.
----------------------------------------------------------------------
----------------------------------------------------------------------
CCP4 Packed Compression Notice
The CBF_PACKED and CBF_PACKED_V2 compression and decompression code
incorporated in CBFlib is derived in large part from the J. P. Abrahams
pack_c.c compression code in CCP4. This code is incorporated in CBFlib
under the GPL and the LGPL with both the permission Jan Pieter Abrahams,
the original author of pack_c.c (email from Jan Pieter Abrahams of 15
January 2007) and of the CCP4 project (email from Martyn Winn on 12
January 2007). The cooperation of J. P. Abrahams and of the CCP4 project
is gratefully acknowledged.
----------------------------------------------------------------------
----------------------------------------------------------------------
Updated 7 April 2007. yaya@bernstein-plus-sons.com
./CBFlib-0.9.2.2/doc/Carray_element_size.html 0000644 0000765 0000765 00000006266 11603702115 017227 0 ustar yaya yaya
(IUCr) CIF Definition save_array_element_size
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The setting of the specified axis in millimetres
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_displacement.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_displacement will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_displacement (e.g.
the mean).
If not specified, the value defaults to to the value of
_diffrn_scan_axis.displacement.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
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HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
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Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the
diffraction data were measured.
Examples:
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
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This item is an text field for use in minimal CBF files to carry
essential header information to be kept with image data
in _array_data.data when the tags that normally carry the
structured metadata for the image have not been populated.
Normally this data item should not appear when the full set
of tags have been populated and _diffrn_data_frame.details
appears.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
This item is an identifier for the convention followed in
constructing the contents of _array_data.header_contents
The permitted values are of the of an image creator identifier
followed by an underscore and a version string. To avoid
confusion about conventions, all creator identifiers
should be registered with the IUCr and the conventions
for all identifiers and versions should be posted on
the MEDSBIO.org web site.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
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The value of _diffrn_detector_element.reference_center_slow is
the slow index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_detector_element.reference_center_units' along the slow
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value givien whould be
representive of the beam center as determined from the ensemble
of settings.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The [2] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
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The method used to obtain monochromatic radiation. If a
monochromator crystal is used, the material and the
indices of the Bragg reflection are specified.
Examples:
'Zr filter'
'Ge 220'
none
'equatorial mounted graphite'
Type: text
Mandatory item: no
Alias: _diffrn_radiation_monochromator
(cif_core.dic
version 2.0.1)
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The pixel-centre-to-pixel-centre distance for a one-step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans
or for uncoupled angular scans at a constant radius
(cylindrical scans) and should not be specified for cases
in which the angle between pixels (rather than the distance
between pixels) is uniform.
See _array_structure_list_axis.angle_increment.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named _diffrn_detector_axis.id
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
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The order of bytes for integer values which require more
than 1 byte.
(IBM-PC's and compatibles and DEC VAXs use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. DEC Alphas can produce/use either
depending on a compiler switch.)
Type: ucode
Mandatory item: yes
The data value must be one of the following:
big_endian
The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
little_endian
The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
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This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differs
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the 'poise' of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
./CBFlib-0.9.2.2/doc/ddl_core_1.4.1.dic 0000644 0000765 0000765 00000046045 11603702115 015331 0 ustar yaya yaya ##############################################################################
# #
# DDL CORE DICTIONARY #
# #
##############################################################################
data_on_this_dictionary
_dictionary_name ddl_core.dic
_dictionary_version 1.4.1
_dictionary_update 2005-06-29
_dictionary_history
;
1991-03-08 "Implementing SMD in STAR: Dictionary Definition Language"
A F P Cook, ORAC Ltd., 8 March 1991. AFPC
1991-06-25 Adjustments and refinement for CIF applications. SRH
1991-09-02 Further refinements prior to "cifdic.c91". SRH
1993-05-10 Additions arising from discussions with Phil Bourne,
Tony Cook, Brian McMahon. SRH
1993-05-11 Further adjustments and Cyclops tests. SRH
1993-05-14 Proposed additional changes. PEB
1993-05-17 Further adjustments. SRH
1993-06-01 Refinements and additions. SRH
1993-07-19 Some tidying up. SRH
1993-08-10 Final checks before Beijing. SRH
1993-12-12 Following the Cambridge meeting with FHA and AFPC. SRH
1993-12-16 Following discussions with Brian McMahon in Chester. SRH
1993-12-17 Further adjustments. SRH
1994-02-18 Add _include_file provisions. SRH
1994-08-08 Install _type_construct definitions and apply. SRH
1994-08-24 Adjustments following Brian McMahon's comments. SRH
1994-11-16 Changes following Brussels workshop. SRH
1995-05-16 Changes to _units definitions. SRH
2005-02-09 Minor corrections to spelling and punctuation. Reference
to REGEX specifications updated. NJA
2005-06-11 Structural change to rationalise DDL1 dictionary against
specification documents in IT Vol. G. Initial global_ block
removed, "_enumeration_default none" added to definition of
_type_conditions and "_enumeration_default .*" to definition
of _type_construct. BMcM
2005-06-20 Minor corrections to reflect proof corrections for Chapter
4.9 of IT Vol. G. NJA
2005-06-29 Allow use of 'su' as synonym for 'esd' in _type_conditions
and describe 'esd' as 'deprecated'. BMcM
;
data_category
_definition
; Character string which identifies the natural grouping of data
items to which the specified data item belongs. If the data
item belongs in a looped list, then it must be grouped only with
items from the same category, but there may be more than one
looped list of the same category provided that each loop has its
own independent reference item (see _list_reference).
;
_name '_category'
_category category
_type char
data_definition
_definition
; The text description of the defined item.
;
_name '_definition'
_category definition
_type char
data_dictionary_history
_definition
; A chronological record of the changes to the dictionary file
containing the definition. Normally this item is stored in the
separate data block labelled data_on_this_dictionary.
;
_name '_dictionary_history'
_category dictionary
_type char
data_dictionary_name
_definition
; The name string which identifies the generic identity of
the dictionary. The standard construction for these names is
_.dic
Normally this item is stored in the separate data block
labelled data_on_this_dictionary.
;
_name '_dictionary_name'
_category dictionary
_type char
loop_ _example ddl_core.dic cif_core.dic
data_dictionary_update
_definition
; The date that the dictionary was last updated.
Normally this item is stored in the separate data block
labelled data_on_this_dictionary.
;
_name '_dictionary_update'
_category dictionary
_type char
_type_construct
(_chronology_year)-(_chronology_month)-(_chronology_day)
data_dictionary_version
_definition
; The dictionary version number. Version numbers cannot decrease
with updates. Normally this item is stored in the separate data
block labelled data_on_this_dictionary.
;
_name '_dictionary_version'
_category dictionary
_type numb
data_enumeration
_definition
; Permitted value(s) for the defined item.
;
_name '_enumeration'
_category enumeration
_type char
_list both
_list_mandatory yes
data_enumeration_default
_definition
; The default value for the defined item if it is not specified
explicitly. If a data value is not declared, the default is
assumed to be the "most likely" or "natural" value.
;
_name '_enumeration_default'
_category enumeration_default
_type char
data_enumeration_detail
_definition
; A description of the permitted value(s) for the defined item, as
identified by _enumeration.
;
_name '_enumeration_detail'
_category enumeration
_type char
_list both
_list_reference '_enumeration'
data_enumeration_range
_definition
; The range of values permitted for a defined item. This can
apply to 'numb' or 'char' items which have a preordained
sequence (e.g. numbers or alphabetical characters).
The minimum value 'min' and maximum value 'max' are separated
by a colon character. If 'max' is omitted, then the item can
have any permitted value greater than or equal to 'min'.
;
_name '_enumeration_range'
_category enumeration_range
_type char
_type_construct (_sequence_minimum):((_sequence_maximum)?)
loop_ _example -4:10 a:z B:R 0:
data_example
_definition
; An example value of the defined item.
;
_name '_example'
_category example
_type char
_list both
_list_mandatory yes
data_example_detail
_definition
; A description of an example value for the defined item.
;
_name '_example_detail'
_category example
_type char
_list both
_list_reference '_example'
data_list
_definition
; Signals whether the defined item is declared in a looped list.
;
_name '_list'
_category list
_type char
loop_ _enumeration
_enumeration_detail yes 'can only be declared in a looped list'
no 'cannot be declared in a looped list'
both 'declaration in a looped list optional'
_enumeration_default no
data_list_level
_definition
; Specifies the level of the loop structure in which a defined
item with the attribute _list 'yes' or 'both' must be declared.
;
_name '_list_level'
_category list
_type numb
_enumeration_range 1:
_enumeration_default 1
data_list_link_child
_definition
; Identifies data item(s) by name which must have a value which
matches that of the defined item. These items are referred to
as "child" references because they depend on the existence
of the defined item.
;
_name '_list_link_child'
_category list_link_child
_type char
_list both
data_list_link_parent
_definition
; Identifies a data item by name which must have a value which
matches that of the defined item, and which must be present in
the same data block as the defined item. This provides for a
reference to the "parent" data item.
;
_name '_list_link_parent'
_category list_link_parent
_type char
_list both
data_list_mandatory
_definition
; Signals whether the defined item must be present in the loop
structure containing other items of the designated _category.
This property is transferrable to another data item which is
identified by _related_item and has _related_function set as
'alternate'.
;
_name '_list_mandatory'
_category list
_type char
loop_ _enumeration
_enumeration_detail
yes 'required item in this category of looped list'
no 'optional item in this category of looped list'
_enumeration_default no
data_list_reference
_definition
; Identifies the data item, or items, which must be present
(collectively) in a looped list with the defined data item
for the loop structure to be valid. The data item(s)
identified by _list_reference provide a unique access code
to each loop packet. Note that this property may be
transferred to another item with _related_function 'alternate'.
;
_name '_list_reference'
_category list_reference
_type char
_list both
data_list_uniqueness
_definition
; Identifies data items which, collectively, must have unique
values for the loop structure of the designated _category items
to be valid. This attribute is specified in the
definition of a data item with _list_mandatory set to 'yes'.
;
_name '_list_uniqueness'
_category list_uniqueness
_type char
_list both
data_name
_definition
; The data name(s) of the defined item(s). If data items are
closely related or represent an irreducible set, their names
may be declared as a looped sequence in the same definition.
;
_name '_name'
_category name
_type char
_list both
loop_ _example '_atom_site_label'
'_atom_attach_all _atom_attach_ring'
'_index_h _index_k _index_l'
'_matrix_11 _matrix_12 _matrix_21 _matrix_22'
data_related_item
_definition
; Identifies data item(s) which have a classified relationship
to the defined data item. The nature of this relationship is
specified by _related_function.
;
_name '_related_item'
_category related
_type char
_list both
_list_mandatory yes
data_related_function
_definition
; Specifies the relationship between the defined item and the
item specified by _related_item. The following classifications
are recognized.
'alternate' signals that the item referred to in _related_item
has attributes that permit it to be used as an alternative to the
defined item for validation purposes.
'convention' signals that the item referred to in _related_item
is equivalent to the defined item except for a predefined
convention which requires a different _enumeration set.
'conversion' signals that the item referred to in _related_item
is equivalent to the defined item except that different scaling
or conversion factors are applied.
'replace' signals that the item referred to in _related_item
may be used identically to replace the defined item.
;
_name '_related_function'
_category related
_type char
_list yes
_list_reference '_related_item'
loop_ _enumeration
_enumeration_detail
alternate 'used alternatively for validation tests'
convention 'equivalent except for defined convention'
conversion 'equivalent except for conversion factor'
replace 'new definition replaces the current one'
data_type
_definition
; The type specification of the defined item.
Type 'numb' identifies items which must have values that are
identifiable numbers. The acceptable syntax for these numbers
is application-dependent, but the formats illustrated by the
following identical numbers are considered to be interchangeable:
42 42.000 0.42E2 .42E+2 4.2E1 420000D-4 0.0000042D+07
Type 'char' identifies items which need not be interpretable
numbers. The specification of these items must comply with the
STAR syntax specification of either a 'contiguous single-line
string' bounded by blanks or blank-quotes, or a 'text string'
bounded by semicolons as the first character of a line.
Type 'null' identifies items which appear in the dictionary
for data-definition and descriptive purposes. These items
serve no function outside the dictionary files.
;
_name '_type'
_category type
_type char
loop_ _enumeration
_enumeration_detail numb 'numerically interpretable string'
char 'character or text string'
null 'for dictionary purposes only'
data_type_conditions
_definition
; Codes defining conditions on the _type specification.
'su' permits a number string to contain an appended standard
uncertainty number enclosed within parentheses. E.g. 4.37(5)
'esd' is a deprecated synonym for 'su', arising from the
former use of the term 'estimated standard deviation'
for 'standard uncertainty', and permitting a number string to
contain an appended standard deviation within parentheses.
E.g. 4.37(5)
'seq' permits data to be declared as a sequence of values
separated by a comma <,> or a colon <:>.
* The sequence v1,v2,v3,. signals that v1, v2, v3, etc.
are alternative values.
* The sequence v1:v2 signals that v1 and v2 are the boundary
values of a continuous range of values satisfying the
requirements of _enumeration for the defined item.
Combinations of alternative and range sequences are permitted.
;
_name '_type_conditions'
_category type_conditions
_type char
_list both
_enumeration_default none
loop_ _enumeration
_enumeration_detail
none 'no extra conditions apply to the defined _type'
esd 'synonym for su'
seq 'data may be declared as a permitted sequence'
su 'numbers *may* have s.u.'s appended within parentheses'
data_type_construct
_definition
; String of characters specifying the construction of the data
value for the defined data item. The construction is composed
of two entities:
(1) data names
(2) construction characters
The rules of construction conform to the regular expression
(REGEX) specifications detailed in IEEE (1991) and International
Tables for Crystallography Volume G, Chapter 2.5.
Ref: IEEE (1991). IEEE Standard for Information Technology -
Portable Operating System Interface (POSIX) - Part 2: Shell
and Utilities, Vol. 1, IEEE Standard 1003.2-1992. New York:
The Institute of Electrical Engineers. International Tables for
Crystallography (2005). Vol. G, Definition and Exchange of
Crystallographic Data, edited by S. R. Hall and B. McMahon.
Heidelberg: Springer.
;
_name '_type_construct'
_category type_construct
_type char
_enumeration_default .*
_example (_year)-(_month)-(_day)
_example_detail 'a typical construction for _date'
data_units
_definition
; A unique code which identifies the units of the defined data
item. A description of the units is provided in _units_detail.
;
_name '_units'
_category units
_type char
loop_ _example
_example_detail K 'kelvins'
C 'degrees Celsius'
rad 'radians'
e 'electrons'
V 'volts'
Dal 'daltons'
m 'metres'
kg 'kilograms'
s 'seconds'
data_units_detail
_definition
; A description of the numerical units applicable to the defined
item and identified by the code _units.
;
_name '_units_detail'
_category units
_type char
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
./CBFlib-0.9.2.2/doc/Iarray_structure_list.array_id.html 0000644 0000765 0000765 00000005205 11603702115 021426 0 ustar yaya yaya
(IUCr) CIF Definition save__array_structure_list.array_id
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
./CBFlib-0.9.2.2/doc/cif_img_1.3.2_IUCr.dic 0000644 0000765 0000765 00000547125 11603702115 016042 0 ustar yaya yaya ##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.3.2 #
# of 2005-06-25 #
# #
# by Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook #
# #
# This dictionary was adapted from format discussed at the imgCIF Workshop, #
# held at BNL Oct 1997 and the Crystallographic Binary File Format Draft #
# Proposal by Andrew Hammersley. The first DDL 2.1 Version was created by #
# John Westbrook. This version was drafted by Herbert J. Bernstein and #
# incorporates comments by I. David Brown, John Westbrook, Brian McMahon, #
# Bob Sweet, Paul Ellis, Harry Powell, Wilfred Li, Gotzon Madariaga, #
# Frances C. Bernstein and others. #
##############################################################################
data_cif_img.dic
_dictionary.title cif_img.dic
_dictionary.version 1.3.2
_dictionary.datablock_id cif_img.dic
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.gain
# _array_intensities.gain_esd
# _array_intensities.linearity
# _array_intensities.offset
# _array_intensities.scaling
# _array_intensities.overload
# _array_intensities.undefined_value
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.encoding_type
# _array_structure.id
#
# category ARRAY_STRUCTURE_LIST
#
# _array_structure_list.axis_set_id
# _array_structure_list.array_id
# _array_structure_list.dimension
# _array_structure_list.direction
# _array_structure_list.index
# _array_structure_list.precedence
#
# category ARRAY_STRUCTURE_LIST_AXIS
#
# _array_structure_list_axis.axis_id
# _array_structure_list_axis.axis_set_id
# _array_structure_list_axis.angle
# _array_structure_list_axis.angle_increment
# _array_structure_list_axis.displacement_increment
# _array_structure_list_axis.angular_pitch
# _array_structure_list_axis.radial_pitch
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.type
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
#
# category DIFFRN_DATA_FRAME
#
# _diffrn_data_frame.array_id
# _diffrn_data_frame.binary_id
# _diffrn_data_frame.detector_element_id
# _diffrn_data_frame.id
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.id
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.axis_id
# _diffrn_detector_axis.detector_id
#
# category DIFFRN_DETECTOR_ELEMENT
#
# _diffrn_detector_element.center[1]
# _diffrn_detector_element.center[2]
# _diffrn_detector_element.id
# _diffrn_detector_element.detector_id
#
# category DIFFRN_MEASUREMENT
#
# _diffrn_measurement.diffrn_id
# _diffrn_measurement.details
# _diffrn_measurement.device
# _diffrn_measurement.device_details
# _diffrn_measurement.device_type
# _diffrn_measurement.id
# _diffrn_measurement.method
# _diffrn_measurement.number_of_axes
# _diffrn_measurement.specimen_support
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.axis_id
# _diffrn_measurement_axis.measurement_device
# _diffrn_measurement_axis.measurement_id
#
# category DIFFRN_RADIATION
#
# _diffrn_radiation.collimation
# _diffrn_radiation.diffrn_id
# _diffrn_radiation.div_x_source
# _diffrn_radiation.div_y_source
# _diffrn_radiation.div_x_y_source
# _diffrn_radiation.filter_edge'
# _diffrn_radiation.inhomogeneity
# _diffrn_radiation.monochromator
# _diffrn_radiation.polarisn_norm
# _diffrn_radiation.polarisn_ratio
# _diffrn_radiation.polarizn_source_norm
# _diffrn_radiation.polarizn_source_ratio
# _diffrn_radiation.probe
# _diffrn_radiation.type
# _diffrn_radiation.xray_symbol
# _diffrn_radiation.wavelength_id
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.date_end
# _diffrn_scan.date_start
# _diffrn_scan.integration_time
# _diffrn_scan.frame_id_start
# _diffrn_scan.frame_id_end
# _diffrn_scan.frames
#
# category DIFFRN_SCAN_AXIS
#
# _diffrn_scan_axis.axis_id
# _diffrn_scan_axis.angle_start
# _diffrn_scan_axis.angle_range
# _diffrn_scan_axis.angle_increment
# _diffrn_scan_axis.angle_rstrt_incr
# _diffrn_scan_axis.displacement_start
# _diffrn_scan_axis.displacement_range
# _diffrn_scan_axis.displacement_increment
# _diffrn_scan_axis.displacement_rstrt_incr
# _diffrn_scan_axis.scan_id
#
# category DIFFRN_SCAN_FRAME
#
# _diffrn_scan_frame.date
# _diffrn_scan_frame.frame_id
# _diffrn_scan_frame.frame_number
# _diffrn_scan_frame.integration_time
# _diffrn_scan_frame.scan_id
#
# category DIFFRN_SCAN_FRAME_AXIS
#
# _diffrn_scan_frame_axis.axis_id
# _diffrn_scan_frame_axis.angle
# _diffrn_scan_frame_axis.angle_increment
# _diffrn_scan_frame_axis.angle_rstrt_incr
# _diffrn_scan_frame_axis.displacement
# _diffrn_scan_frame_axis.displacement_increment
# _diffrn_scan_frame_axis.displacement_rstrt_incr
# _diffrn_scan_frame_axis.frame_id
#
# ***DEPRECATED*** data items
#
# _diffrn_detector_axis.id
# _diffrn_measurement_axis.id
#
# ***DEPRECATED*** category DIFFRN_FRAME_DATA
#
# _diffrn_frame_data.array_id
# _diffrn_frame_data.binary_id
# _diffrn_frame_data.detector_element_id
# _diffrn_frame_data.id
#
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
; Data items in the ARRAY_DATA category are the containers for
the array data items described in the category ARRAY_STRUCTURE.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and is
presented as hexadecimal data. The first character 'H' on the
data lines means hexadecimal. It could have been 'O' for octal
or 'D' for decimal. The second character on the line shows
the number of bytes in each word (in this case '4'), which then
requires eight hexadecimal digits per word. The third character
gives the order of octets within a word, in this case '<'
for the ordering 4321 (i.e. 'big-endian'). Alternatively, the
character '>' could have been used for the ordering 1234
(i.e. 'little-endian'). The block has a 'message digest'
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 2
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id, should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-ID, the value of _array_data.binary_id
should be equal to the value given for X-Binary-ID.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
"--CIF-BINARY-FORMAT-SECTION--" (including the
required initial "--").
The Content-Type may be any of the discrete types permitted
in RFC 2045; 'application/octet-stream' is recommended.
If an octet stream was compressed, the compression should
be specified by the parameter 'conversions="x-CBF_PACKED"'
or the parameter 'conversions="x-CBF_CANONICAL"'.
The Content-Transfer-Encoding may be 'BASE64',
'Quoted-Printable', 'X-BASE8', 'X-BASE10' or
'X-BASE16' for an imgCIF or 'BINARY' for a CBF. The
octal, decimal and hexadecimal transfer encodings are
for convenience in debugging and are not recommended
for archiving and data interchange.
In an imgCIF file, the encoded binary data begin after
the empty line terminating the header. In a CBF, the
raw binary data begin after an empty line terminating
the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (Ctrl-L) page break
1 1A 26 (Ctrl-Z) stop listings in MS-DOS
2 04 04 (Ctrl-D) stop listings in UNIX
3 D5 213 binary section begins
None of these octets are included in the calculation of
the message size or in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. An adjustment is made for
the deprecated binary formats in which eight bytes of binary
header are used for the compression type. In this case,
the eight bytes used for the compression type are subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is 'unsigned 32-bit integer'.
An MD5 message digest may, optionally, be used. The 'RSA Data
Security, Inc. MD5 Message-Digest Algorithm' should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is 'X-BASE8', 'X-BASE10' or
'X-BASE16', the data are presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ('big-
endian') or 1234... ('little-endian'). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as '==' for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is 'H', 'O' or 'D' for hexadecimal, octal or
decimal, n is the number of octets per word and d is '<'
or '>' for the '...4321' and '1234...' octet orderings,
respectively. The '==' padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hexadecimal, octal and decimal formats only,
comments beginning with '#' are permitted to improve
readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three: c1, c2, c3. The resulting 24 bits
are broken into four six-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order four bits of the second octet [(c1 & 3)<<4 | (c2>>4)],
then the bottom four bits of the second octet followed by the
high-order two bits of the last octet [(c2 & 15)<<2 | (c3>>6)],
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
with short groups of octets padded on the right with one '='
if c3 is missing, and with '==' if both c2 and c3 are missing.
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32...38,
42, 48...57, 59, 60, 62, 64...126 and the octet is not a ';'
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
'wrapped' with a terminating '=' (i.e. the MIME conventions
for an implicit line terminator are never used).
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
; Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - a regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.index
_item_description.description
; This item is a pointer to _array_structure_list.index in
the ARRAY_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
; The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
; Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
_array_intensities.gain. If raw, uncorrected values
are presented (e.g. for calibration experiments), the
value of _array_intensities.linearity will be 'raw'
and _array_intensities.gain will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.overload
_array_intensities.undefined_value
image_1 linear 1.2 655535 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
; Detector 'gain'. The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
; The estimated standard deviation in detector 'gain'.
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
; The intensity linearity scaling method used to convert
from the raw intensity to the stored element value:
'linear' is linear.
'offset' means that the value defined by
_array_intensities.offset should be added to each
element value.
'scaling' means that the value defined by
_array_intensities.scaling should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by _array_intensities.scaling is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
'logarithmic_scaled' means that the logarithm base 10 of
raw intensities multiplied by _array_intensities.scaling
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and calculating 10
to the power of this number.
'raw' means that the data are a set of raw values straight
from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
; The value defined by _array_intensities.offset should
be added to each element value.
;
'scaling'
; The value defined by _array_intensities.scaling should be
multiplied with each element value.
;
'scaling_offset'
; The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
; The square root of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
;
'logarithmic_scaled'
; The logarithm base 10 of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
_array_intensities.scaling and calculating 10 to the
power of this number.
;
'raw'
; The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data-fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
; Offset value to add to array element values in the manner
described by the item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
; The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.scaling
_item_description.description
;
Multiplicative scaling value to be applied to array data
in the manner described by item
_array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.undefined_value
_item_description.description
; A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
; Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
_category_key.name '_array_structure.id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
; The order of bytes for integer values which require more
than 1 byte.
(IBM PCs and compatibles, and Dec VAXs use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. Dec Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
; The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
; The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
; Type of data-compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code code
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'none'
; Data are stored in normal format as defined by
_array_structure.encoding_type and
_array_structure.byte_order.
;
'packed'
; Using the 'packed' compression scheme, a CCP4-style packing
(International Tables for Crystallography Volume G,
Section 5.6.3.2)
;
'canonical'
; Using the 'canonical' compression scheme (International Tables
for Crystallography Volume G, Section 5.6.3.1)
;
save_
save__array_structure.encoding_type
_item_description.description
; Data encoding of a single element of array data.
In several cases, the IEEE format is referenced.
See IEEE Standard 754-1985 (IEEE, 1985).
Ref: IEEE (1985). IEEE Standard for Binary Floating-Point
Arithmetic. ANSI/IEEE Std 754-1985. New York: Institute of
Electrical and Electronics Engineers.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure yes
'_array_data.array_id' array_data yes
'_array_structure_list.array_id' array_structure_list yes
'_array_intensities.array_id' array_intensities yes
'_diffrn_data_frame.array_id' diffrn_data_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
; Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left to right (increasing) in the
first dimension and bottom to top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differs
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the 'poise' of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
; The number of elements stored in the array structure in this
dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
; Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
; Indicates the index changes from 1 to the maximum dimension
;
'decreasing'
; Indicates the index changes from the maximum dimension to 1
;
save_
save__array_structure_list.index
_item_description.description
; Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
; Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
; Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets of axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axes: one for the angular
direction and one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes in the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
; The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to
_array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list_axis.angle
_item_description.description
; The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified for this case.
See _array_structure_list_axis.angular_pitch.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
; The pixel-centre-to-pixel-centre distance for a one-step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans
or for uncoupled angular scans at a constant radius
(cylindrical scans) and should not be specified for cases
in which the angle between pixels (rather than the distance
between pixels) is uniform.
See _array_structure_list_axis.angle_increment.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
; The radial distance from one 'cylinder' of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of _array_structure_list_axis.displacement_increment.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
########
# AXIS #
########
save_AXIS
_category.description
; Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection. The location of each
axis is specified by two vectors: the axis itself, given as a unit
vector, and an offset to the base of the unit vector. These vectors
are referenced to a right-handed laboratory coordinate system with
its origin in the sample or specimen:
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
These axes are based on the goniometer, not on the orientation of the
detector, gravity etc. The vectors necessary to specify all other
axes are given by sets of three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right-handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to but significantly
different from the choice in MOSFLM (Leslie & Powell, 2004). In MOSFLM,
X is along the X-ray beam (the CBF/imgCIF Z axis) and Z is along the
rotation axis.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam centre.
The location of the beam centre on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected millimetres from
the (0,0) corner of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, it is necessary to
specify the location of the beam centre on the detector in terms
of the origin of the detector, which is, of course, not coincident
with the centre of the sample.
Ref: Leslie, A. G. W. & Powell, H. (2004). MOSFLM v6.11.
MRC Laboratory of Molecular Biology, Hills Road, Cambridge, England.
http://www.CCP4.ac.uk/dist/x-windows/Mosflm/.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1
This example shows the axis specification of the axes of a kappa-
geometry goniometer [see Stout, G. H. & Jensen, L. H. (1989). X-ray
structure determination. A practical
guide, 2nd ed. p. 134. New York: Wiley Interscience].
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X axis. The next innermost axis, kappa,
is at a 50 degree angle to the X axis, pointed away from the source.
The innermost axis, phi, aligns with the X axis when omega and
phi are at their zero points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
x' = (T-omega) (T-kappa) (T-phi) x
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2
This example show the axis specification of the axes of a
detector, source and gravity. The order has been changed as a
reminder that the ordering of presentation of tokens is not
significant. The centre of rotation of the detector has been taken
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.depends_on specifies the next outermost
axis upon which this axis depends.
This item is a pointer to _axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.equipment specifies the type of
equipment using the axis: 'goniometer', 'detector',
'gravity', 'source' or 'general'.
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: 'rotation' or 'translation' (or 'general' when
the type is not relevant, as for gravity).
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
; Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - a frame containing data from four frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element are
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id.
;
;
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.id
_item_description.description
; The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'slow mode'
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detector(s) used to
measure the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
; The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of
_diffrn_detector.diffrn_id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
; The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id.
The word 'positioner' is a general term used in
instrumentation design for devices that are used to change
the positions of portions of apparatus by linear
translation, rotation or combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
; Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named _diffrn_detector_axis.id,
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
; Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, giving more detailed information
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
is preferable to simply providing the centre of the
detector element.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square, in the pattern
1 2
*
3 4
Note that the beam centre is slightly displaced from each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4.
;
;
loop_
_diffrn_detector_element.detector_id
_diffrn_detector_element.id
_diffrn_detector_element.center[1]
_diffrn_detector_element.center[2]
d1 d1_ccd_1 201.5 -1.5
d1 d1_ccd_2 -1.8 -1.5
d1 d1_ccd_3 201.6 201.4
d1 d1_ccd_4 -1.7 201.5
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.center[1]
_item_description.description
; The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
; The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.id
_item_description.description
; The value of _diffrn_detector_element.id must uniquely
identify each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
; This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the
diffraction data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model x'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector
angle 22.5 degrees
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support
and orient the specimen.
If the value of _diffrn_measurement.device is not given,
it is implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to
measure the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'home-made'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity
measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
;
The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during the collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
; The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id.
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
; Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
; This data item is a pointer to _diffrn_measurement.device
in the DIFFRN_MEASUREMENT category.
;
_item.name
'_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_type.code text
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named _diffrn_measurement_axis.id,
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item.mandatory_code implicit
_item_type.code code
save_
####################
# DIFFRN_RADIATION #
####################
save_DIFFRN_RADIATION
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used for measuring diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
_category_key.name '_diffrn_radiation.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions of
photons in the XZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by pi.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions
of photons in the YZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by pi.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation in degrees squared between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
direction of each photon in XZ plane times the deviations
of the direction of the same photon in the YZ plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that for some synchrotrons, this value is specified in
milliradians squared, in which case a conversion is
needed. To convert a value in milliradians squared to a value
in degrees squared, multiply by 0.180**2 and divide by pi**2.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a
monochromator crystal is used, the material and the
indices of the Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarization ratio of the diffraction beam incident on the
crystal. This is the ratio of the perpendicularly polarized to
the parallel polarized component of the radiation. The
perpendicular component forms an angle of
_diffrn_radiation.polarisn_norm to the normal to the
diffraction plane of the sample (i.e. the plane containing
the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between
the normal to the polarization plane and the laboratory Y
axis as defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monchromator.
This differs from the value of
_diffrn_radiation.polarisn_norm
in that _diffrn_radiation.polarisn_norm refers to
polarization relative to the diffraction plane rather than
to the laboratory axis system.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane should be taken
as the XZ plane and the angle as 0.
See _diffrn_radiation.polarizn_source_ratio.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared)
of the electric vector in the plane of the normal to the
plane of polarization.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane is to be taken
as the XZ plane and the normal is parallel to the Y axis.
Thus, if there was complete polarization in the plane of
polarization, the value of
_diffrn_radiation.polarizn_source_ratio would be 1, and
for an unpolarized beam
_diffrn_radiation.polarizn_source_ratio would have a
value of 0.
If the X axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of 'MONOCHROMATOR' in the Denzo glossary, and values of near
1 should be expected for a bending-magnet source. However,
if the X axis were perpendicular to the polarization plane
(not a common choice), then the Denzo value would be the
negative of _diffrn_radiation.polarizn_source_ratio.
See http://www.hkl-xray.com for information on Denzo and
Otwinowski & Minor (1997).
This differs both in the choice of ratio and choice of
orientation from _diffrn_radiation.polarisn_ratio, which,
unlike _diffrn_radiation.polarizn_source_ratio, is
unbounded.
Reference: Otwinowski, Z. & Minor, W. (1997). 'Processing of
X-ray diffraction data collected in oscillation mode.' Methods
Enzymol. 276, 307-326.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly
recommended that this be given so that the
probe radiation is clearly specified.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'x-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for the probe
radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to
_diffrn_radiation_wavelength.id in the
DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.category_id diffrn_radiation
_item.mandatory_code yes
_item_type.code code
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
; This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
;
_category.id diffrn_refln
_category.mandatory_code no
_category_key.name '_diffrn_refln.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
; This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
; Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
_category_key.name '_diffrn_scan.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. In this example, three rotation axes and one translation axis
at nonzero values are specified, with one axis stepping. There is no
reason why more axes could not have been specified to step. Range
information has been specified, but note that it can be calculated from
the number of frames and the increment, so the data item
_diffrn_scan_axis.angle_range could be dropped.
Both the sweep data and the data for a single frame are specified.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
_diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
_diffrn_scan_frame.integration_time and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustments are made to
scan times and nonlinear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.angle_increment
_diffrn_scan_frame_axis.displacement
_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
; Example 2 - a more extensive example (R. M. Sweet, P. J. Ellis &
H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the goniometer.
This leads to a choice: either the axes of
the detector are defined at the origin, and then a Z setting of -240
is entered, or the axes are defined with the necessary Z offset.
In this case, the setting is used and the offset is left as zero.
This axis is called DETECTOR_Z.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm x 0.150mm, the centre of the first pixel is at (0.075,
0.075) in this coordinate system.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
; Example 3 - Example 2 revised for a spiral scan (R. M. Sweet,
P. J. Ellis & H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the
goniometer, as in Example 2 above, but in this example the
image plate is scanned in a spiral pattern from the outside edge in.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. The rotation axis is called ELEMENT_ROT and the
radial axis is called ELEMENT_RAD. A 150 micrometre radial pitch
and a 75 micrometre 'constant velocity' angular pitch are assumed.
Indexing is carried out first on the rotation axis and the radial axis
is made to be dependent on it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.angle
_array_structure_list_axis.displacement
_array_structure_list_axis.angular_pitch
_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
; The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
; The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
; Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
_diffrn_scan_frame.integration_time, even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
; The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frame_id_end
_item_description.description
; The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frames
_item_description.description
; The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
; Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
; The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.angle_start
_item_description.description
; The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
; The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
; The increment for each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_increment. The
sum of the values of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
; The increment after each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_rstrt_incr. The
sum of the values of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment
and _diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.angle for this
next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
; The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
; The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_increment.
The sum of the values of
_diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_rstrt_incr.
The sum of the values of
_diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.displacement
for this next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
; Data items in the DIFFRN_SCAN_FRAME category describe
the relationships of particular frames to scans.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
; The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame.frame_number
_item_description.description
; The value of this data item is the number of the frame
within the scan, starting with 1. It is not necessarily
the same as the value of _diffrn_scan_frame.frame_id,
but it may be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
; The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of _diffrn_scan.integration_time.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
; Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the
settings of axes for particular frames. Unspecified axes are
assumed to be at their zero points. If, for any given frame,
nonzero values apply for any of the data items in this category,
those values should be given explicitly in this category and not
simply inferred from values in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
; The increment for this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
; The increment after this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment and
_diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.angle for this next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.displacement for this next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
######################## DEPRECATED DATA ITEMS ########################
save__diffrn_detector_axis.id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_detector_axis.id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_measurement_axis.id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
######################### DEPRECATED CATEGORY #########################
#####################
# DIFFRN_FRAME_DATA #
#####################
save_DIFFRN_FRAME_DATA
_category.description
; Data items in the DIFFRN_FRAME_DATA category record
the details about each frame of data.
The items in this category are now in the
DIFFRN_DATA_FRAME category.
The items in the DIFFRN_FRAME_DATA category
are now deprecated. The items from this category
are provided as aliases in version 1.0 of the dictionary
but should not be used for new work.
The items from the old category are provided
in this dictionary for completeness
but should not be used or cited. To avoid
confusion, the example has been removed
and the redundant parent-child links to other
categories have been removed.
;
_category.id diffrn_frame_data
_category.mandatory_code no
loop_
_category_key.name '_diffrn_frame_data.id'
'_diffrn_frame_data.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
THE DIFFRN_FRAME_DATA category is deprecated and should not be used.
;
;
# EXAMPLE REMOVED #
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_frame_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.array_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.binary_id'
_item.category_id diffrn_frame_data
_item.mandatory_code implicit
_item_type.code int
save_
save__diffrn_frame_data.detector_element_id
_item_description.description
;
This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.detector_element_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.id
_item_description.description
; The value of _diffrn_frame_data.id must uniquely identify
each complete frame of data.
DEPRECATED -- DO NOT USE
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_frame_data.id' diffrn_frame_data yes
_item_type.code code
save_
################ END DEPRECATED SECTION ###########
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive) ...
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items (case insensitive)...
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]\
(T[0-2][0-9]:[0-5][0-9]:[0-5][0-9](.[0-9]+)([+-][0-5][0-9]:[0-5][0-9]))?
;
;
Standard format for CIF date and time strings (see
http://www.iucr.org/iucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character "T" followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
decimal fraction on the seconds of time.
Time is local time if no time-zone offset is given.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2))'
'millimetres' 'millimetres (metres * 10^( -3))'
'nanometres' 'nanometres (metres * 10^( -9))'
'angstroms' 'angstroms (metres * 10^(-10))'
'picometres' 'picometres (metres * 10^(-12))'
'femtometres' 'femtometres (metres * 10^(-15))'
#
'reciprocal_metres' 'reciprocal metres (metres^(-1))'
'reciprocal_centimetres'
'reciprocal centimetres ((metres * 10^( -2))^(-1))'
'reciprocal_millimetres'
'reciprocal millimetres ((metres * 10^( -3))^(-1))'
'reciprocal_nanometres'
'reciprocal nanometres ((metres * 10^( -9))^(-1))'
'reciprocal_angstroms'
'reciprocal angstroms ((metres * 10^(-10))^(-1))'
'reciprocal_picometres'
'reciprocal picometres ((metres * 10^(-12))^(-1))'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9))^2'
'angstroms_squared' 'angstroms squared (metres * 10^(-10))^2'
'8pi2_angstroms_squared' '8pi^2 * angstroms squared (metres * 10^(-10))^2'
'picometres_squared' 'picometres squared (metres * 10^(-12))^2'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9))^3'
'angstroms_cubed' 'angstroms cubed (metres * 10^(-10))^3'
'picometres_cubed' 'picometres cubed (metres * 10^(-12))^3'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^( -9))^(-3))
;
'electrons_per_angstroms_cubed'
; electrons per angstroms cubed (electrons/(metres * 10^(-10))^(-3))
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (electrons/(metres * 10^(-12))^(-3))
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.3.2 2005-06-25
; 2005-06-25 ITEM_TYPE_LIST: code, ucode, line, uline regexps updated
to those of current mmCIF; float modified by allowing integers
terminated by a point as valid. The 'time' part of
yyyy-mm-dd types made optional in the regexp. (BM)
2005-06-17 Minor corrections as for proofs for IT G Chapter 4.6
(NJA)
2005-02-21 Minor corrections to spelling and punctuation
(NJA)
2005-01-08 Changes as per Nicola Ashcroft.
+ Updated example 1 for DIFFRN_MEASUREMENT to agree with mmCIF.
+ Spelled out "micrometres" for "um" and "millimetres" for "mm".
+ Removed phrase "which may be stored" from ARRAY_STRUCTURE
description.
+ Removed unused 'byte-offsets' compressions and updated
cites to ITVG for '_array_structure.compression_type'.
(HJB)
;
1.3.1 2003-08-13
;
Changes as per Frances C. Bernstein.
+ Identify initials.
+ Adopt British spelling for centre in text.
+ Set \p and \%Angstrom and powers.
+ Clean up commas and unclear wordings.
+ Clean up tenses in history.
Changes as per Gotzon Madariaga.
+ Fix the ARRAY_DATA example to align '_array_data.binary_id'
and X-Binary-Id.
+ Add a range to '_array_intensities.gain_esd'.
+ In the example of DIFFRN_DETECTOR_ELEMENT,
'_diffrn_detector_element.id' and
'_diffrn_detector_element.detector_id' interchanged.
+ Fix typos for direction, detector and axes.
+ Clarify description of polarisation.
+ Clarify axes in '_diffrn_detector_element.center[1]'
'_diffrn_detector_element.center[2]'.
+ Add local item types for items that are pointers.
(HJB)
;
1.3.0 2003-07-24
;
Changes as per Brian McMahon.
+ Consistently quote tags embedded in text.
+ Clean up introductory comments.
+ Adjust line lengths to fit in 80 character window.
+ Fix several descriptions in AXIS category which
referred to '_axis.type' instead of the current item.
+ Fix erroneous use of deprecated item
'_diffrn_detector_axis.id' in examples for
DIFFRN_SCAN_AXIS.
+ Add deprecated items '_diffrn_detector_axis.id'
and '_diffrn_measurement_axis.id'.
(HJB)
;
1.2.4 2003-07-14
;
Changes as per I. David Brown.
+ Enhance descriptions in DIFFRN_SCAN_AXIS to make them less
dependent on the descriptions in DIFFRN_SCAN_FRAME_AXIS.
+ Provide a copy of the deprecated DIFFRN_FRAME_DATA
category for completeness.
(HJB)
;
1.2.3 2003-07-03
;
Cleanup to conform to ITVG.
+ Correct sign error in ..._cubed units.
+ Correct '_diffrn_radiation.polarisn_norm' range.
(HJB)
;
1.2.2 2003-03-10
;
Correction of typos in various DIFFRN_SCAN_AXIS descriptions.
(HJB)
;
1.2.1 2003-02-22
;
Correction of ATOM_ for ARRAY_ typos in various descriptions.
(HJB)
;
1.2 2003-02-07
;
Corrections to encodings (remove extraneous hyphens) remove
extraneous underscore in '_array_structure.encoding_type'
enumeration. Correct typos in items units list. (HJB)
;
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB.
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li.
;
1.1.1 2001-02-16
;
Several typo corrections by JW.
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS. (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME.
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to '_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source',
'_diffrn_radiation.polarizn_source_norm',
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add '_diffrn_measurement.device' to category key.
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to
allow for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up. (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes. (JW)
+ Correct spelling of diffrn_measurement_axis in '_axis.id'
+ Correct ordering of uses of '_item.mandatory_code' and
'_item_default.value'.
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown. (HJB)
+ Add further comments on '\n' and '\t'.
+ Update ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Change 'meter' to 'metre' throughout.
+ Add missing enumerations to '_array_structure.compression_type'
and make 'none' the default.
+ Remove parent-child relationship between
'_array_structure_list.index' and '_array_structure_list.precedence'.
+ Improve alphabetization.
+ Fix '_array_intensities_gain.esd' related function.
+ Improve comments in AXIS.
+ Fix DIFFRN_FRAME_DATA example.
+ Remove erroneous DIFFRN_MEASUREMENT example.
+ Add '_diffrn_measurement_axis.id' to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data. (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors. (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for '_diffrn_scan.id' definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header. (HJB)
+ Restore '_diffrn_detector.diffrn_id' to DIFFRN_DETECTOR KEY.
+ Add AXIS category.
+ Bring in complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
from cif_mm.dic for clarity.
+ Change '_array_structure.encoding_type' from type code to uline and
added X-Binary-Element-Type to MIME header.
+ Add detector beam centre '_diffrn_detector_element.center[1]' and
'_diffrn_detector_element.center[2]'.
+ Correct item name of '_diffrn_refln.frame_id'.
+ Replace reference to '_array_intensities.undefined' by
'_array_intensities.undefined_value'.
+ Replace references to '_array_intensity.scaling' with
'_array_intensities.scaling'.
+ Add DIFFRN_SCAN... categories.
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft. (HJB)
+ Reflow comment lines over 80 characters and corrected typos.
+ Update examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF. (HJB)
+ Add binary type, which is a text field containing a variant on
MIME encoded data.
+ Change type of '_array_data.data' to binary and specify internal
structure of raw binary data.
+ Add '_array_data.binary_id', and make
'_diffrn_frame_data.binary_id' and '_array_intensities.binary_id'
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft. (JW)
+ Add category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes are made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA is renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE is renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for '_diffrn_frame_data.array_id' is changed from
'_array_structure_list.array_id' to '_array_structure.id'. Item
'_diffrn_detector.array_id' is deleted.
+ Add data item '_diffrn_frame_data.binary_id' to identify data
groups within a binary section. The formal identification of the
binary section is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version is adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley
(AH).
Modifications to the CBF draft. (JW)
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories
have been generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category
ARRAY_DATA. This departs from the CBF notion of data existing
in some special comment. In this description, data is handled as an
ordinary data item encapsulated in a character data type. Although
data this manner deviates from CIF conventions, it does not violate
any DDL 2.1 rules. DDL 2.1 regular expressions can be used to define
the binary representation which will permit some level of data
validation. In this version, the placeholder type code "any" has
been used. This translates to a regular expression which will match
any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary.
It may be possible to use the DDL 2.1 ITEM_STRUCTURE and
ITEM_STRUCTURE_LIST categories to provide the information that is
carried in by the ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By
moving the array structure to the DDL level it would be possible to
define an array type as well as a regular expression defining the
data format.
+ Multiple array sections can be properly handled within a single
datablock.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
./CBFlib-0.9.2.2/doc/Iarray_data.array_id.html 0000644 0000765 0000765 00000005202 11603702115 017241 0 ustar yaya yaya
(IUCr) CIF Definition save__array_data.array_id
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions of
photons in the XZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Data items in the DIFFRN_FRAME_DATA category record
the details about each frame of data.
The items in this category are now in the
DIFFRN_DATA_FRAME category.
The items in the DIFFRN_FRAME_DATA category
are now deprecated. The items from this category
are provided as aliases in the 1.0 dictionary
or, in the case of _diffrn_frame_data.details,
in the 1.4 dictionary. THESE ITEMS SHOULD NOT
BE USED FOR NEW WORK.
The items from the old category are provided
in this dictionary for completeness
but should not be used or cited. To avoid
confusion, the example has been removed
and the redundant parent-child links to other
categories have been removed.
Example:
THE DIFFRN_FRAME_DATA category is deprecated and should not be used.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The [3] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _axis.id in the
AXIS category.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
./CBFlib-0.9.2.2/doc/cif_mm.dic 0000644 0000765 0000765 00012242644 11603702115 014275 0 ustar yaya yaya ###########################################################################
#
# File: mmcif_pdbx.dic
# Date: Fri Jul 29 11:04:31 EDT 2005
#
# Created from files in CVS module dict-mmcif_pdbx.dic unless noted:
# mmcif_pdbx-header.dic
# mmcif_pdbx-data.dic
# mmcif_pdbx-def-1.dic
# ../dict-mmcif_std/mmcif_std-def-2.dic
# mmcif_pdbx-def-2.dic
# mmcif_pdbx-def-3.dic
# mmcif_pdbx-def-4.dic
# mmcif_pdbx-def-5.dic
# mmcif_pdbx-def-6.dic
# ../dict-mmcif_iims/mmcif_iims-def-2.dic
# mmcif_pdbx-def-8.dic
# mmcif_pdbx-def-9.dic
# mmcif_pdbx-def-10.dic
# mmcif_pdbx-def-12.dic
#
###########################################################################
###########################################################################
#
# File: mmcif_pdbx-header.dic
#
# PDB Exchange Data Dictionary
#
# This dictionary supplements the contents of the mmCIF data dictionary
# with additional data items that may be required to store all of the
# information currently included a Protein Data Bank (PDB) format data
# file. Additional data items describing internal processing status
# are also defined here.
#
# The mmCIF dictionary and this supplement provide the provisional
# specifications for the data exchange protocol used by the wwPDB:
# Resource Collaboratory for Structural Bioinformatics (RCSB) PDB,
# Molecular Structure Database (MSD) Group/EBI, PDB Japan (PDBj) at
# Osaka University. This dictionary also includes: data extensions
# for structural genomics projects recommended by International Task
# Force on Data Deposition and Archiving (including protein production),
# NMR and 3D electron microscopy.
#
#
# Header Section
#
##############################################################################
data_mmcif_pdbx.dic
_datablock.id mmcif_pdbx.dic
_datablock.description
;
This data block holds the Protein Data Bank Exchange Data dictionary.
;
_dictionary.title mmcif_pdbx.dic
_dictionary.datablock_id mmcif_pdbx.dic
_dictionary.version 1.019
#
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
0.001 2000-05-23
;
Initial revision based on RCSB local dictionaries
and EBI database schema. J. Westbrook and J. Ionides
;
0.002 2000-06-06
; Changes: (jdw)
+ Added items in refine_hist and exptl_crystal_grow
;
0.003 2000-10-16
; Changes: (jdw)
+ Move enumerations to examples for:
_pdbx_nmr_exptl.type
_pdbx_nmr_ensemble.conformer_selection_criteria
_pdbx_nmr_software.name
_struct_keywords.pdbx_keywords
+ Added _atom_site_anisotrop.pdbx_auth_* items
+ Added _struct_mon_prot_cis.pdbx_
+ Added _struct_conn.pdbx_ptnr3_auth_* items.
;
0.004 2000-10-24
; Changes: (jdw)
+ Added optional timestamps to data items.
+ Repositioned parent items in PDBX_POLY_SEQ_SCHEME.
;
0.005 2000-10-25
; Changes: (jdw)
+ drop category PDBX_DATABASE_REMARK
;
0.006 2000-10-26
;
Changes: (jdw)
+ Added _exptl_crystal_grow.rcsb_pH_range.
+ Added category PDBX_STRUCT_SHEET_HBOND to hold single hydrogen
bond registration between beta sheet strands.
;
0.007 2000-11-09
;
Changes: (jdw)
+ Added mandatory codes for _exptl_crystal_grow.pdbx_details and
_exptl_crystal_grow.pdbx_pH_range.
+ Added missing data types and category ids in category
pdbx_struct_sheet_hbond.
+ Updated data type for atom name references to atcode.
+ Updated aliases for _refine.overall_SU_B and _refine.overall_SU_ML.
+ Trimmed line lengths > 80 characters.
;
0.008 2001-01-22
;
Changes: (jdw)
+ Added item _pdbx_database_status.dep_release_code_sequence
;
0.009 2001-03-02
;
Changes: (jdw)
+ Added missing mandatory codes and reset aliases for
_diffrn_radiation.pdbx_wavelenth_list.
;
0.010 2001-04-18
;
Changes: (jdw)
+ Added missing _item_type.codes for
_refine_hist.number_atoms_solvent
_refine_hist.number_atoms_total
_refine.overall_SU_B
_refine.overall_SU_ML
_refine.pdbx_overall_ESU_R
+ Added CCP4 data items output from REFMAC V5.
;
0.011 2001-06-14
;
Changes: (jdw)
+ Moved enumerations to examples for _pdbx_nmr_spectrometer.field_strength
+ _atom_site.pdb_auth_atom_name data type changed from code to atcode.
;
0.012 2001-06-28
;
Changes: (jdw)
+ _atom_site_anisotrop.pdbx_auth_* aliases corrected.
+ adjust regex for date:time type
;
0.013 2001-07-12
;
Changes: (jdw)
+ enumerations->examples for _pdbx_nmr_representative.selection_criteria and
_pdbx_database_related.db_name.
+ add regex for int and float ranges
;
0.014 2002-02-28
;
Changes: (jdw)
+ Add items for NMR model and PDB insert code to GEOM_BOND, GEOM_ANGLE,
GEOM_CONTACT, and GEOM_TORSION categories.
;
0.015 2002-05-22
;
Changes: (jdw)
+ Add PDBX_ENTITY_NONPOLY and fix missing data type codes.
;
0.016 2002-08-05
;
Changes: (jdw)
+ Add PDBX_AUDIT category.
;
0.017 2002-10-05
;
Changes: (jdw)
+ Final corrections of recommendations for NMR and X-ray deposition for
structural genomics.
;
0.018 2003-07-07
;
Changes: (jdw)
+ Integrated protein production data items.
;
0.019 2003-09-21
;
Changes: (jdw/hy)
+ Added additional phasing items for PDB_EXTRACT.
;
0.020 2003-10-30
;
Changes: (jdw/zf)
+ Fix cases where category keys are not flagged as mandatory
+ Add category PDBX_AUDIT_AUTHOR
;
1.000 2004-04-22
;
Changes: (jdw)
+ New packaging and naming
+ Integrate 3d em definitions
+ Relax enumerations to comply with existing legacy data.
+ Version to 1.000
;
1.001 2004-05-21
;
Changes: (jdw)
+ Fixed incorrect category in _pdbx_audit_author.address
+ Added _citation.pdbx_database_id_DOI
+ Fixed placement of _chem_comp.pdbx_align. Moved this item
to _chem_comp_atom.pdbx_align
;
1.002 2004-06-09
;
Changes: (jdw)
+ Added categories PDBX_DOMAIN, PDBX_SEQUENCE_RANGE,
PDBX_FEATURE_ENTRY, PDBX_FEATURE_ASSEMBLY, PDBX_FEATURE_DOMAIN,
and PDBX_FEATURE_SEQUENCE_RANGE.
;
1.003 2004-06-16
;
Changes: (jdw)
+ Fix miscellaneous unresolved links.
;
1.004 2004-08-04
;
Changes: (jdw)
+ Fix many data type errors in phasing section.
+ Add pdbx_contact_author
;
1.005 2004-09-28
;
Changes: (zkf,jdw)
+ Add missing pdbx_contact_author.postal_code item
+ Add missing pdbx_contact_author.city item
+ Add missing pdbx_contact_author.state_province item
+ Add enumerations in pdbx_contact_author.id
+ Modify enumerations in pdbx_contact_author.role
;
1.006 2004-10-10
;
Changes: (jdw)
+ Update enumerations in cryo-em dictionary.
;
1.007 2004-11-02
;
Changes: (jdw)
+ added pdbx_entity_prod_protocol, pdbx_exptl_crystal_grow_sol,
pdbx_exptl_crystal_grow_comp, and pdbx_exptl_crystal_cryo_treatment
categories
+ relax enumerations in cryo-em dictionary.
+ remove upper-bound for refine.occupancy_max
;
1.008 2004-11-15
;
Changes: (jdw)
+ fix typo in category save frame name pdbx_exptl_crystal_grow_comp.
;
1.009 2005-01-13
;
Changes: (zkf)
+ add _pdbx_database_status.status_code_sf item
+ add _pdbx_database_status.date_of_sf_release item
+ add _pdbx_database_status.status_code_mr item
+ add _pdbx_database_status.date_of_mr_release item
+ add _pdbx_database_status.SG_entry item
+ add _entity_poly.pdbx_target_identifier item
+ add pdbx_SG_project category
+ fixed enumeration values for _software.language
;
1.010 2005-01-25
;
Changes: (jdw)
+ change mandatory doc for _pdbx_database_status.SG_entry
+ fix key in category pdbx_database_PDB_obs_spr
;
1.011 2005-03-08
;
Changes: (jdw)
+ Included extensions from mmCIF dictionary...
Changes: (fzk)
+ add _pdbx_refine_tls_group.beg_auth_asym_id
+ add _pdbx_refine_tls_group.end_auth_asym_id
+ add enumeration values 'SGC' and 'NPPSFA' for
_pdbx_SG_project.initial_of_center
+ add enumeration values 'Structural Genomics Consortium' and
'National Project on Protein Structural and Functional Analyses'
for _pdbx_SG_project.full_name_of_center
+ fix _item_description.description for _entity_poly.pdbx_target_identifier
;
1.012 2005-03-29
;
Changes: (kh/jdw)
+ added preliminary set of extensions for macromolecular powder diffraction
experiments, including:
_pdbx_exptl_pd (category)
_pdbx_exptl_pd.entry.id
_pdbx_exptl_pd.spec_preparation_pH
_pdbx_exptl_pd.spec_preparation_pH_range
_pdbx_exptl_pd.spec_preparation
_diffrn_radiation.pdbx_analyzer
_refine.pdbx_pd_number_of_powder_patterns
_refine.pdbx_pd_number_of_points
_refine.pdbx_pd_meas_number_of_points
_refine.pdbx_pd_proc_ls_prof_R_factor
_refine.pdbx_pd_proc_ls_prof_wR_factor
_refine.pdbx_pd_Marquardt_correlation_coeff
_refine.pdbx_pd_Fsqrd_R_factor
_refine.pdbx_pd_ls_matrix_band_width
Changes: (fzk)
removed 'National Project on Protein Structural and Functional Analyses' from
_pdbx_SG_project.full_name_of_center,
added 'National Project on Protein Structural and Functional Analyses' to
_pdbx_SG_project.project_name
;
1.013 2005-04-05
;
Changes: (jdw)
+ Temporarily remove definitions from Image CIF dictionary
+ Added mandatory code for _cell.reciprocal_angle_beta
+ Added mandatory code for _pdbx_entity_nonpoly.entity_id
+ Fixed category attribute for _reflns_shell.pdbx_chi_squared
+ Changed mandatory code for _software.citation_id
;
1.014 2005-04-08
;
Changes: (jdw)
+ remove _struct_keywords.text from category key
;
1.015 2005-04-15
;
Changes: (jdw)
+ remove _entity_keywords.text from category key
;
1.016 2005-06-24
;
Changes: (jdw)
+ aliases repointed for items in category pdbx_database_remark
+ Added the following items:
_diffrn_detector.pdbx_frames_total
_diffrn_detector.pdbx_collection_time_total
_refine.pdbx_ls_sigma_Fsqd
_reflns.pdbx_Rmerge_I_all
_reflns.pdbx_netI_over_sigmaI
_reflns.pdbx_res_netI_over_av_sigmaI_2
_reflns.pdbx_res_netI_over_sigmaI_2
_reflns_shell.pdbx_netI_over_sigmaI_all
_reflns_shell.pdbx_netI_over_sigmaI_obs
_struct_biol.pdbx_formula_weight
_struct_biol.pdbx_formula_weight_method
_struct_biol_gen.pdbx_PDB_order
_phasing_MAD.pdbx_number_data_sets
_phasing_MAD.pdbx_anom_scat_method
_phasing_MIR.pdbx_number_derivatives
_phasing_set.pdbx_temp_details
+ miscellaneous editorial changes in descriptions and enumerations.
;
1.017 2005-06-27
;
Changes: (BMcM)
+ added _reflns.threshold_expression and _publ_author.email
+ numerous minor changes to wordings of definitions to align with mmcif
version 2.0.09 as released on International Tables G CD-ROM
;
1.018 2005-07-14
;
Changes: (jdw)
+ Added PDB_SOLN_SCATTER* definitions
+ Added _refln.pdbx_[F,I]_[minus,plus] and
_refln.pdbx_[F,I]_[minus,plus]_sigma
+ Extend enumeration for _pdbx_database_status.status_code_sf
;
1.019 2005-07-21
;
Changes: (jdw)
+ Added _struct.pdbx_formula_weight and _struct.pdbx_formula_weight_method
+ Added _refln.pdbx_HL_A_iso, _refln.pdbx_HL_B_iso, _refln.pdbx_HL_C_iso,
and _refln.pdbx_HL_D_iso
+ Added _phasing_set.pdbx_d_res_low/high _pdbx_phasing_MR.native_data_set_id
+ Added category pdbx_feature_monomer
;
### EOF mmcif_pdbx-header.dic
###########################################################################
#
# File: mmcif_pdbx-data.dic
#
# Protein Data Bank Exchange Data Dictionary
#
#
# Data Section
#
#
###########################################################################
##################
## SUB_CATEGORY ##
##################
loop_
_sub_category.id
_sub_category.description
'cartesian_coordinate'
; The collection of x, y, and z components of a position specified
with reference to a Cartesian (orthogonal angstrom) coordinate
system.
;
'cartesian_coordinate_esd'
; The collection of estimated standard deviations of the x, y, and
z components of a position specified with reference to a
Cartesian (orthogonal angstrom) coordinate system.
;
'fractional_coordinate'
; The collection of x, y, and z components of a position specified
with reference to unit cell directions.
;
'fractional_coordinate_esd'
; The collection of estimated standard deviations of the x, y, and
z components of a position specified with reference to unit cell
directions.
;
'matrix'
; The collection of elements of a matrix.
;
miller_index
; The collection of h, k, and l components of the Miller index of
a reflection.
;
'cell_length'
; The collection of a, b, and c axis lengths of a unit cell.
;
'cell_length_esd'
; The collection of estimated standard deviations of the a, b, and
c axis lengths of a unit cell.
;
'cell_angle'
; The collection of alpha, beta, and gamma angles of a unit cell.
;
'cell_angle_esd'
; The collection of estimated standard deviations of the alpha,
beta, and gamma angles of a unit cell.
;
'mm_atom_site_auth_label'
; The collection of asym id, atom id, comp id and seq id
components of an author's alternative specification for
a macromolecular atom site.
;
'mm_atom_site_label'
; The collection of alt id, asym id, atom id, comp id and seq id
components of the label for a macromolecular atom site.
;
'vector'
; The collection of elements of a vector.
;
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the macromolecular dictionary.
;
'atom_group'
'inclusive_group'
; Categories that describe the properties of atoms.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'audit_group'
'inclusive_group'
; Categories that describe dictionary maintenance and
identification.
;
'cell_group'
'inclusive_group'
; Categories that describe the unit cell.
;
'chemical_group'
'inclusive_group'
; Categories that describe chemical properties and nomenclature.
;
'chem_comp_group'
'inclusive_group'
; Categories that describe components of chemical structure.
;
'chem_link_group'
'inclusive_group'
; Categories that describe links between components of
chemical structure.
;
'citation_group'
'inclusive_group'
; Categories that provide bibliographic references.
;
'computing_group'
'inclusive_group'
; Categories that describe the computational details of the
experiment.
;
'compliance_group'
'inclusive_group'
; Categories that are included in this dictionary specifically to
comply with previous dictionaries.
;
'database_group'
'inclusive_group'
; Categories that hold references to entries in databases that
contain related information.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
'em_group'
'inclusive_group'
; Categories that describe 3-dimensional electron microscopy.
;
'entity_group'
'inclusive_group'
; Categories that describe chemical entities.
;
'entry_group'
'inclusive_group'
; Categories that pertain to the entire data block.
;
'exptl_group'
'inclusive_group'
; Categories that hold details of the experimental conditions.
;
'geom_group'
'inclusive_group'
; Categories that hold details of molecular and crystal geometry.
;
'iucr_group'
'inclusive_group'
; Categories that are used for manuscript submission and
internal processing by the staff of the International Union of
Crystallography.
;
'pdb_group'
'inclusive_group'
; Categories that pertain to the file-format or data-processing
codes used by the Protein Data Bank.
;
'phasing_group'
'inclusive_group'
; Categories that describe phasing.
;
'refine_group'
'inclusive_group'
; Categories that describe refinement.
;
'refln_group'
'inclusive_group'
; Categories that describe the details of reflection measurements.
;
'struct_group'
'inclusive_group'
; Categories that contain details about the crystallographic
structure.
;
'symmetry_group'
'inclusive_group'
; Categories that describe symmetry information.
;
'pdbx_group'
'inclusive_group'
; Categories which are part of PDB data exchange protocol.
;
'pdbx_erf_group'
'inclusive_group'
; Categories which are used by RCSB PDB to store derived
and computed data.
;
'ccp4_group'
'inclusive_group'
; Categories from the CCP4 harvest dictionary.
;
'ndb_group'
'inclusive_group'
; Categories which are used by the Nucleic Acid Database.
;
'rcsb_group'
'inclusive_group'
; Categories which are used internally by the RCSB PDB.
;
'protein_production_group'
'inclusive_group'
; Categories which describe the details of protein production.
;
'solution_scattering_group'
'inclusive_group'
; Categories which describe the details of solution scattering experiments.
;
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
#
#
# For some data items, a standard syntax is assumed. The syntax is
# described for each data item in the dictionary, but is summarized here:
#
# Names: The family name(s) followed by a comma, precedes the first
# name(s) or initial(s).
#
# Telephone numbers:
# The international code is given in brackets and any extension
# number is preceded by 'ext'.
#
# Dates: In the form yyyy-mm-dd.
#
##############################################################################
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive) ...
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items (case insensitive)...
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
numbers.
;
name uchar
'_[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+'
; name item types take the form...
;
idname uchar
'[_A-Za-z0-9]+'
; idname item types take the form...
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
'[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]'
;
Standard format for CIF dates.
;
uchar3 uchar
'[+]?[A-Za-z0-9][A-Za-z0-9][A-Za-z0-9]'
;
data item for 3 character codes
;
uchar1 uchar
'[+]?[A-Za-z0-9]'
;
data item for 1 character codes
;
symop char
'([1-9]|[1-9][0-9]|1[0-8][0-9]|19[0-2])(_[1-9][1-9][1-9])?'
; symop item types take the form n_klm, where n refers to the
symmetry operation that is applied to the coordinates in the
ATOM_SITE category identified by _atom_site_label. It must
match a number given in _symmetry_equiv_pos_site_id.
k, l, and m refer to the translations that are subsequently
applied to the symmetry transformed coordinates to generate
the atom used. These translations (x,y,z) are related to
(k,l,m) by
k = 5 + x
l = 5 + y
m = 5 + z
By adding 5 to the translations, the use of negative numbers
is avoided.
;
atcode char
'[][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; Character data type for atom names ...
;
yyyy-mm-dd:hh:mm char
'[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9](-[0-9]?[0-9])?(:[0-9]?[0-9]:[0-9][0-9])?'
;
Standard format for CIF dates with optional time stamp.
;
fax uchar
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive) ...
;
phone uchar
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive) ...
;
email uchar
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive) ...
;
int-range numb
'-?[0-9]+(--?[0-9]+)?'
; int item types are the subset of numbers that are the negative
or positive integers with optional range.
;
float-range numb
'-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?(--?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?)?'
; int item types are the subset of numbers that are the floating
numbers.
;
code30 char
'.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?'
'A string value, not allowed to exceed 30 characters.'
#
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres (metres)'
'centimetres' 'centimetres (metres * 10^( -2))'
'millimetres' 'millimetres (metres * 10^( -3))'
'nanometres' 'nanometres (metres * 10^( -9))'
'angstroms' 'angstroms (metres * 10^(-10))'
'picometres' 'picometres (metres * 10^(-12))'
'femtometres' 'femtometres (metres * 10^(-15))'
#
'reciprocal_metres' 'reciprocal metres (metres^(-1))'
'reciprocal_centimetres'
'reciprocal centimetres ((metres * 10^( -2))^(-1))'
'reciprocal_millimetres'
'reciprocal millimetres ((metres * 10^( -3))^(-1))'
'reciprocal_nanometres'
'reciprocal nanometres ((metres * 10^( -9))^(-1))'
'reciprocal_angstroms'
'reciprocal angstroms ((metres * 10^(-10))^(-1))'
'reciprocal_picometres'
'reciprocal picometres ((metres * 10^(-12))^(-1))'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9))^2'
'angstroms_squared' 'angstroms squared (metres * 10^(-10))^2'
'8pi2_angstroms_squared' '8pi^2 * angstroms squared (metres * 10^(-10))^2'
'picometres_squared' 'picometres squared (metres * 10^(-12))^2'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9))^3'
'angstroms_cubed' 'angstroms cubed (metres * 10^(-10))^3'
'picometres_cubed' 'picometres cubed (metres * 10^(-12))^3'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^( -9))^(-3))
;
'electrons_per_angstroms_cubed'
; electrons per angstroms cubed (electrons/(metres * 10^(-10))^(-3))
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (electrons/(metres * 10^(-12))^(-3))
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'arbitrary'
; arbitrary system of units.
;
#
'angstroms_degrees' 'angstroms * degrees'
#
'degrees_squared' 'degrees squared'
#
'mg_per_ml' 'milliliter per milligram'
#
'ml_per_min' 'milliliter per minute'
#
'milliliters' 'liter / 1000'
#
'milligrams' 'grams / 1000'
#
'megadaltons' 'megadaltons'
'microns_squared' 'microns squared'
'microns' 'microns'
# 'millimeters' 'millimeters'
'electrons_angstrom_squared' 'electrons square angstrom'
'electron_volts' 'electron volts'
# 'mg/ml' 'mg per milliliter'
'millimolar' 'millimolar'
'megagrams_per_cubic_metre' 'megagrams per cubic metre'
'pixels_per_millimetre' 'pixels per millimetre'
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-06
###
### EOF mmcif_pdbx-data.dic
###########################################################################
#
# File: mmcif_std-def-1.dic
#
# mmCIF Data Dictionary (standard defintions)
#
# This data dictionary contains the standard mmCIF data definitions.
#
# Defintion Section 1
#
#
###########################################################################
###############
## ATOM_SITE ##
###############
save_atom_site
_category.description
; Data items in the ATOM_SITE category record details about
the atom sites in a macromolecular crystal structure, such as
the positional coordinates, atomic displacement parameters,
magnetic moments and directions.
The data items for describing anisotropic atomic
displacement factors are only used if the corresponding items
are not given in the ATOM_SITE_ANISOTROP category.
;
_category.id atom_site
_category.mandatory_code no
_category_key.name '_atom_site.id'
loop_
_category_group.id 'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_atom_site.group_PDB
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.footnote_id
_atom_site.auth_seq_id
_atom_site.id
ATOM N N VAL A 11 . 25.369 30.691 11.795 1.00 17.93 . 11 1
ATOM C CA VAL A 11 . 25.970 31.965 12.332 1.00 17.75 . 11 2
ATOM C C VAL A 11 . 25.569 32.010 13.808 1.00 17.83 . 11 3
ATOM O O VAL A 11 . 24.735 31.190 14.167 1.00 17.53 . 11 4
ATOM C CB VAL A 11 . 25.379 33.146 11.540 1.00 17.66 . 11 5
ATOM C CG1 VAL A 11 . 25.584 33.034 10.030 1.00 18.86 . 11 6
ATOM C CG2 VAL A 11 . 23.933 33.309 11.872 1.00 17.12 . 11 7
ATOM N N THR A 12 . 26.095 32.930 14.590 1.00 18.97 4 12 8
ATOM C CA THR A 12 . 25.734 32.995 16.032 1.00 19.80 4 12 9
ATOM C C THR A 12 . 24.695 34.106 16.113 1.00 20.92 4 12 10
ATOM O O THR A 12 . 24.869 35.118 15.421 1.00 21.84 4 12 11
ATOM C CB THR A 12 . 26.911 33.346 17.018 1.00 20.51 4 12 12
ATOM O OG1 THR A 12 3 27.946 33.921 16.183 0.50 20.29 4 12 13
ATOM O OG1 THR A 12 4 27.769 32.142 17.103 0.50 20.59 4 12 14
ATOM C CG2 THR A 12 3 27.418 32.181 17.878 0.50 20.47 4 12 15
ATOM C CG2 THR A 12 4 26.489 33.778 18.426 0.50 20.00 4 12 16
ATOM N N ILE A 13 . 23.664 33.855 16.884 1.00 22.08 . 13 17
ATOM C CA ILE A 13 . 22.623 34.850 17.093 1.00 23.44 . 13 18
ATOM C C ILE A 13 . 22.657 35.113 18.610 1.00 25.77 . 13 19
ATOM O O ILE A 13 . 23.123 34.250 19.406 1.00 26.28 . 13 20
ATOM C CB ILE A 13 . 21.236 34.463 16.492 1.00 22.67 . 13 21
ATOM C CG1 ILE A 13 . 20.478 33.469 17.371 1.00 22.14 . 13 22
ATOM C CG2 ILE A 13 . 21.357 33.986 15.016 1.00 21.75 . 13 23
# - - - - data truncated for brevity - - - -
HETATM C C1 APS C . 1 4.171 29.012 7.116 0.58 17.27 1 300 101
HETATM C C2 APS C . 1 4.949 27.758 6.793 0.58 16.95 1 300 102
HETATM O O3 APS C . 1 4.800 26.678 7.393 0.58 16.85 1 300 103
HETATM N N4 APS C . 1 5.930 27.841 5.869 0.58 16.43 1 300 104
# - - - - data truncated for brevity - - - -
;
save_
save__atom_site.aniso_B[1][1]
_item_description.description
; The [1][1] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site.aniso_B[1][1]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[1][1]_esd'
associated_esd
'_atom_site.aniso_U[1][1]'
conversion_constant
'_atom_site_anisotrop.U[1][1]'
conversion_constant
'_atom_site.aniso_U[1][1]'
alternate_exclusive
'_atom_site_anisotrop.B[1][1]'
alternate_exclusive
'_atom_site_anisotrop.U[1][1]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_B[1][1]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_B[1][1].
;
_item.name '_atom_site.aniso_B[1][1]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[1][1]'
associated_value
'_atom_site.aniso_U[1][1]_esd'
conversion_constant
'_atom_site_anisotrop.U[1][1]_esd'
conversion_constant
'_atom_site.aniso_U[1][1]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[1][1]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[1][1]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_B[1][2]
_item_description.description
; The [1][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site.aniso_B[1][2]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[1][2]_esd'
associated_esd
'_atom_site.aniso_U[1][2]'
conversion_constant
'_atom_site_anisotrop.U[1][2]'
conversion_constant
'_atom_site.aniso_U[1][2]'
alternate_exclusive
'_atom_site_anisotrop.B[1][2]'
alternate_exclusive
'_atom_site_anisotrop.U[1][2]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_B[1][2]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_B[1][2].
;
_item.name '_atom_site.aniso_B[1][2]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[1][2]'
associated_value
'_atom_site.aniso_U[1][2]_esd'
conversion_constant
'_atom_site_anisotrop.U[1][2]_esd'
conversion_constant
'_atom_site.aniso_U[1][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[1][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[1][2]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_B[1][3]
_item_description.description
; The [1][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site.aniso_B[1][3]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[1][3]_esd'
associated_esd
'_atom_site.aniso_U[1][3]'
conversion_constant
'_atom_site_anisotrop.U[1][3]'
conversion_constant
'_atom_site.aniso_U[1][3]'
alternate_exclusive
'_atom_site_anisotrop.B[1][3]'
alternate_exclusive
'_atom_site_anisotrop.U[1][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_B[1][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_B[1][3].
;
_item.name '_atom_site.aniso_B[1][3]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[1][3]'
associated_value
'_atom_site.aniso_U[1][3]_esd'
conversion_constant
'_atom_site_anisotrop.U[1][3]_esd'
conversion_constant
'_atom_site.aniso_U[1][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[1][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[1][3]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_B[2][2]
_item_description.description
; The [2][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site.aniso_B[2][2]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[2][2]_esd'
associated_esd
'_atom_site.aniso_U[2][2]'
conversion_constant
'_atom_site_anisotrop.U[2][2]'
conversion_constant
'_atom_site.aniso_U[2][2]'
alternate_exclusive
'_atom_site_anisotrop.B[2][2]'
alternate_exclusive
'_atom_site_anisotrop.U[2][2]'
alternate_exclusive
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_B[2][2]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_B[2][2].
;
_item.name '_atom_site.aniso_B[2][2]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[2][2]'
associated_value
'_atom_site.aniso_U[2][2]_esd'
conversion_constant
'_atom_site_anisotrop.U[2][2]_esd'
conversion_constant
'_atom_site.aniso_U[2][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[2][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[2][2]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_B[2][3]
_item_description.description
; The [2][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site.aniso_B[2][3]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[2][3]_esd'
associated_esd
'_atom_site.aniso_U[2][3]'
conversion_constant
'_atom_site_anisotrop.U[2][3]'
conversion_constant
'_atom_site.aniso_U[2][3]'
alternate_exclusive
'_atom_site_anisotrop.B[2][3]'
alternate_exclusive
'_atom_site_anisotrop.U[2][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_B[2][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_B[2][3].
;
_item.name '_atom_site.aniso_B[2][3]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[2][3]'
associated_value
'_atom_site.aniso_U[2][3]_esd'
conversion_constant
'_atom_site_anisotrop.U[2][3]_esd'
conversion_constant
'_atom_site.aniso_U[2][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[2][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[2][3]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_B[3][3]
_item_description.description
; The [3][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site.aniso_B[3][3]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[3][3]_esd'
associated_esd
'_atom_site.aniso_U[3][3]'
conversion_constant
'_atom_site_anisotrop.U[3][3]'
conversion_constant
'_atom_site.aniso_U[3][3]'
alternate_exclusive
'_atom_site_anisotrop.B[3][3]'
alternate_exclusive
'_atom_site_anisotrop.U[3][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_B[3][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_B[3][3].
;
_item.name '_atom_site.aniso_B[3][3]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_B[3][3]'
associated_value
'_atom_site.aniso_U[3][3]_esd'
conversion_constant
'_atom_site_anisotrop.U[3][3]_esd'
conversion_constant
'_atom_site.aniso_U[3][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[3][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[3][3]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.aniso_ratio
_item_description.description
; Ratio of the maximum to minimum principal axes of
displacement (thermal) ellipsoids.
;
_item.name '_atom_site.aniso_ratio'
_item.category_id atom_site
_item.mandatory_code no
_item_related.related_name '_atom_site_anisotrop.ratio'
_item_related.function_code alternate_exclusive
loop_
_item_range.maximum
_item_range.minimum . 1.0
1.0 1.0
_item_type.code float
save_
save__atom_site.aniso_U[1][1]
_item_description.description
; The [1][1] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site.aniso_U[1][1]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[1][1]_esd'
associated_esd
'_atom_site.aniso_B[1][1]'
conversion_constant
'_atom_site_anisotrop.B[1][1]'
conversion_constant
'_atom_site.aniso_B[1][1]'
alternate_exclusive
'_atom_site_anisotrop.B[1][1]'
alternate_exclusive
'_atom_site_anisotrop.U[1][1]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site.aniso_U[1][1]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_U[1][1].
;
_item.name '_atom_site.aniso_U[1][1]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[1][1]'
associated_value
'_atom_site.aniso_B[1][1]_esd'
conversion_constant
'_atom_site_anisotrop.B[1][1]_esd'
conversion_constant
'_atom_site.aniso_B[1][1]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[1][1]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[1][1]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site.aniso_U[1][2]
_item_description.description
; The [1][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site.aniso_U[1][2]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[1][2]_esd'
associated_esd
'_atom_site.aniso_B[1][2]'
conversion_constant
'_atom_site_anisotrop.B[1][2]'
conversion_constant
'_atom_site.aniso_B[1][2]'
alternate_exclusive
'_atom_site_anisotrop.B[1][2]'
alternate_exclusive
'_atom_site_anisotrop.U[1][2]'
alternate_exclusive
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site.aniso_U[1][2]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_U[1][2].
;
_item.name '_atom_site.aniso_U[1][2]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[1][2]'
associated_value
'_atom_site.aniso_B[1][2]_esd'
conversion_constant
'_atom_site_anisotrop.B[1][2]_esd'
conversion_constant
'_atom_site.aniso_B[1][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[1][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[1][2]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site.aniso_U[1][3]
_item_description.description
; The [1][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site.aniso_U[1][3]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[1][3]_esd'
associated_esd
'_atom_site.aniso_B[1][3]'
conversion_constant
'_atom_site_anisotrop.B[1][3]'
conversion_constant
'_atom_site.aniso_B[1][3]'
alternate_exclusive
'_atom_site_anisotrop.B[1][3]'
alternate_exclusive
'_atom_site_anisotrop.U[1][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site.aniso_U[1][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_U[1][3].
;
_item.name '_atom_site.aniso_U[1][3]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[1][3]'
associated_value
'_atom_site.aniso_B[1][3]_esd'
conversion_constant
'_atom_site_anisotrop.B[1][3]_esd'
conversion_constant
'_atom_site.aniso_B[1][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[1][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[1][3]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site.aniso_U[2][2]
_item_description.description
; The [2][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site.aniso_U[2][2]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[2][2]_esd'
associated_esd
'_atom_site.aniso_B[2][2]'
conversion_constant
'_atom_site_anisotrop.B[2][2]'
conversion_constant
'_atom_site.aniso_B[2][2]'
alternate_exclusive
'_atom_site_anisotrop.B[2][2]'
alternate_exclusive
'_atom_site_anisotrop.U[2][2]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site.aniso_U[2][2]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_U[2][2].
;
_item.name '_atom_site.aniso_U[2][2]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[2][2]'
associated_value
'_atom_site.aniso_B[2][2]_esd'
conversion_constant
'_atom_site_anisotrop.B[2][2]_esd'
conversion_constant
'_atom_site.aniso_B[2][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[2][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[2][2]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site.aniso_U[2][3]
_item_description.description
; The [2][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site.aniso_U[2][3]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[2][3]_esd'
associated_esd
'_atom_site.aniso_B[2][3]'
conversion_constant
'_atom_site_anisotrop.B[2][3]'
conversion_constant
'_atom_site.aniso_B[2][3]'
alternate_exclusive
'_atom_site_anisotrop.B[2][3]'
alternate_exclusive
'_atom_site_anisotrop.U[2][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site.aniso_U[2][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_U[2][3].
;
_item.name '_atom_site.aniso_U[2][3]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[2][3]'
associated_value
'_atom_site.aniso_B[2][3]_esd'
conversion_constant
'_atom_site_anisotrop.B[2][3]_esd'
conversion_constant
'_atom_site.aniso_B[2][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[2][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[2][3]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site.aniso_U[3][3]
_item_description.description
; The [3][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site.aniso_U[3][3]'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[3][3]_esd'
associated_esd
'_atom_site.aniso_B[3][3]'
conversion_constant
'_atom_site_anisotrop.B[3][3]'
conversion_constant
'_atom_site.aniso_B[3][3]'
alternate_exclusive
'_atom_site_anisotrop.B[3][3]'
alternate_exclusive
'_atom_site_anisotrop.U[3][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site.aniso_U[3][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.aniso_U[3][3].
;
_item.name '_atom_site.aniso_U[3][3]_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.aniso_U[3][3]'
associated_value
'_atom_site.aniso_B[3][3]_esd'
conversion_constant
'_atom_site_anisotrop.B[3][3]_esd'
conversion_constant
'_atom_site.aniso_B[3][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[3][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[3][3]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site.attached_hydrogens
_item_description.description
; The number of hydrogen atoms attached to the atom at this site
excluding any hydrogen atoms for which coordinates (measured or
calculated) are given.
;
_item.name '_atom_site.attached_hydrogens'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_attached_hydrogens'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value 0
loop_
_item_range.maximum
_item_range.minimum 8 8
8 0
0 0
_item_type.code int
loop_
_item_examples.case
_item_examples.detail 2 'water oxygen'
1 'hydroxyl oxygen'
4 'ammonium nitrogen'
save_
save__atom_site.auth_asym_id
_item_description.description
; An alternative identifier for _atom_site.label_asym_id that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_site.auth_asym_id' atom_site yes
'_geom_angle.atom_site_auth_asym_id_1' geom_angle no
'_geom_angle.atom_site_auth_asym_id_2' geom_angle no
'_geom_angle.atom_site_auth_asym_id_3' geom_angle no
'_geom_bond.atom_site_auth_asym_id_1' geom_bond no
'_geom_bond.atom_site_auth_asym_id_2' geom_bond no
'_geom_contact.atom_site_auth_asym_id_1' geom_contact no
'_geom_contact.atom_site_auth_asym_id_2' geom_contact no
'_geom_hbond.atom_site_auth_asym_id_A' geom_hbond no
'_geom_hbond.atom_site_auth_asym_id_D' geom_hbond no
'_geom_hbond.atom_site_auth_asym_id_H' geom_hbond no
'_geom_torsion.atom_site_auth_asym_id_1' geom_torsion no
'_geom_torsion.atom_site_auth_asym_id_2' geom_torsion no
'_geom_torsion.atom_site_auth_asym_id_3' geom_torsion no
'_geom_torsion.atom_site_auth_asym_id_4' geom_torsion no
'_struct_conf.beg_auth_asym_id' struct_conf no
'_struct_conf.end_auth_asym_id' struct_conf no
'_struct_conn.ptnr1_auth_asym_id' struct_conn no
'_struct_conn.ptnr2_auth_asym_id' struct_conn no
'_struct_mon_nucl.auth_asym_id' struct_mon_nucl no
'_struct_mon_prot.auth_asym_id' struct_mon_prot no
'_struct_mon_prot_cis.auth_asym_id' struct_mon_prot_cis no
'_struct_ncs_dom_lim.beg_auth_asym_id' struct_ncs_dom_lim no
'_struct_ncs_dom_lim.end_auth_asym_id' struct_ncs_dom_lim no
'_struct_sheet_range.beg_auth_asym_id' struct_sheet_range no
'_struct_sheet_range.end_auth_asym_id' struct_sheet_range no
'_struct_site_gen.auth_asym_id' struct_site_gen no
loop_
_item_linked.child_name
_item_linked.parent_name
'_geom_angle.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id'
'_geom_angle.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id'
'_geom_angle.atom_site_auth_asym_id_3' '_atom_site.auth_asym_id'
'_geom_bond.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id'
'_geom_bond.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id'
'_geom_contact.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id'
'_geom_contact.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id'
'_geom_hbond.atom_site_auth_asym_id_A' '_atom_site.auth_asym_id'
'_geom_hbond.atom_site_auth_asym_id_D' '_atom_site.auth_asym_id'
'_geom_hbond.atom_site_auth_asym_id_H' '_atom_site.auth_asym_id'
'_geom_torsion.atom_site_auth_asym_id_1' '_atom_site.auth_asym_id'
'_geom_torsion.atom_site_auth_asym_id_2' '_atom_site.auth_asym_id'
'_geom_torsion.atom_site_auth_asym_id_3' '_atom_site.auth_asym_id'
'_geom_torsion.atom_site_auth_asym_id_4' '_atom_site.auth_asym_id'
'_struct_conf.beg_auth_asym_id' '_atom_site.auth_asym_id'
'_struct_conf.end_auth_asym_id' '_atom_site.auth_asym_id'
'_struct_conn.ptnr1_auth_asym_id' '_atom_site.auth_asym_id'
'_struct_conn.ptnr2_auth_asym_id' '_atom_site.auth_asym_id'
'_struct_mon_nucl.auth_asym_id' '_atom_site.auth_asym_id'
'_struct_mon_prot.auth_asym_id' '_atom_site.auth_asym_id'
'_struct_mon_prot_cis.auth_asym_id' '_atom_site.auth_asym_id'
'_struct_ncs_dom_lim.beg_auth_asym_id' '_atom_site.auth_asym_id'
'_struct_ncs_dom_lim.end_auth_asym_id' '_atom_site.auth_asym_id'
'_struct_sheet_range.beg_auth_asym_id' '_atom_site.auth_asym_id'
'_struct_sheet_range.end_auth_asym_id' '_atom_site.auth_asym_id'
'_struct_site_gen.auth_asym_id' '_atom_site.auth_asym_id'
_item_sub_category.id mm_atom_site_auth_label
_item_type.code code
save_
save__atom_site.auth_atom_id
_item_description.description
; An alternative identifier for _atom_site.label_atom_id that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_site.auth_atom_id' atom_site no
'_geom_angle.atom_site_auth_atom_id_1' geom_angle no
'_geom_angle.atom_site_auth_atom_id_2' geom_angle no
'_geom_angle.atom_site_auth_atom_id_3' geom_angle no
'_geom_bond.atom_site_auth_atom_id_1' geom_bond no
'_geom_bond.atom_site_auth_atom_id_2' geom_bond no
'_geom_contact.atom_site_auth_atom_id_1' geom_contact no
'_geom_contact.atom_site_auth_atom_id_2' geom_contact no
'_geom_hbond.atom_site_auth_atom_id_A' geom_hbond no
'_geom_hbond.atom_site_auth_atom_id_D' geom_hbond no
'_geom_hbond.atom_site_auth_atom_id_H' geom_hbond no
'_geom_torsion.atom_site_auth_atom_id_1' geom_torsion no
'_geom_torsion.atom_site_auth_atom_id_2' geom_torsion no
'_geom_torsion.atom_site_auth_atom_id_3' geom_torsion no
'_geom_torsion.atom_site_auth_atom_id_4' geom_torsion no
'_struct_conn.ptnr1_auth_atom_id' struct_conn no
'_struct_conn.ptnr2_auth_atom_id' struct_conn no
'_struct_sheet_hbond.range_1_beg_auth_atom_id' struct_sheet_hbond no
'_struct_sheet_hbond.range_1_end_auth_atom_id' struct_sheet_hbond no
'_struct_sheet_hbond.range_2_beg_auth_atom_id' struct_sheet_hbond no
'_struct_sheet_hbond.range_2_end_auth_atom_id' struct_sheet_hbond no
'_struct_site_gen.auth_atom_id' struct_site_gen no
loop_
_item_linked.child_name
_item_linked.parent_name
'_geom_angle.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id'
'_geom_angle.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id'
'_geom_angle.atom_site_auth_atom_id_3' '_atom_site.auth_atom_id'
'_geom_bond.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id'
'_geom_bond.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id'
'_geom_contact.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id'
'_geom_contact.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id'
'_geom_hbond.atom_site_auth_atom_id_A' '_atom_site.auth_atom_id'
'_geom_hbond.atom_site_auth_atom_id_D' '_atom_site.auth_atom_id'
'_geom_hbond.atom_site_auth_atom_id_H' '_atom_site.auth_atom_id'
'_geom_torsion.atom_site_auth_atom_id_1' '_atom_site.auth_atom_id'
'_geom_torsion.atom_site_auth_atom_id_2' '_atom_site.auth_atom_id'
'_geom_torsion.atom_site_auth_atom_id_3' '_atom_site.auth_atom_id'
'_geom_torsion.atom_site_auth_atom_id_4' '_atom_site.auth_atom_id'
'_struct_conn.ptnr1_auth_atom_id' '_atom_site.auth_atom_id'
'_struct_conn.ptnr2_auth_atom_id' '_atom_site.auth_atom_id'
'_struct_sheet_hbond.range_1_beg_auth_atom_id' '_atom_site.auth_atom_id'
'_struct_sheet_hbond.range_1_end_auth_atom_id' '_atom_site.auth_atom_id'
'_struct_sheet_hbond.range_2_beg_auth_atom_id' '_atom_site.auth_atom_id'
'_struct_sheet_hbond.range_2_end_auth_atom_id' '_atom_site.auth_atom_id'
'_struct_site_gen.auth_atom_id' '_atom_site.auth_atom_id'
_item_sub_category.id mm_atom_site_auth_label
_item_type.code atcode
save_
save__atom_site.auth_comp_id
_item_description.description
; An alternative identifier for _atom_site.label_comp_id that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_site.auth_comp_id' atom_site no
'_geom_angle.atom_site_auth_comp_id_1' geom_angle no
'_geom_angle.atom_site_auth_comp_id_2' geom_angle no
'_geom_angle.atom_site_auth_comp_id_3' geom_angle no
'_geom_bond.atom_site_auth_comp_id_1' geom_bond no
'_geom_bond.atom_site_auth_comp_id_2' geom_bond no
'_geom_contact.atom_site_auth_comp_id_1' geom_contact no
'_geom_contact.atom_site_auth_comp_id_2' geom_contact no
'_geom_hbond.atom_site_auth_comp_id_A' geom_hbond no
'_geom_hbond.atom_site_auth_comp_id_D' geom_hbond no
'_geom_hbond.atom_site_auth_comp_id_H' geom_hbond no
'_geom_torsion.atom_site_auth_comp_id_1' geom_torsion no
'_geom_torsion.atom_site_auth_comp_id_2' geom_torsion no
'_geom_torsion.atom_site_auth_comp_id_3' geom_torsion no
'_geom_torsion.atom_site_auth_comp_id_4' geom_torsion no
'_struct_conf.beg_auth_comp_id' struct_conf no
'_struct_conf.end_auth_comp_id' struct_conf no
'_struct_conn.ptnr1_auth_comp_id' struct_conn no
'_struct_conn.ptnr2_auth_comp_id' struct_conn no
'_struct_mon_nucl.auth_comp_id' struct_mon_nucl no
'_struct_mon_prot.auth_comp_id' struct_mon_prot no
'_struct_mon_prot_cis.auth_comp_id' struct_mon_prot_cis no
'_struct_ncs_dom_lim.beg_auth_comp_id' struct_ncs_dom_lim no
'_struct_ncs_dom_lim.end_auth_comp_id' struct_ncs_dom_lim no
'_struct_sheet_range.beg_auth_comp_id' struct_sheet_range no
'_struct_sheet_range.end_auth_comp_id' struct_sheet_range no
'_struct_site_gen.auth_comp_id' struct_site_gen no
loop_
_item_linked.child_name
_item_linked.parent_name
'_geom_angle.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id'
'_geom_angle.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id'
'_geom_angle.atom_site_auth_comp_id_3' '_atom_site.auth_comp_id'
'_geom_bond.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id'
'_geom_bond.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id'
'_geom_contact.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id'
'_geom_contact.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id'
'_geom_hbond.atom_site_auth_comp_id_A' '_atom_site.auth_comp_id'
'_geom_hbond.atom_site_auth_comp_id_D' '_atom_site.auth_comp_id'
'_geom_hbond.atom_site_auth_comp_id_H' '_atom_site.auth_comp_id'
'_geom_torsion.atom_site_auth_comp_id_1' '_atom_site.auth_comp_id'
'_geom_torsion.atom_site_auth_comp_id_2' '_atom_site.auth_comp_id'
'_geom_torsion.atom_site_auth_comp_id_3' '_atom_site.auth_comp_id'
'_geom_torsion.atom_site_auth_comp_id_4' '_atom_site.auth_comp_id'
'_struct_conf.beg_auth_comp_id' '_atom_site.auth_comp_id'
'_struct_conf.end_auth_comp_id' '_atom_site.auth_comp_id'
'_struct_conn.ptnr1_auth_comp_id' '_atom_site.auth_comp_id'
'_struct_conn.ptnr2_auth_comp_id' '_atom_site.auth_comp_id'
'_struct_mon_nucl.auth_comp_id' '_atom_site.auth_comp_id'
'_struct_mon_prot.auth_comp_id' '_atom_site.auth_comp_id'
'_struct_mon_prot_cis.auth_comp_id' '_atom_site.auth_comp_id'
'_struct_ncs_dom_lim.beg_auth_comp_id' '_atom_site.auth_comp_id'
'_struct_ncs_dom_lim.end_auth_comp_id' '_atom_site.auth_comp_id'
'_struct_sheet_range.beg_auth_comp_id' '_atom_site.auth_comp_id'
'_struct_sheet_range.end_auth_comp_id' '_atom_site.auth_comp_id'
'_struct_site_gen.auth_comp_id' '_atom_site.auth_comp_id'
_item_sub_category.id mm_atom_site_auth_label
_item_type.code code
save_
save__atom_site.auth_seq_id
_item_description.description
; An alternative identifier for _atom_site.label_seq_id that
may be provided by an author in order to match the identification
used in the publication that describes the structure.
Note that this is not necessarily a number, that the values do
not have to be positive, and that the value does not have to
correspond to the value of _atom_site.label_seq_id. The value
of _atom_site.label_seq_id is required to be a sequential list
of positive integers.
The author may assign values to _atom_site.auth_seq_id in any
desired way. For instance, the values may be used to relate
this structure to a numbering scheme in a homologous structure,
including sequence gaps or insertion codes. Alternatively, a
scheme may be used for a truncated polymer that maintains the
numbering scheme of the full length polymer. In all cases, the
scheme used here must match the scheme used in the publication
that describes the structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_site.auth_seq_id' atom_site no
'_geom_angle.atom_site_auth_seq_id_1' geom_angle no
'_geom_angle.atom_site_auth_seq_id_2' geom_angle no
'_geom_angle.atom_site_auth_seq_id_3' geom_angle no
'_geom_bond.atom_site_auth_seq_id_1' geom_bond no
'_geom_bond.atom_site_auth_seq_id_2' geom_bond no
'_geom_contact.atom_site_auth_seq_id_1' geom_contact no
'_geom_contact.atom_site_auth_seq_id_2' geom_contact no
'_geom_hbond.atom_site_auth_seq_id_A' geom_hbond no
'_geom_hbond.atom_site_auth_seq_id_D' geom_hbond no
'_geom_hbond.atom_site_auth_seq_id_H' geom_hbond no
'_geom_torsion.atom_site_auth_seq_id_1' geom_torsion no
'_geom_torsion.atom_site_auth_seq_id_2' geom_torsion no
'_geom_torsion.atom_site_auth_seq_id_3' geom_torsion no
'_geom_torsion.atom_site_auth_seq_id_4' geom_torsion no
'_struct_conf.beg_auth_seq_id' struct_conf no
'_struct_conf.end_auth_seq_id' struct_conf no
'_struct_conn.ptnr1_auth_seq_id' struct_conn no
'_struct_conn.ptnr2_auth_seq_id' struct_conn no
'_struct_mon_nucl.auth_seq_id' struct_mon_nucl no
'_struct_mon_prot.auth_seq_id' struct_mon_prot no
'_struct_mon_prot_cis.auth_seq_id' struct_mon_prot_cis no
'_struct_ncs_dom_lim.beg_auth_seq_id' struct_ncs_dom_lim no
'_struct_ncs_dom_lim.end_auth_seq_id' struct_ncs_dom_lim no
'_struct_sheet_hbond.range_1_beg_auth_seq_id' struct_sheet_hbond no
'_struct_sheet_hbond.range_1_end_auth_seq_id' struct_sheet_hbond no
'_struct_sheet_hbond.range_2_beg_auth_seq_id' struct_sheet_hbond no
'_struct_sheet_hbond.range_2_end_auth_seq_id' struct_sheet_hbond no
'_struct_sheet_range.beg_auth_seq_id' struct_sheet_range no
'_struct_sheet_range.end_auth_seq_id' struct_sheet_range no
'_struct_site_gen.auth_seq_id' struct_site_gen no
loop_
_item_linked.child_name
_item_linked.parent_name
'_geom_angle.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id'
'_geom_angle.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id'
'_geom_angle.atom_site_auth_seq_id_3' '_atom_site.auth_seq_id'
'_geom_bond.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id'
'_geom_bond.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id'
'_geom_contact.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id'
'_geom_contact.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id'
'_geom_hbond.atom_site_auth_seq_id_A' '_atom_site.auth_seq_id'
'_geom_hbond.atom_site_auth_seq_id_D' '_atom_site.auth_seq_id'
'_geom_hbond.atom_site_auth_seq_id_H' '_atom_site.auth_seq_id'
'_geom_torsion.atom_site_auth_seq_id_1' '_atom_site.auth_seq_id'
'_geom_torsion.atom_site_auth_seq_id_2' '_atom_site.auth_seq_id'
'_geom_torsion.atom_site_auth_seq_id_3' '_atom_site.auth_seq_id'
'_geom_torsion.atom_site_auth_seq_id_4' '_atom_site.auth_seq_id'
'_struct_conf.beg_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_conf.end_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_conn.ptnr1_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_conn.ptnr2_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_mon_nucl.auth_seq_id' '_atom_site.auth_seq_id'
'_struct_mon_prot.auth_seq_id' '_atom_site.auth_seq_id'
'_struct_mon_prot_cis.auth_seq_id' '_atom_site.auth_seq_id'
'_struct_ncs_dom_lim.beg_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_ncs_dom_lim.end_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_sheet_hbond.range_1_beg_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_sheet_hbond.range_1_end_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_sheet_hbond.range_2_beg_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_sheet_hbond.range_2_end_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_sheet_range.beg_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_sheet_range.end_auth_seq_id' '_atom_site.auth_seq_id'
'_struct_site_gen.auth_seq_id' '_atom_site.auth_seq_id'
_item_sub_category.id mm_atom_site_auth_label
_item_type.code code
save_
save__atom_site.B_equiv_geom_mean
_item_description.description
; Equivalent isotropic atomic displacement parameter, B~eq~,
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
B~eq~ = (B~i~ B~j~ B~k~)^1/3^
B~n~ = the principal components of the orthogonalized B^ij^
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site.B_equiv_geom_mean'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_B_equiv_geom_mean'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.B_equiv_geom_mean_esd'
associated_esd
'_atom_site.U_equiv_geom_mean'
conversion_constant
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.B_equiv_geom_mean_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.B_equiv_geom_mean.
;
_item.name '_atom_site.B_equiv_geom_mean_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.B_equiv_geom_mean'
associated_value
'_atom_site.U_equiv_geom_mean'
conversion_constant
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.B_iso_or_equiv
_item_description.description
; Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, B~eq~, calculated from the
anisotropic displacement parameters.
B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)]
A = the real space cell lengths
a* = the reciprocal space cell lengths
B^ij^ = 8 pi^2^ U^ij^
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
775-776.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site.B_iso_or_equiv'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_B_iso_or_equiv'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# loop_
# _item_range.maximum
# _item_range.minimum . 0.0
# 0.0 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.B_iso_or_equiv_esd'
associated_esd
'_atom_site.U_iso_or_equiv'
conversion_constant
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.B_iso_or_equiv_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.B_iso_or_equiv.
;
_item.name '_atom_site.B_iso_or_equiv_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.B_iso_or_equiv'
associated_value
'_atom_site.U_iso_or_equiv_esd'
conversion_constant
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site.calc_attached_atom
_item_description.description
; The _atom_site.id of the atom site to which the
'geometry-calculated' atom site is attached.
;
_item.name '_atom_site.calc_attached_atom'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_calc_attached_atom'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
save_
save__atom_site.calc_flag
_item_description.description
; A standard code to signal whether the site coordinates have been
determined from the intensities or calculated from the geometry
of surrounding sites, or have been assigned dummy values. The
abbreviation 'c' may be used in place of 'calc'.
;
_item.name '_atom_site.calc_flag'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_calc_flag'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value d
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail d
'determined from experimental measurements'
calc
'calculated from molecular geometry'
c
'abbreviation for "calc"'
dum
'dummy site with meaningless coordinates'
save_
save__atom_site.Cartn_x
_item_description.description
; The x atom-site coordinate in angstroms specified according to
a set of orthogonal Cartesian axes related to the cell axes as
specified by the description given in
_atom_sites.Cartn_transform_axes.
;
_item.name '_atom_site.Cartn_x'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_Cartn_x'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_site.Cartn_y'
'_atom_site.Cartn_z'
_item_related.related_name '_atom_site.Cartn_x_esd'
_item_related.function_code associated_esd
_item_sub_category.id cartesian_coordinate
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__atom_site.Cartn_x_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.Cartn_x.
;
_item.name '_atom_site.Cartn_x_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_atom_site.Cartn_y_esd'
'_atom_site.Cartn_z_esd'
_item_related.related_name '_atom_site.Cartn_x'
_item_related.function_code associated_value
_item_sub_category.id cartesian_coordinate_esd
_item_type.code float
_item_units.code angstroms
save_
save__atom_site.Cartn_y
_item_description.description
; The y atom-site coordinate in angstroms specified according to
a set of orthogonal Cartesian axes related to the cell axes as
specified by the description given in
_atom_sites.Cartn_transform_axes.
;
_item.name '_atom_site.Cartn_y'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_Cartn_y'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_site.Cartn_x'
'_atom_site.Cartn_z'
_item_related.related_name '_atom_site.Cartn_y_esd'
_item_related.function_code associated_esd
_item_sub_category.id cartesian_coordinate
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__atom_site.Cartn_y_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.Cartn_y.
;
_item.name '_atom_site.Cartn_y_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_atom_site.Cartn_x_esd'
'_atom_site.Cartn_z_esd'
_item_related.related_name '_atom_site.Cartn_y'
_item_related.function_code associated_value
_item_sub_category.id cartesian_coordinate_esd
_item_type.code float
_item_units.code angstroms
save_
save__atom_site.Cartn_z
_item_description.description
; The z atom-site coordinate in angstroms specified according to
a set of orthogonal Cartesian axes related to the cell axes as
specified by the description given in
_atom_sites.Cartn_transform_axes.
;
_item.name '_atom_site.Cartn_z'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_Cartn_z'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_site.Cartn_x'
'_atom_site.Cartn_y'
_item_related.related_name '_atom_site.Cartn_z_esd'
_item_related.function_code associated_esd
_item_sub_category.id cartesian_coordinate
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__atom_site.Cartn_z_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.Cartn_z.
;
_item.name '_atom_site.Cartn_z_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_atom_site.Cartn_x_esd'
'_atom_site.Cartn_y_esd'
_item_related.related_name '_atom_site.Cartn_z'
_item_related.function_code associated_value
_item_sub_category.id cartesian_coordinate_esd
_item_type.code float
_item_units.code angstroms
save_
save__atom_site.chemical_conn_number
_item_description.description
; This data item is a pointer to _chemical_conn_atom.number in the
CHEMICAL_CONN_ATOM category.
;
_item.name '_atom_site.chemical_conn_number'
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_chemical_conn_number'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__atom_site.constraints
_item_description.description
; A description of the constraints applied to parameters at this
site during refinement. See also _atom_site.refinement_flags
and _refine.ls_number_constraints.
;
_item.name '_atom_site.constraints'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_constraints'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
_item_examples.case 'pop=1.0-pop(Zn3)'
save_
save__atom_site.details
_item_description.description
; A description of special aspects of this site. See also
_atom_site.refinement_flags.
;
_item.name '_atom_site.details'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_description'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'Ag/Si disordered'
save_
save__atom_site.disorder_assembly
_item_description.description
; A code which identifies a cluster of atoms that show long-range
positional disorder but are locally ordered. Within each such
cluster of atoms, _atom_site.disorder_group is used to identify
the sites that are simultaneously occupied. This field is only
needed if there is more than one cluster of disordered atoms
showing independent local order.
*** This data item would not in general be used in a
macromolecular data block. ***
;
_item.name '_atom_site.disorder_assembly'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_disorder_assembly'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
save_
save__atom_site.disorder_group
_item_description.description
; A code which identifies a group of positionally disordered atom
sites that are locally simultaneously occupied. Atoms that are
positionally disordered over two or more sites (e.g. the hydrogen
atoms of a methyl group that exists in two orientations) can
be assigned to two or more groups. Sites belonging to the same
group are simultaneously occupied, but those belonging to
different groups are not. A minus prefix (e.g. '-1') is used to
indicate sites disordered about a special position.
*** This data item would not in general be used in a
macromolecular data block. ***
;
_item.name '_atom_site.disorder_group'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_disorder_group'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value .
_item_type.code code
save_
save__atom_site.footnote_id
_item_description.description
; The value of _atom_site.footnote_id must match an ID
specified by _atom_sites_footnote.id in the
ATOM_SITES_FOOTNOTE list.
;
_item.name '_atom_site.footnote_id'
_item.mandatory_code no
save_
save__atom_site.fract_x
_item_description.description
; The x coordinate of the atom-site position specified as a
fraction of _cell.length_a.
;
_item.name '_atom_site.fract_x'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_fract_x'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_site.fract_y'
'_atom_site.fract_z'
_item_related.related_name '_atom_site.fract_x_esd'
_item_related.function_code associated_esd
_item_sub_category.id fractional_coordinate
_item_type.code float
_item_type_conditions.code esd
save_
save__atom_site.fract_x_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.fract_x.
;
_item.name '_atom_site.fract_x_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_atom_site.fract_y_esd'
'_atom_site.fract_z_esd'
_item_related.related_name '_atom_site.fract_x'
_item_related.function_code associated_value
_item_sub_category.id fractional_coordinate_esd
_item_type.code float
save_
save__atom_site.fract_y
_item_description.description
; The y coordinate of the atom-site position specified as a
fraction of _cell.length_b.
;
_item.name '_atom_site.fract_y'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_fract_y'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_site.fract_x'
'_atom_site.fract_z'
_item_related.related_name '_atom_site.fract_y_esd'
_item_related.function_code associated_esd
_item_sub_category.id fractional_coordinate
_item_type.code float
_item_type_conditions.code esd
save_
save__atom_site.fract_y_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.fract_y.
;
_item.name '_atom_site.fract_y_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_atom_site.fract_x_esd'
'_atom_site.fract_z_esd'
_item_related.related_name '_atom_site.fract_y'
_item_related.function_code associated_value
_item_sub_category.id fractional_coordinate_esd
_item_type.code float
save_
save__atom_site.fract_z
_item_description.description
; The z coordinate of the atom-site position specified as a
fraction of _cell.length_c.
;
_item.name '_atom_site.fract_z'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_fract_z'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_site.fract_x'
'_atom_site.fract_y'
_item_related.related_name '_atom_site.fract_z_esd'
_item_related.function_code associated_esd
_item_sub_category.id fractional_coordinate
_item_type.code float
_item_type_conditions.code esd
save_
save__atom_site.fract_z_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.fract_z.
;
_item.name '_atom_site.fract_z_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_atom_site.fract_x_esd'
'_atom_site.fract_y_esd'
_item_related.related_name '_atom_site.fract_z'
_item_related.function_code associated_value
_item_sub_category.id fractional_coordinate_esd
_item_type.code float
save_
save__atom_site.group_PDB
_item_description.description
; The group of atoms to which the atom site belongs. This data
item is provided for compatibility with the original Protein
Data Bank format, and only for that purpose.
;
_item.name '_atom_site.group_PDB'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value ATOM
HETATM
save_
save__atom_site.id
_item_description.description
; The value of _atom_site.id must uniquely identify a record in the
ATOM_SITE list.
Note that this item need not be a number; it can be any unique
identifier.
This data item was introduced to provide compatibility between
small-molecule and macromolecular CIFs. In a small-molecule
CIF, _atom_site_label is the identifier for the atom. In a
macromolecular CIF, the atom identifier is the aggregate of
_atom_site.label_alt_id, _atom_site.label_asym_id,
_atom_site.label_atom_id, _atom_site.label_comp_id and
_atom_site.label_seq_id. For the two types of files to be
compatible, a formal identifier for the category had to be
introduced that was independent of the different modes of
identifying the atoms. For compatibility with older CIFs,
_atom_site_label is aliased to _atom_site.id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_site.id' atom_site yes
'_atom_site_anisotrop.id' atom_site_anisotrop yes
'_geom_angle.atom_site_id_1' geom_angle yes
'_geom_angle.atom_site_id_2' geom_angle yes
'_geom_angle.atom_site_id_3' geom_angle yes
'_geom_bond.atom_site_id_1' geom_bond yes
'_geom_bond.atom_site_id_2' geom_bond yes
'_geom_contact.atom_site_id_1' geom_contact yes
'_geom_contact.atom_site_id_2' geom_contact yes
'_geom_hbond.atom_site_id_A' geom_hbond yes
'_geom_hbond.atom_site_id_D' geom_hbond yes
'_geom_hbond.atom_site_id_H' geom_hbond yes
'_geom_torsion.atom_site_id_1' geom_torsion yes
'_geom_torsion.atom_site_id_2' geom_torsion yes
'_geom_torsion.atom_site_id_3' geom_torsion yes
'_geom_torsion.atom_site_id_4' geom_torsion yes
_item_aliases.alias_name '_atom_site_label'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site_anisotrop.id' '_atom_site.id'
'_geom_angle.atom_site_id_1' '_atom_site.id'
'_geom_angle.atom_site_id_2' '_atom_site.id'
'_geom_angle.atom_site_id_3' '_atom_site.id'
'_geom_bond.atom_site_id_1' '_atom_site.id'
'_geom_bond.atom_site_id_2' '_atom_site.id'
'_geom_contact.atom_site_id_1' '_atom_site.id'
'_geom_contact.atom_site_id_2' '_atom_site.id'
'_geom_hbond.atom_site_id_A' '_atom_site.id'
'_geom_hbond.atom_site_id_D' '_atom_site.id'
'_geom_hbond.atom_site_id_H' '_atom_site.id'
'_geom_torsion.atom_site_id_1' '_atom_site.id'
'_geom_torsion.atom_site_id_2' '_atom_site.id'
'_geom_torsion.atom_site_id_3' '_atom_site.id'
'_geom_torsion.atom_site_id_4' '_atom_site.id'
_item_type.code code
loop_
_item_examples.case '5'
'C12'
'Ca3g28'
'Fe3+17'
'H*251'
'boron2a'
'C_a_phe_83_a_0'
'Zn_Zn_301_A_0'
save_
save__atom_site.label_alt_id
_item_description.description
; A component of the identifier for this atom site.
For further details, see the definition of the ATOM_SITE_ALT
category.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_atom_site.label_alt_id'
_item.mandatory_code yes
_item_sub_category.id mm_atom_site_label
save_
save__atom_site.label_asym_id
_item_description.description
; A component of the identifier for this atom site.
For further details, see the definition of the STRUCT_ASYM
category.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
_item.name '_atom_site.label_asym_id'
_item.mandatory_code yes
_item_sub_category.id mm_atom_site_label
save_
save__atom_site.label_atom_id
_item_description.description
; A component of the identifier for this atom site.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_atom_site.label_atom_id'
_item.mandatory_code yes
_item_sub_category.id mm_atom_site_label
save_
save__atom_site.label_comp_id
_item_description.description
; A component of the identifier for this atom site.
This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_atom_site.label_comp_id'
_item.mandatory_code yes
_item_sub_category.id mm_atom_site_label
save_
save__atom_site.label_entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_atom_site.label_entity_id'
_item.mandatory_code yes
save_
save__atom_site.label_seq_id
_item_description.description
; This data item is a pointer to _entity_poly_seq.num in the
ENTITY_POLY_SEQ category.
;
_item.name '_atom_site.label_seq_id'
_item.mandatory_code yes
save_
save__atom_site.occupancy
_item_description.description
; The fraction of the atom type present at this site.
The sum of the occupancies of all the atom types at this site
may not significantly exceed 1.0 unless it is a dummy site.
;
_item.name '_atom_site.occupancy'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_occupancy'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1.0
# JDW 17-Apr-2003 - Unsupportable restriction.
# loop_
# _item_range.maximum
# _item_range.minimum 1.0 1.0
# 1.0 0.0
# 0.0 0.0
_item_related.related_name '_atom_site.occupancy_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
save_
save__atom_site.occupancy_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.occupancy.
;
_item.name '_atom_site.occupancy_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_atom_site.occupancy'
_item_related.function_code associated_value
_item_type.code float
save_
#save__atom_site.refinement_flags
# _item_description.description
#; A concatenated series of single-letter codes which indicate the
# refinement restraints or constraints applied to this site.
#;
# _item.name '_atom_site.refinement_flags'
# _item.category_id atom_site
# _item.mandatory_code no
# _item_aliases.alias_name '_atom_site_refinement_flags'
# _item_aliases.dictionary cif_core.dic
# _item_aliases.version 2.0.1
# _item_type.code ucode
# loop_
# _item_enumeration.value
# _item_enumeration.detail .
# 'no refinement constraints'
# S
# 'special-position constraint on site'
# G
# 'rigid-group refinement of site'
# R
# 'riding atom site attached to non-riding atom'
# D
# 'distance or angle restraint on site'
# T
# 'thermal displacement constraints'
# U
# 'Uiso or Uij restraint (rigid bond)'
# P
# 'partial occupancy constraint'
# save_
save__atom_site.restraints
_item_description.description
; A description of restraints applied to specific parameters at
this site during refinement. See also _atom_site.refinement_flags
and _refine.ls_number_restraints.
;
_item.name '_atom_site.restraints'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_restraints'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'restrained to planar ring'
save_
save__atom_site.symmetry_multiplicity
_item_description.description
; The multiplicity of a site due to the space-group symmetry as is
given in International Tables for Crystallography Vol. A (2002).
;
_item.name '_atom_site.symmetry_multiplicity'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_symmetry_multiplicity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 192 192
192 1
1 1
_item_type.code int
save_
save__atom_site.thermal_displace_type
_item_description.description
; A standard code used to describe the type of atomic displacement
parameters used for the site.
;
_item.name '_atom_site.thermal_displace_type'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_thermal_displace_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail Uani 'anisotropic Uij'
Uiso 'isotropic U'
Uovl 'overall U'
Umpe 'multipole expansion U'
Bani 'anisotropic Bij'
Biso 'isotropic B'
Bovl 'overall B'
save_
save__atom_site.type_symbol
_item_description.description
; This data item is a pointer to _atom_type.symbol in the
ATOM_TYPE category.
;
_item.name '_atom_site.type_symbol'
_item.mandatory_code yes
_item_aliases.alias_name '_atom_site_type_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__atom_site.U_equiv_geom_mean
_item_description.description
; Equivalent isotropic atomic displacement parameter, U~eq~,
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
U~eq~ = (U~i~ U~j~ U~k~)^1/3^
U~n~ = the principal components of the orthogonalized U^ij^
;
_item.name '_atom_site.U_equiv_geom_mean'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_U_equiv_geom_mean'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 10.0 10.0
10.0 0.0
0.0 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.U_equiv_geom_mean_esd'
associated_esd
'_atom_site.B_equiv_geom_mean'
conversion_constant
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site.U_equiv_geom_mean_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.U_equiv_geom_mean.
;
_item.name '_atom_site.U_equiv_geom_mean_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.U_equiv_geom_mean'
associated_value
'_atom_site.B_equiv_geom_mean'
conversion_constant
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site.U_iso_or_equiv
_item_description.description
; Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, U~eq~, calculated from
anisotropic atomic displacement parameters.
U~eq~ = (1/3) sum~i~[sum~j~(U^ij^ A~i~ A~j~ a*~i~ a*~j~)]
A = the real space cell lengths
a* = the reciprocal space cell lengths
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
775-776.
;
_item.name '_atom_site.U_iso_or_equiv'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_U_iso_or_equiv'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 10.0 10.0
10.0 0.0
0.0 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.U_iso_or_equiv_esd'
associated_esd
'_atom_site.B_iso_or_equiv'
conversion_constant
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site.U_iso_or_equiv_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site.U_iso_or_equiv.
;
_item.name '_atom_site.U_iso_or_equiv_esd'
_item.category_id atom_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site.U_iso_or_equiv'
associated_value
'_atom_site.B_iso_or_equiv_esd'
conversion_constant
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site.Wyckoff_symbol
_item_description.description
; The Wyckoff symbol (letter) as listed in the space-group tables
of International Tables for Crystallography, Vol. A (2002).
;
_item.name '_atom_site.Wyckoff_symbol'
_item.category_id atom_site
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_Wyckoff_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
#########################
## ATOM_SITE_ANISOTROP ##
#########################
save_atom_site_anisotrop
_category.description
; Data items in the ATOM_SITE_ANISOTROP category record details
about anisotropic displacement parameters.
If the ATOM_SITE_ANISOTROP category is used for storing these
data, the corresponding ATOM_SITE data items are not used.
;
_category.id atom_site_anisotrop
_category.mandatory_code no
_category_key.name '_atom_site_anisotrop.id'
loop_
_category_group.id 'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on NDB structure BDL005 of Holbrook, Dickerson &
Kim [Acta Cryst. (1985), B41, 255-262].
;
;
loop_
_atom_site_anisotrop.id
_atom_site_anisotrop.type_symbol
_atom_site_anisotrop.U[1][1]
_atom_site_anisotrop.U[1][2]
_atom_site_anisotrop.U[1][3]
_atom_site_anisotrop.U[2][2]
_atom_site_anisotrop.U[2][3]
_atom_site_anisotrop.U[3][3]
1 O 8642 4866 7299 -342 -258 -1427
2 C 5174 4871 6243 -1885 -2051 -1377
3 C 6202 5020 4395 -1130 -556 -632
4 O 4224 4700 5046 1105 -161 345
5 C 8684 4688 4171 -1850 -433 -292
6 O 11226 5255 3532 -341 2685 1328
7 C 10214 2428 5614 -2610 -1940 902
8 C 4590 3488 5827 751 -770 986
9 N 5014 4434 3447 -17 -1593 539
# ---- abbreviated ----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__atom_site_anisotrop.B[1][1]
_item_description.description
; The [1][1] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site_anisotrop.B[1][1]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_B_11'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[1][1]_esd'
associated_esd
'_atom_site.aniso_U[1][1]'
conversion_constant
'_atom_site_anisotrop.U[1][1]'
conversion_constant
'_atom_site.aniso_B[1][1]'
alternate_exclusive
'_atom_site.aniso_U[1][1]'
alternate_exclusive
'_atom_site_anisotrop.U[1][1]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.B[1][1]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.B[1][1].
;
_item.name '_atom_site_anisotrop.B[1][1]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[1][1]'
associated_value
'_atom_site.aniso_U[1][1]_esd'
conversion_constant
'_atom_site_anisotrop.U[1][1]_esd'
conversion_constant
'_atom_site.aniso_B[1][1]_esd'
alternate_exclusive
'_atom_site.aniso_U[1][1]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[1][1]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.B[1][2]
_item_description.description
; The [1][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site_anisotrop.B[1][2]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_B_12'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[1][2]_esd'
associated_esd
'_atom_site.aniso_U[1][2]'
conversion_constant
'_atom_site_anisotrop.U[1][2]'
conversion_constant
'_atom_site.aniso_B[1][2]'
alternate_exclusive
'_atom_site.aniso_U[1][2]'
alternate_exclusive
'_atom_site_anisotrop.U[1][2]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.B[1][2]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.B[1][2].
;
_item.name '_atom_site_anisotrop.B[1][2]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[1][2]'
associated_value
'_atom_site.aniso_U[1][2]_esd'
conversion_constant
'_atom_site_anisotrop.U[1][2]_esd'
conversion_constant
'_atom_site.aniso_B[1][2]_esd'
alternate_exclusive
'_atom_site.aniso_U[1][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[1][2]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.B[1][3]
_item_description.description
; The [1][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site_anisotrop.B[1][3]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_B_13'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[1][3]_esd'
associated_esd
'_atom_site.aniso_U[1][3]'
conversion_constant
'_atom_site_anisotrop.U[1][3]'
conversion_constant
'_atom_site.aniso_B[1][3]'
alternate_exclusive
'_atom_site.aniso_U[1][3]'
alternate_exclusive
'_atom_site_anisotrop.U[1][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.B[1][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.B[1][3].
;
_item.name '_atom_site_anisotrop.B[1][3]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[1][3]'
associated_value
'_atom_site.aniso_U[1][3]_esd'
conversion_constant
'_atom_site_anisotrop.U[1][3]_esd'
conversion_constant
'_atom_site.aniso_B[1][3]_esd'
alternate_exclusive
'_atom_site.aniso_U[1][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[1][3]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.B[2][2]
_item_description.description
; The [2][2] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site_anisotrop.B[2][2]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_B_22'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[2][2]_esd'
associated_esd
'_atom_site.aniso_U[2][2]'
conversion_constant
'_atom_site_anisotrop.U[2][2]'
conversion_constant
'_atom_site.aniso_B[2][2]'
alternate_exclusive
'_atom_site.aniso_U[2][2]'
alternate_exclusive
'_atom_site_anisotrop.U[2][2]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.B[2][2]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.B[2][2].
;
_item.name '_atom_site_anisotrop.B[2][2]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[2][2]'
associated_value
'_atom_site.aniso_U[2][2]_esd'
conversion_constant
'_atom_site_anisotrop.U[2][2]_esd'
conversion_constant
'_atom_site.aniso_B[2][2]_esd'
alternate_exclusive
'_atom_site.aniso_U[2][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[2][2]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.B[2][3]
_item_description.description
; The [2][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site_anisotrop.B[2][3]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_B_23'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[2][3]_esd'
associated_esd
'_atom_site.aniso_U[2][3]'
conversion_constant
'_atom_site_anisotrop.U[2][3]'
conversion_constant
'_atom_site.aniso_B[2][3]'
alternate_exclusive
'_atom_site.aniso_U[2][3]'
alternate_exclusive
'_atom_site_anisotrop.U[2][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.B[2][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.B[2][3].
;
_item.name '_atom_site_anisotrop.B[2][3]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[2][3]'
associated_value
'_atom_site.aniso_U[2][3]_esd'
conversion_constant
'_atom_site_anisotrop.U[2][3]_esd'
conversion_constant
'_atom_site.aniso_B[2][3]_esd'
alternate_exclusive
'_atom_site.aniso_U[2][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[2][3]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.B[3][3]
_item_description.description
; The [3][3] element of the anisotropic atomic displacement
matrix B, which appears in the structure-factor term as:
T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
_item.name '_atom_site_anisotrop.B[3][3]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_B_33'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[3][3]_esd'
associated_esd
'_atom_site.aniso_U[3][3]'
conversion_constant
'_atom_site_anisotrop.U[3][3]'
conversion_constant
'_atom_site.aniso_B[3][3]'
alternate_exclusive
'_atom_site.aniso_U[3][3]'
alternate_exclusive
'_atom_site_anisotrop.U[3][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.B[3][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.B[3][3].
;
_item.name '_atom_site_anisotrop.B[3][3]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.B[3][3]'
associated_value
'_atom_site.aniso_U[3][3]_esd'
conversion_constant
'_atom_site_anisotrop.U[3][3]_esd'
conversion_constant
'_atom_site.aniso_B[3][3]_esd'
alternate_exclusive
'_atom_site.aniso_U[3][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.U[3][3]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code 8pi2_angstroms_squared
save_
save__atom_site_anisotrop.ratio
_item_description.description
; Ratio of the maximum to minimum principal axes of
displacement (thermal) ellipsoids.
;
_item.name '_atom_site_anisotrop.ratio'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 1.0
1.0 1.0
_item_related.related_name '_atom_site.aniso_ratio'
_item_related.function_code alternate_exclusive
_item_type.code float
save_
save__atom_site_anisotrop.id
_item_description.description
; This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_atom_site_anisotrop.id'
_item.mandatory_code yes
_item_aliases.alias_name '_atom_site_aniso_label'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__atom_site_anisotrop.type_symbol
_item_description.description
; This data item is a pointer to _atom_type.symbol in the
ATOM_TYPE category.
;
_item.name '_atom_site_anisotrop.type_symbol'
_item.mandatory_code yes
_item_aliases.alias_name '_atom_site_aniso_type_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__atom_site_anisotrop.U[1][1]
_item_description.description
; The [1][1] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site_anisotrop.U[1][1]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_11'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[1][1]_esd'
associated_esd
'_atom_site.aniso_B[1][1]'
conversion_constant
'_atom_site_anisotrop.B[1][1]'
conversion_constant
'_atom_site.aniso_B[1][1]'
alternate_exclusive
'_atom_site.aniso_U[1][1]'
alternate_exclusive
'_atom_site_anisotrop.B[1][1]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site_anisotrop.U[1][1]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.U[1][1].
;
_item.name '_atom_site_anisotrop.U[1][1]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[1][1]'
associated_value
'_atom_site.aniso_B[1][1]_esd'
conversion_constant
'_atom_site_anisotrop.B[1][1]_esd'
conversion_constant
'_atom_site.aniso_B[1][1]_esd'
alternate_exclusive
'_atom_site.aniso_U[1][1]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[1][1]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site_anisotrop.U[1][2]
_item_description.description
; The [1][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site_anisotrop.U[1][2]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_12'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[1][2]_esd'
associated_esd
'_atom_site.aniso_B[1][2]'
conversion_constant
'_atom_site_anisotrop.B[1][2]'
conversion_constant
'_atom_site.aniso_B[1][2]'
alternate_exclusive
'_atom_site.aniso_U[1][2]'
alternate_exclusive
'_atom_site_anisotrop.B[1][2]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site_anisotrop.U[1][2]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.U[1][2].
;
_item.name '_atom_site_anisotrop.U[1][2]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[1][2]'
associated_value
'_atom_site.aniso_B[1][2]_esd'
conversion_constant
'_atom_site_anisotrop.B[1][2]_esd'
conversion_constant
'_atom_site.aniso_B[1][2]_esd'
alternate_exclusive
'_atom_site.aniso_U[1][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[1][2]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site_anisotrop.U[1][3]
_item_description.description
; The [1][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site_anisotrop.U[1][3]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_13'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[1][3]_esd'
associated_esd
'_atom_site.aniso_B[1][3]'
conversion_constant
'_atom_site_anisotrop.B[1][3]'
conversion_constant
'_atom_site.aniso_B[1][3]'
alternate_exclusive
'_atom_site.aniso_U[1][3]'
alternate_exclusive
'_atom_site_anisotrop.B[1][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site_anisotrop.U[1][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.U[1][3].
;
_item.name '_atom_site_anisotrop.U[1][3]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[1][3]'
associated_value
'_atom_site.aniso_B[1][3]_esd'
conversion_constant
'_atom_site_anisotrop.B[1][3]_esd'
conversion_constant
'_atom_site.aniso_B[1][3]_esd'
alternate_exclusive
'_atom_site.aniso_U[1][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[1][3]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site_anisotrop.U[2][2]
_item_description.description
; The [2][2] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site_anisotrop.U[2][2]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_22'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[2][2]_esd'
associated_esd
'_atom_site.aniso_B[2][2]'
conversion_constant
'_atom_site_anisotrop.B[2][2]'
conversion_constant
'_atom_site.aniso_B[2][2]'
alternate_exclusive
'_atom_site.aniso_U[2][2]'
alternate_exclusive
'_atom_site_anisotrop.B[2][2]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site_anisotrop.U[2][2]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.U[2][2].
;
_item.name '_atom_site_anisotrop.U[2][2]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[2][2]'
associated_value
'_atom_site.aniso_B[2][2]_esd'
conversion_constant
'_atom_site_anisotrop.B[2][2]_esd'
conversion_constant
'_atom_site.aniso_B[2][2]_esd'
alternate_exclusive
'_atom_site.aniso_U[2][2]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[2][2]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site_anisotrop.U[2][3]
_item_description.description
; The [2][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site_anisotrop.U[2][3]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_23'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[2][3]_esd'
associated_esd
'_atom_site.aniso_B[2][3]'
conversion_constant
'_atom_site_anisotrop.B[2][3]'
conversion_constant
'_atom_site.aniso_B[2][3]'
alternate_exclusive
'_atom_site.aniso_U[2][3]'
alternate_exclusive
'_atom_site_anisotrop.B[2][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site_anisotrop.U[2][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.U[2][3].
;
_item.name '_atom_site_anisotrop.U[2][3]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[2][3]'
associated_value
'_atom_site.aniso_B[2][3]_esd'
conversion_constant
'_atom_site_anisotrop.B[2][3]_esd'
conversion_constant
'_atom_site.aniso_B[2][3]_esd'
alternate_exclusive
'_atom_site.aniso_U[2][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[2][3]_esd'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__atom_site_anisotrop.U[3][3]
_item_description.description
; The [3][3] element of the standard anisotropic atomic
displacement matrix U, which appears in the structure-factor
term as:
T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]}
h = the Miller indices
a* = the reciprocal space cell lengths
These matrix elements may appear with atomic coordinates
in the ATOM_SITE category, or they may appear in the separate
ATOM_SITE_ANISOTROP category, but they may not appear in both
places. Similarly, anisotropic displacements may appear as
either B's or U's, but not as both.
The unique elements of the real symmetric matrix are
entered by row.
;
_item.name '_atom_site_anisotrop.U[3][3]'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_aliases.alias_name '_atom_site_aniso_U_33'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[3][3]_esd'
associated_esd
'_atom_site.aniso_B[3][3]'
conversion_constant
'_atom_site_anisotrop.B[3][3]'
conversion_constant
'_atom_site.aniso_B[3][3]'
alternate_exclusive
'_atom_site.aniso_U[3][3]'
alternate_exclusive
'_atom_site_anisotrop.B[3][3]'
alternate_exclusive
_item_sub_category.id matrix
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_squared
save_
save__atom_site_anisotrop.U[3][3]_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _atom_site_anisotrop.U[3][3].
;
_item.name '_atom_site_anisotrop.U[3][3]_esd'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_atom_site_anisotrop.U[3][3]'
associated_value
'_atom_site.aniso_B[3][3]_esd'
conversion_constant
'_atom_site_anisotrop.B[3][3]_esd'
conversion_constant
'_atom_site.aniso_B[3][3]_esd'
alternate_exclusive
'_atom_site.aniso_U[3][3]_esd'
alternate_exclusive
'_atom_site_anisotrop.B[3][3]_esd'
alternate_exclusive
_item_type.code float
_item_units.code angstroms_squared
save_
################
## ATOM_SITES ##
################
save_atom_sites
_category.description
; Data items in the ATOM_SITES category record details about
the crystallographic cell and cell transformations, which are
common to all atom sites.
;
_category.id atom_sites
_category.mandatory_code no
_category_key.name '_atom_sites.entry_id'
loop_
_category_group.id 'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_atom_sites.entry_id '5HVP'
_atom_sites.Cartn_transform_axes
'c along z, astar along x, b along y'
_atom_sites.Cartn_transf_matrix[1][1] 58.39
_atom_sites.Cartn_transf_matrix[1][2] 0.00
_atom_sites.Cartn_transf_matrix[1][3] 0.00
_atom_sites.Cartn_transf_matrix[2][1] 0.00
_atom_sites.Cartn_transf_matrix[2][2] 86.70
_atom_sites.Cartn_transf_matrix[2][3] 0.00
_atom_sites.Cartn_transf_matrix[3][1] 0.00
_atom_sites.Cartn_transf_matrix[3][2] 0.00
_atom_sites.Cartn_transf_matrix[3][3] 46.27
_atom_sites.Cartn_transf_vector[1] 0.00
_atom_sites.Cartn_transf_vector[2] 0.00
_atom_sites.Cartn_transf_vector[3] 0.00
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__atom_sites.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_atom_sites.entry_id'
_item.mandatory_code yes
save_
save__atom_sites.Cartn_transf_matrix[1][1]
_item_description.description
; The [1][1] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.Cartn_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_matrix[1][1]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_11'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.Cartn_transf_matrix[1][2]
_item_description.description
; The [1][2] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.Cartn_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_matrix[1][2]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_12'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.Cartn_transf_matrix[1][3]
_item_description.description
; The [1][3] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.Cartn_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_matrix[1][3]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_13'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.Cartn_transf_matrix[2][1]
_item_description.description
; The [2][1] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.Cartn_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_matrix[2][1]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_21'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.Cartn_transf_matrix[2][2]
_item_description.description
; The [2][2] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.Cartn_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_matrix[2][2]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_22'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.Cartn_transf_matrix[2][3]
_item_description.description
; The [2][3] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.Cartn_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_matrix[2][3]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_23'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.Cartn_transf_matrix[3][1]
_item_description.description
; The [3][1] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.Cartn_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_matrix[3][1]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_31'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.Cartn_transf_matrix[3][2]
_item_description.description
; The [3][2] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.Cartn_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_matrix[3][2]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_32'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.Cartn_transf_matrix[3][3]
_item_description.description
; The [3][3] element of the 3x3 matrix used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.Cartn_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_matrix[3][3]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_matrix_33'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.Cartn_transf_vector[1]
_item_description.description
; The [1] element of the three-element vector used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The rotation matrix is defined in
_atom_sites.Cartn_transf_matrix[][].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_vector[1]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_vector_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__atom_sites.Cartn_transf_vector[2]
_item_description.description
; The [2] element of the three-element vector used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The rotation matrix is defined in
_atom_sites.Cartn_transf_matrix[][].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_vector[2]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_vector_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__atom_sites.Cartn_transf_vector[3]
_item_description.description
; The [3] element of the three-element vector used to transform
fractional coordinates in the ATOM_SITE category to Cartesian
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The rotation matrix is defined in
_atom_sites.Cartn_transf_matrix[][].
|x'| |11 12 13| |x| |1|
|y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.Cartn_transf_vector[3]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_tran_vector_3'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__atom_sites.Cartn_transform_axes
_item_description.description
; A description of the relative alignment of the crystal cell
axes to the Cartesian orthogonal axes as applied in the
transformation matrix _atom_sites.Cartn_transf_matrix[][].
;
_item.name '_atom_sites.Cartn_transform_axes'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_Cartn_transform_axes'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'a parallel to x; b in the plane of y and z'
save_
save__atom_sites.fract_transf_matrix[1][1]
_item_description.description
; The [1][1] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.fract_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_matrix[1][1]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_matrix_11'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.fract_transf_matrix[1][2]
_item_description.description
; The [1][2] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.fract_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_matrix[1][2]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_matrix_12'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.fract_transf_matrix[1][3]
_item_description.description
; The [1][3] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.fract_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_matrix[1][3]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_matrix_13'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.fract_transf_matrix[2][1]
_item_description.description
; The [2][1] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.fract_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_matrix[2][1]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_matrix_21'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.fract_transf_matrix[2][2]
_item_description.description
; The [2][2] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.fract_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_matrix[2][2]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_matrix_22'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.fract_transf_matrix[2][3]
_item_description.description
; The [2][3] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.fract_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_matrix[2][3]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_matrix_23'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.fract_transf_matrix[3][1]
_item_description.description
; The [3][1] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.fract_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_matrix[3][1]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_matrix_31'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.fract_transf_matrix[3][2]
_item_description.description
; The [3][2] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.fract_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_matrix[3][2]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_matrix_32'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.fract_transf_matrix[3][3]
_item_description.description
; The [3][3] element of the 3x3 matrix used to transform Cartesian
coordinates in the ATOM_SITE category to fractional coordinates
in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x1 translation is defined in
_atom_sites.fract_transf_vector[].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_matrix[3][3]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_matrix_33'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__atom_sites.fract_transf_vector[1]
_item_description.description
; The [1] element of the three-element vector used to transform
Cartesian coordinates in the ATOM_SITE category to fractional
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x3 rotation is defined in
_atom_sites.fract_transf_matrix[][].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_vector[1]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_vector_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__atom_sites.fract_transf_vector[2]
_item_description.description
; The [2] element of the three-element vector used to transform
Cartesian coordinates in the ATOM_SITE category to fractional
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x3 rotation is defined in
_atom_sites.fract_transf_matrix[][].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_vector[2]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_vector_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__atom_sites.fract_transf_vector[3]
_item_description.description
; The [3] element of the three-element vector used to transform
Cartesian coordinates in the ATOM_SITE category to fractional
coordinates in the same category. The axial alignments of this
transformation are described in _atom_sites.Cartn_transform_axes.
The 3x3 rotation is defined in
_atom_sites.fract_transf_matrix[][].
|x'| |11 12 13| |x| |1|
|y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2|
|z'| |31 32 33| |z| |3|
;
_item.name '_atom_sites.fract_transf_vector[3]'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_fract_tran_vector_3'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__atom_sites.solution_primary
_item_description.description
; This code identifies the method used to locate the initial
atom sites.
*** This data item would not in general be used in a
macromolecular data block. ***
;
_item.name '_atom_sites.solution_primary'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_solution_primary'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail difmap 'difference Fourier map'
vecmap 'real-space vector search'
heavy 'heavy-atom method'
direct 'structure-invariant direct methods'
geom 'inferred from neighbouring sites'
disper 'anomalous-dispersion techniques'
isomor 'isomorphous structure methods'
save_
save__atom_sites.solution_secondary
_item_description.description
; This code identifies the method used to locate the
non-hydrogen-atom sites not found by
_atom_sites.solution_primary.
*** This data item would not in general be used in a
macromolecular data block. ***
;
_item.name '_atom_sites.solution_secondary'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_solution_secondary'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail difmap 'difference Fourier map'
vecmap 'real-space vector search'
heavy 'heavy-atom method'
direct 'structure-invariant direct methods'
geom 'inferred from neighbouring sites'
disper 'anomalous-dispersion techniques'
isomor 'isomorphous structure methods'
save_
save__atom_sites.solution_hydrogens
_item_description.description
; This code identifies the method used to locate the
hydrogen atoms.
*** This data item would not in general be used in a
macromolecular data block. ***
;
_item.name '_atom_sites.solution_hydrogens'
_item.category_id atom_sites
_item.mandatory_code no
_item_aliases.alias_name '_atom_sites_solution_hydrogens'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail difmap 'difference Fourier map'
vecmap 'real-space vector search'
heavy 'heavy-atom method'
direct 'structure-invariant direct methods'
geom 'inferred from neighbouring sites'
disper 'anomalous-dispersion techniques'
isomor 'isomorphous structure methods'
save_
####################
## ATOM_SITES_ALT ##
####################
save_atom_sites_alt
_category.description
; Data items in the ATOM_SITES_ALT category record details
about the structural ensembles that should be generated from
atom sites or groups of atom sites that are modelled in
alternative conformations in this data block.
;
_category.id atom_sites_alt
_category.mandatory_code no
_category_key.name '_atom_sites_alt.id'
loop_
_category_group.id 'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_atom_sites_alt.id
_atom_sites_alt.details
.
; Atom sites with the alternative ID set to null are not
modeled in alternative conformations
;
1
; Atom sites with the alternative ID set to 1 have been
modeled in alternative conformations with respect to atom
sites marked with alternative ID 2. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 1 correlate with the conformation of the
inhibitor marked with alternative ID 1. They have been
given an occupancy of 0.58 to match the occupancy assigned
to the inhibitor.
;
2
; Atom sites with the alternative ID set to 2 have been
modeled in alternative conformations with respect to atom
sites marked with alternative ID 1. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 2 correlate with the conformation of the
inhibitor marked with alternative ID 2. They have been
given an occupancy of 0.42 to match the occupancy assigned
to the inhibitor.
;
3
; Atom sites with the alternative ID set to 3 have been
modeled in alternative conformations with respect to
atoms marked with alternative ID 4. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 3 do not correlate with the conformation of the
inhibitor. These atom sites have arbitrarily been given
an occupancy of 0.50.
;
4
; Atom sites with the alternative ID set to 4 have been
modeled in alternative conformations with respect to
atoms marked with alternative ID 3. The conformations of
amino-acid side chains and solvent atoms with alternative
ID set to 4 do not correlate with the conformation of the
inhibitor. These atom sites have arbitrarily been given
an occupancy of 0.50.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__atom_sites_alt.details
_item_description.description
; A description of special aspects of the modelling of atoms in
alternative conformations.
;
_item.name '_atom_sites_alt.details'
_item.category_id atom_sites_alt
_item.mandatory_code no
_item_type.code text
save_
save__atom_sites_alt.id
_item_description.description
; The value of _atom_sites_alt.id must uniquely identify
a record in the ATOM_SITES_ALT list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_sites_alt.id' atom_sites_alt yes
'_atom_site.label_alt_id' atom_site no
'_atom_sites_alt_gen.alt_id' atom_sites_alt_gen yes
'_geom_angle.atom_site_label_alt_id_1' geom_angle no
'_geom_angle.atom_site_label_alt_id_2' geom_angle no
'_geom_angle.atom_site_label_alt_id_3' geom_angle no
'_geom_bond.atom_site_label_alt_id_1' geom_bond no
'_geom_bond.atom_site_label_alt_id_2' geom_bond no
'_geom_contact.atom_site_label_alt_id_1' geom_contact no
'_geom_contact.atom_site_label_alt_id_2' geom_contact no
'_geom_hbond.atom_site_label_alt_id_A' geom_hbond no
'_geom_hbond.atom_site_label_alt_id_D' geom_hbond no
'_geom_hbond.atom_site_label_alt_id_H' geom_hbond no
'_geom_torsion.atom_site_label_alt_id_1' geom_torsion no
'_geom_torsion.atom_site_label_alt_id_2' geom_torsion no
'_geom_torsion.atom_site_label_alt_id_3' geom_torsion no
'_geom_torsion.atom_site_label_alt_id_4' geom_torsion no
'_struct_conn.ptnr1_label_alt_id' struct_conn no
'_struct_conn.ptnr2_label_alt_id' struct_conn no
'_struct_mon_nucl.label_alt_id' struct_mon_nucl yes
'_struct_mon_prot.label_alt_id' struct_mon_prot yes
'_struct_mon_prot_cis.label_alt_id' struct_mon_prot_cis yes
'_struct_ncs_dom_lim.beg_label_alt_id' struct_ncs_dom_lim yes
'_struct_ncs_dom_lim.end_label_alt_id' struct_ncs_dom_lim yes
'_struct_site_gen.label_alt_id' struct_site_gen yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_alt_id' '_atom_sites_alt.id'
'_atom_sites_alt_gen.alt_id' '_atom_sites_alt.id'
'_geom_angle.atom_site_label_alt_id_1' '_atom_site.label_alt_id'
'_geom_angle.atom_site_label_alt_id_2' '_atom_site.label_alt_id'
'_geom_angle.atom_site_label_alt_id_3' '_atom_site.label_alt_id'
'_geom_bond.atom_site_label_alt_id_1' '_atom_site.label_alt_id'
'_geom_bond.atom_site_label_alt_id_2' '_atom_site.label_alt_id'
'_geom_contact.atom_site_label_alt_id_1' '_atom_site.label_alt_id'
'_geom_contact.atom_site_label_alt_id_2' '_atom_site.label_alt_id'
'_geom_hbond.atom_site_label_alt_id_A' '_atom_site.label_alt_id'
'_geom_hbond.atom_site_label_alt_id_D' '_atom_site.label_alt_id'
'_geom_hbond.atom_site_label_alt_id_H' '_atom_site.label_alt_id'
'_geom_torsion.atom_site_label_alt_id_1' '_atom_site.label_alt_id'
'_geom_torsion.atom_site_label_alt_id_2' '_atom_site.label_alt_id'
'_geom_torsion.atom_site_label_alt_id_3' '_atom_site.label_alt_id'
'_geom_torsion.atom_site_label_alt_id_4' '_atom_site.label_alt_id'
'_struct_conn.ptnr1_label_alt_id' '_atom_site.label_alt_id'
'_struct_conn.ptnr2_label_alt_id' '_atom_site.label_alt_id'
'_struct_mon_nucl.label_alt_id' '_atom_site.label_alt_id'
'_struct_mon_prot.label_alt_id' '_atom_site.label_alt_id'
'_struct_mon_prot_cis.label_alt_id' '_atom_site.label_alt_id'
'_struct_ncs_dom_lim.beg_label_alt_id' '_atom_site.label_alt_id'
'_struct_ncs_dom_lim.end_label_alt_id' '_atom_site.label_alt_id'
'_struct_site_gen.label_alt_id' '_atom_site.label_alt_id'
_item_type.code code
loop_
_item_examples.case 'orientation 1'
'molecule abc'
save_
########################
## ATOM_SITES_ALT_ENS ##
########################
save_atom_sites_alt_ens
_category.description
; Data items in the ATOM_SITES_ALT_ENS category record details
about the ensemble structure generated from atoms with various
alternative conformation IDs.
;
_category.id atom_sites_alt_ens
_category.mandatory_code no
_category_key.name '_atom_sites_alt_ens.id'
loop_
_category_group.id 'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_atom_sites_alt_ens.id
_atom_sites_alt_ens.details
'Ensemble 1-A'
; The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the more populated
conformation of the inhibitor (ID=1) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=3) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.
;
'Ensemble 1-B'
; The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the more populated
conformation of the inhibitor (ID=1) and the amino-acid
side chains and solvent structure that correlate with
this inhibitor conformation.
Also included are one set (ID=4) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.
;
'Ensemble 2-A'
; The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the less populated
conformation of the inhibitor (ID=2) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=3) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.
;
'Ensemble 2-B'
; The inhibitor binds to the enzyme in two, roughly twofold
symmetric alternative conformations.
This conformational ensemble includes the less populated
conformation of the inhibitor (ID=2) and the amino-acid
side chains and solvent structure that correlate with this
inhibitor conformation.
Also included are one set (ID=4) of side chains with
alternative conformations when the conformations are not
correlated with the inhibitor conformation.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__atom_sites_alt_ens.details
_item_description.description
; A description of special aspects of the ensemble structure
generated from atoms with various alternative IDs.
;
_item.name '_atom_sites_alt_ens.details'
_item.category_id atom_sites_alt_ens
_item.mandatory_code no
_item_type.code text
save_
save__atom_sites_alt_ens.id
_item_description.description
; The value of _atom_sites_alt_ens.id must uniquely identify a
record in the ATOM_SITES_ALT_ENS list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_sites_alt_ens.id' atom_sites_alt_ens yes
'_atom_sites_alt_gen.ens_id' atom_sites_alt_gen yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_sites_alt_gen.ens_id' '_atom_sites_alt_ens.id'
_item_type.code code
save_
########################
## ATOM_SITES_ALT_GEN ##
########################
save_atom_sites_alt_gen
_category.description
; Data items in the ATOM_SITES_ALT_GEN category record details
about the interpretation of multiple conformations in the
structure.
;
_category.id atom_sites_alt_gen
_category.mandatory_code no
loop_
_category_key.name '_atom_sites_alt_gen.ens_id'
'_atom_sites_alt_gen.alt_id'
loop_
_category_group.id 'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_atom_sites_alt_gen.ens_id
_atom_sites_alt_gen.alt_id
'Ensemble 1-A' .
'Ensemble 1-A' 1
'Ensemble 1-A' 3
'Ensemble 1-B' .
'Ensemble 1-B' 1
'Ensemble 1-B' 4
'Ensemble 2-A' .
'Ensemble 2-A' 2
'Ensemble 2-A' 3
'Ensemble 2-B' .
'Ensemble 2-B' 2
'Ensemble 2-B' 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__atom_sites_alt_gen.alt_id
_item_description.description
; This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_atom_sites_alt_gen.alt_id'
_item.mandatory_code yes
save_
save__atom_sites_alt_gen.ens_id
_item_description.description
; This data item is a pointer to _atom_sites_alt_ens.id in the
ATOM_SITES_ALT_ENS category.
;
_item.name '_atom_sites_alt_gen.ens_id'
_item.mandatory_code yes
save_
#########################
## ATOM_SITES_FOOTNOTE ##
#########################
save_atom_sites_footnote
_category.description
; Data items in the ATOM_SITES_FOOTNOTE category record detailed
comments about an atom site or a group of atom sites.
;
_category.id atom_sites_footnote
_category.mandatory_code no
_category_key.name '_atom_sites_footnote.id'
loop_
_category_group.id 'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_atom_sites_footnote.id
_atom_sites_footnote.text
1
; The inhibitor binds to the enzyme in two alternative
orientations. The two orientations have been assigned
alternative IDs *1* and *2*.
;
2
; Side chains of these residues adopt alternative
orientations that correlate with the alternative
orientations of the inhibitor.
Side chains with alternative ID *1* and occupancy 0.58
correlate with inhibitor orientation *1*.
Side chains with alternative ID *2* and occupancy 0.42
correlate with inhibitor orientation *2*.
;
3
; The positions of these water molecules correlate with
the alternative orientations of the inhibitor.
Water molecules with alternative ID *1* and occupancy 0.58
correlate with inhibitor orientation *1*.
Water molecules with alternative ID *2* and occupancy 0.42
correlate with inhibitor orientation *2*.
;
4
; Side chains of these residues adopt alternative
orientations that do not correlate with the alternative
orientation of the inhibitor.
;
5
; The positions of these water molecules correlate with
alternative orientations of amino-acid side chains that
do not correlate with alternative orientations of the
inhibitor.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__atom_sites_footnote.id
_item_description.description
; A code that identifies the footnote.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_sites_footnote.id' atom_sites_footnote yes
'_atom_site.footnote_id' atom_site no
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.footnote_id' '_atom_sites_footnote.id'
_item_type.code code
loop_
_item_examples.case 'a'
'b'
'1'
'2'
save_
save__atom_sites_footnote.text
_item_description.description
; The text of the footnote. Footnotes are used to describe
an atom site or a group of atom sites in the ATOM_SITE list.
For example, footnotes may be used to indicate atoms for which
the electron density is very weak, or atoms for which static
disorder has been modelled.
;
_item.name '_atom_sites_footnote.text'
_item.category_id atom_sites_footnote
_item.mandatory_code no
_item_type.code text
save_
###############
## ATOM_TYPE ##
###############
save_atom_type
_category.description
; Data items in the ATOM_TYPE category record details about the
properties of the atoms that occupy the atom sites, such as the
atomic scattering factors.
;
_category.id atom_type
_category.mandatory_code no
_category_key.name '_atom_type.symbol'
loop_
_category_group.id 'inclusive_group'
'atom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_atom_type.symbol
_atom_type.oxidation_number
_atom_type.scat_Cromer_Mann_a1
_atom_type.scat_Cromer_Mann_a2
_atom_type.scat_Cromer_Mann_a3
_atom_type.scat_Cromer_Mann_a4
_atom_type.scat_Cromer_Mann_b1
_atom_type.scat_Cromer_Mann_b2
_atom_type.scat_Cromer_Mann_b3
_atom_type.scat_Cromer_Mann_b4
_atom_type.scat_Cromer_Mann_c
C 0 2.31000 20.8439 1.02000 10.2075
1.58860 0.568700 0.865000 51.6512 0.21560
N 0 12.2126 0.005700 3.13220 9.89330
2.01250 28.9975 1.16630 0.582600 -11.529
O 0 3.04850 13.2771 2.28680 5.70110
1.54630 0.323900 0.867000 32.9089 0.250800
S 0 6.90530 1.46790 5.20340 22.2151
1.43790 0.253600 1.58630 56.1720 0.866900
CL -1 18.2915 0.006600 7.20840 1.17170
6.53370 19.5424 2.33860 60.4486 -16.378
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
loop_
_atom_type.symbol
_atom_type.oxidation_number
_atom_type.number_in_cell
_atom_type.scat_dispersion_real
_atom_type.scat_dispersion_imag
_atom_type.scat_source
C 0 72 .017 .009 International_Tables_Vol_IV_Table_2.2B
H 0 100 0 0 International_Tables_Vol_IV_Table_2.2B
O 0 12 .047 .032 International_Tables_Vol_IV_Table_2.2B
N 0 4 .029 .018 International_Tables_Vol_IV_Table_2.2B
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__atom_type.analytical_mass_percent
_item_description.description
; Mass percentage of this atom type derived from chemical analysis.
;
_item.name '_atom_type.analytical_mass_percent'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_analytical_mass_%'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__atom_type.description
_item_description.description
; A description of the atom(s) designated by this atom type. In
most cases, this is the element name and oxidation state of
a single atom species. For disordered or nonstoichiometric
structures it will describe a combination of atom species.
;
_item.name '_atom_type.description'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_description'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'deuterium'
'0.34Fe+0.66Ni'
save_
save__atom_type.number_in_cell
_item_description.description
; Total number of atoms of this atom type in the unit cell.
;
_item.name '_atom_type.number_in_cell'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_number_in_cell'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__atom_type.oxidation_number
_item_description.description
; Formal oxidation state of this atom type in the structure.
;
_item.name '_atom_type.oxidation_number'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_oxidation_number'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 0
loop_
_item_range.maximum
_item_range.minimum 8 8
8 -8
-8 -8
_item_type.code int
save_
save__atom_type.radius_bond
_item_description.description
; The effective intramolecular bonding radius in angstroms
of this atom type.
;
_item.name '_atom_type.radius_bond'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_radius_bond'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 5.0 5.0
5.0 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__atom_type.radius_contact
_item_description.description
; The effective intermolecular bonding radius in angstroms
of this atom type.
;
_item.name '_atom_type.radius_contact'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_radius_contact'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 5.0 5.0
5.0 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__atom_type.scat_Cromer_Mann_a1
_item_description.description
; The Cromer-Mann scattering-factor coefficient a1 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
;
_item.name '_atom_type.scat_Cromer_Mann_a1'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_
save__atom_type.scat_Cromer_Mann_a2
_item_description.description
; The Cromer-Mann scattering-factor coefficient a2 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
;
_item.name '_atom_type.scat_Cromer_Mann_a2'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_
save__atom_type.scat_Cromer_Mann_a3
_item_description.description
; The Cromer-Mann scattering-factor coefficient a3 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
;
_item.name '_atom_type.scat_Cromer_Mann_a3'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a3'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_
save__atom_type.scat_Cromer_Mann_a4
_item_description.description
; The Cromer-Mann scattering-factor coefficient a4 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
;
_item.name '_atom_type.scat_Cromer_Mann_a4'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_a4'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_
save__atom_type.scat_Cromer_Mann_b1
_item_description.description
; The Cromer-Mann scattering-factor coefficient b1 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
;
_item.name '_atom_type.scat_Cromer_Mann_b1'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_
save__atom_type.scat_Cromer_Mann_b2
_item_description.description
; The Cromer-Mann scattering-factor coefficient b2 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
;
_item.name '_atom_type.scat_Cromer_Mann_b2'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_
save__atom_type.scat_Cromer_Mann_b3
_item_description.description
; The Cromer-Mann scattering-factor coefficient b3 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
;
_item.name '_atom_type.scat_Cromer_Mann_b3'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b3'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b4'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_
save__atom_type.scat_Cromer_Mann_b4
_item_description.description
; The Cromer-Mann scattering-factor coefficient b4 used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
;
_item.name '_atom_type.scat_Cromer_Mann_b4'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_b4'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_c'
_item_type.code float
save_
save__atom_type.scat_Cromer_Mann_c
_item_description.description
; The Cromer-Mann scattering-factor coefficient c used to
calculate the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or: International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5.
;
_item.name '_atom_type.scat_Cromer_Mann_c'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_Cromer_Mann_c'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_atom_type.scat_Cromer_Mann_a1'
'_atom_type.scat_Cromer_Mann_a2'
'_atom_type.scat_Cromer_Mann_a3'
'_atom_type.scat_Cromer_Mann_a4'
'_atom_type.scat_Cromer_Mann_b1'
'_atom_type.scat_Cromer_Mann_b2'
'_atom_type.scat_Cromer_Mann_b3'
'_atom_type.scat_Cromer_Mann_b4'
_item_type.code float
save_
save__atom_type.scat_dispersion_imag
_item_description.description
; The imaginary component of the anomalous-dispersion
scattering factor, f'', in electrons for this atom type and
the radiation identified by _diffrn_radiation_wavelength.id.
;
_item.name '_atom_type.scat_dispersion_imag'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_dispersion_imag'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value 0.0
_item_dependent.dependent_name
'_atom_type.scat_dispersion_real'
_item_type.code float
save_
save__atom_type.scat_dispersion_real
_item_description.description
; The real component of the anomalous-dispersion
scattering factor, f', in electrons for this atom type and
the radiation identified by _diffrn_radiation_wavelength.id.
;
_item.name '_atom_type.scat_dispersion_real'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_dispersion_real'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value 0.0
_item_dependent.dependent_name
'_atom_type.scat_dispersion_imag'
_item_type.code float
save_
save__atom_type.scat_length_neutron
_item_description.description
; The bound coherent scattering length in femtometres for the
atom type at the isotopic composition used for the diffraction
experiment.
;
_item.name '_atom_type.scat_length_neutron'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_length_neutron'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_units.code femtometres
save_
save__atom_type.scat_source
_item_description.description
; Reference to the source of the scattering factors or scattering
lengths used for this atom type.
;
_item.name '_atom_type.scat_source'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_source'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'International Tables Vol. IV Table 2.4.6B'
save_
save__atom_type.scat_versus_stol_list
_item_description.description
; A table of scattering factors as a function of sin theta over
lambda. This table should be well commented to indicate the
items present. Regularly formatted lists are strongly
recommended.
;
_item.name '_atom_type.scat_versus_stol_list'
_item.category_id atom_type
_item.mandatory_code no
_item_aliases.alias_name '_atom_type_scat_versus_stol_list'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__atom_type.symbol
_item_description.description
; The code used to identify the atom species (singular or plural)
representing this atom type. Normally this code is the element
symbol. The code may be composed of any character except
an underscore with the additional proviso that digits designate
an oxidation state and must be followed by a + or - character.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_atom_type.symbol' atom_type yes
'_atom_site.type_symbol' atom_site yes
'_atom_site_anisotrop.type_symbol' atom_site_anisotrop yes
'_chemical_conn_atom.type_symbol' chemical_conn_atom yes
'_chem_comp_atom.type_symbol' chem_comp_atom yes
'_phasing_MIR_der_site.atom_type_symbol'
phasing_MIR_der_site yes
_item_aliases.alias_name '_atom_type_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.type_symbol' '_atom_type.symbol'
'_atom_site_anisotrop.type_symbol' '_atom_type.symbol'
'_chemical_conn_atom.type_symbol' '_atom_type.symbol'
'_chem_comp_atom.type_symbol' '_atom_type.symbol'
'_phasing_MIR_der_site.atom_type_symbol' '_atom_type.symbol'
_item_type.code code
loop_
_item_examples.case 'C'
'Cu2+'
'H(SDS)'
'dummy'
'FeNi'
save_
###########
## AUDIT ##
###########
save_audit
_category.description
; Data items in the AUDIT category record details about the
creation and subsequent updating of the data block.
Note that these items apply only to the creation and updating of
the data block, and should not be confused with the data items
in the JOURNAL category that record different stages in the
publication of the material in the data block.
;
_category.id audit
_category.mandatory_code no
_category_key.name '_audit.revision_id'
loop_
_category_group.id 'inclusive_group'
'audit_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_audit.revision_id 1
_audit.creation_date '1992-12-08'
_audit.creation_method
; Created by hand from PDB entry 5HVP, from the J. Biol.
Chem. paper describing this structure and from
laboratory records
;
_audit.update_record
; 1992-12-09 adjusted to reflect comments from B. McKeever
1992-12-10 adjusted to reflect comments from H. Berman
1992-12-12 adjusted to reflect comments from K. Watenpaugh
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_audit.creation_date 1991-03-20
_audit.creation_method from_xtal_archive_file_using_CIFIO
_audit.update_record
; 1991-04-09 text and data added by Tony Willis.
1991-04-15 rec'd by co-editor as manuscript HL0007.
1991-04-17 adjustments based on first referee report.
1991-04-18 adjustments based on second referee report.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__audit.creation_date
_item_description.description
; A date that the data block was created. The date format is
yyyy-mm-dd.
;
_item.name '_audit.creation_date'
_item.category_id audit
_item.mandatory_code no
_item_aliases.alias_name '_audit_creation_date'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code yyyy-mm-dd
_item_examples.case '1990-07-12'
save_
save__audit.creation_method
_item_description.description
; A description of how data were entered into the data block.
;
_item.name '_audit.creation_method'
_item.category_id audit
_item.mandatory_code no
_item_aliases.alias_name '_audit_creation_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'spawned by the program QBEE'
save_
save__audit.revision_id
_item_description.description
; The value of _audit.revision_id must uniquely identify a record
in the AUDIT list.
;
_item.name '_audit.revision_id'
_item.category_id audit
_item.mandatory_code yes
_item_type.code code
_item_examples.case 'rev1'
save_
save__audit.update_record
_item_description.description
; A record of any changes to the data block. The update format is
a date (yyyy-mm-dd) followed by a description of the changes.
The latest update entry is added to the bottom of this record.
;
_item.name '_audit.update_record'
_item.category_id audit
_item.mandatory_code no
_item_aliases.alias_name '_audit_update_record'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case '1990-07-15 Updated by the Co-editor'
save_
##################
## AUDIT_AUTHOR ##
##################
save_audit_author
_category.description
; Data items in the AUDIT_AUTHOR category record details about
the author(s) of the data block.
;
_category.id audit_author
_category.mandatory_code no
_category_key.name '_audit_author.name'
loop_
_category_group.id 'inclusive_group'
'audit_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_audit_author.name
_audit_author.address
'Fitzgerald, Paula M.D.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'McKeever, Brian M.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'Van Middlesworth, J.F.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
'Springer, James P.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__audit_author.address
_item_description.description
; The address of an author of this data block. If there are
multiple authors, _audit_author.address is looped with
_audit_author.name.
;
_item.name '_audit_author.address'
_item.category_id audit_author
_item.mandatory_code no
_item_aliases.alias_name '_audit_author_address'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Department
Institute
Street
City and postcode
COUNTRY
;
save_
save__audit_author.name
_item_description.description
; The name of an author of this data block. If there are multiple
authors, _audit_author.name is looped with _audit_author.address.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
_item.name '_audit_author.name'
_item.category_id audit_author
_item.mandatory_code yes
_item_aliases.alias_name '_audit_author_name'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
save_
###################
## AUDIT_CONFORM ##
###################
save_audit_conform
_category.description
; Data items in the AUDIT_CONFORM category describe the
dictionary versions against which the data names appearing in
the current data block are conformant.
;
_category.id audit_conform
_category.mandatory_code no
loop_
_category_key.name '_audit_conform.dict_name'
'_audit_conform.dict_version'
loop_
_category_group.id 'inclusive_group'
'audit_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - any file conforming to the current CIF core dictionary.
;
;
_audit_conform.dict_name cif_core.dic
_audit_conform.dict_version 2.3.1
_audit_conform.dict_location
ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__audit_conform.dict_location
_item_description.description
; A file name or uniform resource locator (URL) for the
dictionary to which the current data block conforms.
;
_item.name '_audit_conform.dict_location'
_item.category_id audit_conform
_item.mandatory_code no
_item_aliases.alias_name '_audit_conform_dict_location'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__audit_conform.dict_name
_item_description.description
; The string identifying the highest-level dictionary defining
data names used in this file.
;
_item.name '_audit_conform.dict_name'
_item.category_id audit_conform
_item.mandatory_code no
_item_aliases.alias_name '_audit_conform_dict_name'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__audit_conform.dict_version
_item_description.description
; The version number of the dictionary to which the current
data block conforms.
;
_item.name '_audit_conform.dict_version'
_item.category_id audit_conform
_item.mandatory_code no
_item_aliases.alias_name '_audit_conform_dict_version'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
##########################
## AUDIT_CONTACT_AUTHOR ##
##########################
save_audit_contact_author
_category.description
; Data items in the AUDIT_CONTACT_AUTHOR category record details
about the name and address of the author to be contacted
concerning the content of this data block.
;
_category.id audit_contact_author
_category.mandatory_code no
_category_key.name '_audit_contact_author.name'
loop_
_category_group.id 'inclusive_group'
'audit_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_audit_contact_author.name 'Fitzgerald, Paula M.D.'
_audit_contact_author.address
; Department of Biophysical Chemistry
Merck Research Laboratories
PO Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
_audit_contact_author.phone '1(908)5945510'
_audit_contact_author.fax '1(908)5946645'
_audit_contact_author.email 'paula_fitzgerald@merck.com'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__audit_contact_author.address
_item_description.description
; The mailing address of the author of the data block to whom
correspondence should be addressed.
;
_item.name '_audit_contact_author.address'
_item.category_id audit_contact_author
_item.mandatory_code no
_item_aliases.alias_name '_audit_contact_author_address'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Department
Institute
Street
City and postcode
COUNTRY
;
save_
save__audit_contact_author.email
_item_description.description
; The electronic mail address of the author of the data block to
whom correspondence should be addressed, in a form recognizable
to international networks. The format of e-mail
addresses is given in Section 3.4, Address Specification, of
Internet Message Format, RFC 2822, P. Resnick (Editor),
Network Standards Group, April 2001.
;
_item.name '_audit_contact_author.email'
_item.category_id audit_contact_author
_item.mandatory_code no
_item_aliases.alias_name '_audit_contact_author_email'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'name@host.domain.country'
'bm@iucr.org'
save_
save__audit_contact_author.fax
_item_description.description
; The facsimile telephone number of the author of the data
block to whom correspondence should be addressed.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number with no spaces.
;
_item.name '_audit_contact_author.fax'
_item.category_id audit_contact_author
_item.mandatory_code no
_item_aliases.alias_name '_audit_contact_author_fax'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case '12(34)9477334'
'12()349477334'
save_
save__audit_contact_author.name
_item_description.description
; The name of the author of the data block to whom correspondence
should be addressed.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
_item.name '_audit_contact_author.name'
_item.category_id audit_contact_author
_item.mandatory_code yes
_item_aliases.alias_name '_audit_contact_author_name'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
save_
save__audit_contact_author.phone
_item_description.description
; The telephone number of the author of the data block to whom
correspondence should be addressed.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number and any extension number prefixed by 'x',
with no spaces.
;
_item.name '_audit_contact_author.phone'
_item.category_id audit_contact_author
_item.mandatory_code no
_item_aliases.alias_name '_audit_contact_author_phone'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case '12(34)9477330'
'12()349477330'
'12(34)9477330x5543'
save_
##########
## CELL ##
##########
save_cell
_category.description
; Data items in the CELL category record details about the
crystallographic cell parameters.
;
_category.id cell
_category.mandatory_code no
_category_key.name '_cell.entry_id'
loop_
_category_group.id 'inclusive_group'
'cell_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_cell.entry_id '5HVP'
_cell.length_a 58.39
_cell.length_a_esd 0.05
_cell.length_b 86.70
_cell.length_b_esd 0.12
_cell.length_c 46.27
_cell.length_c_esd 0.06
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 90.00
_cell.volume 234237
_cell.details
; The cell parameters were refined every twenty frames during
data integration. The cell lengths given are the mean of
55 such refinements; the esds given are the root mean
square deviations of these 55 observations from that mean.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_cell.length_a 5.959
_cell.length_a_esd 0.001
_cell.length_b 14.956
_cell.length_b_esd 0.001
_cell.length_c 19.737
_cell.length_c_esd 0.003
_cell.angle_alpha 90.0
_cell.angle_beta 90.0
_cell.angle_gamma 90.0
_cell.volume 1759.0
_cell.volume_esd 0.3
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__cell.angle_alpha
_item_description.description
; Unit-cell angle alpha of the reported structure in degrees.
;
_item.name '_cell.angle_alpha'
_item.category_id cell
_item.mandatory_code no
_item_aliases.alias_name '_cell_angle_alpha'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 90.0
loop_
_item_dependent.dependent_name
'_cell.angle_beta'
'_cell.angle_gamma'
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 0.0
0.0 0.0
_item_related.related_name '_cell.angle_alpha_esd'
_item_related.function_code associated_esd
_item_sub_category.id cell_angle
_item_type.code float
_item_type_conditions.code esd
_item_units.code degrees
save_
save__cell.angle_alpha_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _cell.angle_alpha.
;
_item.name '_cell.angle_alpha_esd'
_item.category_id cell
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_cell.angle_beta_esd'
'_cell.angle_gamma_esd'
_item_related.related_name '_cell.angle_alpha'
_item_related.function_code associated_value
_item_sub_category.id cell_angle_esd
_item_type.code float
_item_units.code degrees
save_
save__cell.angle_beta
_item_description.description
; Unit-cell angle beta of the reported structure in degrees.
;
_item.name '_cell.angle_beta'
_item.category_id cell
_item.mandatory_code no
_item_aliases.alias_name '_cell_angle_beta'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 90.0
loop_
_item_dependent.dependent_name
'_cell.angle_alpha'
'_cell.angle_gamma'
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 0.0
0.0 0.0
_item_related.related_name '_cell.angle_beta_esd'
_item_related.function_code associated_esd
_item_sub_category.id cell_angle
_item_type.code float
_item_type_conditions.code esd
_item_units.code degrees
save_
save__cell.angle_beta_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _cell.angle_beta.
;
_item.name '_cell.angle_beta_esd'
_item.category_id cell
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_cell.angle_alpha_esd'
'_cell.angle_gamma_esd'
_item_related.related_name '_cell.angle_beta'
_item_related.function_code associated_value
_item_sub_category.id cell_angle_esd
_item_type.code float
_item_units.code degrees
save_
save__cell.angle_gamma
_item_description.description
; Unit-cell angle gamma of the reported structure in degrees.
;
_item.name '_cell.angle_gamma'
_item.category_id cell
_item.mandatory_code no
_item_aliases.alias_name '_cell_angle_gamma'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 90.0
loop_
_item_dependent.dependent_name
'_cell.angle_alpha'
'_cell.angle_beta'
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 0.0
0.0 0.0
_item_related.related_name '_cell.angle_gamma_esd'
_item_related.function_code associated_esd
_item_sub_category.id cell_angle
_item_type.code float
_item_type_conditions.code esd
_item_units.code degrees
save_
save__cell.angle_gamma_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _cell.angle_gamma.
;
_item.name '_cell.angle_gamma_esd'
_item.category_id cell
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_cell.angle_alpha_esd'
'_cell.angle_beta_esd'
_item_related.related_name '_cell.angle_gamma'
_item_related.function_code associated_value
_item_sub_category.id cell_angle_esd
_item_type.code float
_item_units.code degrees
save_
save__cell.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_cell.entry_id'
_item.mandatory_code yes
save_
save__cell.details
_item_description.description
; A description of special aspects of the cell choice, noting
possible alternative settings.
;
_item.name '_cell.details'
_item.category_id cell
_item.mandatory_code no
_item_aliases.alias_name '_cell_special_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'pseudo-orthorhombic'
'standard setting from 45 deg rotation around c'
save_
save__cell.formula_units_Z
_item_description.description
; The number of the formula units in the unit cell as specified
by _chemical_formula.structural, _chemical_formula.moiety or
_chemical_formula.sum.
;
_item.name '_cell.formula_units_Z'
_item.category_id cell
_item.mandatory_code no
_item_aliases.alias_name '_cell_formula_units_Z'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__cell.length_a
_item_description.description
; Unit-cell length a corresponding to the structure reported in
angstroms.
;
_item.name '_cell.length_a'
_item.category_id cell
_item.mandatory_code no
_item_aliases.alias_name '_cell_length_a'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_cell.length_b'
'_cell.length_c'
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_cell.length_a_esd'
_item_related.function_code associated_esd
_item_sub_category.id cell_length
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__cell.length_a_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _cell.length_a.
;
_item.name '_cell.length_a_esd'
_item.category_id cell
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_cell.length_b_esd'
'_cell.length_c_esd'
_item_related.related_name '_cell.length_a'
_item_related.function_code associated_value
_item_sub_category.id cell_length_esd
_item_type.code float
_item_units.code angstroms
save_
save__cell.length_b
_item_description.description
; Unit-cell length b corresponding to the structure reported in
angstroms.
;
_item.name '_cell.length_b'
_item.category_id cell
_item.mandatory_code no
_item_aliases.alias_name '_cell_length_b'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_cell.length_a'
'_cell.length_c'
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_cell.length_b_esd'
_item_related.function_code associated_esd
_item_sub_category.id cell_length
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__cell.length_b_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _cell.length_b.
;
_item.name '_cell.length_b_esd'
_item.category_id cell
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_cell.length_a_esd'
'_cell.length_c_esd'
_item_related.related_name '_cell.length_b'
_item_related.function_code associated_value
_item_sub_category.id cell_length_esd
_item_type.code float
_item_units.code angstroms
save_
save__cell.length_c
_item_description.description
; Unit-cell length c corresponding to the structure reported in
angstroms.
;
_item.name '_cell.length_c'
_item.category_id cell
_item.mandatory_code no
_item_aliases.alias_name '_cell_length_c'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_cell.length_a'
'_cell.length_b'
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_cell.length_c_esd'
_item_related.function_code associated_esd
_item_sub_category.id cell_length
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__cell.length_c_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _cell.length_c.
;
_item.name '_cell.length_c_esd'
_item.category_id cell
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_cell.length_a_esd'
'_cell.length_b_esd'
_item_related.related_name '_cell.length_c'
_item_related.function_code associated_value
_item_sub_category.id cell_length_esd
_item_type.code float
_item_units.code angstroms
save_
save__cell.volume
_item_description.description
; Cell volume V in angstroms cubed.
V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~
+ 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^
a = _cell.length_a
b = _cell.length_b
c = _cell.length_c
alpha = _cell.angle_alpha
beta = _cell.angle_beta
gamma = _cell.angle_gamma
;
_item.name '_cell.volume'
_item.category_id cell
_item.mandatory_code no
_item_aliases.alias_name '_cell_volume'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_cell.volume_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_cubed
save_
save__cell.volume_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _cell.volume.
;
_item.name '_cell.volume_esd'
_item.category_id cell
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_cell.volume'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms_cubed
save_
save__cell.Z_PDB
_item_description.description
; The number of the polymeric chains in a unit cell. In the case
of heteropolymers, Z is the number of occurrences of the most
populous chain.
This data item is provided for compatibility with the original
Protein Data Bank format, and only for that purpose.
;
_item.name '_cell.Z_PDB'
_item.category_id cell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
######################
## CELL_MEASUREMENT ##
######################
save_cell_measurement
_category.description
; Data items in the CELL_MEASUREMENT category record details
about the measurement of the crystallographic cell parameters.
;
_category.id cell_measurement
_category.mandatory_code no
_category_key.name '_cell_measurement.entry_id'
loop_
_category_group.id 'inclusive_group'
'cell_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_cell_measurement.entry_id '5HVP'
_cell_measurement.temp 293
_cell_measurement.temp_esd 3
_cell_measurement.theta_min 11
_cell_measurement.theta_max 31
_cell_measurement.wavelength 1.54
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_cell_measurement.temp 293
_cell_measurement.reflns_used 25
_cell_measurement.theta_min 25
_cell_measurement.theta_max 31
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__cell_measurement.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_cell_measurement.entry_id'
_item.mandatory_code yes
save_
save__cell_measurement.pressure
_item_description.description
; The pressure in kilopascals at which the unit-cell parameters
were measured (not the pressure at which the sample was
synthesized).
;
_item.name '_cell_measurement.pressure'
_item.category_id cell_measurement
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_pressure'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_cell_measurement.pressure_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code kilopascals
save_
save__cell_measurement.pressure_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _cell_measurement.pressure.
;
_item.name '_cell_measurement.pressure_esd'
_item.category_id cell_measurement
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_cell_measurement.pressure'
_item_related.function_code associated_value
_item_type.code float
_item_units.code kilopascals
save_
save__cell_measurement.radiation
_item_description.description
; Description of the radiation used to measure the unit-cell data.
See also _cell_measurement.wavelength.
;
_item.name '_cell_measurement.radiation'
_item.category_id cell_measurement
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_radiation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'neutron'
'Cu K\a'
'synchrotron'
save_
save__cell_measurement.reflns_used
_item_description.description
; The total number of reflections used to determine the unit cell.
These reflections may be specified as CELL_MEASUREMENT_REFLN
data items.
;
_item.name '_cell_measurement.reflns_used'
_item.category_id cell_measurement
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_reflns_used'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__cell_measurement.temp
_item_description.description
; The temperature in kelvins at which the unit-cell parameters
were measured (not the temperature of synthesis).
;
_item.name '_cell_measurement.temp'
_item.category_id cell_measurement
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_temperature'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_cell_measurement.temp_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code kelvins
save_
save__cell_measurement.temp_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _cell_measurement.temp.
;
_item.name '_cell_measurement.temp_esd'
_item.category_id cell_measurement
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_cell_measurement.temp'
_item_related.function_code associated_value
_item_type.code float
_item_units.code kelvins
save_
save__cell_measurement.theta_max
_item_description.description
; The maximum theta angle of reflections used to measure
the unit cell in degrees.
;
_item.name '_cell_measurement.theta_max'
_item.category_id cell_measurement
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_theta_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
save__cell_measurement.theta_min
_item_description.description
; The minimum theta angle of reflections used to measure
the unit cell in degrees.
;
_item.name '_cell_measurement.theta_min'
_item.category_id cell_measurement
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_theta_min'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
save__cell_measurement.wavelength
_item_description.description
; The wavelength in angstroms of the radiation used to measure
the unit cell. If this is not specified, the wavelength is
assumed to be that specified in the category
DIFFRN_RADIATION_WAVELENGTH.
;
_item.name '_cell_measurement.wavelength'
_item.category_id cell_measurement
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_wavelength'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
############################
## CELL_MEASUREMENT_REFLN ##
############################
save_cell_measurement_refln
_category.description
; Data items in the CELL_MEASUREMENT_REFLN category record
details about the reflections used to determine the
crystallographic cell parameters.
The CELL_MEASUREMENT_REFLN data items would in general be used
only for diffractometer data.
;
_category.id cell_measurement_refln
_category.mandatory_code no
loop_
_category_key.name '_cell_measurement_refln.index_h'
'_cell_measurement_refln.index_k'
'_cell_measurement_refln.index_l'
loop_
_category_group.id 'inclusive_group'
'cell_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room
temperature (unpublished).
;
;
loop_
_cell_measurement_refln.index_h
_cell_measurement_refln.index_k
_cell_measurement_refln.index_l
_cell_measurement_refln.theta
-2 4 1 8.67
0 3 2 9.45
3 0 2 9.46
-3 4 1 8.93
-2 1 -2 7.53
10 0 0 23.77
0 10 0 23.78
-5 4 1 11.14
# - - - - data truncated for brevity - - - -
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__cell_measurement_refln.index_h
_item_description.description
; Miller index h of a reflection used for measurement of the unit
cell.
;
_item.name '_cell_measurement_refln.index_h'
_item.category_id cell_measurement_refln
_item.mandatory_code yes
_item_aliases.alias_name '_cell_measurement_refln_index_h'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_cell_measurement_refln.index_k'
'_cell_measurement_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__cell_measurement_refln.index_k
_item_description.description
; Miller index k of a reflection used for measurement of the unit
cell.
;
_item.name '_cell_measurement_refln.index_k'
_item.category_id cell_measurement_refln
_item.mandatory_code yes
_item_aliases.alias_name '_cell_measurement_refln_index_k'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_cell_measurement_refln.index_h'
'_cell_measurement_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__cell_measurement_refln.index_l
_item_description.description
; Miller index l of a reflection used for measurement of the unit
cell.
;
_item.name '_cell_measurement_refln.index_l'
_item.category_id cell_measurement_refln
_item.mandatory_code yes
_item_aliases.alias_name '_cell_measurement_refln_index_l'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_cell_measurement_refln.index_h'
'_cell_measurement_refln.index_k'
_item_sub_category.id miller_index
_item_type.code int
save_
save__cell_measurement_refln.theta
_item_description.description
; Theta angle for a reflection used for measurement of
the unit cell in degrees.
;
_item.name '_cell_measurement_refln.theta'
_item.category_id cell_measurement_refln
_item.mandatory_code no
_item_aliases.alias_name '_cell_measurement_refln_theta'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
###############
## CHEM_COMP ##
###############
save_chem_comp
_category.description
; Data items in the CHEM_COMP category give details about each
of the chemical components from which the relevant chemical
structures can be constructed, such as name, mass or charge.
The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND,
CHEM_COMP_ANGLE etc. describe the detailed geometry of these
chemical components.
;
_category.id chem_comp
_category.mandatory_code no
_category_key.name '_chem_comp.id'
loop_
_category_group.id 'inclusive_group'
'chem_comp_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_chem_comp.id
_chem_comp.model_source
_chem_comp.name
phe '1987 Protin/Prolsq Ideals file' phenylalanine
val '1987 Protin/Prolsq Ideals file' alanine
# - - - - data truncated for brevity - - - -
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_comp.formula
_item_description.description
; The formula for the chemical component. Formulae are written
according to the following rules:
(1) Only recognized element symbols may be used.
(2) Each element symbol is followed by a 'count' number. A count
of '1' may be omitted.
(3) A space or parenthesis must separate each cluster of
(element symbol + count), but in general parentheses are
not used.
(4) The order of elements depends on whether carbon is
present or not. If carbon is present, the order should be:
C, then H, then the other elements in alphabetical order
of their symbol. If carbon is not present, the elements
are listed purely in alphabetic order of their symbol. This
is the 'Hill' system used by Chemical Abstracts.
;
_item.name '_chem_comp.formula'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'C18 H19 N7 O8 S'
save_
save__chem_comp.formula_weight
_item_description.description
; Formula mass in daltons of the chemical component.
;
_item.name '_chem_comp.formula_weight'
_item.category_id chem_comp
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1.0
1.0 1.0
_item_type.code float
save_
save__chem_comp.id
_item_description.description
; The value of _chem_comp.id must uniquely identify each item in
the CHEM_COMP list.
For protein polymer entities, this is the three-letter code for
the amino acid.
For nucleic acid polymer entities, this is the one-letter code
for the base.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chem_comp.id' chem_comp yes
'_atom_site.label_comp_id' atom_site no
'_chem_comp.mon_nstd_parent_comp_id' chem_comp no
'_chem_comp_atom.comp_id' chem_comp_atom yes
'_chem_comp_angle.comp_id' chem_comp_angle yes
'_chem_comp_bond.comp_id' chem_comp_bond yes
'_chem_comp_chir.comp_id' chem_comp_chir yes
'_chem_comp_chir_atom.comp_id' chem_comp_chir_atom yes
'_chem_comp_plane.comp_id' chem_comp_plane yes
'_chem_comp_plane_atom.comp_id' chem_comp_plane_atom yes
'_chem_comp_tor.comp_id' chem_comp_tor yes
'_chem_comp_tor_value.comp_id' chem_comp_tor_value yes
'_entity_poly_seq.mon_id' entity_poly_seq yes
'_geom_angle.atom_site_label_comp_id_1' geom_angle no
'_geom_angle.atom_site_label_comp_id_2' geom_angle no
'_geom_angle.atom_site_label_comp_id_3' geom_angle no
'_geom_bond.atom_site_label_comp_id_1' geom_bond no
'_geom_bond.atom_site_label_comp_id_2' geom_bond no
'_geom_contact.atom_site_label_comp_id_1' geom_contact no
'_geom_contact.atom_site_label_comp_id_2' geom_contact no
'_geom_hbond.atom_site_label_comp_id_A' geom_hbond no
'_geom_hbond.atom_site_label_comp_id_D' geom_hbond no
'_geom_hbond.atom_site_label_comp_id_H' geom_hbond no
'_geom_torsion.atom_site_label_comp_id_1' geom_torsion no
'_geom_torsion.atom_site_label_comp_id_2' geom_torsion no
'_geom_torsion.atom_site_label_comp_id_3' geom_torsion no
'_geom_torsion.atom_site_label_comp_id_4' geom_torsion no
'_struct_conf.beg_label_comp_id' struct_conf yes
'_struct_conf.end_label_comp_id' struct_conf yes
'_struct_conn.ptnr1_label_comp_id' struct_conn yes
'_struct_conn.ptnr2_label_comp_id' struct_conn yes
'_struct_mon_nucl.label_comp_id' struct_mon_nucl yes
'_struct_mon_prot.label_comp_id' struct_mon_prot yes
'_struct_mon_prot_cis.label_comp_id' struct_mon_prot_cis yes
'_struct_ncs_dom_lim.beg_label_comp_id' struct_ncs_dom_lim yes
'_struct_ncs_dom_lim.end_label_comp_id' struct_ncs_dom_lim yes
'_struct_ref_seq_dif.db_mon_id' struct_ref_seq_dif yes
'_struct_ref_seq_dif.mon_id' struct_ref_seq_dif yes
'_struct_sheet_range.beg_label_comp_id' struct_sheet_range yes
'_struct_sheet_range.end_label_comp_id' struct_sheet_range yes
'_struct_site_gen.label_comp_id' struct_site_gen yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_comp_id' '_chem_comp.id'
'_chem_comp.mon_nstd_parent_comp_id' '_chem_comp.id'
'_chem_comp_atom.comp_id' '_chem_comp.id'
'_chem_comp_chir.comp_id' '_chem_comp.id'
'_chem_comp_chir_atom.comp_id' '_chem_comp.id'
'_chem_comp_plane.comp_id' '_chem_comp.id'
'_chem_comp_plane_atom.comp_id' '_chem_comp.id'
'_entity_poly_seq.mon_id' '_chem_comp.id'
'_chem_comp_angle.comp_id' '_chem_comp_atom.comp_id'
'_chem_comp_bond.comp_id' '_chem_comp_atom.comp_id'
'_chem_comp_tor.comp_id' '_chem_comp_atom.comp_id'
'_chem_comp_tor_value.comp_id' '_chem_comp_atom.comp_id'
'_geom_angle.atom_site_label_comp_id_1' '_atom_site.label_comp_id'
'_geom_angle.atom_site_label_comp_id_2' '_atom_site.label_comp_id'
'_geom_angle.atom_site_label_comp_id_3' '_atom_site.label_comp_id'
'_geom_bond.atom_site_label_comp_id_1' '_atom_site.label_comp_id'
'_geom_bond.atom_site_label_comp_id_2' '_atom_site.label_comp_id'
'_geom_contact.atom_site_label_comp_id_1' '_atom_site.label_comp_id'
'_geom_contact.atom_site_label_comp_id_2' '_atom_site.label_comp_id'
'_geom_hbond.atom_site_label_comp_id_A' '_atom_site.label_comp_id'
'_geom_hbond.atom_site_label_comp_id_D' '_atom_site.label_comp_id'
'_geom_hbond.atom_site_label_comp_id_H' '_atom_site.label_comp_id'
'_geom_torsion.atom_site_label_comp_id_1' '_atom_site.label_comp_id'
'_geom_torsion.atom_site_label_comp_id_2' '_atom_site.label_comp_id'
'_geom_torsion.atom_site_label_comp_id_3' '_atom_site.label_comp_id'
'_geom_torsion.atom_site_label_comp_id_4' '_atom_site.label_comp_id'
'_struct_conf.beg_label_comp_id' '_atom_site.label_comp_id'
'_struct_conf.end_label_comp_id' '_atom_site.label_comp_id'
'_struct_conn.ptnr1_label_comp_id' '_atom_site.label_comp_id'
'_struct_conn.ptnr2_label_comp_id' '_atom_site.label_comp_id'
'_struct_mon_nucl.label_comp_id' '_atom_site.label_comp_id'
'_struct_mon_prot.label_comp_id' '_atom_site.label_comp_id'
'_struct_mon_prot_cis.label_comp_id' '_atom_site.label_comp_id'
'_struct_ncs_dom_lim.beg_label_comp_id' '_atom_site.label_comp_id'
'_struct_ncs_dom_lim.end_label_comp_id' '_atom_site.label_comp_id'
'_struct_ref_seq_dif.db_mon_id' '_chem_comp.id'
'_struct_ref_seq_dif.mon_id' '_chem_comp.id'
'_struct_sheet_range.beg_label_comp_id' '_atom_site.label_comp_id'
'_struct_sheet_range.end_label_comp_id' '_atom_site.label_comp_id'
'_struct_site_gen.label_comp_id' '_atom_site.label_comp_id'
_item_type.code ucode
loop_
_item_examples.case 'ala'
'val'
'A'
'C'
save_
save__chem_comp.model_details
_item_description.description
; A description of special aspects of the generation of the
coordinates for the model of the component.
;
_item.name '_chem_comp.model_details'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code text
_item_examples.case 'geometry idealized but not minimized'
save_
save__chem_comp.model_erf
_item_description.description
; A pointer to an external reference file from which the atomic
description of the component is taken.
;
_item.name '_chem_comp.model_erf'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code line
save_
save__chem_comp.model_source
_item_description.description
; The source of the coordinates for the model of the component.
;
_item.name '_chem_comp.model_source'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'CSD entry ABCDEF'
'built using Quanta/Charmm'
save_
save__chem_comp.mon_nstd_class
_item_description.description
; A description of the class of a nonstandard monomer if the
nonstandard monomer represents a modification of a
standard monomer.
;
_item.name '_chem_comp.mon_nstd_class'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'iodinated base'
'phosphorylated amino acid'
'brominated base'
'modified amino acid'
'glycosylated amino acid'
save_
save__chem_comp.mon_nstd_details
_item_description.description
; A description of special details of a nonstandard monomer.
;
_item.name '_chem_comp.mon_nstd_details'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code text
save_
save__chem_comp.mon_nstd_flag
_item_description.description
; 'yes' indicates that this is a 'standard' monomer, 'no'
indicates that it is 'nonstandard'. Nonstandard monomers
should be described in more detail using the
_chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
_chem_comp.mon_nstd_details data items.
;
_item.name '_chem_comp.mon_nstd_flag'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code ucode
_item_default.value no
loop_
_item_enumeration.value
_item_enumeration.detail no 'the monomer is nonstandard'
n 'abbreviation for "no"'
yes 'the monomer is standard'
y 'abbreviation for "yes"'
save_
save__chem_comp.mon_nstd_parent
_item_description.description
; The name of the parent monomer of the nonstandard monomer,
if the nonstandard monomer represents a modification of a
standard monomer.
;
_item.name '_chem_comp.mon_nstd_parent'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'tyrosine'
'cytosine'
save_
save__chem_comp.mon_nstd_parent_comp_id
_item_description.description
; The identifier for the parent component of the nonstandard
component.
This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_chem_comp.mon_nstd_parent_comp_id'
_item.mandatory_code no
save_
save__chem_comp.name
_item_description.description
; The full name of the component.
;
_item.name '_chem_comp.name'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'alanine'
'valine'
'adenine'
'cytosine'
save_
save__chem_comp.number_atoms_all
_item_description.description
; The total number of atoms in the component.
;
_item.name '_chem_comp.number_atoms_all'
_item.category_id chem_comp
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__chem_comp.number_atoms_nh
_item_description.description
; The number of non-hydrogen atoms in the component.
;
_item.name '_chem_comp.number_atoms_nh'
_item.category_id chem_comp
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__chem_comp.one_letter_code
_item_description.description
; For standard polymer components, the one-letter code for
the component. If there is not a standard one-letter code
for this component, or if this is a non-polymer
component, the one-letter code should be given as 'X'.
This code may be preceded by a '+' character to indicate
that the component is a modification of a standard
component.
;
_item.name '_chem_comp.one_letter_code'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code uchar1
loop_
_item_examples.case
_item_examples.detail A 'alanine or adenine'
B 'ambiguous asparagine/aspartic acid'
R 'arginine'
N 'asparagine'
D 'aspartic acid'
C 'cysteine or cystine or cytosine'
Q 'glutamine'
E 'glutamic acid'
Z 'ambiguous glutamine/glutamic acid'
G 'glycine or guanine'
H 'histidine'
I 'isoleucine'
L 'leucine'
K 'lysine'
M 'methionine'
F 'phenylalanine'
P 'proline'
S 'serine'
T 'threonine or thymine'
W 'tryptophan'
Y 'tyrosine'
V 'valine'
U 'uracil'
O 'water'
X 'other'
save_
save__chem_comp.three_letter_code
_item_description.description
; For standard polymer components, the three-letter code for
the component. If there is not a standard three-letter code
for this component, or if this is a non-polymer
component, the three-letter code should be given as 'UNK'.
This code may be preceded by a '+' character to indicate
that the component is a modification of a standard
component.
;
_item.name '_chem_comp.three_letter_code'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code uchar3
loop_
_item_examples.case
_item_examples.detail ALA 'alanine'
ARG 'arginine'
ASN 'asparagine'
ASP 'aspartic acid'
ASX 'ambiguous asparagine/aspartic acid'
CYS 'cysteine'
GLN 'glutamine'
GLU 'glutamic acid'
GLY 'glycine'
GLX 'ambiguous glutamine/glutamic acid'
HIS 'histidine'
ILE 'isoleucine'
LEU 'leucine'
LYS 'lysine'
MET 'methionine'
PHE 'phenylalanine'
PRO 'proline'
SER 'serine'
THR 'threonine'
TRP 'tryptophan'
TRY 'tyrosine'
VAL 'valine'
1MA '1-methyladenosine'
5MC '5-methylcytosine'
OMC '2(prime)-O-methylcytodine'
1MG '1-methylguanosine'
2MG 'N(2)-methylguanosine'
M2G 'N(2)-dimethylguanosine'
7MG '7-methylguanosine'
0MG '2(prime)-O-methylguanosine'
H2U 'dihydrouridine'
5MU 'ribosylthymidine'
PSU 'pseudouridine'
ACE 'acetic acid'
FOR 'formic acid'
HOH 'water'
UNK 'other'
save_
save__chem_comp.type
_item_description.description
; For standard polymer components, the type of the monomer.
Note that monomers that will form polymers are of three types:
linking monomers, monomers with some type of N-terminal (or 5')
cap and monomers with some type of C-terminal (or 3') cap.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chem_comp.type' chem_comp yes
'_chem_comp_link.type_comp_1' chem_comp_link yes
'_chem_comp_link.type_comp_2' chem_comp_link yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_chem_comp_link.type_comp_1' '_chem_comp.type'
'_chem_comp_link.type_comp_2' '_chem_comp.type'
_item_type.code uline
loop_
_item_enumeration.value 'D-peptide linking'
'L-peptide linking'
'D-peptide NH3 amino terminus'
'L-peptide NH3 amino terminus'
'D-peptide COOH carboxy terminus'
'L-peptide COOH carboxy terminus'
'DNA linking'
'RNA linking'
'DNA OH 5 prime terminus'
'RNA OH 5 prime terminus'
'DNA OH 3 prime terminus'
'RNA OH 3 prime terminus'
'D-saccharide 1,4 and 1,4 linking'
'L-saccharide 1,4 and 1,4 linking'
'D-saccharide 1,4 and 1,6 linking'
'L-saccharide 1,4 and 1,6 linking'
'L-saccharide'
'D-saccharide'
'saccharide'
'non-polymer'
'other'
save_
#####################
## CHEM_COMP_ANGLE ##
#####################
save_chem_comp_angle
_category.description
; Data items in the CHEM_COMP_ANGLE category record details about
angles in a chemical component. Angles are designated by three
atoms, with the second atom forming the vertex of the angle.
Target values may be specified as angles in degrees, as a
distance between the first and third atoms, or both.
;
_category.id chem_comp_angle
_category.mandatory_code no
loop_
_category_key.name '_chem_comp_angle.comp_id'
'_chem_comp_angle.atom_id_1'
'_chem_comp_angle.atom_id_2'
'_chem_comp_angle.atom_id_3'
loop_
_category_group.id 'inclusive_group'
'chem_comp_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_dist
phe N CA C xxx.xx x.xx
phe CA C O xxx.xx x.xx
phe CB CA C xxx.xx x.xx
phe CB CA N xxx.xx x.xx
phe CA CB CG xxx.xx x.xx
phe CB CG CD1 xxx.xx x.xx
phe CB CG CD2 xxx.xx x.xx
phe CD1 CG CD2 xxx.xx x.xx
phe CG CD1 CE1 xxx.xx x.xx
phe CD1 CE1 CZ xxx.xx x.xx
phe CE1 CZ CE2 xxx.xx x.xx
phe CZ CE2 CD2 xxx.xx x.xx
phe CG CD2 CE2 xxx.xx x.xx
val N CA C xxx.xx x.xx
val CA C O xxx.xx x.xx
val CB CA C xxx.xx x.xx
val CB CA N xxx.xx x.xx
val CA CB CG1 xxx.xx x.xx
val CA CB CG2 xxx.xx x.xx
val CG1 CB CG2 xxx.xx x.xx
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_comp_angle.atom_id_1
_item_description.description
; The ID of the first of the three atoms that define the angle.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_angle.atom_id_1'
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_comp_angle.atom_id_2'
'_chem_comp_angle.atom_id_3'
save_
save__chem_comp_angle.atom_id_2
_item_description.description
; The ID of the second of the three atoms that define the angle.
The second atom is taken to be the apex of the angle.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_angle.atom_id_2'
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_comp_angle.atom_id_1'
'_chem_comp_angle.atom_id_3'
save_
save__chem_comp_angle.atom_id_3
_item_description.description
; The ID of the third of the three atoms that define the angle.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_angle.atom_id_3'
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_comp_angle.atom_id_1'
'_chem_comp_angle.atom_id_2'
save_
save__chem_comp_angle.comp_id
_item_description.description
; This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_chem_comp_angle.comp_id'
_item.mandatory_code yes
save_
save__chem_comp_angle.value_angle
_item_description.description
; The value that should be taken as the target value for the angle
associated with the specified atoms, expressed in degrees.
;
_item.name '_chem_comp_angle.value_angle'
_item.category_id chem_comp_angle
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 0.0
0.0 0.0
_item_related.related_name '_chem_comp_angle.value_angle_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code degrees
save_
save__chem_comp_angle.value_angle_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_comp_angle.value_angle.
;
_item.name '_chem_comp_angle.value_angle_esd'
_item.category_id chem_comp_angle
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 0.0
0.0 0.0
_item_related.related_name '_chem_comp_angle.value_angle'
_item_related.function_code associated_value
_item_type.code float
_item_units.code degrees
save_
save__chem_comp_angle.value_dist
_item_description.description
; The value that should be taken as the target value for the angle
associated with the specified atoms, expressed as the distance
between the atoms specified by _chem_comp_angle.atom_id_1 and
_chem_comp_angle.atom_id_3.
;
_item.name '_chem_comp_angle.value_dist'
_item.category_id chem_comp_angle
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_comp_angle.value_dist_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__chem_comp_angle.value_dist_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_comp_angle.value_dist.
;
_item.name '_chem_comp_angle.value_dist_esd'
_item.category_id chem_comp_angle
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_comp_angle.value_dist'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
####################
## CHEM_COMP_ATOM ##
####################
save_chem_comp_atom
_category.description
; Data items in the CHEM_COMP_ATOM category record details about
the atoms in a chemical component. Specifying the atomic
coordinates for the components in this category is an
alternative to specifying the structure of the component
via bonds, angles, planes etc. in the appropriate
CHEM_COMP subcategories.
;
_category.id chem_comp_atom
_category.mandatory_code no
loop_
_category_key.name '_chem_comp_atom.comp_id'
'_chem_comp_atom.atom_id'
loop_
_category_group.id 'inclusive_group'
'chem_comp_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.substruct_code
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
phe N N main 1.20134 0.84658 0.00000
phe CA C main 0.00000 0.00000 0.00000
phe C C main -1.25029 0.88107 0.00000
phe O O main -2.18525 0.66029 -0.78409
phe CB C side 0.00662 -1.03603 1.11081
phe CG C side 0.03254 -0.49711 2.50951
phe CD1 C side -1.15813 -0.12084 3.13467
phe CE1 C side -1.15720 0.38038 4.42732
phe CZ C side 0.05385 0.51332 5.11032
phe CE2 C side 1.26137 0.11613 4.50975
phe CD2 C side 1.23668 -0.38351 3.20288
val N N main 1.20134 0.84658 0.00000
val CA C main 0.00000 0.00000 0.00000
val C C main -1.25029 0.88107 0.00000
val O O main -2.18525 0.66029 -0.78409
val CB C side 0.05260 -0.99339 1.17429
val CG1 C side -0.13288 -0.31545 2.52668
val CG2 C side -0.94265 -2.12930 0.99811
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_comp_atom.alt_atom_id
_item_description.description
; An alternative identifier for the atom. This data item would be
used in cases where alternative nomenclatures exist for labelling
atoms in a group.
;
_item.name '_chem_comp_atom.alt_atom_id'
_item.category_id chem_comp_atom
_item.mandatory_code no
_item_type.code line
save_
save__chem_comp_atom.atom_id
_item_description.description
; The value of _chem_comp_atom.atom_id must uniquely identify
each atom in each monomer in the CHEM_COMP_ATOM list.
The atom identifiers need not be unique over all atoms in the
data block; they need only be unique for each atom in a
component.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chem_comp_atom.atom_id' chem_comp_atom yes
'_atom_site.label_atom_id' atom_site no
'_chem_comp_angle.atom_id_1' chem_comp_angle yes
'_chem_comp_angle.atom_id_2' chem_comp_angle yes
'_chem_comp_angle.atom_id_3' chem_comp_angle yes
'_chem_comp_bond.atom_id_1' chem_comp_bond yes
'_chem_comp_bond.atom_id_2' chem_comp_bond yes
'_chem_comp_chir.atom_id' chem_comp_chir yes
'_chem_comp_chir_atom.atom_id' chem_comp_chir_atom yes
'_chem_comp_plane_atom.atom_id' chem_comp_plane_atom yes
'_chem_comp_tor.atom_id_1' chem_comp_tor yes
'_chem_comp_tor.atom_id_2' chem_comp_tor yes
'_chem_comp_tor.atom_id_3' chem_comp_tor yes
'_chem_comp_tor.atom_id_4' chem_comp_tor yes
'_geom_angle.atom_site_label_atom_id_1' geom_angle no
'_geom_angle.atom_site_label_atom_id_2' geom_angle no
'_geom_angle.atom_site_label_atom_id_3' geom_angle no
'_geom_bond.atom_site_label_atom_id_1' geom_bond no
'_geom_bond.atom_site_label_atom_id_2' geom_bond no
'_geom_contact.atom_site_label_atom_id_1' geom_contact no
'_geom_contact.atom_site_label_atom_id_2' geom_contact no
'_geom_hbond.atom_site_label_atom_id_A' geom_hbond no
'_geom_hbond.atom_site_label_atom_id_D' geom_hbond no
'_geom_hbond.atom_site_label_atom_id_H' geom_hbond no
'_geom_torsion.atom_site_label_atom_id_1' geom_torsion no
'_geom_torsion.atom_site_label_atom_id_2' geom_torsion no
'_geom_torsion.atom_site_label_atom_id_3' geom_torsion no
'_geom_torsion.atom_site_label_atom_id_4' geom_torsion no
'_struct_conn.ptnr1_label_atom_id' struct_conn yes
'_struct_conn.ptnr2_label_atom_id' struct_conn yes
'_struct_sheet_hbond.range_1_beg_label_atom_id'
struct_sheet_hbond yes
'_struct_sheet_hbond.range_1_end_label_atom_id'
struct_sheet_hbond yes
'_struct_sheet_hbond.range_2_beg_label_atom_id'
struct_sheet_hbond yes
'_struct_sheet_hbond.range_2_end_label_atom_id'
struct_sheet_hbond yes
'_struct_site_gen.label_atom_id' struct_site_gen yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_atom_id' '_chem_comp_atom.atom_id'
'_chem_comp_angle.atom_id_1' '_chem_comp_atom.atom_id'
'_chem_comp_angle.atom_id_2' '_chem_comp_atom.atom_id'
'_chem_comp_angle.atom_id_3' '_chem_comp_atom.atom_id'
'_chem_comp_bond.atom_id_1' '_chem_comp_atom.atom_id'
'_chem_comp_bond.atom_id_2' '_chem_comp_atom.atom_id'
'_chem_comp_chir.atom_id' '_chem_comp_atom.atom_id'
'_chem_comp_chir_atom.atom_id' '_chem_comp_atom.atom_id'
'_chem_comp_plane_atom.atom_id' '_chem_comp_atom.atom_id'
'_chem_comp_tor.atom_id_1' '_chem_comp_atom.atom_id'
'_chem_comp_tor.atom_id_2' '_chem_comp_atom.atom_id'
'_chem_comp_tor.atom_id_3' '_chem_comp_atom.atom_id'
'_chem_comp_tor.atom_id_4' '_chem_comp_atom.atom_id'
'_geom_angle.atom_site_label_atom_id_1' '_atom_site.label_atom_id'
'_geom_angle.atom_site_label_atom_id_2' '_atom_site.label_atom_id'
'_geom_angle.atom_site_label_atom_id_3' '_atom_site.label_atom_id'
'_geom_bond.atom_site_label_atom_id_1' '_atom_site.label_atom_id'
'_geom_bond.atom_site_label_atom_id_2' '_atom_site.label_atom_id'
'_geom_contact.atom_site_label_atom_id_1' '_atom_site.label_atom_id'
'_geom_contact.atom_site_label_atom_id_2' '_atom_site.label_atom_id'
'_geom_hbond.atom_site_label_atom_id_A' '_atom_site.label_atom_id'
'_geom_hbond.atom_site_label_atom_id_D' '_atom_site.label_atom_id'
'_geom_hbond.atom_site_label_atom_id_H' '_atom_site.label_atom_id'
'_geom_torsion.atom_site_label_atom_id_1' '_atom_site.label_atom_id'
'_geom_torsion.atom_site_label_atom_id_2' '_atom_site.label_atom_id'
'_geom_torsion.atom_site_label_atom_id_3' '_atom_site.label_atom_id'
'_geom_torsion.atom_site_label_atom_id_4' '_atom_site.label_atom_id'
'_struct_conn.ptnr1_label_atom_id' '_atom_site.label_atom_id'
'_struct_conn.ptnr2_label_atom_id' '_atom_site.label_atom_id'
'_struct_sheet_hbond.range_1_beg_label_atom_id'
'_atom_site.label_atom_id'
'_struct_sheet_hbond.range_1_end_label_atom_id'
'_atom_site.label_atom_id'
'_struct_sheet_hbond.range_2_beg_label_atom_id'
'_atom_site.label_atom_id'
'_struct_sheet_hbond.range_2_end_label_atom_id'
'_atom_site.label_atom_id'
'_struct_site_gen.label_atom_id' '_atom_site.label_atom_id'
_item_type.code atcode
save_
save__chem_comp_atom.charge
_item_description.description
; The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
;
_item.name '_chem_comp_atom.charge'
_item.category_id chem_comp_atom
_item.mandatory_code no
_item_default.value 0
loop_
_item_range.maximum
_item_range.minimum 8 8
8 -8
-8 -8
_item_type.code int
loop_
_item_examples.case
_item_examples.detail 1 'for an ammonium nitrogen'
-1 'for a chloride ion'
save_
save__chem_comp_atom.model_Cartn_x
_item_description.description
; The x component of the coordinates for this atom in this
component specified as orthogonal angstroms. The choice of
reference axis frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, not to atom sites in the ATOM_SITE
list.
;
_item.name '_chem_comp_atom.model_Cartn_x'
_item.category_id chem_comp_atom
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_chem_comp_atom.model_Cartn_y'
'_chem_comp_atom.model_Cartn_z'
_item_related.related_name '_chem_comp_atom.model_Cartn_x_esd'
_item_related.function_code associated_esd
_item_sub_category.id cartesian_coordinate
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__chem_comp_atom.model_Cartn_x_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_comp_atom.model_Cartn_x.
;
_item.name '_chem_comp_atom.model_Cartn_x_esd'
_item.category_id chem_comp_atom
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_chem_comp_atom.model_Cartn_y_esd'
'_chem_comp_atom.model_Cartn_z_esd'
_item_related.related_name '_chem_comp_atom.model_Cartn_x'
_item_related.function_code associated_value
_item_sub_category.id cartesian_coordinate_esd
_item_type.code float
_item_units.code angstroms
save_
save__chem_comp_atom.model_Cartn_y
_item_description.description
; The y component of the coordinates for this atom in this
component specified as orthogonal angstroms. The choice of
reference axis frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, not to atom sites in the ATOM_SITE
list.
;
_item.name '_chem_comp_atom.model_Cartn_y'
_item.category_id chem_comp_atom
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_chem_comp_atom.model_Cartn_x'
'_chem_comp_atom.model_Cartn_z'
_item_related.related_name '_chem_comp_atom.model_Cartn_y_esd'
_item_related.function_code associated_esd
_item_sub_category.id cartesian_coordinate
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__chem_comp_atom.model_Cartn_y_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_comp_atom.model_Cartn_y.
;
_item.name '_chem_comp_atom.model_Cartn_y_esd'
_item.category_id chem_comp_atom
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_chem_comp_atom.model_Cartn_x_esd'
'_chem_comp_atom.model_Cartn_z_esd'
_item_related.related_name '_chem_comp_atom.model_Cartn_y'
_item_related.function_code associated_value
_item_sub_category.id cartesian_coordinate_esd
_item_type.code float
_item_units.code angstroms
save_
save__chem_comp_atom.model_Cartn_z
_item_description.description
; The z component of the coordinates for this atom in this
component specified as orthogonal angstroms. The choice of
reference axis frame for the coordinates is arbitrary.
The set of coordinates input for the entity here is intended to
correspond to the atomic model used to generate restraints for
structure refinement, not to atom sites in the ATOM_SITE
list.
;
_item.name '_chem_comp_atom.model_Cartn_z'
_item.category_id chem_comp_atom
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_chem_comp_atom.model_Cartn_x'
'_chem_comp_atom.model_Cartn_y'
_item_related.related_name '_chem_comp_atom.model_Cartn_z_esd'
_item_related.function_code associated_esd
_item_sub_category.id cartesian_coordinate
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__chem_comp_atom.model_Cartn_z_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_comp_atom.model_Cartn_z.
;
_item.name '_chem_comp_atom.model_Cartn_z_esd'
_item.category_id chem_comp_atom
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_chem_comp_atom.model_Cartn_x_esd'
'_chem_comp_atom.model_Cartn_y_esd'
_item_related.related_name '_chem_comp_atom.model_Cartn_z'
_item_related.function_code associated_value
_item_sub_category.id cartesian_coordinate_esd
_item_type.code float
_item_units.code angstroms
save_
save__chem_comp_atom.comp_id
_item_description.description
; This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_chem_comp_atom.comp_id'
_item.mandatory_code yes
save_
save__chem_comp_atom.partial_charge
_item_description.description
; The partial charge assigned to this atom.
;
_item.name '_chem_comp_atom.partial_charge'
_item.category_id chem_comp_atom
_item.mandatory_code no
_item_type.code float
save_
save__chem_comp_atom.substruct_code
_item_description.description
; This data item assigns the atom to a substructure of the
component, if appropriate.
;
_item.name '_chem_comp_atom.substruct_code'
_item.category_id chem_comp_atom
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail main 'main chain of an amino acid'
side 'side chain of an amino acid'
base 'base of a nucleic acid'
phos 'phosphate of a nucleic acid'
sugar 'sugar of a nucleic acid'
none 'not appropriate for this monomer'
save_
#save_chem_comp_atom.type_energy
# _item_description.description
#; This data item is a pointer to _atom_type_energy.type in the
# ATOM_TYPE_ENERGY category.
#;
# save_
save__chem_comp_atom.type_symbol
_item_description.description
; This data item is a pointer to _atom_type.symbol in the
ATOM_TYPE category.
;
_item.name '_chem_comp_atom.type_symbol'
_item.mandatory_code yes
save_
####################
## CHEM_COMP_BOND ##
####################
save_chem_comp_bond
_category.description
; Data items in the CHEM_COMP_BOND category record details about
the bonds between atoms in a chemical component. Target values
may be specified as bond orders, as a distance between the two
atoms, or both.
;
_category.id chem_comp_bond
_category.mandatory_code no
loop_
_category_key.name '_chem_comp_bond.comp_id'
'_chem_comp_bond.atom_id_1'
'_chem_comp_bond.atom_id_2'
loop_
_category_group.id 'inclusive_group'
'chem_comp_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
phe N CA sing
phe CA C sing
phe C O doub
phe CB CA sing
phe CB CG sing
phe CG CD1 arom
phe CD1 CE1 arom
phe CE1 CZ arom
phe CZ CE2 arom
phe CE2 CD2 arom
phe CD2 CG arom
val N CA sing
val CA C sing
val C O doub
val CB CA sing
val CB CG1 sing
val CB CG2 sing
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_comp_bond.atom_id_1
_item_description.description
; The ID of the first of the two atoms that define the bond.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_bond.atom_id_1'
_item.mandatory_code yes
_item_dependent.dependent_name
'_chem_comp_bond.atom_id_2'
save_
save__chem_comp_bond.atom_id_2
_item_description.description
; The ID of the second of the two atoms that define the bond.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_bond.atom_id_2'
_item.mandatory_code yes
_item_dependent.dependent_name
'_chem_comp_bond.atom_id_1'
save_
save__chem_comp_bond.comp_id
_item_description.description
; This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_chem_comp_bond.comp_id'
_item.mandatory_code yes
save_
save__chem_comp_bond.value_order
_item_description.description
; The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a bond
order.
;
_item.name '_chem_comp_bond.value_order'
_item.category_id chem_comp_bond
_item.mandatory_code no
_item_default.value sing
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail sing 'single bond'
doub 'double bond'
trip 'triple bond'
quad 'quadruple bond'
arom 'aromatic bond'
poly 'polymeric bond'
delo 'delocalized double bond'
pi 'pi bond'
save_
save__chem_comp_bond.value_dist
_item_description.description
; The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a
distance.
;
_item.name '_chem_comp_bond.value_dist'
_item.category_id chem_comp_bond
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_comp_bond.value_dist_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__chem_comp_bond.value_dist_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_comp_bond.value_dist.
;
_item.name '_chem_comp_bond.value_dist_esd'
_item.category_id chem_comp_bond
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_comp_bond.value_dist'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
####################
## CHEM_COMP_CHIR ##
####################
save_chem_comp_chir
_category.description
; Data items in the CHEM_COMP_CHIR category provide details about
the chiral centres in a chemical component. The atoms bonded
to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM
category.
;
_category.id chem_comp_chir
_category.mandatory_code no
loop_
_category_key.name '_chem_comp_chir.comp_id'
'_chem_comp_chir.id'
loop_
_category_group.id 'inclusive_group'
'chem_comp_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id
phe phe1 CA
val val1 CA
# - - - - data truncated for brevity - - - -
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_comp_chir.atom_id
_item_description.description
; The ID of the atom that is a chiral centre.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_chir.atom_id'
_item.mandatory_code yes
save_
save__chem_comp_chir.atom_config
_item_description.description
; The chiral configuration of the atom that is a chiral centre.
;
_item.name '_chem_comp_chir.atom_config'
_item.category_id chem_comp_chir
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail R 'absolute configuration R'
S 'absolute configuration S'
save_
save__chem_comp_chir.id
_item_description.description
; The value of _chem_comp_chir.id must uniquely identify a record
in the CHEM_COMP_CHIR list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chem_comp_chir.id' chem_comp_chir yes
'_chem_comp_chir_atom.chir_id' chem_comp_chir_atom yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_chem_comp_chir_atom.chir_id' '_chem_comp_chir.id'
_item_type.code code
save_
save__chem_comp_chir.comp_id
_item_description.description
; This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_chem_comp_chir.comp_id'
_item.mandatory_code yes
save_
save__chem_comp_chir.number_atoms_all
_item_description.description
; The total number of atoms bonded to the atom specified by
_chem_comp_chir.atom_id.
;
_item.name '_chem_comp_chir.number_atoms_all'
_item.category_id chem_comp_chir
_item.mandatory_code no
_item_type.code int
save_
save__chem_comp_chir.number_atoms_nh
_item_description.description
; The number of non-hydrogen atoms bonded to the atom specified by
_chem_comp_chir.atom_id.
;
_item.name '_chem_comp_chir.number_atoms_nh'
_item.category_id chem_comp_chir
_item.mandatory_code no
_item_type.code int
save_
save__chem_comp_chir.volume_flag
_item_description.description
; A flag to indicate whether a chiral volume should match the
standard value in both magnitude and sign, or in magnitude only.
;
_item.name '_chem_comp_chir.volume_flag'
_item.category_id chem_comp_chir
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail sign 'match magnitude and sign'
nosign 'match magnitude only'
save_
save__chem_comp_chir.volume_three
_item_description.description
; The chiral volume, V~c~, for chiral centres that involve a chiral
atom bonded to three non-hydrogen atoms and one hydrogen atom.
V~c~ = V1 * (V2 X V3)
V1 = the vector distance from the atom specified by
_chem_comp_chir.atom_id to the first atom in the
CHEM_COMP_CHIR_ATOM list
V2 = the vector distance from the atom specified by
_chem_comp_chir.atom_id to the second atom in the
CHEM_COMP_CHIR_ATOM list
V3 = the vector distance from the atom specified by
_chem_comp_chir.atom_id to the third atom in the
CHEM_COMP_CHIR_ATOM list
* = the vector dot product
X = the vector cross product
;
_item.name '_chem_comp_chir.volume_three'
_item.category_id chem_comp_chir
_item.mandatory_code no
_item_related.related_name '_chem_comp_chir.volume_three_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_cubed
save_
save__chem_comp_chir.volume_three_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_comp_chir.volume_three.
;
_item.name '_chem_comp_chir.volume_three_esd'
_item.category_id chem_comp_chir
_item.mandatory_code no
_item_related.related_name '_chem_comp_chir.volume_three'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms_cubed
save_
#########################
## CHEM_COMP_CHIR_ATOM ##
#########################
save_chem_comp_chir_atom
_category.description
; Data items in the CHEM_COMP_CHIR_ATOM category enumerate the
atoms bonded to a chiral atom within a chemical component.
;
_category.id chem_comp_chir_atom
_category.mandatory_code no
loop_
_category_key.name '_chem_comp_chir_atom.chir_id'
'_chem_comp_chir_atom.atom_id'
'_chem_comp_chir_atom.comp_id'
loop_
_category_group.id 'inclusive_group'
'chem_comp_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_chem_comp_chir_atom.comp_id
_chem_comp_chir_atom.chir_id
_chem_comp_chir_atom.atom_id
phe 1 N
phe 1 C
phe 1 CB
val 1 N
val 1 C
val 1 CB
# - - - - data truncated for brevity - - - -
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_comp_chir_atom.atom_id
_item_description.description
; The ID of an atom bonded to the chiral atom.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_chir_atom.atom_id'
_item.mandatory_code yes
save_
save__chem_comp_chir_atom.chir_id
_item_description.description
; This data item is a pointer to _chem_comp_chir.id in the
CHEM_COMP_CHIR category.
;
_item.name '_chem_comp_chir_atom.chir_id'
_item.mandatory_code yes
save_
save__chem_comp_chir_atom.comp_id
_item_description.description
; This data item is a pointer to _chem_comp.id in the
CHEM_COMP category.
;
_item.name '_chem_comp_chir_atom.comp_id'
_item.mandatory_code yes
save_
save__chem_comp_chir_atom.dev
_item_description.description
; The standard uncertainty (estimated standard deviation)
of the position of this atom from the plane defined by
all of the atoms in the plane.
;
_item.name '_chem_comp_chir_atom.dev'
_item.category_id chem_comp_chir_atom
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
####################
## CHEM_COMP_LINK ##
####################
save_chem_comp_link
_category.description
; Data items in the CHEM_COMP_LINK category give details about
the links between chemical components.
;
_category.id chem_comp_link
_category.mandatory_code no
_category_key.name '_chem_comp_link.link_id'
loop_
_category_group.id 'inclusive_group'
'chem_link_group'
# loop_
# _category_examples.detail
# _category_examples.case
# # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# ;
# Example 1 - from nucleotide external reference dictionary Nucleic
# Database Project 1997.
# ;
# ;
# _chem_comp_link.link_id ribose_adenine
# _chem_comp_link.type_comp_1 ribose
# _chem_comp_link.type_comp_2 adenine
# _chem_comp_link.details
# ;
# Defines the linkage between adenine base and ribose sugar
# ;
# ;
# # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_comp_link.link_id
_item_description.description
; This data item is a pointer to _chem_link.id in the
CHEM_LINK category.
;
_item.name '_chem_comp_link.link_id'
_item.mandatory_code yes
save_
save__chem_comp_link.details
_item_description.description
; A description of special aspects of a link between
chemical components in the structure.
;
_item.name '_chem_comp_link.details'
_item.category_id chem_comp_link
_item.mandatory_code no
_item_type.code text
save_
save__chem_comp_link.type_comp_1
_item_description.description
; The type of the first of the two components joined by the
link.
This data item is a pointer to _chem_comp.type in the CHEM_COMP
category.
;
_item.name '_chem_comp_link.type_comp_1'
_item.mandatory_code yes
save_
save__chem_comp_link.type_comp_2
_item_description.description
; The type of the second of the two components joined by the
link.
This data item is a pointer to _chem_comp.type in the CHEM_COMP
category.
;
_item.name '_chem_comp_link.type_comp_2'
_item.mandatory_code yes
save_
#####################
## CHEM_COMP_PLANE ##
#####################
save_chem_comp_plane
_category.description
; Data items in the CHEM_COMP_PLANE category provide identifiers
for the planes in a chemical component. The atoms in the plane
are specified in the CHEM_COMP_PLANE_ATOM category.
;
_category.id chem_comp_plane
_category.mandatory_code no
loop_
_category_key.name '_chem_comp_plane.comp_id'
'_chem_comp_plane.id'
loop_
_category_group.id 'inclusive_group'
'chem_comp_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_chem_comp_plane.comp_id
_chem_comp_plane.id
phe phe1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_comp_plane.id
_item_description.description
; The value of _chem_comp_plane.id must uniquely identify a record
in the CHEM_COMP_PLANE list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chem_comp_plane.id' chem_comp_plane yes
'_chem_comp_plane_atom.plane_id' chem_comp_plane_atom yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_chem_comp_plane_atom.plane_id' '_chem_comp_plane.id'
_item_type.code code
save_
save__chem_comp_plane.comp_id
_item_description.description
; This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_chem_comp_plane.comp_id'
_item.mandatory_code yes
save_
save__chem_comp_plane.number_atoms_all
_item_description.description
; The total number of atoms in the plane.
;
_item.name '_chem_comp_plane.number_atoms_all'
_item.category_id chem_comp_plane
_item.mandatory_code no
_item_type.code int
save_
save__chem_comp_plane.number_atoms_nh
_item_description.description
; The number of non-hydrogen atoms in the plane.
;
_item.name '_chem_comp_plane.number_atoms_nh'
_item.category_id chem_comp_plane
_item.mandatory_code no
_item_type.code int
save_
##########################
## CHEM_COMP_PLANE_ATOM ##
##########################
save_chem_comp_plane_atom
_category.description
; Data items in the CHEM_COMP_PLANE_ATOM category enumerate the
atoms in a plane within a chemical component.
;
_category.id chem_comp_plane_atom
_category.mandatory_code no
loop_
_category_key.name '_chem_comp_plane_atom.plane_id'
'_chem_comp_plane_atom.atom_id'
'_chem_comp_plane_atom.comp_id'
loop_
_category_group.id 'inclusive_group'
'chem_comp_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.atom_id
phe1 phe CB
phe1 phe CG
phe1 phe CD1
phe1 phe CE1
phe1 phe CZ
phe1 phe CE2
phe1 phe CD2
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_comp_plane_atom.atom_id
_item_description.description
; The ID of an atom involved in the plane.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_plane_atom.atom_id'
_item.mandatory_code yes
save_
save__chem_comp_plane_atom.comp_id
_item_description.description
; This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_chem_comp_plane_atom.comp_id'
_item.mandatory_code yes
save_
save__chem_comp_plane_atom.plane_id
_item_description.description
; This data item is a pointer to _chem_comp_plane.id in the
CHEM_COMP_PLANE category.
;
_item.name '_chem_comp_plane_atom.plane_id'
_item.mandatory_code yes
save_
save__chem_comp_plane_atom.dist_esd
_item_description.description
; This data item is the standard deviation of the
out-of-plane distance for this atom.
;
_item.name '_chem_comp_plane_atom.dist_esd'
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
####################
## CHEM_COMP_TOR ##
####################
save_chem_comp_tor
_category.description
; Data items in the CHEM_COMP_TOR category record details about
the torsion angles in a chemical component. As torsion angles
can have more than one target value, the target values are
specified in the CHEM_COMP_TOR_VALUE category.
;
_category.id chem_comp_tor
_category.mandatory_code no
loop_
_category_key.name '_chem_comp_tor.comp_id'
'_chem_comp_tor.id'
loop_
_category_group.id 'inclusive_group'
'chem_comp_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
phe phe_chi1 N CA CB CG
phe phe_chi2 CA CB CG CD1
phe phe_ring1 CB CG CD1 CE1
phe phe_ring2 CB CG CD2 CE2
phe phe_ring3 CG CD1 CE1 CZ
phe phe_ring4 CD1 CE1 CZ CE2
phe phe_ring5 CE1 CZ CE2 CD2
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_comp_tor.atom_id_1
_item_description.description
; The ID of the first of the four atoms that define the torsion
angle.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_tor.atom_id_1'
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_comp_tor.atom_id_2'
'_chem_comp_tor.atom_id_3'
'_chem_comp_tor.atom_id_4'
save_
save__chem_comp_tor.atom_id_2
_item_description.description
; The ID of the second of the four atoms that define the torsion
angle.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_tor.atom_id_2'
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_comp_tor.atom_id_1'
'_chem_comp_tor.atom_id_3'
'_chem_comp_tor.atom_id_4'
save_
save__chem_comp_tor.atom_id_3
_item_description.description
; The ID of the third of the four atoms that define the torsion
angle.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_tor.atom_id_3'
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_comp_tor.atom_id_1'
'_chem_comp_tor.atom_id_2'
'_chem_comp_tor.atom_id_4'
save_
save__chem_comp_tor.atom_id_4
_item_description.description
; The ID of the fourth of the four atoms that define the torsion
angle.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_tor.atom_id_4'
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_comp_tor.atom_id_1'
'_chem_comp_tor.atom_id_2'
'_chem_comp_tor.atom_id_3'
save_
save__chem_comp_tor.id
_item_description.description
; The value of _chem_comp_tor.id must uniquely identify a
record in the CHEM_COMP_TOR list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chem_comp_tor.id' chem_comp_tor yes
'_chem_comp_tor_value.tor_id' chem_comp_tor_value yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_chem_comp_tor_value.tor_id' '_chem_comp_tor.id'
_item_type.code code
save_
save__chem_comp_tor.comp_id
_item_description.description
; This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_chem_comp_tor.comp_id'
_item.mandatory_code yes
save_
##########################
## CHEM_COMP_TOR_VALUE ##
##########################
save_chem_comp_tor_value
_category.description
; Data items in the CHEM_COMP_TOR_VALUE category record details
about the target values for the torsion angles enumerated in the
CHEM_COMP_TOR list. Target values may be specified as angles
in degrees, as a distance between the first and fourth atoms, or
both.
;
_category.id chem_comp_tor_value
_category.mandatory_code no
loop_
_category_key.name '_chem_comp_tor_value.tor_id'
'_chem_comp_tor_value.comp_id'
loop_
_category_group.id 'inclusive_group'
'chem_comp_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_chem_comp_tor_value.tor_id
_chem_comp_tor_value.comp_id
_chem_comp_tor_value.angle
_chem_comp_tor_value.dist
phe_chi1 phe -60.0 2.88
phe_chi1 phe 180.0 3.72
phe_chi1 phe 60.0 2.88
phe_chi2 phe 90.0 3.34
phe_chi2 phe -90.0 3.34
phe_ring1 phe 180.0 3.75
phe_ring2 phe 180.0 3.75
phe_ring3 phe 0.0 2.80
phe_ring4 phe 0.0 2.80
phe_ring5 phe 0.0 2.80
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_comp_tor_value.comp_id
_item_description.description
; This data item is a pointer to _chem_comp_atom.comp_id in the
CHEM_COMP_ATOM category.
;
_item.name '_chem_comp_tor_value.comp_id'
_item.mandatory_code yes
save_
save__chem_comp_tor_value.tor_id
_item_description.description
; This data item is a pointer to _chem_comp_tor.id in the
CHEM_COMP_TOR category.
;
_item.name '_chem_comp_tor_value.tor_id'
_item.mandatory_code yes
save_
save__chem_comp_tor_value.angle
_item_description.description
; A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed in
degrees.
;
_item.name '_chem_comp_tor_value.angle'
_item.category_id chem_comp_tor_value
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 -180.0
-180.0 -180.0
_item_related.related_name '_chem_comp_tor_value.angle_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code degrees
save_
save__chem_comp_tor_value.angle_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_comp_tor_value.angle.
;
_item.name '_chem_comp_tor_value.angle_esd'
_item.category_id chem_comp_tor_value
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 -180.0
-180.0 -180.0
_item_related.related_name '_chem_comp_tor_value.angle'
_item_related.function_code associated_value
_item_type.code float
_item_units.code degrees
save_
save__chem_comp_tor_value.dist
_item_description.description
; A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed as
the distance between the atoms specified by
_chem_comp_tor.atom_id_1 and _chem_comp_tor.atom_id_4 in the
referenced record in the CHEM_COMP_TOR list. Note that the
torsion angle cannot be fully specified by a distance (for
instance, a torsion angle of -60 degree will yield the same
distance as a 60 degree angle). However, the distance
specification can be useful for refinement in situations
in which the angle is already close to the desired value.
;
_item.name '_chem_comp_tor_value.dist'
_item.category_id chem_comp_tor_value
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_comp_tor_value.dist_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__chem_comp_tor_value.dist_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_comp_tor_value.dist.
;
_item.name '_chem_comp_tor_value.dist_esd'
_item.category_id chem_comp_tor_value
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_comp_tor_value.dist'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
###############
## CHEM_LINK ##
###############
save_chem_link
_category.description
; Data items in the CHEM_LINK category give details about
the links between chemical components.
;
_category.id chem_link
_category.mandatory_code no
_category_key.name '_chem_link.id'
loop_
_category_group.id 'inclusive_group'
'chem_link_group'
save_
save__chem_link.id
_item_description.description
; The value of _chem_link.id must uniquely identify each
item in the CHEM_LINK list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chem_link.id' chem_link yes
'_chem_link_angle.link_id' chem_link_angle yes
'_chem_link_bond.link_id' chem_link_bond yes
'_chem_link_chir.link_id' chem_link_chir yes
'_chem_link_plane.link_id' chem_link_plane yes
'_chem_link_tor.link_id' chem_link_tor yes
'_chem_comp_link.link_id' chem_comp_link yes
'_entity_link.link_id' entity_link yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_chem_link_angle.link_id' '_chem_link.id'
'_chem_link_bond.link_id' '_chem_link.id'
'_chem_link_chir.link_id' '_chem_link.id'
'_chem_link_plane.link_id' '_chem_link.id'
'_chem_link_tor.link_id' '_chem_link.id'
'_chem_comp_link.link_id' '_chem_link.id'
'_entity_link.link_id' '_chem_link.id'
_item_type.code code
loop_
_item_examples.case 'peptide'
'oligosaccharide 1,4'
'DNA'
save_
save__chem_link.details
_item_description.description
; A description of special aspects of a link between
chemical components in the structure.
;
_item.name '_chem_link.details'
_item.category_id chem_link
_item.mandatory_code no
_item_type.code text
save_
#####################
## CHEM_LINK_ANGLE ##
#####################
save_chem_link_angle
_category.description
; Data items in the CHEM_LINK_ANGLE category record details
about angles in a link between chemical components.
;
_category.id chem_link_angle
_category.mandatory_code no
loop_
_category_key.name '_chem_link_angle.link_id'
'_chem_link_angle.atom_id_1'
'_chem_link_angle.atom_id_2'
'_chem_link_angle.atom_id_3'
loop_
_category_group.id 'inclusive_group'
'chem_link_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47,
392-400] as interpreted by J. P. Priestle (1995). Consistent
Stereochemical Dictionaries for Refinement and Model
Building. CCP4 Daresbury Study Weekend,
DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury
Laboratory.
;
;
loop_
_chem_link_angle.link_id
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
_chem_link_angle.atom_id_1
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.atom_3_comp_id
PEPTIDE 111.2 2.8 N 1 CA 1 C 1
PEPTIDE 120.8 1.7 CA 1 C 1 O 1
PEPTIDE 116.2 2.0 CA 1 C 1 N 2
PEPTIDE 123.0 1.6 O 1 C 1 N 2
PEPTIDE 121.7 1.8 C 1 N 2 CA 2
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_link_angle.atom_1_comp_id
_item_description.description
; This data item indicates whether atom 1 is found in the first
or the second of the two components connected by the link.
;
_item.name '_chem_link_angle.atom_1_comp_id'
_item.category_id chem_link_angle
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_chem_link_angle.atom_2_comp_id'
'_chem_link_angle.atom_3_comp_id'
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_angle.atom_2_comp_id
_item_description.description
; This data item indicates whether atom 2 is found in the first
or the second of the two components connected by the link.
;
_item.name '_chem_link_angle.atom_2_comp_id'
_item.category_id chem_link_angle
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_chem_link_angle.atom_1_comp_id'
'_chem_link_angle.atom_3_comp_id'
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_angle.atom_3_comp_id
_item_description.description
; This data item indicates whether atom 3 is found in the first
or the second of the two components connected by the link.
;
_item.name '_chem_link_angle.atom_3_comp_id'
_item.category_id chem_link_angle
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_chem_link_angle.atom_1_comp_id'
'_chem_link_angle.atom_2_comp_id'
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_angle.atom_id_1
_item_description.description
; The ID of the first of the three atoms that define the angle.
An atom with this ID must exist in the component of the type
specified by _chem_comp_link.type_comp_1 (or
_chem_comp_link.type_comp_2, where the appropriate data item
is indicated by the value of _chem_comp_angle.atom_1_comp_id).
;
_item.name '_chem_link_angle.atom_id_1'
_item.category_id chem_link_angle
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_link_angle.atom_id_2'
'_chem_link_angle.atom_id_3'
_item_type.code code
save_
save__chem_link_angle.atom_id_2
_item_description.description
; The ID of the second of the three atoms that define the angle.
The second atom is taken to be the apex of the angle.
An atom with this ID must exist in the component of the type
specified by _chem_comp_link.type_comp_1 (or
_chem_comp_link.type_comp_2, where the appropriate data item
is indicated by the value of _chem_comp_angle.atom_2_comp_id).
;
_item.name '_chem_link_angle.atom_id_2'
_item.category_id chem_link_angle
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_link_angle.atom_id_1'
'_chem_link_angle.atom_id_3'
_item_type.code code
save_
save__chem_link_angle.atom_id_3
_item_description.description
; The ID of the third of the three atoms that define the angle.
An atom with this ID must exist in the component of the type
specified by _chem_comp_link.type_comp_1 (or
_chem_comp_link.type_comp_2, where the appropriate data item
is indicated by the value of _chem_comp_angle.atom_3_comp_id).
;
_item.name '_chem_link_angle.atom_id_3'
_item.category_id chem_link_angle
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_link_angle.atom_id_1'
'_chem_link_angle.atom_id_2'
_item_type.code code
save_
save__chem_link_angle.link_id
_item_description.description
; This data item is a pointer to _chem_link.id in the CHEM_LINK
category.
;
_item.name '_chem_link_angle.link_id'
_item.mandatory_code yes
save_
save__chem_link_angle.value_angle
_item_description.description
; The value that should be taken as the target value for the angle
associated with the specified atoms, expressed in degrees.
;
_item.name '_chem_link_angle.value_angle'
_item.category_id chem_link_angle
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 0.0
0.0 0.0
_item_related.related_name '_chem_link_angle.value_angle_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code degrees
save_
save__chem_link_angle.value_angle_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_link_angle.value_angle.
;
_item.name '_chem_link_angle.value_angle_esd'
_item.category_id chem_link_angle
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 0.0
0.0 0.0
_item_related.related_name '_chem_link_angle.value_angle'
_item_related.function_code associated_value
_item_type.code float
_item_units.code degrees
save_
save__chem_link_angle.value_dist
_item_description.description
; The value that should be taken as the target value for the angle
associated with the specified atoms, expressed as the distance
between the atoms specified by _chem_comp_angle.atom_id_1 and
_chem_comp_angle.atom_id_3.
;
_item.name '_chem_link_angle.value_dist'
_item.category_id chem_link_angle
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_link_angle.value_dist_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__chem_link_angle.value_dist_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_comp_angle.value_dist.
;
_item.name '_chem_link_angle.value_dist_esd'
_item.category_id chem_link_angle
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_link_angle.value_dist'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
####################
## CHEM_LINK_BOND ##
####################
save_chem_link_bond
_category.description
; Data items in the CHEM_LINK_BOND category record details about
bonds in a link between components in the chemical structure.
;
_category.id chem_link_bond
_category.mandatory_code no
loop_
_category_key.name '_chem_link_bond.link_id'
'_chem_link_bond.atom_id_1'
'_chem_link_bond.atom_id_2'
loop_
_category_group.id 'inclusive_group'
'chem_link_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47,
392-400] as interpreted by J. P. Priestle (1995). Consistent
Stereochemical Dictionaries for Refinement and Model
Building. CCP4 Daresbury Study Weekend,
DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury
Laboratory.
;
;
loop_
_chem_link_bond.link_id
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
_chem_link_bond.atom_id_1
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.atom_2_comp_id
PEPTIDE 1.458 0.019 N 1 CA 1
PEPTIDE 1.525 0.021 CA 1 C 1
PEPTIDE 1.329 0.014 C 1 N 2
PEPTIDE 1.231 0.020 C 1 O 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chem_link_bond.atom_1_comp_id
_item_description.description
; This data item indicates whether atom 1 is found in the first
or the second of the two components connected by the link.
;
_item.name '_chem_link_bond.atom_1_comp_id'
_item.category_id chem_link_bond
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_chem_link_bond.atom_2_comp_id'
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_bond.atom_2_comp_id
_item_description.description
; This data item indicates whether atom 2 is found in the first
or the second of the two chemical components connected by
the link.
;
_item.name '_chem_link_bond.atom_2_comp_id'
_item.category_id chem_link_bond
_item.mandatory_code no
_item_dependent.dependent_name
'_chem_link_bond.atom_1_comp_id'
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_bond.atom_id_1
_item_description.description
; The ID of the first of the two atoms that define the bond.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the
linkage sense.
;
_item.name '_chem_link_bond.atom_id_1'
_item.category_id chem_link_bond
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_link_bond.atom_id_2'
_item_type.code code
save_
save__chem_link_bond.atom_id_2
_item_description.description
; The ID of the second of the two atoms that define the bond.
As this data item does not point to a specific atom in a
specific component, it is not a child in the linkage sense.
;
_item.name '_chem_link_bond.atom_id_2'
_item.category_id chem_link_bond
_item.mandatory_code yes
_item_dependent.dependent_name
'_chem_link_bond.atom_id_1'
_item_type.code code
save_
save__chem_link_bond.link_id
_item_description.description
; This data item is a pointer to _chem_link.id in the CHEM_LINK
category.
;
_item.name '_chem_link_bond.link_id'
_item.mandatory_code yes
save_
save__chem_link_bond.value_dist
_item_description.description
; The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a
distance.
;
_item.name '_chem_link_bond.value_dist'
_item.category_id chem_link_bond
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_link_bond.value_dist_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__chem_link_bond.value_dist_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_link_bond.value_dist.
;
_item.name '_chem_link_bond.value_dist_esd'
_item.category_id chem_link_bond
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_link_bond.value_dist'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
save__chem_link_bond.value_order
_item_description.description
; The value that should be taken as the target for the chemical
bond associated with the specified atoms, expressed as a bond
order.
;
_item.name '_chem_link_bond.value_order'
_item.category_id chem_link_bond
_item.mandatory_code no
_item_default.value sing
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail sing 'single bond'
doub 'double bond'
trip 'triple bond'
quad 'quadruple bond'
arom 'aromatic bond'
poly 'polymeric bond'
delo 'delocalized double bond'
pi 'pi bond'
save_
####################
## CHEM_LINK_CHIR ##
####################
save_chem_link_chir
_category.description
; Data items in the CHEM_LINK_CHIR category provide details about
the chiral centres in a link between two chemical components.
The atoms bonded to the chiral atom are specified in the
CHEM_LINK_CHIR_ATOM category.
;
_category.id chem_link_chir
_category.mandatory_code no
loop_
_category_key.name '_chem_link_chir.link_id'
'_chem_link_chir.id'
loop_
_category_group.id 'inclusive_group'
'chem_link_group'
save_
save__chem_link_chir.atom_comp_id
_item_description.description
; This data item indicates whether the chiral atom is found in the
first or the second of the two components connected by the
link.
;
_item.name '_chem_link_chir.atom_comp_id'
_item.category_id chem_link_chir
_item.mandatory_code no
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_chir.atom_id
_item_description.description
; The ID of the atom that is a chiral centre.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
;
_item.name '_chem_link_chir.atom_id'
_item.mandatory_code yes
_item_type.code code
save_
save__chem_link_chir.atom_config
_item_description.description
; The chiral configuration of the atom that is a chiral centre.
;
_item.name '_chem_link_chir.atom_config'
_item.category_id chem_link_chir
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail R 'absolute configuration R'
S 'absolute configuration S'
save_
save__chem_link_chir.id
_item_description.description
; The value of _chem_link_chir.id must uniquely identify a record
in the CHEM_LINK_CHIR list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chem_link_chir.id' chem_link_chir yes
'_chem_link_chir_atom.chir_id' chem_link_chir_atom yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_chem_link_chir_atom.chir_id' '_chem_link_chir.id'
_item_type.code code
save_
save__chem_link_chir.link_id
_item_description.description
; This data item is a pointer to _chem_link.id in the CHEM_LINK
category.
;
_item.name '_chem_link_chir.link_id'
_item.mandatory_code yes
save_
save__chem_link_chir.number_atoms_all
_item_description.description
; The total number of atoms bonded to the atom specified by
_chem_link_chir.atom_id.
;
_item.name '_chem_link_chir.number_atoms_all'
_item.category_id chem_link_chir
_item.mandatory_code no
_item_type.code int
save_
save__chem_link_chir.number_atoms_nh
_item_description.description
; The number of non-hydrogen atoms bonded to the atom specified by
_chem_link_chir.atom_id.
;
_item.name '_chem_link_chir.number_atoms_nh'
_item.category_id chem_link_chir
_item.mandatory_code no
_item_type.code int
save_
save__chem_link_chir.volume_flag
_item_description.description
; A flag to indicate whether a chiral volume should match the
standard value in both magnitude and sign, or in magnitude only.
;
_item.name '_chem_link_chir.volume_flag'
_item.category_id chem_link_chir
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail sign 'match magnitude and sign'
nosign 'match magnitude only'
save_
save__chem_link_chir.volume_three
_item_description.description
; The chiral volume, V(c), for chiral centres that involve a chiral
atom bonded to three non-hydrogen atoms and one hydrogen atom.
V~c~ = V1 * (V2 X V3)
V1 = the vector distance from the atom specified by
_chem_link_chir.atom_id to the first atom in the
CHEM_LINK_CHIR_ATOM list
V2 = the vector distance from the atom specified by
_chem_link_chir.atom_id to the second atom in the
CHEM_LINK_CHIR_ATOM list
V3 = the vector distance from the atom specified by
_chem_link_chir.atom_id to the third atom in the
CHEM_LINK_CHIR_ATOM list
* = the vector dot product
X = the vector cross product
;
_item.name '_chem_link_chir.volume_three'
_item.category_id chem_link_chir
_item.mandatory_code no
_item_related.related_name '_chem_link_chir.volume_three_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms_cubed
save_
save__chem_link_chir.volume_three_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_link_chir.volume_three.
;
_item.name '_chem_link_chir.volume_three_esd'
_item.category_id chem_link_chir
_item.mandatory_code no
_item_related.related_name '_chem_link_chir.volume_three'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms_cubed
save_
#########################
## CHEM_LINK_CHIR_ATOM ##
#########################
save_chem_link_chir_atom
_category.description
; Data items in the CHEM_LINK_CHIR_ATOM category enumerate the
atoms bonded to a chiral atom in a link between two
chemical components.
;
_category.id chem_link_chir_atom
_category.mandatory_code no
loop_
_category_key.name '_chem_link_chir_atom.chir_id'
'_chem_link_chir_atom.atom_id'
loop_
_category_group.id 'inclusive_group'
'chem_link_group'
save_
save__chem_link_chir_atom.atom_comp_id
_item_description.description
; This data item indicates whether the atom bonded to a chiral
atom is found in the first or the second of the two components
connected by the link.
;
_item.name '_chem_link_chir_atom.atom_comp_id'
_item.category_id chem_link_chir_atom
_item.mandatory_code no
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_chir_atom.atom_id
_item_description.description
; The ID of an atom bonded to the chiral atom.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
;
_item.name '_chem_link_chir_atom.atom_id'
_item.mandatory_code yes
_item_type.code code
save_
save__chem_link_chir_atom.chir_id
_item_description.description
; This data item is a pointer to _chem_link_chir.id in the
CHEM_LINK_CHIR category.
;
_item.name '_chem_link_chir_atom.chir_id'
_item.mandatory_code yes
save_
save__chem_link_chir_atom.dev
_item_description.description
; The standard uncertainty (estimated standard deviation)
of the position of this atom from the plane defined by
all of the atoms in the plane.
;
_item.name '_chem_link_chir_atom.dev'
_item.category_id chem_link_chir_atom
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
#####################
## CHEM_LINK_PLANE ##
#####################
save_chem_link_plane
_category.description
; Data items in the CHEM_LINK_PLANE category provide identifiers
for the planes in a link between two chemical components.
The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM
category.
;
_category.id chem_link_plane
_category.mandatory_code no
loop_
_category_key.name '_chem_link_plane.link_id'
'_chem_link_plane.id'
loop_
_category_group.id 'inclusive_group'
'chem_link_group'
save_
save__chem_link_plane.id
_item_description.description
; The value of _chem_link_plane.id must uniquely identify a record
in the CHEM_LINK_PLANE list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chem_link_plane.id' chem_link_plane yes
'_chem_link_plane_atom.plane_id' chem_link_plane_atom yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_chem_link_plane_atom.plane_id' '_chem_link_plane.id'
_item_type.code code
save_
save__chem_link_plane.link_id
_item_description.description
; This data item is a pointer to _chem_link.id in the CHEM_LINK
category.
;
_item.name '_chem_link_plane.link_id'
_item.mandatory_code yes
save_
save__chem_link_plane.number_atoms_all
_item_description.description
; The total number of atoms in the plane.
;
_item.name '_chem_link_plane.number_atoms_all'
_item.category_id chem_link_plane
_item.mandatory_code no
_item_type.code int
save_
save__chem_link_plane.number_atoms_nh
_item_description.description
; The number of non-hydrogen atoms in the plane.
;
_item.name '_chem_link_plane.number_atoms_nh'
_item.category_id chem_link_plane
_item.mandatory_code no
_item_type.code int
save_
##########################
## CHEM_LINK_PLANE_ATOM ##
##########################
save_chem_link_plane_atom
_category.description
; Data items in the CHEM_LINK_PLANE_ATOM category enumerate the
atoms in a plane in a link between two chemical components.
;
_category.id chem_link_plane_atom
_category.mandatory_code no
loop_
_category_key.name '_chem_link_plane_atom.plane_id'
'_chem_link_plane_atom.atom_id'
loop_
_category_group.id 'inclusive_group'
'chem_link_group'
save_
save__chem_link_plane_atom.atom_comp_id
_item_description.description
; This data item indicates whether the atom in a plane is found in
the first or the second of the two components connected by the
link.
;
_item.name '_chem_link_plane_atom.atom_comp_id'
_item.category_id chem_link_plane_atom
_item.mandatory_code no
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_plane_atom.atom_id
_item_description.description
; The ID of an atom involved in the plane.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
;
_item.name '_chem_link_plane_atom.atom_id'
_item.mandatory_code yes
_item_type.code code
save_
save__chem_link_plane_atom.plane_id
_item_description.description
; This data item is a pointer to _chem_link_plane.id in the
CHEM_LINK_PLANE category.
;
_item.name '_chem_link_plane_atom.plane_id'
_item.mandatory_code yes
save_
###################
## CHEM_LINK_TOR ##
###################
save_chem_link_tor
_category.description
; Data items in the CHEM_LINK_TOR category record details about
the torsion angles in a link between two chemical components.
As torsion angles can have more than one target value, the
target values are specified in the CHEM_LINK_TOR_VALUE category.
;
_category.id chem_link_tor
_category.mandatory_code no
loop_
_category_key.name '_chem_link_tor.link_id'
'_chem_link_tor.id'
loop_
_category_group.id 'inclusive_group'
'chem_link_group'
save_
save__chem_link_tor.atom_1_comp_id
_item_description.description
; This data item indicates whether atom 1 is found in the first
or the second of the two components connected by the link.
;
_item.name '_chem_link_tor.atom_1_comp_id'
_item.category_id chem_link_tor
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_chem_link_tor.atom_2_comp_id'
'_chem_link_tor.atom_3_comp_id'
'_chem_link_tor.atom_4_comp_id'
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_tor.atom_2_comp_id
_item_description.description
; This data item indicates whether atom 2 is found in the first
or the second of the two components connected by the link.
;
_item.name '_chem_link_tor.atom_2_comp_id'
_item.category_id chem_link_tor
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_chem_link_tor.atom_1_comp_id'
'_chem_link_tor.atom_3_comp_id'
'_chem_link_tor.atom_4_comp_id'
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_tor.atom_3_comp_id
_item_description.description
; This data item indicates whether atom 3 is found in the first
or the second of the two components connected by the link.
;
_item.name '_chem_link_tor.atom_3_comp_id'
_item.category_id chem_link_tor
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_chem_link_tor.atom_1_comp_id'
'_chem_link_tor.atom_2_comp_id'
'_chem_link_tor.atom_4_comp_id'
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_tor.atom_4_comp_id
_item_description.description
; This data item indicates whether atom 4 is found in the first
or the second of the two components connected by the link.
;
_item.name '_chem_link_tor.atom_4_comp_id'
_item.category_id chem_link_tor
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_chem_link_tor.atom_1_comp_id'
'_chem_link_tor.atom_2_comp_id'
'_chem_link_tor.atom_3_comp_id'
loop_
_item_enumeration.value
_item_enumeration.detail 1 'the atom is in component 1'
2 'the atom is in component 2'
_item_type.code ucode
save_
save__chem_link_tor.atom_id_1
_item_description.description
; The ID of the first of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
;
_item.name '_chem_link_tor.atom_id_1'
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_link_tor.atom_id_2'
'_chem_link_tor.atom_id_3'
'_chem_link_tor.atom_id_4'
_item_type.code code
save_
save__chem_link_tor.atom_id_2
_item_description.description
; The ID of the second of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
;
_item.name '_chem_link_tor.atom_id_2'
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_link_tor.atom_id_1'
'_chem_link_tor.atom_id_3'
'_chem_link_tor.atom_id_4'
_item_type.code code
save_
save__chem_link_tor.atom_id_3
_item_description.description
; The ID of the third of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
;
_item.name '_chem_link_tor.atom_id_3'
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_link_tor.atom_id_1'
'_chem_link_tor.atom_id_2'
'_chem_link_tor.atom_id_4'
_item_type.code code
save_
save__chem_link_tor.atom_id_4
_item_description.description
; The ID of the fourth of the four atoms that define the torsion
angle.
As this data item does not point to a specific atom in a
specific chemical component, it is not a child in the linkage
sense.
;
_item.name '_chem_link_tor.atom_id_4'
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_chem_link_tor.atom_id_1'
'_chem_link_tor.atom_id_2'
'_chem_link_tor.atom_id_3'
_item_type.code code
save_
save__chem_link_tor.id
_item_description.description
; The value of _chem_link_tor.id must uniquely identify a
record in the CHEM_LINK_TOR list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chem_link_tor.id' chem_link_tor yes
'_chem_link_tor_value.tor_id' chem_link_tor_value yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_chem_link_tor_value.tor_id' '_chem_link_tor.id'
_item_type.code code
save_
save__chem_link_tor.link_id
_item_description.description
; This data item is a pointer to _chem_link.id in the CHEM_LINK
category.
;
_item.name '_chem_link_tor.link_id'
_item.mandatory_code yes
save_
#########################
## CHEM_LINK_TOR_VALUE ##
#########################
save_chem_link_tor_value
_category.description
; Data items in the CHEM_LINK_TOR_VALUE category record details
about the target values for the torsion angles enumerated in the
CHEM_LINK_TOR list. Target values may be specified as angles
in degrees, as a distance between the first and fourth atoms, or
both.
;
_category.id chem_link_tor_value
_category.mandatory_code no
_category_key.name '_chem_link_tor_value.tor_id'
loop_
_category_group.id 'inclusive_group'
'chem_link_group'
save_
save__chem_link_tor_value.tor_id
_item_description.description
; This data item is a pointer to _chem_link_tor.id in the
CHEM_LINK_TOR category.
;
_item.name '_chem_link_tor_value.tor_id'
_item.mandatory_code yes
save_
save__chem_link_tor_value.angle
_item_description.description
; A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed in
degrees.
;
_item.name '_chem_link_tor_value.angle'
_item.category_id chem_link_tor_value
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 -180.0
-180.0 -180.0
_item_related.related_name '_chem_link_tor_value.angle_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code degrees
save_
save__chem_link_tor_value.angle_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_link_tor_value.angle.
;
_item.name '_chem_link_tor_value.angle_esd'
_item.category_id chem_link_tor_value
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 -180.0
-180.0 -180.0
_item_related.related_name '_chem_link_tor_value.angle'
_item_related.function_code associated_value
_item_type.code float
_item_units.code degrees
save_
save__chem_link_tor_value.dist
_item_description.description
; A value that should be taken as a potential target value for the
torsion angle associated with the specified atoms, expressed as
the distance between the atoms specified by
_chem_link_tor.atom_id_1 and _chem_link_tor.atom_id_4 in the
referenced record in the CHEM_LINK_TOR list. Note that the
torsion angle cannot be fully specified by a distance (for
instance, a torsion angle of -60 degree will yield the same
distance as a 60 degree angle). However, the distance
specification can be useful for refinement in situations in
which the angle is already close to the desired value.
;
_item.name '_chem_link_tor_value.dist'
_item.category_id chem_link_tor_value
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_link_tor_value.dist_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__chem_link_tor_value.dist_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _chem_link_tor_value.dist.
;
_item.name '_chem_link_tor_value.dist_esd'
_item.category_id chem_link_tor_value
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_chem_link_tor_value.dist'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
##############
## CHEMICAL ##
##############
save_chemical
_category.description
; Data items in the CHEMICAL category would not in general be
used in a macromolecular CIF. See instead the ENTITY data
items.
Data items in the CHEMICAL category record details about the
composition and chemical properties of the compounds. The
formula data items must agree with those that specify the
density, unit-cell and Z values.
;
_category.id chemical
_category.mandatory_code no
_category_key.name '_chemical.entry_id'
loop_
_category_group.id 'inclusive_group'
'chemical_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan
[Acta Cryst. (1996), C52, 765-767].
;
;
_chemical.entry_id '9597gaus'
_chemical.name_systematic
trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chemical.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_chemical.entry_id'
_item.mandatory_code yes
save_
save__chemical.compound_source
_item_description.description
; Description of the source of the compound under study, or of the
parent molecule if a simple derivative is studied. This includes
the place of discovery for minerals or the actual source of a
natural product.
;
_item.name '_chemical.compound_source'
_item.category_id chemical
_item.mandatory_code no
_item_aliases.alias_name '_chemical_compound_source'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'From Norilsk (USSR)'
'Extracted from the bark of Cinchona Naturalis'
save_
save__chemical.melting_point
_item_description.description
; The temperature in kelvins at which the crystalline solid changes
to a liquid.
;
_item.name '_chemical.melting_point'
_item.category_id chemical
_item.mandatory_code no
_item_aliases.alias_name '_chemical_melting_point'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code kelvins
save_
save__chemical.name_common
_item_description.description
; Trivial name by which the compound is commonly known.
;
_item.name '_chemical.name_common'
_item.category_id chemical
_item.mandatory_code no
_item_aliases.alias_name '_chemical_name_common'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case '1-bromoestradiol'
save_
save__chemical.name_mineral
_item_description.description
; Mineral name accepted by the International Mineralogical
Association. Use only for natural minerals. See also
_chemical.compound_source.
;
_item.name '_chemical.name_mineral'
_item.category_id chemical
_item.mandatory_code no
_item_aliases.alias_name '_chemical_name_mineral'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'chalcopyrite'
save_
save__chemical.name_structure_type
_item_description.description
; Commonly used structure-type name. Usually only applied to
minerals or inorganic compounds.
;
_item.name '_chemical.name_structure_type'
_item.category_id chemical
_item.mandatory_code no
_item_aliases.alias_name '_chemical_name_structure_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'perovskite'
'sphalerite'
'A15'
save_
save__chemical.name_systematic
_item_description.description
; IUPAC or Chemical Abstracts full name of the compound.
;
_item.name '_chemical.name_systematic'
_item.category_id chemical
_item.mandatory_code no
_item_aliases.alias_name '_chemical_name_systematic'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case '1-bromoestra-1,3,5(10)-triene-3,17\b-diol'
save_
########################
## CHEMICAL_CONN_ATOM ##
########################
save_chemical_conn_atom
_category.description
; Data items in the CHEMICAL_CONN_ATOM category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND
categories record details about the two-dimensional (2D)
chemical structure of the molecular species. They allow
a 2D chemical diagram to be reconstructed for use in a
publication or in a database search for structural and
substructural relationships.
The CHEMICAL_CONN_ATOM data items provide information about the
chemical properties of the atoms in the structure. In cases
where crystallographic and molecular symmetry elements coincide,
they must also contain symmetry-generated atoms, so that the
CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always
describe a complete chemical entity.
;
_category.id chemical_conn_atom
_category.mandatory_code no
_category_key.name '_chemical_conn_atom.number'
loop_
_category_group.id 'inclusive_group'
'chemical_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
;
;
loop_
_chemical_conn_atom.number
_chemical_conn_atom.type_symbol
_chemical_conn_atom.display_x
_chemical_conn_atom.display_y
_chemical_conn_atom.NCA
_chemical_conn_atom.NH
1 S .39 .81 1 0
2 S .39 .96 2 0
3 N .14 .88 3 0
4 C .33 .88 3 0
5 C .11 .96 2 2
6 C .03 .96 2 2
7 C .03 .80 2 2
8 C .11 .80 2 2
9 S .54 .81 1 0
10 S .54 .96 2 0
11 N .80 .88 3 0
12 C .60 .88 3 0
13 C .84 .96 2 2
14 C .91 .96 2 2
15 C .91 .80 2 2
16 C .84 .80 2 2
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chemical_conn_atom.charge
_item_description.description
; The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
;
_item.name '_chemical_conn_atom.charge'
_item.category_id chemical_conn_atom
_item.mandatory_code no
_item_aliases.alias_name '_chemical_conn_atom_charge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 0
loop_
_item_range.maximum
_item_range.minimum 8 8
8 -8
-8 -8
_item_type.code int
loop_
_item_examples.case
_item_examples.detail 1 'for an ammonium nitrogen'
-1 'for a chloride ion'
save_
save__chemical_conn_atom.display_x
_item_description.description
; The 2D Cartesian x coordinate of the position of this atom in a
recognizable chemical diagram. The coordinate origin is at the
lower left corner, the x axis is horizontal and the y axis
is vertical. The coordinates must lie in the range 0.0 to 1.0.
These coordinates can be obtained from projections of a suitable
uncluttered view of the molecular structure.
;
_item.name '_chemical_conn_atom.display_x'
_item.category_id chemical_conn_atom
_item.mandatory_code no
_item_aliases.alias_name '_chemical_conn_atom_display_x'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_dependent.dependent_name
'_chemical_conn_atom.display_y'
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 0.0
0.0 0.0
_item_type.code float
save_
save__chemical_conn_atom.display_y
_item_description.description
; The 2D Cartesian y coordinate of the position of this atom in a
recognizable chemical diagram. The coordinate origin is at the
lower left corner, the x axis is horizontal and the y axis
is vertical. The coordinates must lie in the range 0.0 to 1.0.
These coordinates can be obtained from projections of a suitable
uncluttered view of the molecular structure.
;
_item.name '_chemical_conn_atom.display_y'
_item.category_id chemical_conn_atom
_item.mandatory_code no
_item_aliases.alias_name '_chemical_conn_atom_display_y'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_dependent.dependent_name
'_chemical_conn_atom.display_x'
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 0.0
0.0 0.0
_item_type.code float
save_
save__chemical_conn_atom.NCA
_item_description.description
; The number of connected atoms excluding terminal hydrogen atoms.
;
_item.name '_chemical_conn_atom.NCA'
_item.category_id chemical_conn_atom
_item.mandatory_code no
_item_aliases.alias_name '_chemical_conn_atom_NCA'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__chemical_conn_atom.NH
_item_description.description
; The total number of hydrogen atoms attached to this atom,
regardless of whether they are included in the refinement or
the ATOM_SITE list. This number is the same as
_atom_site.attached_hydrogens only if none of the hydrogen
atoms appear in the ATOM_SITE list.
;
_item.name '_chemical_conn_atom.NH'
_item.category_id chemical_conn_atom
_item.mandatory_code no
_item_aliases.alias_name '_chemical_conn_atom_NH'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__chemical_conn_atom.number
_item_description.description
; The chemical sequence number to be associated with this atom.
Within an ATOM_SITE list, this number must match one of
the _atom_site.chemical_conn_number values.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_chemical_conn_atom.number' chemical_conn_atom yes
'_atom_site.chemical_conn_number' atom_site no
'_chemical_conn_bond.atom_1' chemical_conn_bond yes
'_chemical_conn_bond.atom_2' chemical_conn_bond yes
_item_aliases.alias_name '_chemical_conn_atom_number'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.chemical_conn_number' '_chemical_conn_atom.number'
'_chemical_conn_bond.atom_1' '_chemical_conn_atom.number'
'_chemical_conn_bond.atom_2' '_chemical_conn_atom.number'
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__chemical_conn_atom.type_symbol
_item_description.description
; This data item is a pointer to _atom_type.symbol in the
ATOM_TYPE category.
;
_item.name '_chemical_conn_atom.type_symbol'
_item.mandatory_code yes
_item_aliases.alias_name '_chemical_conn_atom_type_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
########################
## CHEMICAL_CONN_BOND ##
########################
save_chemical_conn_bond
_category.description
; Data items in the CHEMICAL_CONN_BOND category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND
categories record details about the two-dimensional (2D)
chemical structure of the molecular species. They allow a
2D chemical diagram to be reconstructed for use in a
publication or in a database search for structural and
substructural relationships.
The CHEMICAL_CONN_BOND data items specify the connections
between the atoms in the CHEMICAL_CONN_ATOM list and the nature
of the chemical bond between these atoms.
;
_category.id chemical_conn_bond
_category.mandatory_code no
loop_
_category_key.name '_chemical_conn_bond.atom_1'
'_chemical_conn_bond.atom_2'
loop_
_category_group.id 'inclusive_group'
'chemical_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
;
;
loop_
_chemical_conn_bond.atom_1
_chemical_conn_bond.atom_2
_chemical_conn_bond.type
4 1 doub 4 3 sing
4 2 sing 5 3 sing
6 5 sing 7 6 sing
8 7 sing 8 3 sing
10 2 sing 12 9 doub
12 11 sing 12 10 sing
13 11 sing 14 13 sing
15 14 sing 16 15 sing
16 11 sing 17 5 sing
18 5 sing 19 6 sing
20 6 sing 21 7 sing
22 7 sing 23 8 sing
24 8 sing 25 13 sing
26 13 sing 27 14 sing
28 14 sing 29 15 sing
30 15 sing 31 16 sing
32 16 sing
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chemical_conn_bond.atom_1
_item_description.description
; This data item is a pointer to _chemical_conn_atom.number in the
CHEMICAL_CONN_ATOM category.
;
_item.name '_chemical_conn_bond.atom_1'
_item.mandatory_code yes
_item_aliases.alias_name '_chemical_conn_bond_atom_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_dependent.dependent_name
'_chemical_conn_bond.atom_2'
save_
save__chemical_conn_bond.atom_2
_item_description.description
; This data item is a pointer to _chemical_conn_atom.number in the
CHEMICAL_CONN_ATOM category.
;
_item.name '_chemical_conn_bond.atom_2'
_item.mandatory_code yes
_item_aliases.alias_name '_chemical_conn_bond_atom_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_dependent.dependent_name
'_chemical_conn_bond.atom_1'
save_
save__chemical_conn_bond.type
_item_description.description
; The chemical bond type associated with the connection between
the two sites _chemical_conn_bond.atom_1 and
_chemical_conn_bond.atom_2.
;
_item.name '_chemical_conn_bond.type'
_item.category_id chemical_conn_bond
_item.mandatory_code no
_item_aliases.alias_name '_chemical_conn_bond_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value sing
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail sing 'single bond'
doub 'double bond'
trip 'triple bond'
quad 'quadruple bond'
arom 'aromatic bond'
poly 'polymeric bond'
delo 'delocalized double bond'
pi 'pi bond'
save_
######################
## CHEMICAL_FORMULA ##
######################
save_chemical_formula
_category.description
; Data items in the CHEMICAL_FORMULA category would not, in
general, be used in a macromolecular CIF. See instead the
ENTITY data items.
Data items in the CHEMICAL_FORMULA category specify the
composition and chemical properties of the compound. The formula
data items must agree with those that specify the density,
unit-cell and Z values.
The following rules apply to the construction of the data items
_chemical_formula.analytical, _chemical_formula.structural and
_chemical_formula.sum. For the data item
_chemical_formula.moiety, the formula construction is broken up
into residues or moieties, i.e. groups of atoms that form a
molecular unit or molecular ion. The rules given below apply
within each moiety but different requirements apply to the way
that moieties are connected (see _chemical_formula.moiety).
(1) Only recognized element symbols may be used.
(2) Each element symbol is followed by a 'count' number. A count
of '1' may be omitted.
(3) A space or parenthesis must separate each cluster of (element
symbol + count).
(4) Where a group of elements is enclosed in parentheses, the
multiplier for the group must follow the closing parenthesis.
That is, all element and group multipliers are assumed to be
printed as subscripted numbers. (An exception to this rule
exists for _chemical_formula.moiety formulae where pre- and
post-multipliers are permitted for molecular units.)
(5) Unless the elements are ordered in a manner that corresponds
to their chemical structure, as in
_chemical_formula.structural, the order of the elements within
any group or moiety should be: C, then H, then the other
elements in alphabetical order of their symbol. This is the
'Hill' system used by Chemical Abstracts. This ordering is
used in _chemical_formula.moiety and _chemical_formula.sum.
;
_category.id chemical_formula
_category.mandatory_code no
_category_key.name '_chemical_formula.entry_id'
loop_
_category_group.id 'inclusive_group'
'chemical_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_chemical_formula.entry_id 'TOZ'
_chemical_formula.moiety 'C18 H25 N O3'
_chemical_formula.sum 'C18 H25 N O3'
_chemical_formula.weight 303.40
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__chemical_formula.analytical
_item_description.description
; Formula determined by standard chemical analysis including trace
elements. See the CHEMICAL_FORMULA category description for
rules for writing chemical formulae. Parentheses are used only
for standard uncertainties (estimated standard deviations).
;
_item.name '_chemical_formula.analytical'
_item.category_id chemical_formula
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_analytical'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'Fe2.45(2) Ni1.60(3) S4'
save_
save__chemical_formula.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_chemical_formula.entry_id'
_item.mandatory_code yes
save_
save__chemical_formula.iupac
_item_description.description
; Formula expressed in conformance with IUPAC rules for inorganic
and metal-organic compounds where these conflict with the rules
for any other CHEMICAL_FORMULA entries. Typically used for
formatting a formula in accordance with journal rules. This
should appear in the data block in addition to the most
appropriate of the other CHEMICAL_FORMULA data names.
Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry.
Oxford: Blackwell Scientific Publications.
;
_item.name '_chemical_formula.iupac'
_item.category_id chemical_formula
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_iupac'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H'
save_
save__chemical_formula.moiety
_item_description.description
; Formula with each discrete bonded residue or ion shown as a
separate moiety. See the CHEMICAL_FORMULA category description
for rules for writing chemical formulae. In addition to the
general formulae requirements, the following rules apply:
(1) Moieties are separated by commas ','.
(2) The order of elements within a moiety follows general rule
(5) in the CHEMICAL_FORMULA category description.
(3) Parentheses are not used within moieties but may surround
a moiety. Parentheses may not be nested.
(4) Charges should be placed at the end of the moiety. The
charge '+' or '-' may be preceded by a numerical multiplier
and should be separated from the last (element symbol +
count) by a space. Pre- or post-multipliers may be used for
individual moieties.
;
_item.name '_chemical_formula.moiety'
_item.category_id chemical_formula
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_moiety'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'C7 H4 Cl Hg N O3 S'
'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-'
'C12 H16 N2 O6, 5(H2 O1)'
"(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)"
save_
save__chemical_formula.structural
_item_description.description
; See the CHEMICAL_FORMULA category description for the rules for
writing chemical formulae for inorganics, organometallics, metal
complexes etc., in which bonded groups are preserved as
discrete entities within parentheses, with post-multipliers as
required. The order of the elements should give as much
information as possible about the chemical structure.
Parentheses may be used and nested as required. This formula
should correspond to the structure as actually reported, i.e.
trace elements not included in atom-type and atom-site data
should not be included in this formula (see also
_chemical_formula.analytical).
;
_item.name '_chemical_formula.structural'
_item.category_id chemical_formula
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_structural'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Ca ((Cl O3)2 O)2 (H2 O)6'
'(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2'
save_
save__chemical_formula.sum
_item_description.description
; See the CHEMICAL_FORMULA category description for the rules
for writing chemical formulae in which all discrete bonded
residues and ions are summed over the constituent elements,
following the ordering given in general rule (5) in the
CHEMICAL_FORMULA category description. Parentheses are not
normally used.
;
_item.name '_chemical_formula.sum'
_item.category_id chemical_formula
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_sum'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'C18 H19 N7 O8 S'
save_
save__chemical_formula.weight
_item_description.description
; Formula mass in daltons. This mass should correspond to the
formulae given under _chemical_formula.structural,
_chemical_formula.moiety or _chemical_formula.sum and,
together with the Z value and cell parameters, should
yield the density given as _exptl_crystal.density_diffrn.
;
_item.name '_chemical_formula.weight'
_item.category_id chemical_formula
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_weight'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 1.0
1.0 1.0
_item_type.code float
save_
save__chemical_formula.weight_meas
_item_description.description
; Formula mass in daltons measured by a non-diffraction experiment.
;
_item.name '_chemical_formula.weight_meas'
_item.category_id chemical_formula
_item.mandatory_code no
_item_aliases.alias_name '_chemical_formula_weight_meas'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 1.0
1.0 1.0
_item_type.code float
save_
##############
## CITATION ##
##############
save_citation
_category.description
; Data items in the CITATION category record details about the
literature cited as being relevant to the contents of the data
block.
;
_category.id citation
_category.mandatory_code no
_category_key.name '_citation.id'
loop_
_category_group.id 'inclusive_group'
'citation_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_citation.id
_citation.coordinate_linkage
_citation.title
_citation.country
_citation.journal_abbrev
_citation.journal_volume
_citation.journal_issue
_citation.page_first
_citation.page_last
_citation.year
_citation.journal_id_ASTM
_citation.journal_id_ISSN
_citation.journal_id_CSD
_citation.book_title
_citation.book_publisher
_citation.book_id_ISBN
_citation.details
primary yes
; Crystallographic analysis of a complex between human
immunodeficiency virus type 1 protease and acetyl-pepstatin
at 2.0-Angstroms resolution.
;
US 'J. Biol. Chem.' 265 . 14209 14219 1990
HBCHA3 0021-9258 071 . . .
; The publication that directly relates to this coordinate
set.
;
2 no
; Three-dimensional structure of aspartyl-protease from human
immunodeficiency virus HIV-1.
;
UK 'Nature' 337 . 615 619 1989
NATUAS 0028-0836 006 . . .
; Determination of the structure of the unliganded enzyme.
;
3 no
; Crystallization of the aspartylprotease from human
immunodeficiency virus, HIV-1.
;
US 'J. Biol. Chem.' 264 . 1919 1921 1989
HBCHA3 0021-9258 071 . . .
; Crystallization of the unliganded enzyme.
;
4 no
; Human immunodeficiency virus protease. Bacterial expression
and characterization of the purified aspartic protease.
;
US 'J. Biol. Chem.' 264 . 2307 2312 1989
HBCHA3 0021-9258 071 . . .
; Expression and purification of the enzyme.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__citation.abstract
_item_description.description
; Abstract for the citation. This is used most when the
citation is extracted from a bibliographic database that
contains full text or abstract information.
;
_item.name '_citation.abstract'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_abstract'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__citation.abstract_id_CAS
_item_description.description
; The Chemical Abstracts Service (CAS) abstract identifier;
relevant for journal articles.
;
_item.name '_citation.abstract_id_CAS'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_abstract_id_CAS'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__citation.book_id_ISBN
_item_description.description
; The International Standard Book Number (ISBN) code assigned to
the book cited; relevant for books or book chapters.
;
_item.name '_citation.book_id_ISBN'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_book_id_ISBN'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__citation.book_publisher
_item_description.description
; The name of the publisher of the citation; relevant
for books or book chapters.
;
_item.name '_citation.book_publisher'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_book_publisher'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'John Wiley and Sons'
save_
save__citation.book_publisher_city
_item_description.description
; The location of the publisher of the citation; relevant
for books or book chapters.
;
_item.name '_citation.book_publisher_city'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_book_publisher_city'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'London'
save_
save__citation.book_title
_item_description.description
; The title of the book in which the citation appeared; relevant
for books or book chapters.
;
_item.name '_citation.book_title'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_book_title'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__citation.coordinate_linkage
_item_description.description
; _citation.coordinate_linkage states whether this citation
is concerned with precisely the set of coordinates given in the
data block. If, for instance, the publication described the same
structure, but the coordinates had undergone further refinement
prior to the creation of the data block, the value of this data
item would be 'no'.
;
_item.name '_citation.coordinate_linkage'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_coordinate_linkage'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail no
'citation unrelated to current coordinates'
n
'abbreviation for "no"'
yes
'citation related to current coordinates'
y
'abbreviation for "yes"'
save_
save__citation.country
_item_description.description
; The country of publication; relevant for books
and book chapters.
;
_item.name '_citation.country'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_country'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__citation.database_id_Medline
_item_description.description
; Accession number used by Medline to categorize a specific
bibliographic entry.
;
_item.name '_citation.database_id_Medline'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_database_id_Medline'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
_item_examples.case 89064067
save_
save__citation.details
_item_description.description
; A description of special aspects of the relationship
of the contents of the data block to the literature item cited.
;
_item.name '_citation.details'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_special_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case
; citation relates to this precise
coordinate set
;
; citation relates to earlier low-resolution
structure
;
; citation relates to further refinement of
structure reported in citation 2
;
save_
save__citation.id
_item_description.description
; The value of _citation.id must uniquely identify a record in the
CITATION list.
The _citation.id 'primary' should be used to indicate the
citation that the author(s) consider to be the most pertinent to
the contents of the data block.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_citation.id' citation yes
'_citation_author.citation_id' citation_author yes
'_citation_editor.citation_id' citation_editor yes
'_software.citation_id' software no
_item_aliases.alias_name '_citation_id'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_linked.child_name
_item_linked.parent_name
'_citation_author.citation_id' '_citation.id'
'_citation_editor.citation_id' '_citation.id'
'_software.citation_id' '_citation.id'
_item_type.code code
loop_
_item_examples.case 'primary'
'1'
'2'
save_
save__citation.journal_abbrev
_item_description.description
; Abbreviated name of the cited journal as given in the
Chemical Abstracts Service Source Index.
;
_item.name '_citation.journal_abbrev'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_journal_abbrev'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
_item_examples.case 'J. Mol. Biol.'
save_
save__citation.journal_id_ASTM
_item_description.description
; The American Society for Testing and Materials (ASTM) code
assigned to the journal cited (also referred to as the CODEN
designator of the Chemical Abstracts Service); relevant for
journal articles.
;
_item.name '_citation.journal_id_ASTM'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_journal_id_ASTM'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__citation.journal_id_CSD
_item_description.description
; The Cambridge Structural Database (CSD) code assigned to the
journal cited; relevant for journal articles. This is also the
system used at the Protein Data Bank (PDB).
;
_item.name '_citation.journal_id_CSD'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_journal_id_CSD'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
_item_examples.case '0070'
save_
save__citation.journal_id_ISSN
_item_description.description
; The International Standard Serial Number (ISSN) code assigned to
the journal cited; relevant for journal articles.
;
_item.name '_citation.journal_id_ISSN'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_journal_id_ISSN'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__citation.journal_full
_item_description.description
; Full name of the cited journal; relevant for journal articles.
;
_item.name '_citation.journal_full'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_journal_full'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'Journal of Molecular Biology'
save_
save__citation.journal_issue
_item_description.description
; Issue number of the journal cited; relevant for journal
articles.
;
_item.name '_citation.journal_issue'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_journal_issue'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
_item_examples.case '2'
save_
save__citation.journal_volume
_item_description.description
; Volume number of the journal cited; relevant for journal
articles.
;
_item.name '_citation.journal_volume'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_journal_volume'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
_item_examples.case '174'
save_
save__citation.language
_item_description.description
; Language in which the cited article is written.
;
_item.name '_citation.language'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_language'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
_item_examples.case 'German'
save_
save__citation.page_first
_item_description.description
; The first page of the citation; relevant for journal
articles, books and book chapters.
;
_item.name '_citation.page_first'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_page_first'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__citation.page_last
_item_description.description
; The last page of the citation; relevant for journal
articles, books and book chapters.
;
_item.name '_citation.page_last'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_page_last'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__citation.title
_item_description.description
; The title of the citation; relevant for journal articles, books
and book chapters.
;
_item.name '_citation.title'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_title'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Structure of diferric duck ovotransferrin
at 2.35 \%A resolution.
;
save_
save__citation.year
_item_description.description
; The year of the citation; relevant for journal articles, books
and book chapters.
;
_item.name '_citation.year'
_item.category_id citation
_item.mandatory_code no
_item_aliases.alias_name '_citation_year'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
_item_examples.case 1984
save_
#####################
## CITATION_AUTHOR ##
#####################
save_citation_author
_category.description
; Data items in the CITATION_AUTHOR category record details
about the authors associated with the citations in the
CITATION list.
;
_category.id citation_author
_category.mandatory_code no
loop_
_category_key.name '_citation_author.citation_id'
'_citation_author.name'
loop_
_category_group.id 'inclusive_group'
'citation_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_citation_author.citation_id
_citation_author.ordinal
_citation_author.name
primary 1 'Fitzgerald, P.M.D.'
primary 2 'McKeever, B.M.'
primary 3 'Van Middlesworth, J.F.'
primary 4 'Springer, J.P.'
primary 5 'Heimbach, J.C.'
primary 6 'Leu, C.-T.'
primary 7 'Herber, W.K.'
primary 8 'Dixon, R.A.F.'
primary 9 'Darke, P.L.'
2 1 'Navia, M.A.'
2 2 'Fitzgerald, P.M.D.'
2 3 'McKeever, B.M.'
2 4 'Leu, C.-T.'
2 5 'Heimbach, J.C.'
2 6 'Herber, W.K.'
2 7 'Sigal, I.S.'
2 8 'Darke, P.L.'
2 9 'Springer, J.P.'
3 1 'McKeever, B.M.'
3 2 'Navia, M.A.'
3 3 'Fitzgerald, P.M.D.'
3 4 'Springer, J.P.'
3 5 'Leu, C.-T.'
3 6 'Heimbach, J.C.'
3 7 'Herber, W.K.'
3 8 'Sigal, I.S.'
3 9 'Darke, P.L.'
4 1 'Darke, P.L.'
4 2 'Leu, C.-T.'
4 3 'Davis, L.J.'
4 4 'Heimbach, J.C.'
4 5 'Diehl, R.E.'
4 6 'Hill, W.S.'
4 7 'Dixon, R.A.F.'
4 8 'Sigal, I.S.'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__citation_author.citation_id
_item_description.description
; This data item is a pointer to _citation.id in the CITATION
category.
;
_item.name '_citation_author.citation_id'
_item.mandatory_code yes
_item_aliases.alias_name '_citation_author_citation_id'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__citation_author.name
_item_description.description
; Name of an author of the citation; relevant for journal
articles, books and book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
_item.name '_citation_author.name'
_item.category_id citation_author
_item.mandatory_code yes
_item_aliases.alias_name '_citation_author_name'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
save_
save__citation_author.ordinal
_item_description.description
; This data item defines the order of the author's name in the
list of authors of a citation.
;
_item.name '_citation_author.ordinal'
_item.category_id citation_author
_item.mandatory_code no
_item_aliases.alias_name '_citation_author_ordinal'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
#####################
## CITATION_EDITOR ##
#####################
save_citation_editor
_category.description
; Data items in the CITATION_EDITOR category record details
about the editors associated with the books or book chapters
cited in the CITATION list.
;
_category.id citation_editor
_category.mandatory_code no
loop_
_category_key.name '_citation_editor.citation_id'
'_citation_editor.name'
loop_
_category_group.id 'inclusive_group'
'citation_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - hypothetical example.
;
;
loop_
_citation_editor.citation_id
_citation_editor.name
5 'McKeever, B.M.'
5 'Navia, M.A.'
5 'Fitzgerald, P.M.D.'
5 'Springer, J.P.'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__citation_editor.citation_id
_item_description.description
; This data item is a pointer to _citation.id in the CITATION
category.
;
_item.name '_citation_editor.citation_id'
_item.mandatory_code yes
_item_aliases.alias_name '_citation_editor_citation_id'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__citation_editor.name
_item_description.description
; Names of an editor of the citation; relevant for books and
book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
_item.name '_citation_editor.name'
_item.category_id citation_editor
_item.mandatory_code no
_item_aliases.alias_name '_citation_editor_name'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
save_
save__citation_editor.ordinal
_item_description.description
; This data item defines the order of the editor's name in the
list of editors of a citation.
;
_item.name '_citation_editor.ordinal'
_item.category_id citation_editor
_item.mandatory_code no
_item_aliases.alias_name '_citation_editor_ordinal'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
###############
## COMPUTING ##
###############
save_computing
_category.description
; Data items in the COMPUTING category record details about the
computer programs used in the crystal structure analysis.
Data items in this category would not, in general, be used in
a macromolecular CIF. The category SOFTWARE, which allows
a more detailed description of computer programs and
their attributes to be given, would be used instead.
;
_category.id computing
_category.mandatory_code no
_category_key.name '_computing.entry_id'
loop_
_category_group.id 'inclusive_group'
'computing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Rodr\'iguez-Romera, Ruiz-P\'erez & Solans [Acta
Cryst. (1996), C52, 1415-1417].
;
;
_computing.data_collection 'CAD-4 (Enraf-Nonius, 1989)'
_computing.cell_refinement 'CAD-4 (Enraf-Nonius, 1989)'
_computing.data_reduction 'CFEO (Solans, 1978)'
_computing.structure_solution 'SHELXS86 (Sheldrick, 1990)'
_computing.structure_refinement 'SHELXL93 (Sheldrick, 1993)'
_computing.molecular_graphics 'ORTEPII (Johnson, 1976)'
_computing.publication_material 'PARST (Nardelli, 1983)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__computing.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_computing.entry_id'
_item.mandatory_code yes
save_
save__computing.cell_refinement
_item_description.description
; Software used for cell refinement.
Give the program or package name and a brief reference.
;
_item.name '_computing.cell_refinement'
_item.category_id computing
_item.mandatory_code no
_item_aliases.alias_name '_computing_cell_refinement'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'CAD4 (Enraf-Nonius, 1989)'
save_
save__computing.data_collection
_item_description.description
; Software used for data collection.
Give the program or package name and a brief reference.
;
_item.name '_computing.data_collection'
_item.category_id computing
_item.mandatory_code no
_item_aliases.alias_name '_computing_data_collection'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'CAD4 (Enraf-Nonius, 1989)'
save_
save__computing.data_reduction
_item_description.description
; Software used for data reduction.
Give the program or package name and a brief reference.
;
_item.name '_computing.data_reduction'
_item.category_id computing
_item.mandatory_code no
_item_aliases.alias_name '_computing_data_reduction'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
'DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)'
save_
save__computing.molecular_graphics
_item_description.description
; Software used for molecular graphics.
Give the program or package name and a brief reference.
;
_item.name '_computing.molecular_graphics'
_item.category_id computing
_item.mandatory_code no
_item_aliases.alias_name '_computing_molecular_graphics'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'FRODO (Jones, 1986), ORTEP (Johnson, 1965)'
save_
save__computing.publication_material
_item_description.description
; Software used for generating material for publication.
Give the program or package name and a brief reference.
;
_item.name '_computing.publication_material'
_item.category_id computing
_item.mandatory_code no
_item_aliases.alias_name '_computing_publication_material'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__computing.structure_refinement
_item_description.description
; Software used for refinement of the structure.
Give the program or package name and a brief reference.
;
_item.name '_computing.structure_refinement'
_item.category_id computing
_item.mandatory_code no
_item_aliases.alias_name '_computing_structure_refinement'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'SHELX85 (Sheldrick, 1985)'
'X-PLOR (Brunger, 1992)'
save_
save__computing.structure_solution
_item_description.description
; Software used for solution of the structure.
Give the program or package name and a brief reference.
;
_item.name '_computing.structure_solution'
_item.category_id computing
_item.mandatory_code no
_item_aliases.alias_name '_computing_structure_solution'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'SHELX85 (Sheldrick, 1985)'
save_
##############
## DATABASE ##
##############
save_database
_category.description
; Data items in the DATABASE category have been superseded by
data items in the DATABASE_2 category. They are included
here only for compliance with older CIFs.
;
_category.id database
_category.mandatory_code no
_category_key.name '_database.entry_id'
loop_
_category_group.id 'inclusive_group'
'compliance_group'
save_
save__database.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_database.entry_id'
_item.mandatory_code yes
save_
#save__database.code_CAS
# _item_description.description
#; The code assigned by Chemical Abstracts.
#;
# _item.name '_database.code_CAS'
# _item.category_id database
# _item.mandatory_code no
# _item_aliases.alias_name '_database_code_CAS'
# _item_aliases.dictionary cif_core.dic
# _item_aliases.version 2.0.1
# loop_
# _item_related.related_name
# _item_related.function_code '_database_2.database_id'
# replacedby
# '_database_2.database_code'
# replacedby
# _item_type.code line
# save_
#
#save__database.code_CSD
# _item_description.description
#; The code assigned by the Cambridge Structural Database
# (organic and metal-organic compounds).
#;
# _item.name '_database.code_CSD'
# _item.category_id database
# _item.mandatory_code no
# _item_aliases.alias_name '_database_code_CSD'
# _item_aliases.dictionary cif_core.dic
# _item_aliases.version 2.0.1
# loop_
# _item_related.related_name
# _item_related.function_code '_database_2.database_id'
# replacedby
# '_database_2.database_code'
# replacedby
# _item_type.code line
# save_
#
#save__database.code_ICSD
# _item_description.description
#; The code assigned by the Inorganic Crystal Structure Database.
#;
# _item.name '_database.code_ICSD'
# _item.category_id database
# _item.mandatory_code no
# _item_aliases.alias_name '_database_code_ICSD'
# _item_aliases.dictionary cif_core.dic
# _item_aliases.version 2.0.1
# loop_
# _item_related.related_name
# _item_related.function_code '_database_2.database_id'
# replacedby
# '_database_2.database_code'
# replacedby
# _item_type.code line
# save_
#
#save__database.code_MDF
# _item_description.description
#; The code assigned by the Metals Data File (metal structures).
#;
# _item.name '_database.code_MDF'
# _item.category_id database
# _item.mandatory_code no
# _item_aliases.alias_name '_database_code_MDF'
# _item_aliases.dictionary cif_core.dic
# _item_aliases.version 2.0.1
# loop_
# _item_related.related_name
# _item_related.function_code '_database_2.database_id'
# replacedby
# '_database_2.database_code'
# replacedby
# _item_type.code line
# save_
#
#save__database.code_NBS
# _item_description.description
#; The code assigned by the NBS (NIST) Crystal Data Database
# (lattice parameters).
#;
# _item.name '_database.code_NBS'
# _item.category_id database
# _item.mandatory_code no
# _item_aliases.alias_name '_database_code_NBS'
# _item_aliases.dictionary cif_core.dic
# _item_aliases.version 2.0.1
# loop_
# _item_related.related_name
# _item_related.function_code '_database_2.database_id'
# replacedby
# '_database_2.database_code'
# replacedby
# _item_type.code line
# save_
#
#save__database.code_PDF
# _item_description.description
#; The code assigned by the Powder Diffraction File (JCPDS/ICDD).
#;
# _item.name '_database.code_PDF'
# _item.category_id database
# _item.mandatory_code no
# _item_aliases.alias_name '_database_code_PDF'
# _item_aliases.dictionary cif_core.dic
# _item_aliases.version 2.0.1
# loop_
# _item_related.related_name
# _item_related.function_code '_database_2.database_id'
# replacedby
# '_database_2.database_code'
# replacedby
# _item_type.code line
# save_
#
save__database.journal_ASTM
_item_description.description
; The ASTM CODEN designator for a journal as given in the Chemical
Source List maintained by the Chemical Abstracts Service.
;
_item.name '_database.journal_ASTM'
_item.category_id database
_item.mandatory_code no
_item_aliases.alias_name '_database_journal_ASTM'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__database.journal_CSD
_item_description.description
; The journal code used in the Cambridge Structural Database.
;
_item.name '_database.journal_CSD'
_item.category_id database
_item.mandatory_code no
_item_aliases.alias_name '_database_journal_CSD'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
################
## DATABASE_2 ##
################
save_database_2
_category.description
; Data items in the DATABASE_2 category record details about the
database identifiers of the data block.
These data items are assigned by database managers and should
only appear in a data block if they originate from that source.
The name of this category, DATABASE_2, arose because the
category name DATABASE was already in use in the core CIF
dictionary, but was used differently from the way it needed
to be used in the mmCIF dictionary. Since CIF data names
cannot be changed once they have been adopted, a new category
had to be created.
;
_category.id database_2
_category.mandatory_code no
loop_
_category_key.name '_database_2.database_id'
'_database_2.database_code'
loop_
_category_group.id 'inclusive_group'
'database_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_database_2.database_id 'PDB'
_database_2.database_code '5HVP'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__database_2.database_id
_item_description.description
; An abbreviation that identifies the database.
;
_item.name '_database_2.database_id'
_item.category_id database_2
_item.mandatory_code yes
loop_
_item_related.related_name
_item_related.function_code '_database.code_CAS'
replaces
'_database.code_CSD'
replaces
'_database.code_ICSD'
replaces
'_database.code_MDF'
replaces
'_database.code_NBS'
replaces
'_database.code_PDF'
replaces
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail CAS
; Chemical Abstracts
;
CSD
; Cambridge Structural Database
(organic and metal-organic compounds)
;
ICSD
; Inorganic Crystal Structure Database
;
MDF
; Metals Data File (metal structures)
;
NDB
; Nucleic Acid Database
;
NBS
; NBS (NIST) Crystal Data Database
(lattice parameters)
;
PDB
; Protein Data Bank
;
PDF
; Powder Diffraction File (JCPDS/ICDD)
;
RCSB
; Research Collaboratory for Structural Bioinformatics
;
EBI
; European Bioinformatics Institute
;
save_
save__database_2.database_code
_item_description.description
; The code assigned by the database identified in
_database_2.database_id.
;
_item.name '_database_2.database_code'
_item.category_id database_2
_item.mandatory_code yes
loop_
_item_related.related_name
_item_related.function_code '_database.code_CAS'
replaces
'_database.code_CSD'
replaces
'_database.code_ICSD'
replaces
'_database.code_MDF'
replaces
'_database.code_NBS'
replaces
'_database.code_PDF'
replaces
_item_type.code line
loop_
_item_examples.case 1ABC
ABCDEF
save_
#########################
## DATABASE_PDB_CAVEAT ##
#########################
save_database_PDB_caveat
_category.description
; Data items in the DATABASE_PDB_CAVEAT category record details
about features of the data block flagged as 'caveats' by the
Protein Data Bank (PDB).
These data items are included only for consistency with PDB
format files. They should appear in a data block only if that
data block was created by reformatting a PDB format file.
;
_category.id database_PDB_caveat
_category.mandatory_code no
_category_key.name '_database_PDB_caveat.id'
loop_
_category_group.id 'inclusive_group'
'database_group'
'pdb_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - hypothetical example.
;
;
loop_
_database_PDB_caveat.id
_database_PDB_caveat.text
1
; THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS
;
2
; UNCORRECTABLE AT THIS TIME
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__database_PDB_caveat.id
_item_description.description
; A unique identifier for the PDB caveat record.
;
_item.name '_database_PDB_caveat.id'
_item.category_id database_PDB_caveat
_item.mandatory_code yes
_item_type.code int
save_
save__database_PDB_caveat.text
_item_description.description
; The full text of the PDB caveat record.
;
_item.name '_database_PDB_caveat.text'
_item.category_id database_PDB_caveat
_item.mandatory_code no
_item_type.code text
save_
#########################
## DATABASE_PDB_MATRIX ##
#########################
save_database_PDB_matrix
_category.description
; The DATABASE_PDB_MATRIX category provides placeholders for
transformation matrices and vectors used by the Protein Data
Bank (PDB).
These data items are included only for consistency with older
PDB format files. They should appear in a data block only if
that data block was created by reformatting a PDB format file.
;
_category.id database_PDB_matrix
_category.mandatory_code no
_category_key.name '_database_PDB_matrix.entry_id'
loop_
_category_group.id 'inclusive_group'
'database_group'
'pdb_group'
save_
save__database_PDB_matrix.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_database_PDB_matrix.entry_id'
_item.mandatory_code yes
save_
save__database_PDB_matrix.origx[1][1]
_item_description.description
; The [1][1] element of the PDB ORIGX matrix.
;
_item.name '_database_PDB_matrix.origx[1][1]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 1.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.origx[1][2]
_item_description.description
; The [1][2] element of the PDB ORIGX matrix.
;
_item.name '_database_PDB_matrix.origx[1][2]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.origx[1][3]
_item_description.description
; The [1][3] element of the PDB ORIGX matrix.
;
_item.name '_database_PDB_matrix.origx[1][3]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.origx[2][1]
_item_description.description
; The [2][1] element of the PDB ORIGX matrix.
;
_item.name '_database_PDB_matrix.origx[2][1]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.origx[2][2]
_item_description.description
; The [2][2] element of the PDB ORIGX matrix.
;
_item.name '_database_PDB_matrix.origx[2][2]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 1.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.origx[2][3]
_item_description.description
; The [2][3] element of the PDB ORIGX matrix.
;
_item.name '_database_PDB_matrix.origx[2][3]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.origx[3][1]
_item_description.description
; The [3][1] element of the PDB ORIGX matrix.
;
_item.name '_database_PDB_matrix.origx[3][1]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.origx[3][2]
_item_description.description
; The [3][2] element of the PDB ORIGX matrix.
;
_item.name '_database_PDB_matrix.origx[3][2]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.origx[3][3]
_item_description.description
; The [3][3] element of the PDB ORIGX matrix.
;
_item.name '_database_PDB_matrix.origx[3][3]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 1.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.origx_vector[1]
_item_description.description
; The [1] element of the PDB ORIGX vector.
;
_item.name '_database_PDB_matrix.origx_vector[1]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__database_PDB_matrix.origx_vector[2]
_item_description.description
; The [2] element of the PDB ORIGX vector.
;
_item.name '_database_PDB_matrix.origx_vector[2]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__database_PDB_matrix.origx_vector[3]
_item_description.description
; The [3] element of the PDB ORIGX vector.
;
_item.name '_database_PDB_matrix.origx_vector[3]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__database_PDB_matrix.scale[1][1]
_item_description.description
; The [1][1] element of the PDB SCALE matrix.
;
_item.name '_database_PDB_matrix.scale[1][1]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 1.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.scale[1][2]
_item_description.description
; The [1][2] element of the PDB SCALE matrix.
;
_item.name '_database_PDB_matrix.scale[1][2]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.scale[1][3]
_item_description.description
; The [1][3] element of the PDB SCALE matrix.
;
_item.name '_database_PDB_matrix.scale[1][3]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.scale[2][1]
_item_description.description
; The [2][1] element of the PDB SCALE matrix.
;
_item.name '_database_PDB_matrix.scale[2][1]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.scale[2][2]
_item_description.description
; The [2][2] element of the PDB SCALE matrix.
;
_item.name '_database_PDB_matrix.scale[2][2]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 1.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.scale[2][3]
_item_description.description
; The [2][3] element of the PDB SCALE matrix.
;
_item.name '_database_PDB_matrix.scale[2][3]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.scale[3][1]
_item_description.description
; The [3][1] element of the PDB SCALE matrix.
;
_item.name '_database_PDB_matrix.scale[3][1]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.scale[3][2]
_item_description.description
; The [3][2] element of the PDB SCALE matrix.
;
_item.name '_database_PDB_matrix.scale[3][2]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.scale[3][3]
_item_description.description
; The [3][3] element of the PDB SCALE matrix.
;
_item.name '_database_PDB_matrix.scale[3][3]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 1.0
_item_sub_category.id matrix
_item_type.code float
save_
save__database_PDB_matrix.scale_vector[1]
_item_description.description
; The [1] element of the PDB SCALE vector.
;
_item.name '_database_PDB_matrix.scale_vector[1]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__database_PDB_matrix.scale_vector[2]
_item_description.description
; The [2] element of the PDB SCALE vector.
;
_item.name '_database_PDB_matrix.scale_vector[2]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__database_PDB_matrix.scale_vector[3]
_item_description.description
; The [3] element of the PDB SCALE vector.
;
_item.name '_database_PDB_matrix.scale_vector[3]'
_item.category_id database_PDB_matrix
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
#########################
## DATABASE_PDB_REMARK ##
#########################
save_database_PDB_remark
_category.description
; Data items in the DATABASE_PDB_REMARK category record details
about the data block as archived by the Protein Data Bank (PDB).
Some data appearing in PDB REMARK records can be
algorithmically extracted into the appropriate data items
in the data block.
These data items are included only for consistency with older
PDB format files. They should appear in a data block only if
that data block was created by reformatting a PDB format file.
;
_category.id database_PDB_remark
_category.mandatory_code no
_category_key.name '_database_PDB_remark.id'
loop_
_category_group.id 'inclusive_group'
'database_group'
'pdb_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_database_PDB_remark.id
_database_PDB_remark.text
3
; REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J.
KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R
VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION
RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I).
RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF
SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED
STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE
WEIGHTS OF THE CORRESPONDING RESTRAINTS)
DISTANCE RESTRAINTS (ANGSTROMS)
BOND DISTANCE 0.018(0.020)
ANGLE DISTANCE 0.038(0.030)
PLANAR 1-4 DISTANCE 0.043(0.040)
PLANE RESTRAINT (ANGSTROMS) 0.015(0.020)
CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150)
NON-BONDED CONTACT RESTRAINTS (ANGSTROMS)
SINGLE TORSION CONTACT 0.216(0.500)
MULTIPLE TORSION CONTACT 0.207(0.500)
POSSIBLE HYDROGEN BOND 0.245(0.500)
CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES)
PLANAR (OMEGA) 2.6(3.0)
STAGGERED 17.4(15.0)
ORTHONORMAL 18.1(20.0)
;
4
; THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE
THE CHAIN INDICATORS *A* AND *B*.
;
# - - - - data truncated for brevity - - - -
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__database_PDB_remark.id
_item_description.description
; A unique identifier for the PDB remark record.
;
_item.name '_database_PDB_remark.id'
_item.category_id database_PDB_remark
_item.mandatory_code yes
_item_type.code int
save_
save__database_PDB_remark.text
_item_description.description
; The full text of the PDB remark record.
;
_item.name '_database_PDB_remark.text'
_item.category_id database_PDB_remark
_item.mandatory_code no
_item_type.code text
save_
######################
## DATABASE_PDB_REV ##
######################
save_database_PDB_rev
_category.description
; Data items in the DATABASE_PDB_REV category record details
about the history of the data block as archived by the Protein
Data Bank (PDB).
These data items are assigned by the PDB database managers and
should only appear in a data block if they originate from that
source.
;
_category.id database_PDB_rev
_category.mandatory_code no
_category_key.name '_database_PDB_rev.num'
loop_
_category_group.id 'inclusive_group'
'database_group'
'pdb_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_database_PDB_rev.num
_database_PDB_rev.author_name
_database_PDB_rev.date
_database_PDB_rev.date_original
_database_PDB_rev.status
_database_PDB_rev.mod_type
1 'Fitzgerald, Paula M.D' 1991-10-15 1990-04-30
'full release' 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__database_PDB_rev.author_name
_item_description.description
; The name of the person responsible for submitting this revision
to the PDB.
The family name(s) followed by a comma precedes the first
name(s) or initial(s).
;
_item.name '_database_PDB_rev.author_name'
_item.category_id database_PDB_rev
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
save_
save__database_PDB_rev.date
_item_description.description
; Date the PDB revision took place. Taken from the REVDAT record.
;
_item.name '_database_PDB_rev.date'
_item.category_id database_PDB_rev
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__database_PDB_rev.date_original
_item_description.description
; Date the entry first entered the PDB database in the form
yyyy-mm-dd. Taken from the PDB HEADER record.
;
_item.name '_database_PDB_rev.date_original'
_item.category_id database_PDB_rev
_item.mandatory_code no
_item_type.code yyyy-mm-dd
_item_examples.case '1980-08-21'
save_
save__database_PDB_rev.mod_type
_item_description.description
; Taken from the REVDAT record. Refer to the Protein Data Bank
format description at
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
for details.
;
_item.name '_database_PDB_rev.mod_type'
_item.category_id database_PDB_rev
_item.mandatory_code no
_item_type.code int
loop_
_item_enumeration.value
_item_enumeration.detail 0 'initial entry'
1 'all other types of modification'
2 'modifications to CONECT records'
3
; modifications affecting the coordinates
or their transforms (CRYST1, ORIGX, SCALE,
MTRIX, TVECT, ATOM, HETATM, SIGATM
records)
;
4
;
layer 1 to layer 2 revision which may affect
all record types
;
5 'data uniformity processing'
save_
save__database_PDB_rev.num
_item_description.description
; The value of _database_PDB_rev.num must uniquely and
sequentially identify a record in the DATABASE_PDB_REV list.
Note that this item must be a number and that modification
numbers are assigned in increasing numerical order.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_database_PDB_rev.num' database_PDB_rev yes
'_database_PDB_rev_record.rev_num' database_PDB_rev_record yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_database_PDB_rev_record.rev_num' '_database_PDB_rev.num'
_item_type.code int
save_
save__database_PDB_rev.replaced_by
_item_description.description
; The PDB code for a subsequent PDB entry that replaced the
PDB file corresponding to this data block.
;
_item.name '_database_PDB_rev.replaced_by'
_item.category_id database_PDB_rev
_item.mandatory_code no
_item_type.code line
save_
save__database_PDB_rev.replaces
_item_description.description
; The PDB code for a previous PDB entry that was replaced by
the PDB file corresponding to this data block.
;
_item.name '_database_PDB_rev.replaces'
_item.category_id database_PDB_rev
_item.mandatory_code no
_item_type.code line
save_
save__database_PDB_rev.status
_item_description.description
; The status of this revision.
;
_item.name '_database_PDB_rev.status'
_item.category_id database_PDB_rev
_item.mandatory_code no
_item_type.code uline
loop_
_item_enumeration.value 'in preparation'
'prerelease'
'full release'
'obsolete'
save_
#############################
## DATABASE_PDB_REV_RECORD ##
#############################
save_database_PDB_rev_record
_category.description
; Data items in the DATABASE_PDB_REV_RECORD category record
details about specific record types that were changed in a
given revision of a PDB entry.
These data items are assigned by the PDB database managers and
should only appear in a data block if they originate from that
source.
;
_category.id database_PDB_rev_record
_category.mandatory_code no
loop_
_category_key.name '_database_PDB_rev_record.rev_num'
'_database_PDB_rev_record.type'
loop_
_category_group.id 'inclusive_group'
'database_group'
'pdb_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - hypothetical example.
;
;
loop_
_database_PDB_rev_record.rev_num
_database_PDB_rev_record.type
_database_PDB_rev_record.details
1 CONECT
; Error fix - incorrect connection between
atoms 2312 and 2317
;
2 MATRIX 'For consistency with 1995-08-04 style-guide'
3 ORIGX 'Based on new data from author'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__database_PDB_rev_record.details
_item_description.description
; A description of special aspects of the revision of records in
this PDB entry.
;
_item.name '_database_PDB_rev_record.details'
_item.category_id database_PDB_rev_record
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'Based on new data from author'
'For consistency with 1995-08-04 style-guide'
'For consistency with structural class'
save_
save__database_PDB_rev_record.rev_num
_item_description.description
; This data item is a pointer to _database_PDB_rev.num in the
DATABASE_PDB_REV category.
;
_item.name '_database_PDB_rev_record.rev_num'
_item.mandatory_code yes
save_
save__database_PDB_rev_record.type
_item_description.description
; The types of records that were changed in this revision to a
PDB entry.
;
_item.name '_database_PDB_rev_record.type'
_item.category_id database_PDB_rev_record
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case 'CRYST1'
'SCALE'
'MTRIX'
'ATOM'
'HETATM'
save_
########################
## DATABASE_PDB_TVECT ##
########################
save_database_PDB_tvect
_category.description
; The DATABASE_PDB_TVECT category provides placeholders for
the TVECT matrices and vectors used by the Protein Data
Bank (PDB).
These data items are included only for consistency with older
PDB format files. They should appear in a data block only if
the data block was created by reformatting a PDB format file.
;
_category.id database_PDB_tvect
_category.mandatory_code no
_category_key.name '_database_PDB_tvect.id'
loop_
_category_group.id 'inclusive_group'
'database_group'
'pdb_group'
save_
save__database_PDB_tvect.details
_item_description.description
; A description of special aspects of this TVECT.
;
_item.name '_database_PDB_tvect.details'
_item.category_id database_PDB_tvect
_item.mandatory_code no
_item_type.code text
save_
save__database_PDB_tvect.id
_item_description.description
; The value of _database_PDB_tvect.id must uniquely identify a
record in the DATABASE_PDB_TVECT list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_database_PDB_tvect.id'
_item.category_id database_PDB_tvect
_item.mandatory_code yes
_item_type.code code
save_
save__database_PDB_tvect.vector[1]
_item_description.description
; The [1] element of the PDB TVECT vector.
;
_item.name '_database_PDB_tvect.vector[1]'
_item.category_id database_PDB_tvect
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__database_PDB_tvect.vector[2]
_item_description.description
; The [2] element of the PDB TVECT vector.
;
_item.name '_database_PDB_tvect.vector[2]'
_item.category_id database_PDB_tvect
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__database_PDB_tvect.vector[3]
_item_description.description
; The [3] element of the PDB TVECT vector.
;
_item.name '_database_PDB_tvect.vector[3]'
_item.category_id database_PDB_tvect
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
############
## DIFFRN ##
############
save_diffrn
_category.description
; Data items in the DIFFRN category record details about the
diffraction data and their measurement.
;
_category.id diffrn
_category.mandatory_code no
_category_key.name '_diffrn.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn.id 'Set1'
_diffrn.ambient_temp 293(3)
_diffrn.ambient_environment
; Mother liquor from the reservoir of the vapor diffusion
experiment, mounted in room air
;
_diffrn.crystal_support
; 0.7 mm glass capillary, sealed with dental wax
;
_diffrn.crystal_treatment
; Equilibrated in rotating anode radiation enclosure for
18 hours prior to beginning of data collection
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn.id 'd1'
_diffrn.details
; \q scan width (1.0 + 0.14tan\q)\%, \q scan rate 1.2\% per
min. Background counts for 5 sec on each side every scan.
;
_diffrn.ambient_temp 293
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn.ambient_environment
_item_description.description
; The gas or liquid surrounding the sample, if not air.
;
_item.name '_diffrn.ambient_environment'
_item.category_id diffrn
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_ambient_environment'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
#save__diffrn.ambient_pressure
# _item_description.description
#; The mean pressure in kilopascals at which the intensities were
# measured.
#;
# _item.name '_diffrn.ambient_pressure'
# _item.category_id diffrn
# _item.mandatory_code no
# _item_aliases.alias_name '_diffrn_ambient_pressure'
# _item_aliases.dictionary cif_core.dic
# _item_aliases.version 2.0.1
# loop_
# _item_range.maximum
# _item_range.minimum . 0.0
# 0.0 0.0
# _item_related.related_name '_diffrn.ambient_pressure_esd'
# _item_related.function_code associated_esd
# _item_type.code float
# _item_type_conditions.code esd
# _item_units.code kilopascals
# save_
#
#save__diffrn.ambient_pressure_esd
# _item_description.description
#; The standard uncertainty (estimated standard deviation)
# of _diffrn.ambient_pressure.
#;
# _item.name '_diffrn.ambient_pressure_esd'
# _item.category_id diffrn
# _item.mandatory_code no
# _item_default.value 0.0
# _item_related.related_name '_diffrn.ambient_pressure'
# _item_related.function_code associated_value
# _item_type.code float
# _item_units.code kilopascals
# save_
save__diffrn.ambient_temp
_item_description.description
; The mean temperature in kelvins at which the intensities were
measured.
;
_item.name '_diffrn.ambient_temp'
_item.category_id diffrn
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_ambient_temperature'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_diffrn.ambient_temp_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code kelvins
save_
save__diffrn.ambient_temp_details
_item_description.description
; A description of special aspects of temperature control during
data collection.
;
_item.name '_diffrn.ambient_temp_details'
_item.category_id diffrn
_item.mandatory_code no
_item_type.code text
save_
save__diffrn.ambient_temp_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _diffrn.ambient_temp.
;
_item.name '_diffrn.ambient_temp_esd'
_item.category_id diffrn
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_diffrn.ambient_temp'
_item_related.function_code associated_value
_item_type.code float
_item_units.code kelvins
save_
save__diffrn.crystal_id
_item_description.description
; This data item is a pointer to _exptl_crystal.id in the
EXPTL_CRYSTAL category.
;
_item.name '_diffrn.crystal_id'
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_refln_crystal_id'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__diffrn.crystal_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn.crystal_support'
_item.category_id diffrn
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
save__diffrn.crystal_treatment
_item_description.description
; Remarks about how the crystal was treated prior to intensity
measurement. Particularly relevant when intensities were
measured at low temperature.
;
_item.name '_diffrn.crystal_treatment'
_item.category_id diffrn
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_crystal_treatment'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'equilibrated in hutch for 24 hours'
'flash frozen in liquid nitrogen'
'slow cooled with direct air stream'
save_
save__diffrn.details
_item_description.description
; Special details of the diffraction measurement process. Should
include information about source instability, crystal motion,
degradation and so on.
;
_item.name '_diffrn.details'
_item.category_id diffrn
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_special_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__diffrn.id
_item_description.description
; This data item uniquely identifies a set of diffraction
data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn.id' diffrn yes
'_diffrn_detector.diffrn_id' diffrn_detector yes
'_diffrn_measurement.diffrn_id' diffrn_measurement yes
'_diffrn_orient_matrix.diffrn_id' diffrn_orient_matrix yes
'_diffrn_orient_refln.diffrn_id' diffrn_orient_refln yes
'_diffrn_radiation.diffrn_id' diffrn_radiation yes
'_diffrn_refln.diffrn_id' diffrn_refln yes
'_diffrn_reflns.diffrn_id' diffrn_reflns yes
'_diffrn_source.diffrn_id' diffrn_source yes
'_diffrn_standard_refln.diffrn_id' diffrn_standard_refln yes
'_diffrn_standards.diffrn_id' diffrn_standards yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector.diffrn_id' '_diffrn.id'
'_diffrn_measurement.diffrn_id' '_diffrn.id'
'_diffrn_orient_matrix.diffrn_id' '_diffrn.id'
'_diffrn_orient_refln.diffrn_id' '_diffrn.id'
'_diffrn_radiation.diffrn_id' '_diffrn.id'
'_diffrn_refln.diffrn_id' '_diffrn.id'
'_diffrn_reflns.diffrn_id' '_diffrn.id'
'_diffrn_source.diffrn_id' '_diffrn.id'
'_diffrn_standard_refln.diffrn_id' '_diffrn.id'
'_diffrn_standards.diffrn_id' '_diffrn.id'
_item_type.code code
save_
#######################
## DIFFRN_ATTENUATOR ##
#######################
save_diffrn_attenuator
_category.description
; Data items in the DIFFRN_ATTENUATOR category record details
about the diffraction attenuator scales employed.
;
_category.id diffrn_attenuator
_category.mandatory_code no
_category_key.name '_diffrn_attenuator.code'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_attenuator.code 1
_diffrn_attenuator.scale 16.976
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_attenuator.code
_item_description.description
; A code associated with a particular attenuator setting. This
code is referenced by the _diffrn_refln.attenuator_code which is
stored with the diffraction data. See _diffrn_attenuator.scale.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_attenuator.code' diffrn_attenuator yes
_item_aliases.alias_name '_diffrn_attenuator_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.attenuator_code' '_diffrn_attenuator.code'
_item_type.code code
save_
save__diffrn_attenuator.scale
_item_description.description
; The scale factor applied when an intensity measurement is
reduced by an attenuator identified by _diffrn_attenuator.code.
The measured intensity must be multiplied by this scale to
convert it to the same scale as unattenuated intensities.
;
_item.name '_diffrn_attenuator.scale'
_item.category_id diffrn_attenuator
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_attenuator_scale'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 1.0
1.0 1.0
_item_type.code float
save_
#####################
## DIFFRN_DETECTOR ##
#####################
save_diffrn_detector
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
_category_key.name '_diffrn_detector.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
save_
#save__diffrn_detector.dtime
# _item_description.description
#; The deadtime in microseconds of the detectors used to measure
# the diffraction intensities.
#;
# _item.name '_diffrn_detector.dtime'
# _item.category_id diffrn_detector
# _item.mandatory_code no
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version '_diffrn_radiation_detector_dtime'
# cifdic.c91
# 1.0
# '_diffrn_detector_dtime'
# cif_core.dic
# 2.0
# loop_
# _item_range.maximum
# _item_range.minimum . 0.0
# 0.0 0.0
# _item_type.code float
# _item_units.code microseconds
# save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_diffrn_measurement
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the diffraction
data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
_category_key.name '_diffrn_measurement.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model x'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm,
detector angle 22.5 degrees
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type
'Philips PW1100/20 diffractometer'
_diffrn_measurement.method \q/2\q
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support and
orient the specimen.
;
_item.name '_diffrn_measurement.device'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to measure
the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'homemade'
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'profile data from theta/2theta scans'
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
##########################
## DIFFRN_ORIENT_MATRIX ##
##########################
save_diffrn_orient_matrix
_category.description
; Data items in the DIFFRN_ORIENT_MATRIX category record details
about the orientation matrix used in the measurement of the
diffraction data.
;
_category.id diffrn_orient_matrix
_category.mandatory_code no
_category_key.name '_diffrn_orient_matrix.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
;
;
_diffrn_orient_matrix.diffrn_id set1
_diffrn_orient_matrix.type
; reciprocal axis matrix, multiplies hkl vector to generate
diffractometer xyz vector and diffractometer angles
;
_diffrn_orient_matrix.UB[1][1] -0.071479
_diffrn_orient_matrix.UB[1][2] 0.020208
_diffrn_orient_matrix.UB[1][3] 0.039076
_diffrn_orient_matrix.UB[2][1] 0.035372
_diffrn_orient_matrix.UB[2][2] 0.056209
_diffrn_orient_matrix.UB[2][3] 0.078324
_diffrn_orient_matrix.UB[3][1] -0.007470
_diffrn_orient_matrix.UB[3][2] 0.067854
_diffrn_orient_matrix.UB[3][3] -0.017832
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_orient_matrix.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_orient_matrix.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_orient_matrix.type
_item_description.description
; A description of the orientation matrix type and how it should
be applied to define the orientation of the crystal precisely
with respect to the diffractometer axes.
;
_item.name '_diffrn_orient_matrix.type'
_item.category_id diffrn_orient_matrix
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__diffrn_orient_matrix.UB[1][1]
_item_description.description
; The [1][1] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also _diffrn_orient_matrix.type.
;
_item.name '_diffrn_orient_matrix.UB[1][1]'
_item.category_id diffrn_orient_matrix
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_11'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
save_
save__diffrn_orient_matrix.UB[1][2]
_item_description.description
; The [1][2] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also _diffrn_orient_matrix.type.
;
_item.name '_diffrn_orient_matrix.UB[1][2]'
_item.category_id diffrn_orient_matrix
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_12'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_orient_matrix.UB[1][3]
_item_description.description
; The [1][3] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also _diffrn_orient_matrix.type.
;
_item.name '_diffrn_orient_matrix.UB[1][3]'
_item.category_id diffrn_orient_matrix
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_13'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_orient_matrix.UB[2][1]
_item_description.description
; The [2][1] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also _diffrn_orient_matrix.type.
;
_item.name '_diffrn_orient_matrix.UB[2][1]'
_item.category_id diffrn_orient_matrix
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_21'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_orient_matrix.UB[2][2]
_item_description.description
; The [2][2] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also _diffrn_orient_matrix.type.
;
_item.name '_diffrn_orient_matrix.UB[2][2]'
_item.category_id diffrn_orient_matrix
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_22'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_orient_matrix.UB[2][3]
_item_description.description
; The [2][3] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also _diffrn_orient_matrix.type.
;
_item.name '_diffrn_orient_matrix.UB[2][3]'
_item.category_id diffrn_orient_matrix
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_23'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_orient_matrix.UB[3][1]
_item_description.description
; The [3][1] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also _diffrn_orient_matrix.type.
;
_item.name '_diffrn_orient_matrix.UB[3][1]'
_item.category_id diffrn_orient_matrix
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_31'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_orient_matrix.UB[3][2]
_item_description.description
; The [3][2] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also _diffrn_orient_matrix.type.
;
_item.name '_diffrn_orient_matrix.UB[3][2]'
_item.category_id diffrn_orient_matrix
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_32'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_orient_matrix.UB[3][3]
_item_description.description
; The [3][3] element of the 3x3 matrix that defines the dimensions
of the reciprocal cell and its orientation with respect to the
local diffractometer axes. See also _diffrn_orient_matrix.type.
;
_item.name '_diffrn_orient_matrix.UB[3][3]'
_item.category_id diffrn_orient_matrix
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_matrix_UB_33'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
#########################
## DIFFRN_ORIENT_REFLN ##
#########################
save_diffrn_orient_refln
_category.description
; Data items in the DIFFRN_ORIENT_REFLN category record details
about the reflections that define the orientation matrix used in
the measurement of the diffraction intensities.
;
_category.id diffrn_orient_refln
_category.mandatory_code no
loop_
_category_key.name '_diffrn_orient_refln.diffrn_id'
'_diffrn_orient_refln.index_h'
'_diffrn_orient_refln.index_k'
'_diffrn_orient_refln.index_l'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
;
;
_diffrn_orient_refln.diffrn_id myset1
_diffrn_orient_refln.index_h 2
_diffrn_orient_refln.index_k 0
_diffrn_orient_refln.index_l 2
_diffrn_orient_refln.angle_chi -28.45
_diffrn_orient_refln.angle_kappa -11.32
_diffrn_orient_refln.angle_omega 5.33
_diffrn_orient_refln.angle_phi 101.78
_diffrn_orient_refln.angle_psi 0.00
_diffrn_orient_refln.angle_theta 10.66
# ... data abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_orient_refln.angle_chi
_item_description.description
; Diffractometer angle chi of a reflection used to
define the orientation matrix in degrees. See
_diffrn_orient_matrix.UB[][] and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
;
_item.name '_diffrn_orient_refln.angle_chi'
_item.category_id diffrn_orient_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_refln_angle_chi'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.angle_kappa'
'_diffrn_orient_refln.angle_omega'
'_diffrn_orient_refln.angle_phi'
'_diffrn_orient_refln.angle_psi'
'_diffrn_orient_refln.angle_theta'
_item_type.code float
_item_units.code degrees
save_
save__diffrn_orient_refln.angle_kappa
_item_description.description
; Diffractometer angle kappa of a reflection used to
define the orientation matrix in degrees. See
_diffrn_orient_matrix.UB[][] and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
;
_item.name '_diffrn_orient_refln.angle_kappa'
_item.category_id diffrn_orient_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_refln_angle_kappa'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.angle_chi'
'_diffrn_orient_refln.angle_omega'
'_diffrn_orient_refln.angle_phi'
'_diffrn_orient_refln.angle_psi'
'_diffrn_orient_refln.angle_theta'
_item_type.code float
_item_units.code degrees
save_
save__diffrn_orient_refln.angle_omega
_item_description.description
; Diffractometer angle omega of a reflection used to
define the orientation matrix in degrees. See
_diffrn_orient_matrix.UB[][] and the Miller indices in
the DIFFRN_ORIENT_REFLN category.
;
_item.name '_diffrn_orient_refln.angle_omega'
_item.category_id diffrn_orient_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_refln_angle_omega'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.angle_chi'
'_diffrn_orient_refln.angle_kappa'
'_diffrn_orient_refln.angle_phi'
'_diffrn_orient_refln.angle_psi'
'_diffrn_orient_refln.angle_theta'
_item_type.code float
_item_units.code degrees
save_
save__diffrn_orient_refln.angle_phi
_item_description.description
; Diffractometer angle phi of a reflection used to
define the orientation matrix in degrees. See
_diffrn_orient_matrix.UB[][] and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
;
_item.name '_diffrn_orient_refln.angle_phi'
_item.category_id diffrn_orient_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_refln_angle_phi'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.angle_chi'
'_diffrn_orient_refln.angle_kappa'
'_diffrn_orient_refln.angle_omega'
'_diffrn_orient_refln.angle_psi'
'_diffrn_orient_refln.angle_theta'
_item_type.code float
_item_units.code degrees
save_
save__diffrn_orient_refln.angle_psi
_item_description.description
; Diffractometer angle psi of a reflection used to
define the orientation matrix in degrees. See
_diffrn_orient_matrix.UB[][] and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
;
_item.name '_diffrn_orient_refln.angle_psi'
_item.category_id diffrn_orient_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_refln_angle_psi'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.angle_chi'
'_diffrn_orient_refln.angle_kappa'
'_diffrn_orient_refln.angle_omega'
'_diffrn_orient_refln.angle_phi'
'_diffrn_orient_refln.angle_theta'
_item_type.code float
_item_units.code degrees
save_
save__diffrn_orient_refln.angle_theta
_item_description.description
; Diffractometer angle theta of a reflection used to
define the orientation matrix in degrees. See
_diffrn_orient_matrix.UB[][] and the Miller indices
in the DIFFRN_ORIENT_REFLN category.
;
_item.name '_diffrn_orient_refln.angle_theta'
_item.category_id diffrn_orient_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_orient_refln_angle_theta'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.angle_chi'
'_diffrn_orient_refln.angle_kappa'
'_diffrn_orient_refln.angle_omega'
'_diffrn_orient_refln.angle_phi'
'_diffrn_orient_refln.angle_psi'
_item_type.code float
_item_units.code degrees
save_
save__diffrn_orient_refln.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_orient_refln.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_orient_refln.index_h
_item_description.description
; Miller index h of a reflection used to define the orientation
matrix.
;
_item.name '_diffrn_orient_refln.index_h'
_item.category_id diffrn_orient_refln
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_orient_refln_index_h'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.index_k'
'_diffrn_orient_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__diffrn_orient_refln.index_k
_item_description.description
; Miller index k of a reflection used to define the orientation
matrix.
;
_item.name '_diffrn_orient_refln.index_k'
_item.category_id diffrn_orient_refln
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_orient_refln_index_k'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.index_h'
'_diffrn_orient_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__diffrn_orient_refln.index_l
_item_description.description
; Miller index l of a reflection used to define the orientation
matrix.
;
_item.name '_diffrn_orient_refln.index_l'
_item.category_id diffrn_orient_refln
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_orient_refln_index_l'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_orient_refln.index_h'
'_diffrn_orient_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
######################
## DIFFRN_RADIATION ##
######################
save_diffrn_radiation
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used in measuring the diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
_category_key.name '_diffrn_radiation.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a mono-
chromator crystal is used, the material and the indices of the
Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See _diffrn_radiation.polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarization ratio of the diffraction beam incident on the
crystal. This is the ratio of the perpendicularly polarized
to the parallel-polarized component of the radiation. The
perpendicular component forms an angle of
_diffrn_radiation.polarisn_norm to the normal to the
diffraction plane of the sample (i.e. the plane containing
the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; The nature of the radiation used (i.e. the name of the
subatomic particle or the region of the electromagnetic
spectrum). It is strongly recommended that this information
is given, so that the probe radiation can be simply determined.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'x-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for the probe
radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to _diffrn_radiation_wavelength.id
in the DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.mandatory_code yes
save_
#################################
## DIFFRN_RADIATION_WAVELENGTH ##
#################################
save_diffrn_radiation_wavelength
_category.description
; Data items in the DIFFRN_RADIATION_WAVELENGTH category
describe the wavelength of the radiation used to measure the
diffraction intensities. Items may be looped to identify
and assign weights to distinct components of a
polychromatic beam.
;
_category.id diffrn_radiation_wavelength
_category.mandatory_code no
_category_key.name '_diffrn_radiation_wavelength.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 1.54
_diffrn_radiation_wavelength.wt 1.0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation_wavelength.id
_item_description.description
; The code identifying each value of
_diffrn_radiation_wavelength.wavelength.
Items in the DIFFRN_RADIATION_WAVELENGTH category are looped
when multiple wavelengths are used.
This code is used to link with the DIFFRN_REFLN category.
The _diffrn_refln.wavelength_id codes must match one of
the codes defined in this category.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_radiation_wavelength.id' diffrn_radiation_wavelength yes
'_diffrn_radiation.wavelength_id' diffrn_radiation yes
'_diffrn_refln.wavelength_id' diffrn_refln yes
'_refln.wavelength_id' refln yes
_item_aliases.alias_name '_diffrn_radiation_wavelength_id'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_radiation.wavelength_id' '_diffrn_radiation_wavelength.id'
'_diffrn_refln.wavelength_id' '_diffrn_radiation_wavelength.id'
'_refln.wavelength_id' '_diffrn_radiation_wavelength.id'
_item_type.code code
loop_
_item_examples.case 'x1'
'x2'
'neut'
save_
save__diffrn_radiation_wavelength.wavelength
_item_description.description
; The radiation wavelength in angstroms.
;
_item.name '_diffrn_radiation_wavelength.wavelength'
_item.category_id diffrn_radiation_wavelength
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_radiation_wavelength'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation_wavelength.wt
_item_description.description
; The relative weight of a wavelength identified by the code
_diffrn_radiation_wavelength.id in the list of wavelengths.
;
_item.name '_diffrn_radiation_wavelength.wt'
_item.category_id diffrn_radiation_wavelength
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_wavelength_wt'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1.0
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 0.0
0.0 0.0
_item_type.code float
save_
##################
## DIFFRN_REFLN ##
##################
save_diffrn_refln
_category.description
; Data items in the DIFFRN_REFLN category record details about
the intensities in the diffraction data set
identified by _diffrn_refln.diffrn_id.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in the particular diffraction
data set identified by _diffrn_reflns.diffrn_id.
;
_category.id diffrn_refln
_category.mandatory_code no
loop_
_category_key.name '_diffrn_refln.diffrn_id'
'_diffrn_refln.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4 for data set 'set1' reflection 1102.
;
;
_diffrn_refln.diffrn_id set1
_diffrn_refln.id 1102
_diffrn_refln.wavelength_id Cu1fixed
_diffrn_refln.angle_chi 32.21
_diffrn_refln.angle_kappa 20.12
_diffrn_refln.angle_omega 11.54
_diffrn_refln.angle_phi 176.02
_diffrn_refln.angle_psi 0.00
_diffrn_refln.angle_theta 23.08
_diffrn_refln.attenuator_code 'Ni.005'
_diffrn_refln.counts_bg_1 22
_diffrn_refln.counts_bg_2 25
_diffrn_refln.counts_net 3450
_diffrn_refln.counts_peak 321
_diffrn_refln.counts_total 3499
_diffrn_refln.detect_slit_horiz 0.04
_diffrn_refln.detect_slit_vert 0.02
_diffrn_refln.elapsed_time 1.00
_diffrn_refln.index_h 4
_diffrn_refln.index_k 0
_diffrn_refln.index_l 2
_diffrn_refln.intensity_net 202.56
_diffrn_refln.intensity_sigma 2.18
_diffrn_refln.scale_group_code A24
_diffrn_refln.scan_mode om
_diffrn_refln.scan_mode_backgd mo
_diffrn_refln.scan_rate 1.2
_diffrn_refln.scan_time_backgd 900.00
_diffrn_refln.scan_width 1.0
_diffrn_refln.sint_over_lambda 0.25426
_diffrn_refln.standard_code 1
_diffrn_refln.wavelength 1.54184
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_refln.angle_chi
_item_description.description
; The diffractometer angle chi of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_chi'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_chi'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__diffrn_refln.angle_kappa
_item_description.description
; The diffractometer angle kappa of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_kappa'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_kappa'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__diffrn_refln.angle_omega
_item_description.description
; The diffractometer angle omega of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_omega'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_omega'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__diffrn_refln.angle_phi
_item_description.description
; The diffractometer angle phi of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_phi'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_phi'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__diffrn_refln.angle_psi
_item_description.description
; The diffractometer angle psi of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_psi'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_psi'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__diffrn_refln.angle_theta
_item_description.description
; The diffractometer angle theta of a reflection in degrees. This
angle corresponds to the specified orientation matrix
and the original measured cell before any subsequent cell
transformations.
;
_item.name '_diffrn_refln.angle_theta'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_angle_theta'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__diffrn_refln.attenuator_code
_item_description.description
; The code identifying the attenuator setting for this reflection.
This code must match one of the _diffrn_attenuator.code values.
;
_item.name '_diffrn_refln.attenuator_code'
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_attenuator_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__diffrn_refln.counts_bg_1
_item_description.description
; The diffractometer counts for the measurement of the background
before the peak.
;
_item.name '_diffrn_refln.counts_bg_1'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_counts_bg_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__diffrn_refln.counts_bg_2
_item_description.description
; The diffractometer counts for the measurement of the background
after the peak.
;
_item.name '_diffrn_refln.counts_bg_2'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_counts_bg_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__diffrn_refln.counts_net
_item_description.description
; The diffractometer counts for the measurement of net counts after
background removal.
;
_item.name '_diffrn_refln.counts_net'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_counts_net'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__diffrn_refln.counts_peak
_item_description.description
; The diffractometer counts for the measurement of counts for the
peak scan or position.
;
_item.name '_diffrn_refln.counts_peak'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_counts_peak'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__diffrn_refln.counts_total
_item_description.description
; The diffractometer counts for the measurement of total counts
(background plus peak).
;
_item.name '_diffrn_refln.counts_total'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_counts_total'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__diffrn_refln.detect_slit_horiz
_item_description.description
; Total slit aperture in degrees in the diffraction plane.
;
_item.name '_diffrn_refln.detect_slit_horiz'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_detect_slit_horiz'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_refln.detect_slit_vert
_item_description.description
; Total slit aperture in degrees perpendicular to the
diffraction plane.
;
_item.name '_diffrn_refln.detect_slit_vert'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_detect_slit_vert'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_refln.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_refln.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_refln.elapsed_time
_item_description.description
; Elapsed time in minutes from the start of the diffraction
experiment to the measurement of this intensity.
;
_item.name '_diffrn_refln.elapsed_time'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_elapsed_time'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code minutes
save_
save__diffrn_refln.id
_item_description.description
; The value of _diffrn_refln.id must uniquely identify the
reflection in the data set identified by the item
_diffrn_refln.diffrn_id.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_diffrn_refln.id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_refln.index_h
_item_description.description
; Miller index h of a reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Miller indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are given in
_diffrn_reflns.reduction_process. See also
_diffrn_reflns.transf_matrix[][].
;
_item.name '_diffrn_refln.index_h'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_refln_index_h'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_refln.index_h'
'_diffrn_refln.index_k'
_item_sub_category.id miller_index
_item_type.code int
save_
save__diffrn_refln.index_k
_item_description.description
; Miller index k of a reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Miller indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are given in
_diffrn_reflns.reduction_process. See also
_diffrn_reflns.transf_matrix[][].
;
_item.name '_diffrn_refln.index_k'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_refln_index_k'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_refln.index_h'
'_diffrn_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__diffrn_refln.index_l
_item_description.description
; Miller index l of a reflection. The values of
the Miller indices in the DIFFRN_REFLN category need not match
the values of the Miller indices in the REFLN category if a
transformation of the original measured cell has taken place.
Details of the cell transformation are given in
_diffrn_reflns.reduction_process. See also
_diffrn_reflns.transf_matrix[][].
;
_item.name '_diffrn_refln.index_l'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_refln_index_l'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_refln.index_h'
'_diffrn_refln.index_k'
_item_sub_category.id miller_index
_item_type.code int
save_
save__diffrn_refln.intensity_net
_item_description.description
; Net intensity calculated from the diffraction counts after the
attenuator and standard scales have been applied.
;
_item.name '_diffrn_refln.intensity_net'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_intensity_net'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code float
save_
save__diffrn_refln.intensity_sigma
_item_description.description
; Standard uncertainty (estimated standard deviation) of the
intensity calculated from the diffraction counts after the
attenuator and standard scales have been applied.
;
_item.name '_diffrn_refln.intensity_sigma'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_intensity_sigma'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code float
save_
save__diffrn_refln.scale_group_code
_item_description.description
; The code identifying the scale applying to this reflection.
This data item is a pointer to _diffrn_scale_group.code in the
DIFFRN_SCALE_GROUP category.
;
_item.name '_diffrn_refln.scale_group_code'
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_refln_scale_group_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__diffrn_refln.scan_mode
_item_description.description
; The code identifying the mode of scanning for measurements
using a diffractometer.
See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd.
;
_item.name '_diffrn_refln.scan_mode'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_scan_mode'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail om 'omega scan'
ot 'omega/2theta scan'
q 'Q scans (arbitrary reciprocal directions)'
save_
save__diffrn_refln.scan_mode_backgd
_item_description.description
; The code identifying the mode of scanning a reflection to
measure the background intensity.
;
_item.name '_diffrn_refln.scan_mode_backgd'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_scan_mode_backgd'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail st 'stationary counter background'
mo 'moving counter background'
save_
save__diffrn_refln.scan_rate
_item_description.description
; The rate of scanning a reflection in degrees per minute
to measure the intensity.
;
_item.name '_diffrn_refln.scan_rate'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_scan_rate'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees_per_minute
save_
save__diffrn_refln.scan_time_backgd
_item_description.description
; The time spent measuring each background in seconds.
;
_item.name '_diffrn_refln.scan_time_backgd'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_scan_time_backgd'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code seconds
save_
save__diffrn_refln.scan_width
_item_description.description
; The scan width in degrees of the scan mode defined by the code
_diffrn_refln.scan_mode.
;
_item.name '_diffrn_refln.scan_width'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_scan_width'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_refln.sint_over_lambda
_item_description.description
; The (sin theta)/lambda value in reciprocal angstroms for this
reflection.
;
_item.name '_diffrn_refln.sint_over_lambda'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_sint/lambda'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code reciprocal_angstroms
save_
save__diffrn_refln.standard_code
_item_description.description
; The code identifying that this reflection was measured as a
standard intensity.
This data item is a pointer to _diffrn_standard_refln.code in the
DIFFRN_STANDARD_REFLN category.
;
_item.name '_diffrn_refln.standard_code'
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_refln_standard_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__diffrn_refln.wavelength
_item_description.description
; The mean wavelength in angstroms of the radiation used to measure
the intensity of this reflection. This is an important parameter
for data collected using energy-dispersive detectors or the
Laue method.
;
_item.name '_diffrn_refln.wavelength'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_refln_wavelength'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_refln.wavelength_id
_item_description.description
; This data item is a pointer to _diffrn_radiation.wavelength_id in
the DIFFRN_RADIATION category.
;
_item.name '_diffrn_refln.wavelength_id'
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_refln_wavelength_id'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
###################
## DIFFRN_REFLNS ##
###################
save_diffrn_reflns
_category.description
; Data items in the DIFFRN_REFLNS category record details about
the set of intensities measured in the diffraction experiment.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in a diffraction data set.
;
_category.id diffrn_reflns
_category.mandatory_code no
_category_key.name '_diffrn_reflns.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
# loop_
# _category_examples.detail
# _category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_reflns.av_R_equivalents
_item_description.description
; The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent
reflections used to calculate the average intensity av(I). The
avdel(I) term is the average absolute difference between av(I)
and the individual symmetry-equivalent intensities.
;
_item.name '_diffrn_reflns.av_R_equivalents'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_av_R_equivalents'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_reflns.av_sigmaI_over_netI
_item_description.description
; Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections.
;
_item.name '_diffrn_reflns.av_sigmaI_over_netI'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_av_sigmaI/netI'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_reflns.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_reflns.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_reflns.limit_h_max
_item_description.description
; The maximum value of the Miller index h for the
reflection data specified by _diffrn_refln.index_h.
;
_item.name '_diffrn_reflns.limit_h_max'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_h_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__diffrn_reflns.limit_h_min
_item_description.description
; The minimum value of the Miller index h for the
reflection data specified by _diffrn_refln.index_h.
;
_item.name '_diffrn_reflns.limit_h_min'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_h_min'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__diffrn_reflns.limit_k_max
_item_description.description
; The maximum value of the Miller index k for the
reflection data specified by _diffrn_refln.index_k.
;
_item.name '_diffrn_reflns.limit_k_max'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_k_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__diffrn_reflns.limit_k_min
_item_description.description
; The minimum value of the Miller index k for the
reflection data specified by _diffrn_refln.index_k.
;
_item.name '_diffrn_reflns.limit_k_min'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_k_min'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__diffrn_reflns.limit_l_max
_item_description.description
; The maximum value of the Miller index l for the
reflection data specified by _diffrn_refln.index_l.
;
_item.name '_diffrn_reflns.limit_l_max'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_l_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__diffrn_reflns.limit_l_min
_item_description.description
; The minimum value of the Miller index l for the
reflection data specified by _diffrn_refln.index_l.
;
_item.name '_diffrn_reflns.limit_l_min'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_limit_l_min'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__diffrn_reflns.number
_item_description.description
; The total number of measured intensities, excluding reflections
that are classified as systematically absent.
;
_item.name '_diffrn_reflns.number'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_number'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__diffrn_reflns.reduction_process
_item_description.description
; A description of the process used to reduce the intensity data
into structure-factor magnitudes.
;
_item.name '_diffrn_reflns.reduction_process'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_reduction_process'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'data averaged using Fisher test'
save_
save__diffrn_reflns.theta_max
_item_description.description
; Maximum theta angle in degrees for the measured diffraction
intensities.
;
_item.name '_diffrn_reflns.theta_max'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_theta_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_reflns.theta_min
_item_description.description
; Minimum theta angle in degrees for the measured diffraction
intensities.
;
_item.name '_diffrn_reflns.theta_min'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_theta_min'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_reflns.transf_matrix[1][1]
_item_description.description
; The [1][1] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
;
_item.name '_diffrn_reflns.transf_matrix[1][1]'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_11'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_reflns.transf_matrix[1][2]
_item_description.description
; The [1][2] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
;
_item.name '_diffrn_reflns.transf_matrix[1][2]'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_12'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_reflns.transf_matrix[1][3]
_item_description.description
; The [1][3] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
;
_item.name '_diffrn_reflns.transf_matrix[1][3]'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_13'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_reflns.transf_matrix[2][1]
_item_description.description
; The [2][1] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
;
_item.name '_diffrn_reflns.transf_matrix[2][1]'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_21'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_reflns.transf_matrix[2][2]
_item_description.description
; The [2][2] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
;
_item.name '_diffrn_reflns.transf_matrix[2][2]'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_22'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_reflns.transf_matrix[2][3]
_item_description.description
; The [2][3] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
;
_item.name '_diffrn_reflns.transf_matrix[2][3]'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_23'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_reflns.transf_matrix[3][1]
_item_description.description
; The [3][1] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
;
_item.name '_diffrn_reflns.transf_matrix[3][1]'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_31'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_reflns.transf_matrix[3][2]
_item_description.description
; The [3][2] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
;
_item.name '_diffrn_reflns.transf_matrix[3][2]'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_32'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
save__diffrn_reflns.transf_matrix[3][3]
_item_description.description
; The [3][3] element of the 3x3 matrix used to transform Miller
indices in the DIFFRN_REFLN category into the Miller indices in
the REFLN category.
;
_item.name '_diffrn_reflns.transf_matrix[3][3]'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_reflns_transf_matrix_33'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_sub_category.id matrix
_item_type.code float
save_
########################
## DIFFRN_SCALE_GROUP ##
########################
save_diffrn_scale_group
_category.description
; Data items in the DIFFRN_SCALE_GROUP category record details
of the scaling factors applied to place all intensities in the
reflection lists on a common scale.
Scaling groups might, for example, correspond to each film in a
multi-film data set or each crystal in a multi-crystal data set.
;
_category.id diffrn_scale_group
_category.mandatory_code no
_category_key.name '_diffrn_scale_group.code'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on CAD-4 diffractometer data obtained for
Yb(S-C5H4N)2(THF)4.
;
;
_diffrn_scale_group.code A24
_diffrn_scale_group.I_net 1.021
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scale_group.code
_item_description.description
; The value of _diffrn_scale_group.code must uniquely identify a
record in the DIFFRN_SCALE_GROUP list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scale_group.code' diffrn_scale_group yes
'_diffrn_refln.scale_group_code' diffrn_refln yes
_item_aliases.alias_name '_diffrn_scale_group_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.scale_group_code' '_diffrn_scale_group.code'
_item_type.code code
loop_
_item_examples.case '1'
'2'
'c1'
'c2'
save_
save__diffrn_scale_group.I_net
_item_description.description
; The scale for a specific measurement group which is to be
multiplied with the net intensity to place all intensities
in the DIFFRN_REFLN or REFLN list on a common scale.
;
_item.name '_diffrn_scale_group.I_net'
_item.category_id diffrn_scale_group
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_scale_group_I_net'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
###################
## DIFFRN_SOURCE ##
###################
save_diffrn_source
_category.description
; Data items in the DIFFRN_SOURCE category record details of
the source of radiation used in the diffraction experiment.
;
_category.id diffrn_source
_category.mandatory_code no
_category_key.name '_diffrn_source.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_source.diffrn_id 's1'
_diffrn_source.source 'rotating anode'
_diffrn_source.type 'Rigaku RU-200'
_diffrn_source.power 50
_diffrn_source.current 180
_diffrn_source.size '8mm x 0.4 mm broad-focus'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_source.current
_item_description.description
; The current in milliamperes at which the radiation source
was operated.
;
_item.name '_diffrn_source.current'
_item.category_id diffrn_source
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_source_current'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code milliamperes
save_
save__diffrn_source.details
_item_description.description
; A description of special aspects of the radiation source used.
;
_item.name '_diffrn_source.details'
_item.category_id diffrn_source
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_source_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__diffrn_source.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_source.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_source.power
_item_description.description
; The power in kilowatts at which the radiation source
was operated.
;
_item.name '_diffrn_source.power'
_item.category_id diffrn_source
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_source_power'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code kilowatts
save_
save__diffrn_source.size
_item_description.description
; The dimensions of the source as viewed from the sample.
;
_item.name '_diffrn_source.size'
_item.category_id diffrn_source
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_source_size'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '8mm x 0.4 mm fine-focus'
'broad focus'
save_
save__diffrn_source.source
_item_description.description
; The general class of the radiation source.
;
_item.name '_diffrn_source.source'
_item.category_id diffrn_source
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_source'
cifdic.c91
1.0
'_diffrn_source'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'sealed X-ray tube'
'nuclear reactor'
'spallation source'
'electron microscope'
'rotating-anode X-ray tube'
'synchrotron'
save_
save__diffrn_source.target
_item_description.description
; The chemical element symbol for the X-ray target
(usually the anode) used to generate X-rays.
This can also be used for spallation sources.
;
_item.name '_diffrn_source.target'
_item.category_id diffrn_source
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_source_target'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
loop_
_item_enumeration.value
H He Li Be B C N O F Ne Na Mg Al Si P S Cl
Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge
As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag
Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm
Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir
Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U
Np Pu Am Cm Bk Cf Es Fm Md No Lr
save_
save__diffrn_source.type
_item_description.description
; The make, model or name of the source of radiation.
;
_item.name '_diffrn_source.type'
_item.category_id diffrn_source
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_source_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'NSLS beamline X8C'
'Rigaku RU200'
save_
save__diffrn_source.voltage
_item_description.description
; The voltage in kilovolts at which the radiation source was
operated.
;
_item.name '_diffrn_source.voltage'
_item.category_id diffrn_source
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_source_voltage'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code kilovolts
save_
###########################
## DIFFRN_STANDARD_REFLN ##
###########################
save_diffrn_standard_refln
_category.description
; Data items in the DIFFRN_STANDARD_REFLN category record details
about the reflections treated as standards during the measurement
of a set of diffraction intensities.
Note that these are the individual standard reflections, not the
results of the analysis of the standard reflections.
;
_category.id diffrn_standard_refln
_category.mandatory_code no
loop_
_category_key.name '_diffrn_standard_refln.diffrn_id'
'_diffrn_standard_refln.code'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
loop_
_diffrn_standard_refln.diffrn_id
_diffrn_standard_refln.code
_diffrn_standard_refln.index_h
_diffrn_standard_refln.index_k
_diffrn_standard_refln.index_l
s1 1 3 2 4
s1 1 1 9 1
s1 1 3 0 10
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_standard_refln.code
_item_description.description
; The code identifying a reflection measured as a standard
reflection with the indices _diffrn_standard_refln.index_h,
_diffrn_standard_refln.index_k and
_diffrn_standard_refln.index_l. This is the same code as the
_diffrn_refln.standard_code in the DIFFRN_REFLN list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_standard_refln.code' diffrn_standard_refln yes
'_diffrn_refln.standard_code' diffrn_refln yes
_item_aliases.alias_name '_diffrn_standard_refln_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.standard_code' '_diffrn_standard_refln.code'
_item_type.code code
loop_
_item_examples.case '1'
'2'
'c1'
'c2'
save_
save__diffrn_standard_refln.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_standard_refln.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_standard_refln.index_h
_item_description.description
; Miller index h of a standard reflection used in the diffraction
measurement process.
;
_item.name '_diffrn_standard_refln.index_h'
_item.category_id diffrn_standard_refln
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_standard_refln_index_h'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_standard_refln.index_k'
'_diffrn_standard_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__diffrn_standard_refln.index_k
_item_description.description
; Miller index k of a standard reflection used in the diffraction
measurement process.
;
_item.name '_diffrn_standard_refln.index_k'
_item.category_id diffrn_standard_refln
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_standard_refln_index_k'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_standard_refln.index_h'
'_diffrn_standard_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__diffrn_standard_refln.index_l
_item_description.description
; Miller index l of a standard reflection used in the diffraction
measurement process.
;
_item.name '_diffrn_standard_refln.index_l'
_item.category_id diffrn_standard_refln
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_standard_refln_index_l'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_diffrn_standard_refln.index_h'
'_diffrn_standard_refln.index_k'
_item_sub_category.id miller_index
_item_type.code int
save_
######################
## DIFFRN_STANDARDS ##
######################
save_diffrn_standards
_category.description
; Data items in the DIFFRN_STANDARDS category record details
about the set of standard reflections used to monitor intensity
stability during the measurement of diffraction intensities.
Note that these records describe properties common to the set of
standard reflections, not the standard reflections themselves.
;
_category.id diffrn_standards
_category.mandatory_code no
_category_key.name '_diffrn_standards.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_standards.diffrn_id 's1'
_diffrn_standards.number 3
_diffrn_standards.interval_time 120
_diffrn_standards.decay_% 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_standards.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_standards.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_standards.decay_%
_item_description.description
; The percentage decrease in the mean of the intensities
for the set of standard reflections from the start of the
measurement process to the end. This value usually
affords a measure of the overall decay in crystal quality
during the diffraction measurement process. Negative values
are used in exceptional instances where the final intensities
are greater than the initial ones.
;
_item.name '_diffrn_standards.decay_%'
_item.category_id diffrn_standards
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_standards_decay_%'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 100.0 100.0
100.0 .
_item_type.code float
save_
save__diffrn_standards.interval_count
_item_description.description
; The number of reflection intensities between the measurement of
standard reflection intensities.
;
_item.name '_diffrn_standards.interval_count'
_item.category_id diffrn_standards
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_standards_interval_count'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__diffrn_standards.interval_time
_item_description.description
; The time in minutes between the measurement of standard
reflection intensities.
;
_item.name '_diffrn_standards.interval_time'
_item.category_id diffrn_standards
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_standards_interval_time'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code float
_item_units.code minutes
save_
save__diffrn_standards.number
_item_description.description
; The number of unique standard reflections used during the
measurement of the diffraction intensities.
;
_item.name '_diffrn_standards.number'
_item.category_id diffrn_standards
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_standards_number'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__diffrn_standards.scale_sigma
_item_description.description
; The standard uncertainty (estimated standard deviation) of
the individual mean standard scales applied to the intensity
data.
;
_item.name '_diffrn_standards.scale_sigma'
_item.category_id diffrn_standards
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_standards_scale_sigma'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
############
## ENTITY ##
############
save_entity
_category.description
; Data items in the ENTITY category record details (such as
chemical composition, name and source) about the molecular
entities that are present in the crystallographic structure.
Items in the various ENTITY subcategories provide a full
chemical description of these molecular entities.
Entities are of three types: polymer, non-polymer and water.
Note that the water category includes only water; ordered
solvent such as sulfate ion or acetone would be described as
individual non-polymer entities.
The ENTITY category is specific to macromolecular CIF
applications and replaces the function of the CHEMICAL category
in the CIF core.
It is important to remember that the ENTITY data are not the
result of the crystallographic experiment; those results are
represented by the ATOM_SITE data items. ENTITY data items
describe the chemistry of the molecules under investigation
and can most usefully be thought of as the ideal groups to which
the structure is restrained or constrained during refinement.
It is also important to remember that entities do not correspond
directly to the enumeration of the contents of the asymmetric
unit. Entities are described only once, even in those structures
that contain multiple observations of an entity. The
STRUCT_ASYM data items, which reference the entity list,
describe and label the contents of the asymmetric unit.
;
_category.id entity
_category.mandatory_code no
_category_key.name '_entity.id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_entity.id
_entity.type
_entity.formula_weight
_entity.details
1 polymer 10916
; The enzymatically competent form of HIV
protease is a dimer. This entity
corresponds to one monomer of an active dimer.
;
2 non-polymer '762' .
3 water 18 .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__entity.details
_item_description.description
; A description of special aspects of the entity.
;
_item.name '_entity.details'
_item.category_id entity
_item.mandatory_code no
_item_type.code text
save_
save__entity.formula_weight
_item_description.description
; Formula mass in daltons of the entity.
;
_item.name '_entity.formula_weight'
_item.category_id entity
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1.0
1.0 1.0
_item_type.code float
save_
save__entity.id
_item_description.description
; The value of _entity.id must uniquely identify a record in the
ENTITY list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity.id' entity yes
'_atom_site.label_entity_id' atom_site no
'_entity_keywords.entity_id' entity_keywords yes
'_entity_link.entity_id_1' entity_link yes
'_entity_link.entity_id_2' entity_link yes
'_entity_name_com.entity_id' entity_name_com yes
'_entity_name_sys.entity_id' entity_name_sys yes
'_entity_poly.entity_id' entity_poly yes
'_entity_poly_seq.entity_id' entity_poly_seq yes
'_entity_src_gen.entity_id' entity_src_gen yes
'_entity_src_nat.entity_id' entity_src_nat yes
'_struct_asym.entity_id' struct_asym yes
'_struct_ref.entity_id' struct_ref yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_entity_id' '_entity.id'
'_entity_keywords.entity_id' '_entity.id'
'_entity_link.entity_id_1' '_entity.id'
'_entity_link.entity_id_2' '_entity.id'
'_entity_name_com.entity_id' '_entity.id'
'_entity_name_sys.entity_id' '_entity.id'
'_entity_poly.entity_id' '_entity.id'
'_entity_poly_seq.entity_id' '_entity_poly.entity_id'
'_entity_src_gen.entity_id' '_entity.id'
'_entity_src_nat.entity_id' '_entity.id'
'_struct_asym.entity_id' '_entity.id'
'_struct_ref.entity_id' '_entity.id'
save_
save__entity.src_method
_item_description.description
; The method by which the sample for the entity was produced.
Entities isolated directly from natural sources (tissues, soil
samples etc.) are expected to have further information in the
ENTITY_SRC_NAT category. Entities isolated from genetically
manipulated sources are expected to have further information in
the ENTITY_SRC_GEN category.
;
_item.name '_entity.src_method'
_item.category_id entity
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail nat
; entity isolated from a natural source
;
man
; entity isolated from a genetically
manipulated source
;
syn
; entity obtained synthetically
;
save_
save__entity.type
_item_description.description
; Defines the type of the entity.
Polymer entities are expected to have corresponding
ENTITY_POLY and associated entries.
Non-polymer entities are expected to have corresponding
CHEM_COMP and associated entries.
Water entities are not expected to have corresponding
entries in the ENTITY category.
;
_item.name '_entity.type'
_item.category_id entity
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail polymer 'entity is a polymer'
non-polymer 'entity is not a polymer'
water 'water in the solvent model'
save_
#####################
## ENTITY_KEYWORDS ##
#####################
save_entity_keywords
_category.description
; Data items in the ENTITY_KEYWORDS category specify keywords
relevant to the molecular entities. Note that this list of
keywords is separate from the list that is used for the
STRUCT_BIOL data items and is intended to provide only the
information that one would know about the molecular entity *if
one did not know its structure*. Hence polypeptides are simply
polypeptides, not cytokines or beta-alpha-barrels, and
polyribonucleic acids are simply poly-RNA, not transfer-
RNA.
;
_category.id entity_keywords
_category.mandatory_code no
_category_key.name '_entity_keywords.entity_id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_entity_keywords.entity_id
_entity_keywords.text
2 'natural product, inhibitor, reduced peptide'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__entity_keywords.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_entity_keywords.entity_id'
_item.mandatory_code yes
save_
save__entity_keywords.text
_item_description.description
; Keywords describing this entity.
;
_item.name '_entity_keywords.text'
_item.category_id entity_keywords
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'polypeptide'
'natural product'
'polysaccharide'
save_
#################
## ENTITY_LINK ##
#################
save_entity_link
_category.description
; Data items in the ENTITY_LINK category give details about
the links between entities.
;
_category.id entity_link
_category.mandatory_code no
_category_key.name '_entity_link.link_id'
loop_
_category_group.id 'inclusive_group'
'chem_link_group'
save_
save__entity_link.link_id
_item_description.description
; This data item is a pointer to _chem_link.id in the
CHEM_LINK category.
;
_item.name '_entity_link.link_id'
_item.mandatory_code yes
save_
save__entity_link.details
_item_description.description
; A description of special aspects of a link between
chemical components in the structure.
;
_item.name '_entity_link.details'
_item.category_id entity_link
_item.mandatory_code no
_item_type.code text
save_
save__entity_link.entity_id_1
_item_description.description
; The entity ID of the first of the two entities joined by the
link.
This data item is a pointer to _entity.id in the ENTITY
category.
;
_item.name '_entity_link.entity_id_1'
_item.mandatory_code yes
save_
save__entity_link.entity_id_2
_item_description.description
; The entity ID of the second of the two entities joined by the
link.
This data item is a pointer to _entity.id in the ENTITY
category.
;
_item.name '_entity_link.entity_id_2'
_item.mandatory_code yes
save_
save__entity_link.entity_seq_num_1
_item_description.description
; For a polymer entity, the sequence number in the first of
the two entities containing the link.
This data item is a pointer to _entity_poly_seq.num in the
ENTITY_POLY_SEQ category.
;
_item.name '_entity_link.entity_seq_num_1'
_item.mandatory_code no
save_
save__entity_link.entity_seq_num_2
_item_description.description
; For a polymer entity, the sequence number in the second of
the two entities containing the link.
This data item is a pointer to _entity_poly_seq.num in the
ENTITY_POLY_SEQ category.
;
_item.name '_entity_link.entity_seq_num_2'
_item.mandatory_code no
save_
#####################
## ENTITY_NAME_COM ##
#####################
save_entity_name_com
_category.description
; Data items in the ENTITY_NAME_COM category record the common name
or names associated with the entity. In some cases, the entity
name may not be the same as the name of the biological structure.
For example, haemoglobin alpha chain would be the entity common
name, not haemoglobin.
;
_category.id entity_name_com
_category.mandatory_code no
loop_
_category_key.name '_entity_name_com.entity_id'
'_entity_name_com.name'
loop_
_category_group.id 'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_entity_name_com.entity_id
_entity_name_com.name
1 'HIV-1 protease monomer'
1 'HIV-1 PR monomer'
2 'acetyl-pepstatin'
2 'acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine'
3 'water'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__entity_name_com.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_entity_name_com.entity_id'
_item.mandatory_code yes
save_
save__entity_name_com.name
_item_description.description
; A common name for the entity.
;
_item.name '_entity_name_com.name'
_item.category_id entity_name_com
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'HIV protease monomer'
'hemoglobin alpha chain'
'2-fluoro-1,4-dichloro benzene'
'arbutin'
save_
#####################
## ENTITY_NAME_SYS ##
#####################
save_entity_name_sys
_category.description
; Data items in the ENTITY_NAME_SYS category record the systematic
name or names associated with the entity and the system that
was used to construct the systematic name. In some cases, the
entity name may not be the same as the name of the biological
structure.
;
_category.id entity_name_sys
_category.mandatory_code no
loop_
_category_key.name '_entity_name_sys.entity_id'
'_entity_name_sys.name'
loop_
_category_group.id 'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_entity_name_sys.entity_id
_entity_name_sys.name
1 'EC 3.4.23.16'
2 'acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta'
3 water
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__entity_name_sys.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_entity_name_sys.entity_id'
_item.mandatory_code yes
save_
save__entity_name_sys.name
_item_description.description
; The systematic name for the entity.
;
_item.name '_entity_name_sys.name'
_item.category_id entity_name_sys
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'hydroquinone-beta-D-pyranoside'
'EC 2.1.1.1'
'2-fluoro-1,4-dichlorobenzene'
save_
save__entity_name_sys.system
_item_description.description
; The system used to generate the systematic name of the entity.
;
_item.name '_entity_name_sys.system'
_item.category_id entity_name_sys
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'Chemical Abstracts conventions'
'enzyme convention'
'Sigma catalog'
save_
#################
## ENTITY_POLY ##
#################
save_entity_poly
_category.description
; Data items in the ENTITY_POLY category record details about the
polymer, such as the type of the polymer, the number of
monomers and whether it has nonstandard features.
;
_category.id entity_poly
_category.mandatory_code no
_category_key.name '_entity_poly.entity_id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.nstd_chirality
_entity_poly.nstd_linkage
_entity_poly.nstd_monomer
_entity_poly.type_details
1 polypeptide(L) no no no .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__entity_poly.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_entity_poly.entity_id'
_item.mandatory_code yes
save_
save__entity_poly.nstd_chirality
_item_description.description
; A flag to indicate whether the polymer contains at least
one monomer unit with chirality different from that specified in
_entity_poly.type.
;
_item.name '_entity_poly.nstd_chirality'
_item.category_id entity_poly
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail no
; polymer contains no monomers with different
chirality
;
n
; abbreviation for "no"
;
yes
; polymer contains at least one monomer with
different chirality
;
y
; abbreviation for "yes"
;
save_
save__entity_poly.nstd_linkage
_item_description.description
; A flag to indicate whether the polymer contains at least
one monomer-to-monomer link different from that implied by
_entity_poly.type.
;
_item.name '_entity_poly.nstd_linkage'
_item.category_id entity_poly
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail no
'polymer contains no different links'
n
'abbreviation for "no"'
yes
; polymer contains at least one different
link
;
y
'abbreviation for "yes"'
save_
save__entity_poly.nstd_monomer
_item_description.description
; A flag to indicate whether the polymer contains at least
one monomer that is not considered standard.
;
_item.name '_entity_poly.nstd_monomer'
_item.category_id entity_poly
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail no
'polymer contains no nonstandard monomers'
n
'abbreviation for "no"'
yes
; polymer contains at least one nonstandard
monomer
;
y
'abbreviation for "yes"'
save_
save__entity_poly.number_of_monomers
_item_description.description
; The number of monomers in the polymer.
;
_item.name '_entity_poly.number_of_monomers'
_item.category_id entity_poly
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__entity_poly.type
_item_description.description
; The type of the polymer.
;
_item.name '_entity_poly.type'
_item.category_id entity_poly
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value 'polypeptide(D)'
'polypeptide(L)'
'polydeoxyribonucleotide'
'polyribonucleotide'
'polysaccharide(D)'
'polysaccharide(L)'
'other'
save_
save__entity_poly.type_details
_item_description.description
; A description of special aspects of the polymer type.
;
_item.name '_entity_poly.type_details'
_item.category_id entity_poly
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'monomer Ala 16 is a D-amino acid'
'the oligomer contains alternating RNA and DNA units'
save_
#####################
## ENTITY_POLY_SEQ ##
#####################
save_entity_poly_seq
_category.description
; Data items in the ENTITY_POLY_SEQ category specify the sequence
of monomers in a polymer. Allowance is made for the possibility
of microheterogeneity in a sample by allowing a given sequence
number to be correlated with more than one monomer ID. The
corresponding ATOM_SITE entries should reflect this
heterogeneity.
;
_category.id entity_poly_seq
_category.mandatory_code no
loop_
_category_key.name '_entity_poly_seq.entity_id'
'_entity_poly_seq.num'
'_entity_poly_seq.mon_id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
1 1 PRO 1 2 GLN 1 3 ILE 1 4 THR 1 5 LEU
1 6 TRP 1 7 GLN 1 8 ARG 1 9 PRO 1 10 LEU
1 11 VAL 1 12 THR 1 13 ILE 1 14 LYS 1 15 ILE
1 16 GLY 1 17 GLY 1 18 GLN 1 19 LEU 1 20 LYS
1 21 GLU 1 22 ALA 1 23 LEU 1 24 LEU 1 25 ASP
# - - - - data truncated for brevity - - - -
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__entity_poly_seq.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_entity_poly_seq.entity_id'
_item.mandatory_code yes
save_
save__entity_poly_seq.hetero
_item_description.description
; A flag to indicate whether this monomer in the polymer is
heterogeneous in sequence. This would be rare.
;
_item.name '_entity_poly_seq.hetero'
_item.category_id entity_poly_seq
_item.mandatory_code no
_item_default.value no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail no
'sequence is not heterogeneous at this monomer'
n
'abbreviation for "no"'
yes
'sequence is heterogeneous at this monomer'
y
'abbreviation for "yes"'
save_
save__entity_poly_seq.mon_id
_item_description.description
; This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_entity_poly_seq.mon_id'
_item.mandatory_code yes
save_
save__entity_poly_seq.num
_item_description.description
; The value of _entity_poly_seq.num must uniquely and sequentially
identify a record in the ENTITY_POLY_SEQ list.
Note that this item must be a number and that the sequence
numbers must progress in increasing numerical order.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entity_poly_seq.num' entity_poly_seq yes
'_atom_site.label_seq_id' atom_site no
'_entity_link.entity_seq_num_1' entity_link no
'_entity_link.entity_seq_num_2' entity_link no
'_geom_angle.atom_site_label_seq_id_1' geom_angle no
'_geom_angle.atom_site_label_seq_id_2' geom_angle no
'_geom_angle.atom_site_label_seq_id_3' geom_angle no
'_geom_bond.atom_site_label_seq_id_1' geom_bond no
'_geom_bond.atom_site_label_seq_id_2' geom_bond no
'_geom_contact.atom_site_label_seq_id_1' geom_contact no
'_geom_contact.atom_site_label_seq_id_2' geom_contact no
'_geom_hbond.atom_site_label_seq_id_A' geom_hbond no
'_geom_hbond.atom_site_label_seq_id_D' geom_hbond no
'_geom_hbond.atom_site_label_seq_id_H' geom_hbond no
'_geom_torsion.atom_site_label_seq_id_1' geom_torsion no
'_geom_torsion.atom_site_label_seq_id_2' geom_torsion no
'_geom_torsion.atom_site_label_seq_id_3' geom_torsion no
'_geom_torsion.atom_site_label_seq_id_4' geom_torsion no
'_struct_conf.beg_label_seq_id' struct_conf yes
'_struct_conf.end_label_seq_id' struct_conf yes
'_struct_conn.ptnr1_label_seq_id' struct_conn yes
'_struct_conn.ptnr2_label_seq_id' struct_conn yes
'_struct_mon_nucl.label_seq_id' struct_mon_nucl yes
'_struct_mon_prot.label_seq_id' struct_mon_prot yes
'_struct_mon_prot_cis.label_seq_id' struct_mon_prot_cis yes
'_struct_ncs_dom_lim.beg_label_seq_id' struct_ncs_dom_lim yes
'_struct_ncs_dom_lim.end_label_seq_id' struct_ncs_dom_lim yes
'_struct_ref_seq.seq_align_beg' struct_ref_seq yes
'_struct_ref_seq.seq_align_end' struct_ref_seq yes
'_struct_ref_seq_dif.seq_num' struct_ref_seq_dif yes
'_struct_sheet_hbond.range_1_beg_label_seq_id' struct_sheet_hbond yes
'_struct_sheet_hbond.range_1_end_label_seq_id' struct_sheet_hbond yes
'_struct_sheet_hbond.range_2_beg_label_seq_id' struct_sheet_hbond yes
'_struct_sheet_hbond.range_2_end_label_seq_id' struct_sheet_hbond yes
'_struct_sheet_range.beg_label_seq_id' struct_sheet_range yes
'_struct_sheet_range.end_label_seq_id' struct_sheet_range yes
'_struct_site_gen.label_seq_id' struct_site_gen yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_seq_id' '_entity_poly_seq.num'
'_entity_link.entity_seq_num_1' '_entity_poly_seq.num'
'_entity_link.entity_seq_num_2' '_entity_poly_seq.num'
'_geom_angle.atom_site_label_seq_id_1' '_atom_site.label_seq_id'
'_geom_angle.atom_site_label_seq_id_2' '_atom_site.label_seq_id'
'_geom_angle.atom_site_label_seq_id_3' '_atom_site.label_seq_id'
'_geom_bond.atom_site_label_seq_id_1' '_atom_site.label_seq_id'
'_geom_bond.atom_site_label_seq_id_2' '_atom_site.label_seq_id'
'_geom_contact.atom_site_label_seq_id_1' '_atom_site.label_seq_id'
'_geom_contact.atom_site_label_seq_id_2' '_atom_site.label_seq_id'
'_geom_hbond.atom_site_label_seq_id_A' '_atom_site.label_seq_id'
'_geom_hbond.atom_site_label_seq_id_D' '_atom_site.label_seq_id'
'_geom_hbond.atom_site_label_seq_id_H' '_atom_site.label_seq_id'
'_geom_torsion.atom_site_label_seq_id_1' '_atom_site.label_seq_id'
'_geom_torsion.atom_site_label_seq_id_2' '_atom_site.label_seq_id'
'_geom_torsion.atom_site_label_seq_id_3' '_atom_site.label_seq_id'
'_geom_torsion.atom_site_label_seq_id_4' '_atom_site.label_seq_id'
'_struct_conf.beg_label_seq_id' '_atom_site.label_seq_id'
'_struct_conf.end_label_seq_id' '_atom_site.label_seq_id'
'_struct_conn.ptnr1_label_seq_id' '_atom_site.label_seq_id'
'_struct_conn.ptnr2_label_seq_id' '_atom_site.label_seq_id'
'_struct_mon_nucl.label_seq_id' '_atom_site.label_seq_id'
'_struct_mon_prot.label_seq_id' '_atom_site.label_seq_id'
'_struct_mon_prot_cis.label_seq_id' '_atom_site.label_seq_id'
'_struct_ncs_dom_lim.beg_label_seq_id' '_atom_site.label_seq_id'
'_struct_ncs_dom_lim.end_label_seq_id' '_atom_site.label_seq_id'
'_struct_ref_seq.seq_align_beg' '_entity_poly_seq.num'
'_struct_ref_seq.seq_align_end' '_entity_poly_seq.num'
'_struct_ref_seq_dif.seq_num' '_entity_poly_seq.num'
'_struct_sheet_hbond.range_1_beg_label_seq_id' '_atom_site.label_seq_id'
'_struct_sheet_hbond.range_1_end_label_seq_id' '_atom_site.label_seq_id'
'_struct_sheet_hbond.range_2_beg_label_seq_id' '_atom_site.label_seq_id'
'_struct_sheet_hbond.range_2_end_label_seq_id' '_atom_site.label_seq_id'
'_struct_sheet_range.beg_label_seq_id' '_atom_site.label_seq_id'
'_struct_sheet_range.end_label_seq_id' '_atom_site.label_seq_id'
'_struct_site_gen.label_seq_id' '_atom_site.label_seq_id'
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
####################
## ENTITY_SRC_GEN ##
####################
save_entity_src_gen
_category.description
; Data items in the ENTITY_SRC_GEN category record details of
the source from which the entity was obtained in cases
where the source was genetically manipulated. The
following are treated separately: items pertaining to the tissue
from which the gene was obtained, items pertaining to the host
organism for gene expression and items pertaining to the actual
producing organism (plasmid).
;
_category.id entity_src_gen
_category.mandatory_code no
_category_key.name '_entity_src_gen.entity_id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_entity_src_gen.entity_id
_entity_src_gen.gene_src_common_name
_entity_src_gen.gene_src_genus
_entity_src_gen.gene_src_species
_entity_src_gen.gene_src_strain
_entity_src_gen.host_org_common_name
_entity_src_gen.host_org_genus
_entity_src_gen.host_org_species
_entity_src_gen.plasmid_name
1 'HIV-1' '?' '?' 'NY-5'
'bacteria' 'Escherichia' 'coli' 'pB322'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__entity_src_gen.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_entity_src_gen.entity_id'
_item.mandatory_code yes
save_
save__entity_src_gen.gene_src_common_name
_item_description.description
; The common name of the natural organism from which the gene was
obtained.
;
_item.name '_entity_src_gen.gene_src_common_name'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'man'
'yeast'
'bacteria'
save_
save__entity_src_gen.gene_src_details
_item_description.description
; A description of special aspects of the natural organism from
which the gene was obtained.
;
_item.name '_entity_src_gen.gene_src_details'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
save_
save__entity_src_gen.gene_src_genus
_item_description.description
; The genus of the natural organism from which the gene was
obtained.
;
_item.name '_entity_src_gen.gene_src_genus'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'Homo'
'Saccharomyces'
'Escherichia'
save_
save__entity_src_gen.gene_src_species
_item_description.description
; The species of the natural organism from which the gene was
obtained.
;
_item.name '_entity_src_gen.gene_src_species'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'sapiens'
'cerevisiae'
'coli'
save_
save__entity_src_gen.gene_src_strain
_item_description.description
; The strain of the natural organism from which the gene was
obtained, if relevant.
;
_item.name '_entity_src_gen.gene_src_strain'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'DH5a'
'BMH 71-18'
save_
save__entity_src_gen.gene_src_tissue
_item_description.description
; The tissue of the natural organism from which the gene was
obtained.
;
_item.name '_entity_src_gen.gene_src_tissue'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'heart'
'liver'
'eye lens'
save_
save__entity_src_gen.gene_src_tissue_fraction
_item_description.description
; The subcellular fraction of the tissue of the natural organism
from which the gene was obtained.
;
_item.name '_entity_src_gen.gene_src_tissue_fraction'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'mitochondria'
'nucleus'
'membrane'
save_
save__entity_src_gen.host_org_common_name
_item_description.description
; The common name of the organism that served as host for the
production of the entity.
;
_item.name '_entity_src_gen.host_org_common_name'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'yeast'
'bacteria'
save_
save__entity_src_gen.host_org_details
_item_description.description
; A description of special aspects of the organism that served as
host for the production of the entity.
;
_item.name '_entity_src_gen.host_org_details'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
save_
save__entity_src_gen.host_org_genus
_item_description.description
; The genus of the organism that served as host for the production
of the entity.
;
_item.name '_entity_src_gen.host_org_genus'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'Saccharomyces'
'Escherichia'
save_
save__entity_src_gen.host_org_species
_item_description.description
; The species of the organism that served as host for the
production of the entity.
;
_item.name '_entity_src_gen.host_org_species'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'cerevisiae'
'coli'
save_
save__entity_src_gen.host_org_strain
_item_description.description
; The strain of the organism that served as host for the
production of the entity.
;
_item.name '_entity_src_gen.host_org_strain'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'DH5a'
'BMH 71-18'
save_
save__entity_src_gen.plasmid_details
_item_description.description
; A description of special aspects of the plasmid that produced the
entity in the host organism.
;
_item.name '_entity_src_gen.plasmid_details'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
save_
save__entity_src_gen.plasmid_name
_item_description.description
; The name of the plasmid that produced the entity in the host
organism.
;
_item.name '_entity_src_gen.plasmid_name'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'pET3C'
'pT123sab'
save_
####################
## ENTITY_SRC_NAT ##
####################
save_entity_src_nat
_category.description
; Data items in the ENTITY_SRC_NAT category record details of
the source from which the entity was obtained in cases
where the entity was isolated directly from a natural tissue.
;
_category.id entity_src_nat
_category.mandatory_code no
_category_key.name '_entity_src_nat.entity_id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_entity_src_nat.entity_id
_entity_src_nat.common_name
_entity_src_nat.genus
_entity_src_nat.species
_entity_src_nat.details
2 'bacteria' 'Actinomycetes' '?'
; Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka
Prefecture University, and provided to us by Dr. Ben
Dunn, University of Florida, and Dr. J. Kay, University
of Wales.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__entity_src_nat.common_name
_item_description.description
; The common name of the organism from which the entity
was isolated.
;
_item.name '_entity_src_nat.common_name'
_item.category_id entity_src_nat
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'man'
'yeast'
'bacteria'
save_
save__entity_src_nat.details
_item_description.description
; A description of special aspects of the organism from which the
entity was isolated.
;
_item.name '_entity_src_nat.details'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
save_
save__entity_src_nat.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_entity_src_nat.entity_id'
_item.mandatory_code yes
save_
save__entity_src_nat.genus
_item_description.description
; The genus of the organism from which the entity was isolated.
;
_item.name '_entity_src_nat.genus'
_item.category_id entity_src_nat
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'Homo'
'Saccharomyces'
'Escherichia'
save_
save__entity_src_nat.species
_item_description.description
; The species of the organism from which the entity was isolated.
;
_item.name '_entity_src_nat.species'
_item.category_id entity_src_nat
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'sapiens'
'cerevisiae'
'coli'
save_
save__entity_src_nat.strain
_item_description.description
; The strain of the organism from which the entity was isolated.
;
_item.name '_entity_src_nat.strain'
_item.category_id entity_src_nat
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'DH5a'
'BMH 71-18'
save_
save__entity_src_nat.tissue
_item_description.description
; The tissue of the organism from which the entity was isolated.
;
_item.name '_entity_src_nat.tissue'
_item.category_id entity_src_nat
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'heart'
'liver'
'eye lens'
save_
save__entity_src_nat.tissue_fraction
_item_description.description
; The subcellular fraction of the tissue of the organism from
which the entity was isolated.
;
_item.name '_entity_src_nat.tissue_fraction'
_item.category_id entity_src_nat
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'mitochondria'
'nucleus'
'membrane'
save_
###########
## ENTRY ##
###########
save_entry
_category.description
; There is only one item in the ENTRY category, _entry.id. This
data item gives a name to this entry and is indirectly a key to
the categories (such as CELL, GEOM, EXPTL) that describe
information pertinent to the entire data block.
;
_category.id entry
_category.mandatory_code no
_category_key.name '_entry.id'
loop_
_category_group.id 'inclusive_group'
'entry_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_entry.id '5HVP'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_entry.id 'TOZ'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__entry.id
_item_description.description
; The value of _entry.id identifies the data block.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_entry.id' entry yes
'_atom_sites.entry_id' atom_sites yes
'_cell.entry_id' cell yes
'_cell_measurement.entry_id' cell_measurement yes
'_chemical.entry_id' chemical yes
'_chemical_formula.entry_id' chemical_formula yes
'_computing.entry_id' computing yes
'_database.entry_id' database yes
'_database_PDB_matrix.entry_id' database_PDB_matrix yes
'_entry_link.entry_id' entry_link yes
'_exptl.entry_id' exptl yes
'_geom.entry_id' geom yes
'_journal.entry_id' journal yes
'_phasing_averaging.entry_id' phasing_averaging yes
'_phasing_isomorphous.entry_id' phasing_isomorphous yes
'_phasing_MAD.entry_id' phasing_MAD yes
'_phasing_MIR.entry_id' phasing_MIR yes
'_publ.entry_id' publ yes
'_publ_manuscript_incl.entry_id' publ_manuscript_incl yes
'_refine.entry_id' refine yes
'_refine_analyze.entry_id' refine_analyze yes
'_reflns.entry_id' reflns yes
'_struct.entry_id' struct yes
'_struct_keywords.entry_id' struct_keywords yes
'_struct_mon_details.entry_id' struct_mon_details yes
'_symmetry.entry_id' symmetry yes
_item_aliases.alias_name '_audit_block_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_sites.entry_id' '_entry.id'
'_cell.entry_id' '_entry.id'
'_cell_measurement.entry_id' '_entry.id'
'_chemical.entry_id' '_entry.id'
'_chemical_formula.entry_id' '_entry.id'
'_computing.entry_id' '_entry.id'
'_database.entry_id' '_entry.id'
'_database_PDB_matrix.entry_id' '_entry.id'
'_entry_link.entry_id' '_entry.id'
'_exptl.entry_id' '_entry.id'
'_geom.entry_id' '_entry.id'
'_journal.entry_id' '_entry.id'
'_phasing_averaging.entry_id' '_entry.id'
'_phasing_isomorphous.entry_id' '_entry.id'
'_phasing_MAD.entry_id' '_entry.id'
'_phasing_MIR.entry_id' '_entry.id'
'_publ.entry_id' '_entry.id'
'_publ_manuscript_incl.entry_id' '_entry.id'
'_refine.entry_id' '_entry.id'
'_refine_analyze.entry_id' '_entry.id'
'_reflns.entry_id' '_entry.id'
'_struct.entry_id' '_entry.id'
'_struct_keywords.entry_id' '_entry.id'
'_struct_mon_details.entry_id' '_entry.id'
'_symmetry.entry_id' '_entry.id'
_item_type.code code
save_
save_entry_link
_category.description
; Data items in the ENTRY_LINK category record the
relationships between the current data block
identified by _entry.id and other data blocks
within the current file which may be referenced
in the current data block.
;
_category.id entry_link
_category.mandatory_code no
loop_
_category_key.name '_entry_link.id'
'_entry_link.entry_id'
loop_
_category_group.id 'inclusive_group'
'entry_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - example file for the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
;
;
loop_
_entry_link.id
_entry_link.entry_id
_entry_link.details
KSE_COM KSE_TEXT
'experimental data common to ref./mod. structures'
KSE_REF KSE_TEXT 'reference structure'
KSE_MOD KSE_TEXT 'modulated structure'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__entry_link.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_entry_link.entry_id'
_item.mandatory_code yes
save_
save__entry_link.id
_item_description.description
; The value of _entry_link.id identifies a data block
related to the current data block.
;
_item.name '_entry_link.id'
_item.category_id entry_link
_item.mandatory_code yes
_item_aliases.alias_name '_audit_link_block_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
save_
save__entry_link.details
_item_description.description
; A description of the relationship between the data blocks
identified by _entry_link.id and _entry_link.entry_id.
;
_item.name '_entry_link.details'
_item.category_id entry_link
_item.mandatory_code no
_item_aliases.alias_name '_audit_link_block_description'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
###########
## EXPTL ##
###########
save_exptl
_category.description
; Data items in the EXPTL category record details about the
experimental work prior to the intensity measurements and
details about the absorption-correction technique employed.
;
_category.id exptl
_category.mandatory_code no
_category_key.name '_exptl.entry_id'
loop_
_category_group.id 'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4.
;
;
_exptl.entry_id datablock1
_exptl.absorpt_coefficient_mu 1.22
_exptl.absorpt_correction_T_max 0.896
_exptl.absorpt_correction_T_min 0.802
_exptl.absorpt_correction_type integration
_exptl.absorpt_process_details
; Gaussian grid method from SHELX76
Sheldrick, G. M., "SHELX-76: structure determination and
refinement program", Cambridge University, UK, 1976
;
_exptl.crystals_number 1
_exptl.details
; Enraf-Nonius LT2 liquid nitrogen variable-temperature
device used
;
_exptl.method 'single-crystal x-ray diffraction'
_exptl.method_details
; graphite monochromatized Cu K(alpha) fixed tube and
Enraf-Nonius CAD4 diffractometer used
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__exptl.absorpt_coefficient_mu
_item_description.description
; The absorption coefficient mu in reciprocal millimetres
calculated from the atomic content of the cell, the density and
the radiation wavelength.
;
_item.name '_exptl.absorpt_coefficient_mu'
_item.category_id exptl
_item.mandatory_code no
_item_aliases.alias_name '_exptl_absorpt_coefficient_mu'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code reciprocal_millimetres
save_
save__exptl.absorpt_correction_T_max
_item_description.description
; The maximum transmission factor for the crystal and radiation.
The maximum and minimum transmission factors are also referred
to as the absorption correction
A or 1/A*.
;
_item.name '_exptl.absorpt_correction_T_max'
_item.category_id exptl
_item.mandatory_code no
_item_aliases.alias_name '_exptl_absorpt_correction_T_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 0.0
0.0 0.0
_item_type.code float
save_
save__exptl.absorpt_correction_T_min
_item_description.description
; The minimum transmission factor for the crystal and radiation.
The maximum and minimum transmission factors are also referred
to as the absorption correction
A or 1/A*.
;
_item.name '_exptl.absorpt_correction_T_min'
_item.category_id exptl
_item.mandatory_code no
_item_aliases.alias_name '_exptl_absorpt_correction_T_min'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 0.0
0.0 0.0
_item_type.code float
save_
save__exptl.absorpt_correction_type
_item_description.description
; The absorption correction type and method. The value
'empirical' should NOT be used unless more detailed
information is not available.
;
_item.name '_exptl.absorpt_correction_type'
_item.category_id exptl
_item.mandatory_code no
_item_aliases.alias_name '_exptl_absorpt_correction_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail analytical 'analytical from crystal shape'
cylinder 'cylindrical'
empirical 'empirical from intensities'
gaussian 'Gaussian from crystal shape'
integration 'integration from crystal shape'
multi-scan 'symmetry-related measurements'
none 'no correction applied'
numerical 'numerical from crystal shape'
psi-scan 'psi-scan corrections'
refdelf 'refined from delta-F'
sphere 'spherical'
save_
save__exptl.absorpt_process_details
_item_description.description
; Description of the absorption process applied to the
intensities. A literature reference should be supplied for
psi-scan techniques.
;
_item.name '_exptl.absorpt_process_details'
_item.category_id exptl
_item.mandatory_code no
_item_aliases.alias_name '_exptl_absorpt_process_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'Tompa analytical'
save_
save__exptl.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_exptl.entry_id'
_item.mandatory_code yes
save_
save__exptl.crystals_number
_item_description.description
; The total number of crystals used in the measurement of
intensities.
;
_item.name '_exptl.crystals_number'
_item.category_id exptl
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystals_number'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__exptl.details
_item_description.description
; Any special information about the experimental work prior to the
intensity measurement. See also _exptl_crystal.preparation.
;
_item.name '_exptl.details'
_item.category_id exptl
_item.mandatory_code no
_item_aliases.alias_name '_exptl_special_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__exptl.method
_item_description.description
; The method used in the experiment.
;
_item.name '_exptl.method'
_item.category_id exptl
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case 'single-crystal x-ray diffraction'
'single-crystal neutron diffraction'
'single-crystal electron diffraction'
'fiber x-ray diffraction'
'fiber neutron diffraction'
'fiber electron diffraction'
'single-crystal joint x-ray and neutron diffraction'
'single-crystal joint x-ray and electron diffraction'
'solution nmr'
'solid-state nmr'
'theoretical model'
'other'
save_
save__exptl.method_details
_item_description.description
; A description of special aspects of the experimental method.
;
_item.name '_exptl.method_details'
_item.category_id exptl
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case '29 structures'
'minimized average structure'
save_
###################
## EXPTL_CRYSTAL ##
###################
save_exptl_crystal
_category.description
; Data items in the EXPTL_CRYSTAL category record the results of
experimental measurements on the crystal or crystals used,
such as shape, size or density.
;
_category.id exptl_crystal
_category.mandatory_code no
_category_key.name '_exptl_crystal.id'
loop_
_category_group.id 'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4.
;
;
_exptl_crystal.id xst2l
_exptl_crystal.colour 'pale yellow'
_exptl_crystal.density_diffrn 1.113
_exptl_crystal.density_Matthews 1.01
_exptl_crystal.density_meas 1.11
_exptl_crystal.density_meas_temp 294.5
_exptl_crystal.density_method 'neutral buoyancy'
_exptl_crystal.density_percent_sol 0.15
# P = 1 - (1.23*N*MMass) / V
_exptl_crystal.description 'hexagonal rod, uncut'
_exptl_crystal.F_000 202
_exptl_crystal.preparation
; hanging drop, crystal soaked in 10% ethylene glycol for
10 h, then placed in nylon loop at data collection time
;
_exptl_crystal.size_max 0.30
_exptl_crystal.size_mid 0.20
_exptl_crystal.size_min 0.05
_exptl_crystal.size_rad 0.025
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - using separate items to define upper and lower
limits for a value.
;
; _exptl_crystal.density_meas_gt 2.5
_exptl_crystal.density_meas_lt 5.0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 3 - here the density was measured at some
unspecified temperature below room temperature.
;
; _exptl_crystal.density_meas_temp_lt 300
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__exptl_crystal.colour
_item_description.description
; The colour of the crystal.
;
_item.name '_exptl_crystal.colour'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_colour'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
_item_examples.case 'dark green'
save_
save__exptl_crystal.density_diffrn
_item_description.description
; Density values calculated from the crystal cell and contents. The
units are megagrams per cubic metre (grams per cubic centimetre).
;
_item.name '_exptl_crystal.density_diffrn'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_density_diffrn'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__exptl_crystal.density_Matthews
_item_description.description
; The density of the crystal, expressed as the ratio of the
volume of the asymmetric unit to the molecular mass of a
monomer of the structure, in units of angstroms^3^ per dalton.
Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
;
_item.name '_exptl_crystal.density_Matthews'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code float
save_
#save__exptl_crystal.density_meas
# _item_description.description
#; Density values measured using standard chemical and physical
# methods. The units are megagrams per cubic metre (grams per
# cubic centimetre).
#;
# _item.name '_exptl_crystal.density_meas'
# _item.category_id exptl_crystal
# _item.mandatory_code no
# _item_aliases.alias_name '_exptl_crystal_density_meas'
# _item_aliases.dictionary cif_core.dic
# _item_aliases.version 2.0.1
# loop_
# _item_range.maximum
# _item_range.minimum . 0.0
# 0.0 0.0
# _item_type.code float
# save_
#
#save__exptl_crystal.density_meas_temp
# _item_description.description
#; The temperature in kelvins at which _exptl_crystal.density_meas
# was determined.
#;
# _item.name '_exptl_crystal.density_meas_temp'
# _item.category_id exptl_crystal
# _item.mandatory_code no
# _item_aliases.alias_name '_exptl_crystal_density_meas_temp'
# _item_aliases.dictionary cif_core.dic
# _item_aliases.version 2.0.1
# loop_
# _item_range.maximum
# _item_range.minimum . 0.0
# 0.0 0.0
# _item_type.code float
# _item_units.code kelvins
# save_
save__exptl_crystal.density_method
_item_description.description
; The method used to measure _exptl_crystal.density_meas.
;
_item.name '_exptl_crystal.density_method'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_density_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__exptl_crystal.density_percent_sol
_item_description.description
; Density value P calculated from the crystal cell and contents,
expressed as per cent solvent.
P = 1 - (1.23 N MMass) / V
N = the number of molecules in the unit cell
MMass = the molecular mass of each molecule (gm/mole)
V = the volume of the unit cell (A^3^)
1.23 = a conversion factor evaluated as:
(0.74 cm^3^/g) (10^24^ A^3^/cm^3^)
--------------------------------------
(6.02*10^23^) molecules/mole
where 0.74 is an assumed value for the partial specific
volume of the molecule
;
_item.name '_exptl_crystal.density_percent_sol'
_item.category_id exptl_crystal
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__exptl_crystal.description
_item_description.description
; A description of the quality and habit of the crystal.
The crystal dimensions should not normally be reported here;
use instead the specific items in the EXPTL_CRYSTAL category
relating to size for the gross dimensions of the crystal and
data items in the EXPTL_CRYSTAL_FACE category to describe the
relationship between individual faces.
;
_item.name '_exptl_crystal.description'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_description'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__exptl_crystal.F_000
_item_description.description
; The effective number of electrons in the crystal unit cell
contributing to F(000). This may contain dispersion contributions
and is calculated as
F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^
f~r~ = real part of the scattering factors at theta = 0 degree
f~i~ = imaginary part of the scattering factors at
theta = 0 degree
the sum is taken over each atom in the unit cell
;
_item.name '_exptl_crystal.F_000'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_F_000'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__exptl_crystal.id
_item_description.description
; The value of _exptl_crystal.id must uniquely identify a record in
the EXPTL_CRYSTAL list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_exptl_crystal.id' exptl_crystal yes
'_exptl_crystal_face.crystal_id' exptl_crystal_face yes
'_exptl_crystal_grow.crystal_id' exptl_crystal_grow yes
'_exptl_crystal_grow_comp.crystal_id' exptl_crystal_grow_comp yes
'_diffrn.crystal_id' diffrn yes
'_refln.crystal_id' refln yes
_item_aliases.alias_name '_exptl_crystal_id'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn.crystal_id' '_exptl_crystal.id'
'_exptl_crystal_grow.crystal_id' '_exptl_crystal.id'
'_exptl_crystal_face.crystal_id' '_exptl_crystal.id'
'_exptl_crystal_grow_comp.crystal_id' '_exptl_crystal.id'
'_refln.crystal_id' '_exptl_crystal.id'
_item_type.code code
save_
save__exptl_crystal.preparation
_item_description.description
; Details of crystal growth and preparation of the crystal (e.g.
mounting) prior to the intensity measurements.
;
_item.name '_exptl_crystal.preparation'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_preparation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'mounted in an argon-filled quartz capillary'
save_
save__exptl_crystal.size_max
_item_description.description
; The maximum dimension of the crystal. This item may appear in a
list with _exptl_crystal.id if multiple crystals are used in the
experiment.
;
_item.name '_exptl_crystal.size_max'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_size_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__exptl_crystal.size_mid
_item_description.description
; The medial dimension of the crystal. This item may appear in a
list with _exptl_crystal.id if multiple crystals are used in the
experiment.
;
_item.name '_exptl_crystal.size_mid'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_size_mid'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__exptl_crystal.size_min
_item_description.description
; The minimum dimension of the crystal. This item may appear in a
list with _exptl_crystal.id if multiple crystals are used in the
experiment.
;
_item.name '_exptl_crystal.size_min'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_size_min'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__exptl_crystal.size_rad
_item_description.description
; The radius of the crystal, if the crystal is a sphere or a
cylinder. This item may appear in a list with _exptl_crystal.id
if multiple crystals are used in the experiment.
;
_item.name '_exptl_crystal.size_rad'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_size_rad'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
########################
## EXPTL_CRYSTAL_FACE ##
########################
save_exptl_crystal_face
_category.description
; Data items in the EXPTL_CRYSTAL_FACE category record details
of the crystal faces.
;
_category.id exptl_crystal_face
_category.mandatory_code no
loop_
_category_key.name '_exptl_crystal_face.crystal_id'
'_exptl_crystal_face.index_h'
'_exptl_crystal_face.index_k'
'_exptl_crystal_face.index_l'
loop_
_category_group.id 'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4
for the 100 face of crystal xstl1.
;
;
_exptl_crystal_face.crystal_id xstl1
_exptl_crystal_face.index_h 1
_exptl_crystal_face.index_k 0
_exptl_crystal_face.index_l 0
_exptl_crystal_face.diffr_chi 42.56
_exptl_crystal_face.diffr_kappa 30.23
_exptl_crystal_face.diffr_phi -125.56
_exptl_crystal_face.diffr_psi -0.34
_exptl_crystal_face.perp_dist 0.025
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__exptl_crystal_face.crystal_id
_item_description.description
; This data item is a pointer to _exptl_crystal.id in the
EXPTL_CRYSTAL category.
;
_item.name '_exptl_crystal_face.crystal_id'
_item.mandatory_code yes
save_
save__exptl_crystal_face.diffr_chi
_item_description.description
; The chi diffractometer setting angle in degrees for a specific
crystal face associated with _exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.diffr_chi'
_item.category_id exptl_crystal_face
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_face_diffr_chi'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__exptl_crystal_face.diffr_kappa
_item_description.description
; The kappa diffractometer setting angle in degrees for a specific
crystal face associated with _exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.diffr_kappa'
_item.category_id exptl_crystal_face
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_face_diffr_kappa'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__exptl_crystal_face.diffr_phi
_item_description.description
; The phi diffractometer setting angle in degrees for a specific
crystal face associated with _exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.diffr_phi'
_item.category_id exptl_crystal_face
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_face_diffr_phi'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__exptl_crystal_face.diffr_psi
_item_description.description
; The psi diffractometer setting angle in degrees for a specific
crystal face associated with _exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.diffr_psi'
_item.category_id exptl_crystal_face
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_face_diffr_psi'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__exptl_crystal_face.index_h
_item_description.description
; Miller index h of the crystal face associated with the value
_exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.index_h'
_item.category_id exptl_crystal_face
_item.mandatory_code yes
_item_aliases.alias_name '_exptl_crystal_face_index_h'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_exptl_crystal_face.index_k'
'_exptl_crystal_face.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__exptl_crystal_face.index_k
_item_description.description
; Miller index k of the crystal face associated with the value
_exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.index_k'
_item.category_id exptl_crystal_face
_item.mandatory_code yes
_item_aliases.alias_name '_exptl_crystal_face_index_k'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_exptl_crystal_face.index_h'
'_exptl_crystal_face.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__exptl_crystal_face.index_l
_item_description.description
; Miller index l of the crystal face associated with the value
_exptl_crystal_face.perp_dist.
;
_item.name '_exptl_crystal_face.index_l'
_item.category_id exptl_crystal_face
_item.mandatory_code yes
_item_aliases.alias_name '_exptl_crystal_face_index_l'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_exptl_crystal_face.index_h'
'_exptl_crystal_face.index_k'
_item_sub_category.id miller_index
_item_type.code int
save_
save__exptl_crystal_face.perp_dist
_item_description.description
; The perpendicular distance in millimetres from the face to the
centre of rotation of the crystal.
;
_item.name '_exptl_crystal_face.perp_dist'
_item.category_id exptl_crystal_face
_item.mandatory_code no
_item_aliases.alias_name '_exptl_crystal_face_perp_dist'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
########################
## EXPTL_CRYSTAL_GROW ##
########################
save_exptl_crystal_grow
_category.description
; Data items in the EXPTL_CRYSTAL_GROW category record details
about the conditions and methods used to grow the crystal.
;
_category.id exptl_crystal_grow
_category.mandatory_code no
_category_key.name '_exptl_crystal_grow.crystal_id'
loop_
_category_group.id 'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method 'hanging drop'
_exptl_crystal_grow.apparatus 'Linbro plates'
_exptl_crystal_grow.atmosphere 'room air'
_exptl_crystal_grow.pH 4.7
_exptl_crystal_grow.temp 18(3)
_exptl_crystal_grow.time 'approximately 2 days'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__exptl_crystal_grow.apparatus
_item_description.description
; The physical apparatus in which the crystal was grown.
;
_item.name '_exptl_crystal_grow.apparatus'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'Linbro plate'
'sandwich box'
'ACA plates'
save_
save__exptl_crystal_grow.atmosphere
_item_description.description
; The nature of the gas or gas mixture in which the crystal was
grown.
;
_item.name '_exptl_crystal_grow.atmosphere'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'room air'
'nitrogen'
'argon'
save_
save__exptl_crystal_grow.crystal_id
_item_description.description
; This data item is a pointer to _exptl_crystal.id in the
EXPTL_CRYSTAL category.
;
_item.name '_exptl_crystal_grow.crystal_id'
_item.mandatory_code yes
save_
save__exptl_crystal_grow.details
_item_description.description
; A description of special aspects of the crystal growth.
;
_item.name '_exptl_crystal_grow.details'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
; Solution 2 was prepared as a well solution and
mixed. A droplet containing 2 \ml of solution
1 was delivered onto a cover slip; 2 \ml of
solution 2 was added to the droplet without
mixing.
;
; Crystal plates were originally stored at room
temperature for 1 week but no nucleation
occurred. They were then transferred to 4
degrees C, at which temperature well formed
single crystals grew in 2 days.
;
; The dependence on pH for successful crystal
growth is very sharp. At pH 7.4 only showers
of tiny crystals grew, at pH 7.5 well formed
single crystals grew, at pH 7.6 no
crystallization occurred at all.
;
save_
save__exptl_crystal_grow.method
_item_description.description
; The method used to grow the crystals.
;
_item.name '_exptl_crystal_grow.method'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'batch precipitation'
'batch dialysis'
'hanging drop vapor diffusion'
'sitting drop vapor diffusion'
save_
save__exptl_crystal_grow.method_ref
_item_description.description
; A literature reference that describes the method used to grow
the crystals.
;
_item.name '_exptl_crystal_grow.method_ref'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'McPherson et al., 1988'
save_
save__exptl_crystal_grow.pH
_item_description.description
; The pH at which the crystal was grown. If more than one pH was
employed during the crystallization process, the final pH should
be noted here and the protocol involving multiple pH values
should be described in _exptl_crystal_grow.details.
;
_item.name '_exptl_crystal_grow.pH'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
loop_
_item_examples.case 7.4
7.6
4.3
save_
save__exptl_crystal_grow.pressure
_item_description.description
; The ambient pressure in kilopascals at which the crystal was
grown.
;
_item.name '_exptl_crystal_grow.pressure'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_exptl_crystal_grow.pressure_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code kilopascals
save_
save__exptl_crystal_grow.pressure_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _exptl_crystal_grow.pressure.
;
_item.name '_exptl_crystal_grow.pressure_esd'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_exptl_crystal_grow.pressure'
_item_related.function_code associated_value
_item_type.code float
_item_units.code kilopascals
save_
save__exptl_crystal_grow.seeding
_item_description.description
; A description of the protocol used for seeding the crystal
growth.
;
_item.name '_exptl_crystal_grow.seeding'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'macroseeding'
; Microcrystals were introduced from a previous
crystal growth experiment by transfer with a
human hair.
;
save_
save__exptl_crystal_grow.seeding_ref
_item_description.description
; A literature reference that describes the protocol used to seed
the crystal.
;
_item.name '_exptl_crystal_grow.seeding_ref'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
_item_type.code text
_item_examples.case 'Stura et al., 1989'
save_
save__exptl_crystal_grow.temp
_item_description.description
; The temperature in kelvins at which the crystal was grown.
If more than one temperature was employed during the
crystallization process, the final temperature should be noted
here and the protocol involving multiple temperatures should be
described in _exptl_crystal_grow.details.
;
_item.name '_exptl_crystal_grow.temp'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_exptl_crystal_grow.temp_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code kelvins
save_
save__exptl_crystal_grow.temp_details
_item_description.description
; A description of special aspects of temperature control during
crystal growth.
;
_item.name '_exptl_crystal_grow.temp_details'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
_item_type.code text
save_
save__exptl_crystal_grow.temp_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _exptl_crystal_grow.temp.
;
_item.name '_exptl_crystal_grow.temp_esd'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_exptl_crystal_grow.temp'
_item_related.function_code associated_value
_item_type.code float
_item_units.code kelvins
save_
save__exptl_crystal_grow.time
_item_description.description
; The approximate time that the crystal took to grow to the size
used for data collection.
;
_item.name '_exptl_crystal_grow.time'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'overnight'
'2-4 days'
'6 months'
save_
#############################
## EXPTL_CRYSTAL_GROW_COMP ##
#############################
save_exptl_crystal_grow_comp
_category.description
; Data items in the EXPTL_CRYSTAL_GROW_COMP category record
details about the components of the solutions that were 'mixed'
(by whatever means) to produce the crystal.
In general, solution 1 is the solution that contains the
molecule to be crystallized and solution 2 is the solution
that contains the precipitant. However, the number of solutions
required to describe the crystallization protocol is not limited
to 2.
Details of the crystallization protocol should be given in
_exptl_crystal_grow_comp.details using the solutions
described in EXPTL_CRYSTAL_GROW_COMP.
;
_category.id exptl_crystal_grow_comp
_category.mandatory_code no
loop_
_category_key.name '_exptl_crystal_grow_comp.id'
'_exptl_crystal_grow_comp.crystal_id'
loop_
_category_group.id 'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_exptl_crystal_grow_comp.crystal_id
_exptl_crystal_grow_comp.id
_exptl_crystal_grow_comp.sol_id
_exptl_crystal_grow_comp.name
_exptl_crystal_grow_comp.volume
_exptl_crystal_grow_comp.conc
_exptl_crystal_grow_comp.details
1 1 1 'HIV-1 protease' '0.002 ml' '6 mg/ml'
; The protein solution was in a buffer containing 25 mM NaCl,
100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide
;
1 2 2 'NaCl' '0.200 ml' '4 M' 'in 3 mM NaAzide'
1 3 2 'Acetic Acid' '0.047 ml' '100 mM' 'in 3 mM NaAzide'
1 4 2 'Na Acetate' '0.053 ml' '100 mM'
; in 3 mM NaAzide. Buffer components were mixed to produce a
pH of 4.7 according to a ratio calculated from the pKa. The
actual pH of solution 2 was not measured.
;
1 5 2 'water' '0.700 ml' 'neat' 'in 3 mM NaAzide'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__exptl_crystal_grow_comp.conc
_item_description.description
; The concentration of the solution component.
;
_item.name '_exptl_crystal_grow_comp.conc'
_item.category_id exptl_crystal_grow_comp
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case '200 \ml'
'0.1 ml'
save_
save__exptl_crystal_grow_comp.details
_item_description.description
; A description of any special aspects of the solution component.
When the solution component is the one that contains the
macromolecule, this could be the specification of the buffer in
which the macromolecule was stored. When the solution component
is a buffer component, this could be the methods (or formula)
used to achieve a desired pH.
;
_item.name '_exptl_crystal_grow_comp.details'
_item.category_id exptl_crystal_grow_comp
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'in 3 mM NaAzide'
; The protein solution was in a buffer
containing 25 mM NaCl, 100 mM NaMES/MES
buffer, pH 7.5, 3 mM NaAzide
;
; in 3 mM NaAzide. Buffer components were mixed
to produce a pH of 4.7 according to a ratio
calculated from the pKa. The actual pH of
solution 2 was not measured.
;
save_
save__exptl_crystal_grow_comp.crystal_id
_item_description.description
; This data item is a pointer to _exptl_crystal.id in the
EXPTL_CRYSTAL category.
;
_item.name '_exptl_crystal_grow_comp.crystal_id'
_item.mandatory_code yes
save_
save__exptl_crystal_grow_comp.id
_item_description.description
; The value of _exptl_crystal_grow_comp.id must uniquely identify
each item in the EXPTL_CRYSTAL_GROW_COMP list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_exptl_crystal_grow_comp.id'
_item.category_id exptl_crystal_grow_comp
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case '1'
'A'
'protein in buffer'
save_
save__exptl_crystal_grow_comp.name
_item_description.description
; A common name for the component of the solution.
;
_item.name '_exptl_crystal_grow_comp.name'
_item.category_id exptl_crystal_grow_comp
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'protein in buffer'
'acetic acid'
save_
save__exptl_crystal_grow_comp.sol_id
_item_description.description
; An identifier for the solution to which the given solution
component belongs.
;
_item.name '_exptl_crystal_grow_comp.sol_id'
_item.category_id exptl_crystal_grow_comp
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case '1'
'well solution'
'solution A'
save_
save__exptl_crystal_grow_comp.volume
_item_description.description
; The volume of the solution component.
;
_item.name '_exptl_crystal_grow_comp.volume'
_item.category_id exptl_crystal_grow_comp
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case '200 \ml'
'0.1 ml'
save_
##########
## GEOM ##
##########
save_geom
_category.description
; Data items in the GEOM and related (GEOM_ANGLE,
GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION)
categories record details about the molecular
geometry as calculated from the contents of the ATOM, CELL
and SYMMETRY data.
Geometry data are therefore redundant, in that they can be
calculated from other more fundamental quantities in the data
block. However, they provide a check on the correctness of
both sets of data and enable the most important geometric data
to be identified for publication by setting the appropriate
publication flag.
;
_category.id geom
_category.mandatory_code no
_category_key.name '_geom.entry_id'
loop_
_category_group.id 'inclusive_group'
'geom_group'
save_
save__geom.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_geom.entry_id'
_item.mandatory_code yes
save_
save__geom.details
_item_description.description
; A description of geometry not covered by the
existing data names in the GEOM categories, such as
least-squares planes.
;
_item.name '_geom.details'
_item.category_id geom
_item.mandatory_code no
_item_aliases.alias_name '_geom_special_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
################
## GEOM_ANGLE ##
################
save_geom_angle
_category.description
; Data items in the GEOM_ANGLE category record details about the
bond angles as calculated from the contents
of the ATOM, CELL and SYMMETRY data.
;
_category.id geom_angle
_category.mandatory_code no
loop_
_category_key.name '_geom_angle.atom_site_id_1'
'_geom_angle.atom_site_id_2'
'_geom_angle.atom_site_id_3'
'_geom_angle.site_symmetry_1'
'_geom_angle.site_symmetry_2'
'_geom_angle.site_symmetry_3'
loop_
_category_group.id 'inclusive_group'
'geom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
loop_
_geom_angle.atom_site_id_1
_geom_angle.atom_site_id_2
_geom_angle.atom_site_id_3
_geom_angle.value
_geom_angle.value_esd
_geom_angle.site_symmetry_1
_geom_angle.site_symmetry_2
_geom_angle.site_symmetry_3
_geom_angle.publ_flag
C2 O1 C5 111.6 0.2 1_555 1_555 1_555 yes
O1 C2 C3 110.9 0.2 1_555 1_555 1_555 yes
O1 C2 O21 122.2 0.3 1_555 1_555 1_555 yes
C3 C2 O21 127.0 0.3 1_555 1_555 1_555 yes
C2 C3 N4 101.3 0.2 1_555 1_555 1_555 yes
C2 C3 C31 111.3 0.2 1_555 1_555 1_555 yes
C2 C3 H3 107 1 1_555 1_555 1_555 no
N4 C3 C31 116.7 0.2 1_555 1_555 1_555 yes
# - - - - data truncated for brevity - - - -
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__geom_angle.atom_site_id_1
_item_description.description
; The identifier of the first of the three atom sites that define
the angle.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_angle.atom_site_id_1'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_angle_atom_site_label_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_geom_angle.atom_site_id_2'
'_geom_angle.atom_site_id_3'
save_
save__geom_angle.atom_site_label_alt_id_1
_item_description.description
; An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_alt_id_1'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_atom_id_1
_item_description.description
; An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_atom_id_1'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_comp_id_1
_item_description.description
; An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_comp_id_1'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_seq_id_1
_item_description.description
; An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_seq_id_1'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_asym_id_1
_item_description.description
; An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_asym_id_1'
_item.mandatory_code no
save_
save__geom_angle.atom_site_id_2
_item_description.description
; The identifier of the second of the three atom sites that define
the angle. The second atom is taken to be the apex of the angle.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_angle.atom_site_id_2'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_angle_atom_site_label_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_geom_angle.atom_site_id_1'
'_geom_angle.atom_site_id_3'
save_
save__geom_angle.atom_site_label_alt_id_2
_item_description.description
; An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_alt_id_2'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_atom_id_2
_item_description.description
; An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_atom_id_2'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_comp_id_2
_item_description.description
; An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_comp_id_2'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_seq_id_2
_item_description.description
; An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_seq_id_2'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_asym_id_2
_item_description.description
; An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_asym_id_2'
_item.mandatory_code no
save_
save__geom_angle.atom_site_id_3
_item_description.description
; The identifier of the third of the three atom sites that define
the angle.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_angle.atom_site_id_3'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_angle_atom_site_label_3'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_geom_angle.atom_site_id_1'
'_geom_angle.atom_site_id_2'
save_
save__geom_angle.atom_site_label_alt_id_3
_item_description.description
; An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_alt_id_3'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_atom_id_3
_item_description.description
; An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_atom_id_3'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_comp_id_3
_item_description.description
; An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_comp_id_3'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_seq_id_3
_item_description.description
; An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_seq_id_3'
_item.mandatory_code no
save_
save__geom_angle.atom_site_label_asym_id_3
_item_description.description
; An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_label_asym_id_3'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_asym_id_1
_item_description.description
; An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_asym_id_1'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_atom_id_1
_item_description.description
; An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_atom_id_1'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_comp_id_1
_item_description.description
; An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_comp_id_1'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_seq_id_1
_item_description.description
; An optional identifier of the first of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_seq_id_1'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_atom_id_2
_item_description.description
; An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_atom_id_2'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_asym_id_2
_item_description.description
; An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_asym_id_2'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_comp_id_2
_item_description.description
; An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_comp_id_2'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_seq_id_2
_item_description.description
; An optional identifier of the second of the three atom sites
that define the angle.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_seq_id_2'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_atom_id_3
_item_description.description
; An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_atom_id_3'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_asym_id_3
_item_description.description
; An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_asym_id_3'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_comp_id_3
_item_description.description
; An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_comp_id_3'
_item.mandatory_code no
save_
save__geom_angle.atom_site_auth_seq_id_3
_item_description.description
; An optional identifier of the third of the three atom sites that
define the angle.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_angle.atom_site_auth_seq_id_3'
_item.mandatory_code no
save_
save__geom_angle.publ_flag
_item_description.description
; This code signals whether the angle is referred to in a
publication or should be placed in a table of significant angles.
;
_item.name '_geom_angle.publ_flag'
_item.category_id geom_angle
_item.mandatory_code no
_item_aliases.alias_name '_geom_angle_publ_flag'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail no 'do not include angle in special list'
n 'abbreviation for "no"'
yes 'do include angle in special list'
y 'abbreviation for "yes"'
save_
save__geom_angle.site_symmetry_1
_item_description.description
; The symmetry code of the first of the three atom sites that
define the angle.
;
_item.name '_geom_angle.site_symmetry_1'
_item.category_id geom_angle
_item.mandatory_code yes
_item_aliases.alias_name '_geom_angle_site_symmetry_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__geom_angle.site_symmetry_2
_item_description.description
; The symmetry code of the second of the three atom sites that
define the angle.
;
_item.name '_geom_angle.site_symmetry_2'
_item.category_id geom_angle
_item.mandatory_code yes
_item_aliases.alias_name '_geom_angle_site_symmetry_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__geom_angle.site_symmetry_3
_item_description.description
; The symmetry code of the third of the three atom sites that
define the angle.
;
_item.name '_geom_angle.site_symmetry_3'
_item.category_id geom_angle
_item.mandatory_code yes
_item_aliases.alias_name '_geom_angle_site_symmetry_3'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__geom_angle.value
_item_description.description
; Angle in degrees defined by the three sites
_geom_angle.atom_site_id_1, _geom_angle.atom_site_id_2 and
_geom_angle.atom_site_id_3.
;
_item.name '_geom_angle.value'
_item.category_id geom_angle
_item.mandatory_code no
_item_aliases.alias_name '_geom_angle'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_geom_angle.value_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code degrees
save_
save__geom_angle.value_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _geom_angle.value.
;
_item.name '_geom_angle.value_esd'
_item.category_id geom_angle
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_geom_angle.value'
_item_related.function_code associated_value
_item_type.code float
_item_units.code degrees
save_
###############
## GEOM_BOND ##
###############
save_geom_bond
_category.description
; Data items in the GEOM_BOND category record details about
the bond lengths as calculated from the contents
of the ATOM, CELL and SYMMETRY data.
;
_category.id geom_bond
_category.mandatory_code no
loop_
_category_key.name '_geom_bond.atom_site_id_1'
'_geom_bond.atom_site_id_2'
'_geom_bond.site_symmetry_1'
'_geom_bond.site_symmetry_2'
loop_
_category_group.id 'inclusive_group'
'geom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
loop_
_geom_bond.atom_site_id_1
_geom_bond.atom_site_id_2
_geom_bond.dist
_geom_bond.dist_esd
_geom_bond.site_symmetry_1
_geom_bond.site_symmetry_2
_geom_bond.publ_flag
O1 C2 1.342 0.004 1_555 1_555 yes
O1 C5 1.439 0.003 1_555 1_555 yes
C2 C3 1.512 0.004 1_555 1_555 yes
C2 O21 1.199 0.004 1_555 1_555 yes
C3 N4 1.465 0.003 1_555 1_555 yes
C3 C31 1.537 0.004 1_555 1_555 yes
C3 H3 1.00 0.03 1_555 1_555 no
N4 C5 1.472 0.003 1_555 1_555 yes
# - - - - data truncated for brevity - - - -
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__geom_bond.atom_site_id_1
_item_description.description
; The identifier of the first of the two atom sites that define the
bond.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_bond.atom_site_id_1'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_bond_atom_site_label_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_dependent.dependent_name
'_geom_bond.atom_site_id_2'
save_
save__geom_bond.atom_site_label_alt_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_label_alt_id_1'
_item.mandatory_code no
save_
save__geom_bond.atom_site_label_atom_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_label_atom_id_1'
_item.mandatory_code no
save_
save__geom_bond.atom_site_label_comp_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_label_comp_id_1'
_item.mandatory_code no
save_
save__geom_bond.atom_site_label_seq_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_label_seq_id_1'
_item.mandatory_code no
save_
save__geom_bond.atom_site_label_asym_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_label_asym_id_1'
_item.mandatory_code no
save_
save__geom_bond.atom_site_id_2
_item_description.description
; The identifier of the second of the two atom sites that define
the bond.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_bond.atom_site_id_2'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_bond_atom_site_label_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_dependent.dependent_name
'_geom_bond.atom_site_id_1'
save_
save__geom_bond.atom_site_label_alt_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_label_alt_id_2'
_item.mandatory_code no
save_
save__geom_bond.atom_site_label_atom_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_label_atom_id_2'
_item.mandatory_code no
save_
save__geom_bond.atom_site_label_comp_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_label_comp_id_2'
_item.mandatory_code no
save_
save__geom_bond.atom_site_label_seq_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_label_seq_id_2'
_item.mandatory_code no
save_
save__geom_bond.atom_site_label_asym_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_label_asym_id_2'
_item.mandatory_code no
save_
save__geom_bond.atom_site_auth_atom_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_auth_atom_id_1'
_item.mandatory_code no
save_
save__geom_bond.atom_site_auth_asym_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_auth_asym_id_1'
_item.mandatory_code no
save_
save__geom_bond.atom_site_auth_comp_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_auth_comp_id_1'
_item.mandatory_code no
save_
save__geom_bond.atom_site_auth_seq_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_auth_seq_id_1'
_item.mandatory_code no
save_
save__geom_bond.atom_site_auth_atom_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_auth_atom_id_2'
_item.mandatory_code no
save_
save__geom_bond.atom_site_auth_asym_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_auth_asym_id_2'
_item.mandatory_code no
save_
save__geom_bond.atom_site_auth_comp_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_auth_comp_id_2'
_item.mandatory_code no
save_
save__geom_bond.atom_site_auth_seq_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the bond.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_bond.atom_site_auth_seq_id_2'
_item.mandatory_code no
save_
save__geom_bond.dist
_item_description.description
; The intramolecular bond distance in angstroms.
;
_item.name '_geom_bond.dist'
_item.category_id geom_bond
_item.mandatory_code no
_item_aliases.alias_name '_geom_bond_distance'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_geom_bond.dist_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__geom_bond.dist_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _geom_bond.dist.
;
_item.name '_geom_bond.dist_esd'
_item.category_id geom_bond
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_geom_bond.dist'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
save__geom_bond.publ_flag
_item_description.description
; This code signals whether the bond distance is referred to in a
publication or should be placed in a list of significant bond
distances.
;
_item.name '_geom_bond.publ_flag'
_item.category_id geom_bond
_item.mandatory_code no
_item_aliases.alias_name '_geom_bond_publ_flag'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail no 'do not include bond in special list'
n 'abbreviation for "no"'
yes 'do include bond in special list'
y 'abbreviation for "yes"'
save_
save__geom_bond.site_symmetry_1
_item_description.description
; The symmetry code of the first of the two atom sites that
define the bond.
;
_item.name '_geom_bond.site_symmetry_1'
_item.category_id geom_bond
_item.mandatory_code yes
_item_aliases.alias_name '_geom_bond_site_symmetry_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__geom_bond.site_symmetry_2
_item_description.description
; The symmetry code of the second of the two atom sites that
define the bond.
;
_item.name '_geom_bond.site_symmetry_2'
_item.category_id geom_bond
_item.mandatory_code yes
_item_aliases.alias_name '_geom_bond_site_symmetry_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
##################
## GEOM_CONTACT ##
##################
save_geom_contact
_category.description
; Data items in the GEOM_CONTACT category record details about
interatomic contacts as calculated from the contents
of the ATOM, CELL and SYMMETRY data.
;
_category.id geom_contact
_category.mandatory_code no
loop_
_category_key.name '_geom_contact.atom_site_id_1'
'_geom_contact.atom_site_id_2'
'_geom_contact.site_symmetry_1'
'_geom_contact.site_symmetry_2'
loop_
_category_group.id 'inclusive_group'
'geom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
[Acta Cryst. (1992), C48, 2262-2264].
;
;
loop_
_geom_contact.atom_site_id_1
_geom_contact.atom_site_id_2
_geom_contact.dist
_geom_contact.dist_esd
_geom_contact.site_symmetry_1
_geom_contact.site_symmetry_2
_geom_contact.publ_flag
O(1) O(2) 2.735 0.003 . . yes
H(O1) O(2) 1.82 . . . no
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__geom_contact.atom_site_id_1
_item_description.description
; The identifier of the first of the two atom sites that define the
contact.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_contact.atom_site_id_1'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_contact_atom_site_label_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_dependent.dependent_name
'_geom_contact.atom_site_id_2'
save_
save__geom_contact.atom_site_label_alt_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_label_alt_id_1'
_item.mandatory_code no
save_
save__geom_contact.atom_site_label_atom_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_label_atom_id_1'
_item.mandatory_code no
save_
save__geom_contact.atom_site_label_comp_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_label_comp_id_1'
_item.mandatory_code no
save_
save__geom_contact.atom_site_label_seq_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_label_seq_id_1'
_item.mandatory_code no
save_
save__geom_contact.atom_site_label_asym_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_label_asym_id_1'
_item.mandatory_code no
save_
save__geom_contact.atom_site_id_2
_item_description.description
; The identifier of the second of the two atom sites that define
the contact.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_contact.atom_site_id_2'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_contact_atom_site_label_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_dependent.dependent_name
'_geom_contact.atom_site_id_1'
save_
save__geom_contact.atom_site_label_alt_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_label_alt_id_2'
_item.mandatory_code no
save_
save__geom_contact.atom_site_label_atom_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_label_atom_id_2'
_item.mandatory_code no
save_
save__geom_contact.atom_site_label_comp_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_label_comp_id_2'
_item.mandatory_code no
save_
save__geom_contact.atom_site_label_seq_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_label_seq_id_2'
_item.mandatory_code no
save_
save__geom_contact.atom_site_label_asym_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_label_asym_id_2'
_item.mandatory_code no
save_
save__geom_contact.atom_site_auth_atom_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_auth_atom_id_1'
_item.mandatory_code no
save_
save__geom_contact.atom_site_auth_asym_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_auth_asym_id_1'
_item.mandatory_code no
save_
save__geom_contact.atom_site_auth_comp_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_auth_comp_id_1'
_item.mandatory_code no
save_
save__geom_contact.atom_site_auth_seq_id_1
_item_description.description
; An optional identifier of the first of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_auth_seq_id_1'
_item.mandatory_code no
save_
save__geom_contact.atom_site_auth_atom_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_auth_atom_id_2'
_item.mandatory_code no
save_
save__geom_contact.atom_site_auth_asym_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_auth_asym_id_2'
_item.mandatory_code no
save_
save__geom_contact.atom_site_auth_comp_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_auth_comp_id_2'
_item.mandatory_code no
save_
save__geom_contact.atom_site_auth_seq_id_2
_item_description.description
; An optional identifier of the second of the two atom sites that
define the contact.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_contact.atom_site_auth_seq_id_2'
_item.mandatory_code no
save_
save__geom_contact.dist
_item_description.description
; The interatomic contact distance in angstroms.
;
_item.name '_geom_contact.dist'
_item.category_id geom_contact
_item.mandatory_code no
_item_aliases.alias_name '_geom_contact_distance'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_geom_contact.dist_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__geom_contact.dist_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _geom_contact.dist.
;
_item.name '_geom_contact.dist_esd'
_item.category_id geom_contact
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_geom_contact.dist'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
save__geom_contact.publ_flag
_item_description.description
; This code signals whether the contact distance is referred to
in a publication or should be placed in a list of significant
contact distances.
;
_item.name '_geom_contact.publ_flag'
_item.category_id geom_contact
_item.mandatory_code no
_item_aliases.alias_name '_geom_contact_publ_flag'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail no 'do not include distance in special list'
n 'abbreviation for "no"'
yes 'do include distance in special list'
y 'abbreviation for "yes"'
save_
save__geom_contact.site_symmetry_1
_item_description.description
; The symmetry code of the first of the two atom sites that
define the contact.
;
_item.name '_geom_contact.site_symmetry_1'
_item.category_id geom_contact
_item.mandatory_code yes
_item_aliases.alias_name '_geom_contact_site_symmetry_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__geom_contact.site_symmetry_2
_item_description.description
; The symmetry code of the second of the two atom sites that
define the contact.
;
_item.name '_geom_contact.site_symmetry_2'
_item.category_id geom_contact
_item.mandatory_code yes
_item_aliases.alias_name '_geom_contact_site_symmetry_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
################
## GEOM_HBOND ##
################
save_geom_hbond
_category.description
; Data items in the GEOM_HBOND category record details about
hydrogen bonds as calculated from the contents of the ATOM,
CELL and SYMMETRY data.
;
_category.id geom_hbond
_category.mandatory_code no
loop_
_category_key.name '_geom_hbond.atom_site_id_A'
'_geom_hbond.atom_site_id_D'
'_geom_hbond.atom_site_id_H'
'_geom_hbond.site_symmetry_A'
'_geom_hbond.site_symmetry_D'
'_geom_hbond.site_symmetry_H'
loop_
_category_group.id 'inclusive_group'
'geom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer,
Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779].
;
;
loop_
_geom_hbond.atom_site_id_D
_geom_hbond.atom_site_id_H
_geom_hbond.atom_site_id_A
_geom_hbond.dist_DH
_geom_hbond.dist_HA
_geom_hbond.dist_DA
_geom_hbond.angle_DHA
_geom_hbond.publ_flag
N6 HN6 OW 0.888 1.921 2.801 169.6 yes
OW HO2 O7 0.917 1.923 2.793 153.5 yes
OW HO1 N10 0.894 1.886 2.842 179.7 yes
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__geom_hbond.angle_DHA
_item_description.description
; The angle in degrees defined by the donor-, hydrogen- and
acceptor-atom sites in a hydrogen bond.
;
_item.name '_geom_hbond.angle_DHA'
_item.category_id geom_hbond
_item.mandatory_code no
_item_aliases.alias_name '_geom_hbond_angle_DHA'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_geom_hbond.angle_DHA_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__geom_hbond.angle_DHA_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _geom_hbond.angle_DHA.
;
_item.name '_geom_hbond.angle_DHA_esd'
_item.category_id geom_hbond
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_geom_hbond.angle_DHA'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
save__geom_hbond.atom_site_id_A
_item_description.description
; The identifier of the acceptor-atom site that defines the
hydrogen bond.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_hbond.atom_site_id_A'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_hbond_atom_site_label_A'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_geom_hbond.atom_site_id_D'
'_geom_hbond.atom_site_id_H'
save_
save__geom_hbond.atom_site_label_alt_id_A
_item_description.description
; An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_alt_id_A'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_asym_id_A
_item_description.description
; An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_asym_id_A'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_atom_id_A
_item_description.description
; An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_atom_id_A'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_comp_id_A
_item_description.description
; An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_comp_id_A'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_seq_id_A
_item_description.description
; An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_seq_id_A'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_id_D
_item_description.description
; The identifier of the donor-atom site that defines the hydrogen
bond.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_hbond.atom_site_id_D'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_hbond_atom_site_label_D'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_geom_hbond.atom_site_id_A'
'_geom_hbond.atom_site_id_H'
save_
save__geom_hbond.atom_site_label_alt_id_D
_item_description.description
; An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_alt_id_D'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_asym_id_D
_item_description.description
; An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_asym_id_D'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_atom_id_D
_item_description.description
; An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_atom_id_D'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_comp_id_D
_item_description.description
; An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_comp_id_D'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_seq_id_D
_item_description.description
; An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_seq_id_D'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_id_H
_item_description.description
; The identifier of the hydrogen-atom site that defines the
hydrogen bond.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_hbond.atom_site_id_H'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_hbond_atom_site_label_H'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_geom_hbond.atom_site_id_A'
'_geom_hbond.atom_site_id_D'
save_
save__geom_hbond.atom_site_label_alt_id_H
_item_description.description
; An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_alt_id_H'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_asym_id_H
_item_description.description
; An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_asym_id_H'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_atom_id_H
_item_description.description
; An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_atom_id_H'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_comp_id_H
_item_description.description
; An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_comp_id_H'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_label_seq_id_H
_item_description.description
; An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_label_seq_id_H'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_asym_id_A
_item_description.description
; An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_asym_id_A'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_atom_id_A
_item_description.description
; An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_atom_id_A'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_comp_id_A
_item_description.description
; An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_comp_id_A'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_seq_id_A
_item_description.description
; An optional identifier of the acceptor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_seq_id_A'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_asym_id_D
_item_description.description
; An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_asym_id_D'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_atom_id_D
_item_description.description
; An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_atom_id_D'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_comp_id_D
_item_description.description
; An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_comp_id_D'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_seq_id_D
_item_description.description
; An optional identifier of the donor-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_seq_id_D'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_asym_id_H
_item_description.description
; An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_asym_id_H'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_atom_id_H
_item_description.description
; An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_atom_id_H'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_comp_id_H
_item_description.description
; An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_comp_id_H'
_item.mandatory_code no
save_
save__geom_hbond.atom_site_auth_seq_id_H
_item_description.description
; An optional identifier of the hydrogen-atom site that defines
the hydrogen bond.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_hbond.atom_site_auth_seq_id_H'
_item.mandatory_code no
save_
save__geom_hbond.dist_DA
_item_description.description
; The distance in angstroms between the donor- and acceptor-atom
sites in a hydrogen bond.
;
_item.name '_geom_hbond.dist_DA'
_item.category_id geom_hbond
_item.mandatory_code no
_item_aliases.alias_name '_geom_hbond_distance_DA'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_geom_hbond.dist_DA_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__geom_hbond.dist_DA_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
in angstroms of _geom_hbond.dist_DA.
;
_item.name '_geom_hbond.dist_DA_esd'
_item.category_id geom_hbond
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_geom_hbond.dist_DH'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
save__geom_hbond.dist_DH
_item_description.description
; The distance in angstroms between the donor- and hydrogen-atom
sites in a hydrogen bond.
;
_item.name '_geom_hbond.dist_DH'
_item.category_id geom_hbond
_item.mandatory_code no
_item_aliases.alias_name '_geom_hbond_distance_DH'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_geom_hbond.dist_DH_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__geom_hbond.dist_DH_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
in angstroms of _geom_hbond.dist_DH.
;
_item.name '_geom_hbond.dist_DH_esd'
_item.category_id geom_hbond
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_geom_hbond.dist_DH'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
save__geom_hbond.dist_HA
_item_description.description
; The distance in angstroms between the hydrogen- and acceptor-
atom sites in a hydrogen bond.
;
_item.name '_geom_hbond.dist_HA'
_item.category_id geom_hbond
_item.mandatory_code no
_item_aliases.alias_name '_geom_hbond_distance_HA'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_geom_hbond.dist_HA_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__geom_hbond.dist_HA_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
in angstroms of _geom_hbond.dist_HA.
;
_item.name '_geom_hbond.dist_HA_esd'
_item.category_id geom_hbond
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_geom_hbond.dist_HA'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
save__geom_hbond.publ_flag
_item_description.description
; This code signals whether the hydrogen-bond information is
referred to in a publication or should be placed in a table of
significant hydrogen-bond geometry.
;
_item.name '_geom_hbond.publ_flag'
_item.category_id geom_hbond
_item.mandatory_code no
_item_aliases.alias_name '_geom_hbond_publ_flag'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail no 'do not include bond in special list'
n 'abbreviation for "no"'
yes 'do include bond in special list'
y 'abbreviation for "yes"'
save_
save__geom_hbond.site_symmetry_A
_item_description.description
; The symmetry code of the acceptor-atom site that defines the
hydrogen bond.
;
_item.name '_geom_hbond.site_symmetry_A'
_item.category_id geom_hbond
_item.mandatory_code yes
_item_aliases.alias_name '_geom_hbond_site_symmetry_A'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__geom_hbond.site_symmetry_D
_item_description.description
; The symmetry code of the donor-atom site that defines the
hydrogen bond.
;
_item.name '_geom_hbond.site_symmetry_D'
_item.category_id geom_hbond
_item.mandatory_code yes
_item_aliases.alias_name '_geom_hbond_site_symmetry_D'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__geom_hbond.site_symmetry_H
_item_description.description
; The symmetry code of the hydrogen-atom site that defines the
hydrogen bond.
;
_item.name '_geom_hbond.site_symmetry_H'
_item.category_id geom_hbond
_item.mandatory_code yes
_item_aliases.alias_name '_geom_hbond_site_symmetry_H'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
##################
## GEOM_TORSION ##
##################
save_geom_torsion
_category.description
; Data items in the GEOM_TORSION category record details about
torsion angles as calculated from the
contents of the ATOM, CELL and SYMMETRY data.
The vector direction _geom_torsion.atom_site_id_2 to
_geom_torsion.atom_site_id_3 is the viewing direction, and the
torsion angle is the angle of twist required to superimpose the
projection of the vector between site 2 and site 1 onto the
projection of the vector between site 3 and site 4. Clockwise
torsions are positive, anticlockwise torsions are negative.
Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
;
_category.id geom_torsion
_category.mandatory_code no
loop_
_category_key.name '_geom_torsion.atom_site_id_1'
'_geom_torsion.atom_site_id_2'
'_geom_torsion.atom_site_id_3'
'_geom_torsion.atom_site_id_4'
'_geom_torsion.site_symmetry_1'
'_geom_torsion.site_symmetry_2'
'_geom_torsion.site_symmetry_3'
'_geom_torsion.site_symmetry_4'
loop_
_category_group.id 'inclusive_group'
'geom_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
[Acta Cryst. (1992), C48, 2262-2264].
;
;
loop_
_geom_torsion.atom_site_id_1
_geom_torsion.atom_site_id_2
_geom_torsion.atom_site_id_3
_geom_torsion.atom_site_id_4
_geom_torsion.value
_geom_torsion.site_symmetry_1
_geom_torsion.site_symmetry_2
_geom_torsion.site_symmetry_3
_geom_torsion.site_symmetry_4
_geom_torsion.publ_flag
C(9) O(2) C(7) C(2) 71.8 . . . . yes
C(7) O(2) C(9) C(10) -168.0 . . . 2_666 yes
C(10) O(3) C(8) C(6) -167.7 . . . . yes
C(8) O(3) C(10) C(9) -69.7 . . . 2_666 yes
O(1) C(1) C(2) C(3) -179.5 . . . . no
O(1) C(1) C(2) C(7) -0.6 . . . . no
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__geom_torsion.atom_site_id_1
_item_description.description
; The identifier of the first of the four atom sites that define
the torsion angle.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_torsion.atom_site_id_1'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_torsion_atom_site_label_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_geom_torsion.atom_site_id_2'
'_geom_torsion.atom_site_id_3'
'_geom_torsion.atom_site_id_4'
save_
save__geom_torsion.atom_site_label_alt_id_1
_item_description.description
; An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_alt_id_1'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_atom_id_1
_item_description.description
; An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_atom_id_1'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_comp_id_1
_item_description.description
; An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_comp_id_1'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_seq_id_1
_item_description.description
; An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_seq_id_1'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_asym_id_1
_item_description.description
; An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_asym_id_1'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_id_2
_item_description.description
; The identifier of the second of the four atom sites that define
the torsion angle.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_torsion.atom_site_id_2'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_torsion_atom_site_label_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_geom_torsion.atom_site_id_1'
'_geom_torsion.atom_site_id_3'
'_geom_torsion.atom_site_id_4'
save_
save__geom_torsion.atom_site_label_alt_id_2
_item_description.description
; An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_alt_id_2'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_atom_id_2
_item_description.description
; An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_atom_id_2'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_comp_id_2
_item_description.description
; An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_comp_id_2'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_seq_id_2
_item_description.description
; An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_seq_id_2'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_asym_id_2
_item_description.description
; An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_asym_id_2'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_id_3
_item_description.description
; The identifier of the third of the four atom sites that define
the torsion angle.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_torsion.atom_site_id_3'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_torsion_atom_site_label_3'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_geom_torsion.atom_site_id_1'
'_geom_torsion.atom_site_id_2'
'_geom_torsion.atom_site_id_4'
save_
save__geom_torsion.atom_site_label_alt_id_3
_item_description.description
; An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_alt_id_3'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_atom_id_3
_item_description.description
; An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_atom_id_3'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_comp_id_3
_item_description.description
; An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_comp_id_3'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_seq_id_3
_item_description.description
; An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_seq_id_3'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_asym_id_3
_item_description.description
; An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_asym_id_3'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_id_4
_item_description.description
; The identifier of the fourth of the four atom sites that define
the torsion angle.
This data item is a pointer to _atom_site.id in the ATOM_SITE
category.
;
_item.name '_geom_torsion.atom_site_id_4'
_item.mandatory_code yes
_item_aliases.alias_name '_geom_torsion_atom_site_label_4'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_geom_torsion.atom_site_id_1'
'_geom_torsion.atom_site_id_2'
'_geom_torsion.atom_site_id_3'
save_
save__geom_torsion.atom_site_label_alt_id_4
_item_description.description
; An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_alt_id_4'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_atom_id_4
_item_description.description
; An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_atom_id_4'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_comp_id_4
_item_description.description
; An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_comp_id_4'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_seq_id_4
_item_description.description
; An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_seq_id_4'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_label_asym_id_4
_item_description.description
; An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_label_asym_id_4'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_atom_id_1
_item_description.description
; An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_atom_id_1'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_asym_id_1
_item_description.description
; An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_asym_id_1'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_comp_id_1
_item_description.description
; An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_comp_id_1'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_seq_id_1
_item_description.description
; An optional identifier of the first of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_seq_id_1'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_atom_id_2
_item_description.description
; An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_atom_id_2'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_asym_id_2
_item_description.description
; An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_asym_id_2'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_comp_id_2
_item_description.description
; An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_comp_id_2'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_seq_id_2
_item_description.description
; An optional identifier of the second of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_seq_id_2'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_atom_id_3
_item_description.description
; An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_atom_id_3'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_asym_id_3
_item_description.description
; An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_asym_id_3'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_comp_id_3
_item_description.description
; An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_comp_id_3'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_seq_id_3
_item_description.description
; An optional identifier of the third of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_seq_id_3'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_atom_id_4
_item_description.description
; An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_atom_id_4'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_asym_id_4
_item_description.description
; An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_asym_id_4'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_comp_id_4
_item_description.description
; An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_comp_id_4'
_item.mandatory_code no
save_
save__geom_torsion.atom_site_auth_seq_id_4
_item_description.description
; An optional identifier of the fourth of the four atom sites that
define the torsion angle.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_geom_torsion.atom_site_auth_seq_id_4'
_item.mandatory_code no
save_
save__geom_torsion.publ_flag
_item_description.description
; This code signals whether the torsion angle is referred to in a
publication or should be placed in a table of significant
torsion angles.
;
_item.name '_geom_torsion.publ_flag'
_item.category_id geom_torsion
_item.mandatory_code no
_item_aliases.alias_name '_geom_torsion_publ_flag'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail no 'do not include angle in special list'
n 'abbreviation for "no"'
yes 'do include angle in special list'
y 'abbreviation for "yes"'
save_
save__geom_torsion.site_symmetry_1
_item_description.description
; The symmetry code of the first of the four atom sites that
define the torsion angle.
;
_item.name '_geom_torsion.site_symmetry_1'
_item.category_id geom_torsion
_item.mandatory_code yes
_item_aliases.alias_name '_geom_torsion_site_symmetry_1'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__geom_torsion.site_symmetry_2
_item_description.description
; The symmetry code of the second of the four atom sites that
define the torsion angle.
;
_item.name '_geom_torsion.site_symmetry_2'
_item.category_id geom_torsion
_item.mandatory_code yes
_item_aliases.alias_name '_geom_torsion_site_symmetry_2'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__geom_torsion.site_symmetry_3
_item_description.description
; The symmetry code of the third of the four atom sites that
define the torsion angle.
;
_item.name '_geom_torsion.site_symmetry_3'
_item.category_id geom_torsion
_item.mandatory_code yes
_item_aliases.alias_name '_geom_torsion_site_symmetry_3'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__geom_torsion.site_symmetry_4
_item_description.description
; The symmetry code of the fourth of the four atom sites that
define the torsion angle.
;
_item.name '_geom_torsion.site_symmetry_4'
_item.category_id geom_torsion
_item.mandatory_code yes
_item_aliases.alias_name '_geom_torsion_site_symmetry_4'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__geom_torsion.value
_item_description.description
; The value of the torsion angle in degrees.
;
_item.name '_geom_torsion.value'
_item.category_id geom_torsion
_item.mandatory_code no
_item_aliases.alias_name '_geom_torsion'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_geom_torsion.value_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code degrees
save_
save__geom_torsion.value_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _geom_torsion.value.
;
_item.name '_geom_torsion.value_esd'
_item.category_id geom_torsion
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_geom_torsion.value'
_item_related.function_code associated_value
_item_type.code float
_item_units.code degrees
save_
#############
## JOURNAL ##
#############
save_journal
_category.description
; Data items in the JOURNAL category record details about the
book-keeping by the journal staff when processing
a data block submitted for publication.
The creator of a data block will not normally specify these data.
The data names are not defined in the dictionary because they are
for journal use only.
;
_category.id journal
_category.mandatory_code no
_category_key.name '_journal.entry_id'
loop_
_category_group.id 'inclusive_group'
'iucr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith
& Tozer (1991). Acta Cryst. C47, 2276-2277].
;
;
_journal.entry_id 'TOZ'
_journal.date_recd_electronic 1991-04-15
_journal.date_from_coeditor 1991-04-18
_journal.date_accepted 1991-04-18
_journal.date_printers_first 1991-08-07
_journal.date_proofs_out 1991-08-07
_journal.coeditor_code HL0007
_journal.techeditor_code C910963
_journal.coden_ASTM ACSCEE
_journal.name_full 'Acta Crystallographica Section C'
_journal.year 1991
_journal.volume 47
_journal.issue NOV91
_journal.page_first 2276
_journal.page_last 2277
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__journal.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_journal.entry_id'
_item.mandatory_code yes
save_
save__journal.coden_ASTM
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.coden_ASTM'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_coden_ASTM'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.coden_Cambridge
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.coden_Cambridge'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_coden_Cambridge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.coeditor_address
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.coeditor_address'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_coeditor_address'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__journal.coeditor_code
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.coeditor_code'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_coeditor_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.coeditor_email
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.coeditor_email'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_coeditor_email'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.coeditor_fax
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.coeditor_fax'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_coeditor_fax'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.coeditor_name
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.coeditor_name'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_coeditor_name'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.coeditor_notes
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.coeditor_notes'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_coeditor_notes'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__journal.coeditor_phone
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.coeditor_phone'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_coeditor_phone'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.data_validation_number
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.data_validation_number'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_data_validation_number'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
save_
save__journal.date_accepted
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.date_accepted'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_date_accepted'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code yyyy-mm-dd
save_
save__journal.date_from_coeditor
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.date_from_coeditor'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_date_from_coeditor'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code yyyy-mm-dd
save_
save__journal.date_to_coeditor
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.date_to_coeditor'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_date_to_coeditor'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code yyyy-mm-dd
save_
save__journal.date_printers_final
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.date_printers_final'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_date_printers_final'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code yyyy-mm-dd
save_
save__journal.date_printers_first
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.date_printers_first'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_date_printers_first'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code yyyy-mm-dd
save_
save__journal.date_proofs_in
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.date_proofs_in'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_date_proofs_in'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code yyyy-mm-dd
save_
save__journal.date_proofs_out
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.date_proofs_out'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_date_proofs_out'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code yyyy-mm-dd
save_
save__journal.date_recd_copyright
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.date_recd_copyright'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_date_recd_copyright'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code yyyy-mm-dd
save_
save__journal.date_recd_electronic
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.date_recd_electronic'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_date_recd_electronic'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code yyyy-mm-dd
save_
save__journal.date_recd_hard_copy
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.date_recd_hard_copy'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_date_recd_hard_copy'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code yyyy-mm-dd
save_
save__journal.issue
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.issue'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_issue'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.language
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.language'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_language'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.name_full
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.name_full'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_name_full'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.page_first
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.page_first'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_page_first'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.page_last
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.page_last'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_page_last'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.paper_category
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.paper_category'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_paper_category'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.suppl_publ_number
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.suppl_publ_number'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_suppl_publ_number'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.suppl_publ_pages
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.suppl_publ_pages'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_suppl_publ_pages'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.techeditor_address
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.techeditor_address'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_techeditor_address'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__journal.techeditor_code
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.techeditor_code'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_techeditor_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.techeditor_email
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.techeditor_email'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_techeditor_email'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.techeditor_fax
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.techeditor_fax'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_techeditor_fax'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.techeditor_name
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.techeditor_name'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_techeditor_name'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.techeditor_notes
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.techeditor_notes'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_techeditor_notes'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__journal.techeditor_phone
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.techeditor_phone'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_techeditor_phone'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.volume
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.volume'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_volume'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal.year
_item_description.description
; Journal data items are defined by the journal staff.
;
_item.name '_journal.year'
_item.category_id journal
_item.mandatory_code no
_item_aliases.alias_name '_journal_year'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
###################
## JOURNAL_INDEX ##
###################
save_journal_index
_category.description
; Data items in the JOURNAL_INDEX category are used to list terms
used to generate the journal indexes.
The creator of a data block will not normally specify these data
items.
;
_category.id journal_index
_category.mandatory_code no
loop_
_category_key.name '_journal_index.type'
'_journal_index.term'
loop_
_category_group.id 'inclusive_group'
'iucr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell
[Acta Cryst. (1994), C50, 2067-2069].
;
;
loop_
_journal_index.type
_journal_index.term
_journal_index.subterm
O C16H19NO4 .
S alkaloids (-)-norcocaine
S (-)-norcocaine .
S
; [2R,3S-(2\b,3\b)]-methyl
3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate
;
.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__journal_index.subterm
_item_description.description
; Journal index data items are defined by the journal staff.
;
_item.name '_journal_index.subterm'
_item.category_id journal_index
_item.mandatory_code no
_item_aliases.alias_name '_journal_index_subterm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal_index.term
_item_description.description
; Journal index data items are defined by the journal staff.
;
_item.name '_journal_index.term'
_item.category_id journal_index
_item.mandatory_code no
_item_aliases.alias_name '_journal_index_term'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__journal_index.type
_item_description.description
; Journal index data items are defined by the journal staff.
;
_item.name '_journal_index.type'
_item.category_id journal_index
_item.mandatory_code no
_item_aliases.alias_name '_journal_index_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
#############
## PHASING ##
#############
save_phasing
_category.description
; Data items in the PHASING category record details about the
phasing of the structure, listing the various methods used in
the phasing process. Details about the application of each
method are listed in the appropriate subcategories.
;
_category.id phasing
_category.mandatory_code no
_category_key.name '_phasing.method'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - hypothetical example.
;
;
loop_
_phasing.method
'mir'
'averaging'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing.method
_item_description.description
; A listing of the method or methods used to phase this
structure.
;
_item.name '_phasing.method'
_item.category_id phasing
_item.mandatory_code yes
_item_type.code ucode
loop_
_item_examples.case
_item_examples.detail abinitio
; phasing by ab initio methods
;
averaging
; phase improvement by averaging over multiple
images of the structure
;
dm
; phasing by direct methods
;
isas
; phasing by iterative single-wavelength
anomalous scattering
;
isir
; phasing by iterative single-wavelength
isomorphous replacement
;
isomorphous
; phasing beginning with phases calculated from
an isomorphous structure
;
mad
; phasing by multiple-wavelength anomalous
dispersion
;
mir
; phasing by multiple isomorphous replacement
;
miras
; phasing by multiple isomorphous replacement
with anomalous scattering
;
mr
; phasing by molecular replacement
;
sir
; phasing by single isomorphous replacement
;
siras
; phasing by single isomorphous replacement
with anomalous scattering
;
save_
#######################
## PHASING_AVERAGING ##
#######################
save_phasing_averaging
_category.description
; Data items in the PHASING_AVERAGING category record details
about the phasing of the structure where methods involving
averaging of multiple observations of the molecule in the
asymmetric unit are involved.
;
_category.id phasing_averaging
_category.mandatory_code no
_category_key.name '_phasing_averaging.entry_id'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - hypothetical example.
;
;
_phasing_averaging.entry_id 'EXAMHYPO'
_phasing_averaging.method
; Iterative threefold averaging alternating with phase
extensions by 0.5 reciprocal lattice units per cycle.
;
_phasing_averaging.details
; The position of the threefold axis was redetermined every
five cycles.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_averaging.details
_item_description.description
; A description of special aspects of the averaging process.
;
_item.name '_phasing_averaging.details'
_item.category_id phasing_averaging
_item.mandatory_code no
_item_type.code text
save_
save__phasing_averaging.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_phasing_averaging.entry_id'
_item.mandatory_code yes
save_
save__phasing_averaging.method
_item_description.description
; A description of the phase-averaging phasing method used to
phase this structure.
Note that this is not the computer program used, which is
described in the SOFTWARE category, but rather the method
itself.
This data item should be used to describe significant
methodological options used within the phase-averaging program.
;
_item.name '_phasing_averaging.method'
_item.category_id phasing_averaging
_item.mandatory_code no
_item_type.code text
save_
#########################
## PHASING_ISOMORPHOUS ##
#########################
save_phasing_isomorphous
_category.description
; Data items in the PHASING_ISOMORPHOUS category record details
about the phasing of the structure where a model isomorphous
to the structure being phased was used to generate the initial
phases.
;
_category.id phasing_isomorphous
_category.mandatory_code no
_category_key.name '_phasing_isomorphous.entry_id'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 4PHV and laboratory records for the
structure corresponding to PDB entry 4PHV.
;
;
_phasing_isomorphous.parent 'PDB entry 5HVP'
_phasing_isomorphous.details
; The inhibitor and all solvent atoms were removed from the
parent structure before beginning refinement. All static
disorder present in the parent structure was also removed.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_isomorphous.details
_item_description.description
; A description of special aspects of the isomorphous phasing.
;
_item.name '_phasing_isomorphous.details'
_item.category_id phasing_isomorphous
_item.mandatory_code no
_item_type.code text
_item_examples.case
; Residues 13-18 were eliminated from the
starting model as it was anticipated that
binding of the inhibitor would cause a
structural rearrangement in this part of the
structure.
;
save_
save__phasing_isomorphous.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_phasing_isomorphous.entry_id'
_item.mandatory_code yes
save_
save__phasing_isomorphous.method
_item_description.description
; A description of the isomorphous-phasing method used to
phase this structure.
Note that this is not the computer program used, which is
described in the SOFTWARE category, but rather the method
itself.
This data item should be used to describe significant
methodological options used within the isomorphous phasing
program.
;
_item.name '_phasing_isomorphous.method'
_item.category_id phasing_isomorphous
_item.mandatory_code no
_item_type.code text
_item_examples.case
; Iterative threefold averaging alternating with
phase extension by 0.5 reciprocal lattice
units per cycle.
;
save_
save__phasing_isomorphous.parent
_item_description.description
; Reference to the structure used to generate starting phases
if the structure referenced in this data block was phased
by virtue of being isomorphous to a known structure (e.g.
a mutant that crystallizes in the same space group as the
wild-type protein.)
;
_item.name '_phasing_isomorphous.parent'
_item.category_id phasing_isomorphous
_item.mandatory_code no
_item_type.code text
save_
#################
## PHASING_MAD ##
#################
save_phasing_MAD
_category.description
; Data items in the PHASING_MAD category record details about
the phasing of the structure where methods involving
multiple-wavelength anomalous-dispersion techniques are involved.
;
_category.id phasing_MAD
_category.mandatory_code no
_category_key.name '_phasing_MAD.entry_id'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
;
;
_phasing_MAD.entry_id 'NCAD'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_MAD.details
_item_description.description
; A description of special aspects of the MAD phasing.
;
_item.name '_phasing_MAD.details'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code text
save_
save__phasing_MAD.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_phasing_MAD.entry_id'
_item.mandatory_code yes
save_
save__phasing_MAD.method
_item_description.description
; A description of the MAD phasing method used to phase
this structure.
Note that this is not the computer program used, which is
described in the SOFTWARE category, but rather the method
itself.
This data item should be used to describe significant
methodological options used within the MAD phasing program.
;
_item.name '_phasing_MAD.method'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code text
save_
#######################
## PHASING_MAD_CLUST ##
#######################
save_phasing_MAD_clust
_category.description
; Data items in the PHASING_MAD_CLUST category record details
about a cluster of experiments that contributed to the
generation of a set of phases.
;
_category.id phasing_MAD_clust
_category.mandatory_code no
loop_
_category_key.name '_phasing_MAD_clust.expt_id'
'_phasing_MAD_clust.id'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
;
;
loop_
_phasing_MAD_clust.id
_phasing_MAD_clust.expt_id
_phasing_MAD_clust.number_set
'4 wavelength' 1 4
'5 wavelength' 1 5
'5 wavelength' 2 5
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_MAD_clust.expt_id
_item_description.description
; This data item is a pointer to _phasing_MAD_expt.id in the
PHASING_MAD_EXPT category.
;
_item.name '_phasing_MAD_clust.expt_id'
_item.mandatory_code yes
save_
save__phasing_MAD_clust.id
_item_description.description
; The value of _phasing_MAD_clust.id must, together with
_phasing_MAD_clust.expt_id, uniquely identify a record in the
PHASING_MAD_CLUST list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_phasing_MAD_clust.id' phasing_MAD_clust yes
'_phasing_MAD_set.clust_id' phasing_MAD_set yes
'_phasing_MAD_ratio.clust_id' phasing_MAD_ratio yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_phasing_MAD_set.clust_id' '_phasing_MAD_clust.id'
'_phasing_MAD_ratio.clust_id' '_phasing_MAD_clust.id'
_item_type.code code
save_
save__phasing_MAD_clust.number_set
_item_description.description
; The number of data sets in this cluster of data sets.
;
_item.name '_phasing_MAD_clust.number_set'
_item.category_id phasing_MAD_clust
_item.mandatory_code no
_item_type.code int
save_
######################
## PHASING_MAD_EXPT ##
######################
save_phasing_MAD_expt
_category.description
; Data items in the PHASING_MAD_EXPT category record details about
a MAD phasing experiment, such as the number of experiments that
were clustered together to produce a set of phases or the
statistics for those phases.
;
_category.id phasing_MAD_expt
_category.mandatory_code no
_category_key.name '_phasing_MAD_expt.id'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
;
;
loop_
_phasing_MAD_expt.id
_phasing_MAD_expt.number_clust
_phasing_MAD_expt.R_normal_all
_phasing_MAD_expt.R_normal_anom_scat
_phasing_MAD_expt.delta_delta_phi
_phasing_MAD_expt.delta_phi_sigma
_phasing_MAD_expt.mean_fom
1 2 0.063 0.451 58.5 20.3 0.88
2 1 0.051 0.419 36.8 18.2 0.93
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_MAD_expt.delta_delta_phi
_item_description.description
; The difference between two independent determinations of
_phasing_MAD_expt.delta_phi.
;
_item.name '_phasing_MAD_expt.delta_delta_phi'
_item.category_id phasing_MAD_expt
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_expt.delta_phi
_item_description.description
; The phase difference between F~t~(h), the structure factor due
to normal scattering from all atoms, and F~a~(h), the structure
factor due to normal scattering from only the anomalous
scatterers.
;
_item.name '_phasing_MAD_expt.delta_phi'
_item.category_id phasing_MAD_expt
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_phasing_MAD_expt.delta_phi_sigma'
_item_related.function_code associated_esd
save_
save__phasing_MAD_expt.delta_phi_sigma
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_MAD_expt.delta_phi.
;
_item.name '_phasing_MAD_expt.delta_phi_sigma'
_item.category_id phasing_MAD_expt
_item.mandatory_code no
_item_related.related_name '_phasing_MAD_expt.delta_phi'
_item_related.function_code associated_value
_item_type.code float
save_
save__phasing_MAD_expt.id
_item_description.description
; The value of _phasing_MAD_expt.id must uniquely identify each
record in the PHASING_MAD_EXPT list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_phasing_MAD_expt.id' phasing_MAD_expt yes
'_phasing_MAD_clust.expt_id' phasing_MAD_clust yes
'_phasing_MAD_set.expt_id' phasing_MAD_set yes
'_phasing_MAD_ratio.expt_id' phasing_MAD_ratio yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_phasing_MAD_clust.expt_id' '_phasing_MAD_expt.id'
'_phasing_MAD_set.expt_id' '_phasing_MAD_expt.id'
'_phasing_MAD_ratio.expt_id' '_phasing_MAD_expt.id'
_item_type.code code
save_
save__phasing_MAD_expt.mean_fom
_item_description.description
; The mean figure of merit.
;
_item.name '_phasing_MAD_expt.mean_fom'
_item.category_id phasing_MAD_expt
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_expt.number_clust
_item_description.description
; The number of clusters of data sets in this phasing experiment.
;
_item.name '_phasing_MAD_expt.number_clust'
_item.category_id phasing_MAD_expt
_item.mandatory_code no
_item_type.code int
save_
save__phasing_MAD_expt.R_normal_all
_item_description.description
; Definition...
;
_item.name '_phasing_MAD_expt.R_normal_all'
_item.category_id phasing_MAD_expt
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_expt.R_normal_anom_scat
_item_description.description
; Definition...
;
_item.name '_phasing_MAD_expt.R_normal_anom_scat'
_item.category_id phasing_MAD_expt
_item.mandatory_code no
_item_type.code float
save_
#######################
## PHASING_MAD_RATIO ##
#######################
save_phasing_MAD_ratio
_category.description
; Data items in the PHASING_MAD_RATIO category record
the ratios of phasing statistics between pairs of data sets
in a MAD phasing experiment, in given shells of resolution.
;
_category.id phasing_MAD_ratio
_category.mandatory_code no
loop_
_category_key.name '_phasing_MAD_ratio.clust_id'
'_phasing_MAD_ratio.expt_id'
'_phasing_MAD_ratio.wavelength_1'
'_phasing_MAD_ratio.wavelength_2'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
;
;
loop_
_phasing_MAD_ratio.expt_id
_phasing_MAD_ratio.clust_id
_phasing_MAD_ratio.wavelength_1
_phasing_MAD_ratio.wavelength_2
_phasing_MAD_ratio.d_res_low
_phasing_MAD_ratio.d_res_high
_phasing_MAD_ratio.ratio_two_wl
_phasing_MAD_ratio.ratio_one_wl
_phasing_MAD_ratio.ratio_one_wl_centric
1 '4 wavelength' 1.4013 1.4013 20.00 4.00 . 0.084 0.076
1 '4 wavelength' 1.4013 1.3857 20.00 4.00 0.067 . .
1 '4 wavelength' 1.4013 1.3852 20.00 4.00 0.051 . .
1 '4 wavelength' 1.4013 1.3847 20.00 4.00 0.044 . .
1 '4 wavelength' 1.3857 1.3857 20.00 4.00 . 0.110 0.049
1 '4 wavelength' 1.3857 1.3852 20.00 4.00 0.049 . .
1 '4 wavelength' 1.3857 1.3847 20.00 4.00 0.067 . .
1 '4 wavelength' 1.3852 1.3852 20.00 4.00 . 0.149 0.072
1 '4 wavelength' 1.3852 1.3847 20.00 4.00 0.039 . .
1 '4 wavelength' 1.3847 1.3847 20.00 4.00 . 0.102 0.071
1 '4 wavelength' 1.4013 1.4013 4.00 3.00 . 0.114 0.111
1 '4 wavelength' 1.4013 1.3857 4.00 3.00 0.089 . .
1 '4 wavelength' 1.4013 1.3852 4.00 3.00 0.086 . .
1 '4 wavelength' 1.4013 1.3847 4.00 3.00 0.077 . .
1 '4 wavelength' 1.3857 1.3857 4.00 3.00 . 0.140 0.127
1 '4 wavelength' 1.3857 1.3852 4.00 3.00 0.085 . .
1 '4 wavelength' 1.3857 1.3847 4.00 3.00 0.089 . .
1 '4 wavelength' 1.3852 1.3852 4.00 3.00 . 0.155 0.119
1 '4 wavelength' 1.3852 1.3847 4.00 3.00 0.082 . .
1 '4 wavelength' 1.3847 1.3847 4.00 3.00 . 0.124 0.120
1 '5 wavelength' 1.3857 1.3857 20.00 4.00 . 0.075 0.027
1 '5 wavelength' 1.3857 1.3852 20.00 4.00 0.041 . .
1 '5 wavelength' 1.3857 1.3847 20.00 4.00 0.060 . .
1 '5 wavelength' 1.3857 1.3784 20.00 4.00 0.057 . .
1 '5 wavelength' 1.3857 1.2862 20.00 4.00 0.072 . .
1 '5 wavelength' 1.3852 1.3852 20.00 4.00 . 0.105 0.032
1 '5 wavelength' 1.3852 1.3847 20.00 4.00 0.036 . .
1 '5 wavelength' 1.3852 1.3784 20.00 4.00 0.044 . .
1 '5 wavelength' 1.3852 1.2862 20.00 4.00 0.065 . .
1 '5 wavelength' 1.3847 1.3847 20.00 4.00 . 0.072 0.031
1 '5 wavelength' 1.3847 1.3784 20.00 4.00 0.040 . .
1 '5 wavelength' 1.3847 1.2862 20.00 4.00 0.059 . .
1 '5 wavelength' 1.3784 1.3784 20.00 4.00 . 0.059 0.032
1 '5 wavelength' 1.3784 1.2862 20.00 4.00 0.059 . .
1 '5 wavelength' 1.2862 1.3847 20.00 4.00 . 0.058 0.028
1 '5 wavelength' 1.3857 1.3857 4.00 3.00 . 0.078 0.075
1 '5 wavelength' 1.3857 1.3852 4.00 3.00 0.059 . .
1 '5 wavelength' 1.3857 1.3847 4.00 3.00 0.067 . .
1 '5 wavelength' 1.3857 1.3784 4.00 3.00 0.084 . .
1 '5 wavelength' 1.3857 1.2862 4.00 3.00 0.073 . .
1 '5 wavelength' 1.3852 1.3852 4.00 3.00 . 0.101 0.088
1 '5 wavelength' 1.3852 1.3847 4.00 3.00 0.066 . .
1 '5 wavelength' 1.3852 1.3784 4.00 3.00 0.082 . .
1 '5 wavelength' 1.3852 1.2862 4.00 3.00 0.085 . .
1 '5 wavelength' 1.3847 1.3847 4.00 3.00 . 0.097 0.074
1 '5 wavelength' 1.3847 1.3784 4.00 3.00 0.081 . .
1 '5 wavelength' 1.3847 1.2862 4.00 3.00 0.085 . .
1 '5 wavelength' 1.3784 1.3784 4.00 3.00 . 0.114 0.089
1 '5 wavelength' 1.3784 1.2862 4.00 3.00 0.103 . .
1 '5 wavelength' 1.2862 1.2862 4.00 3.00 . 0.062 0.060
2 '5 wavelength' 0.7263 0.7263 15.00 3.00 . 0.035 0.026
2 '5 wavelength' 0.7263 0.7251 15.00 3.00 0.028 . .
2 '5 wavelength' 0.7263 0.7284 15.00 3.00 0.023 . .
2 '5 wavelength' 0.7263 0.7246 15.00 3.00 0.025 . .
2 '5 wavelength' 0.7263 0.7217 15.00 3.00 0.026 . .
2 '5 wavelength' 0.7251 0.7251 15.00 3.00 . 0.060 0.026
2 '5 wavelength' 0.7251 0.7284 15.00 3.00 0.029 . .
2 '5 wavelength' 0.7251 0.7246 15.00 3.00 0.031 . .
2 '5 wavelength' 0.7251 0.7217 15.00 3.00 0.035 . .
2 '5 wavelength' 0.7284 0.7284 15.00 3.00 . 0.075 0.030
2 '5 wavelength' 0.7284 0.7246 15.00 3.00 0.023 . .
2 '5 wavelength' 0.7284 0.7217 15.00 3.00 0.027 . .
2 '5 wavelength' 0.7246 0.7246 15.00 3.00 . 0.069 0.026
2 '5 wavelength' 0.7246 0.7217 15.00 3.00 0.024 . .
2 '5 wavelength' 0.7217 0.7284 15.00 3.00 . 0.060 0.028
2 '5 wavelength' 0.7263 0.7263 3.00 1.90 . 0.060 0.050
2 '5 wavelength' 0.7263 0.7251 3.00 1.90 0.056 . .
2 '5 wavelength' 0.7263 0.7284 3.00 1.90 0.055 . .
2 '5 wavelength' 0.7263 0.7246 3.00 1.90 0.053 . .
2 '5 wavelength' 0.7263 0.7217 3.00 1.90 0.056 . .
2 '5 wavelength' 0.7251 0.7251 3.00 1.90 . 0.089 0.050
2 '5 wavelength' 0.7251 0.7284 3.00 1.90 0.054 . .
2 '5 wavelength' 0.7251 0.7246 3.00 1.90 0.058 . .
2 '5 wavelength' 0.7251 0.7217 3.00 1.90 0.063 . .
2 '5 wavelength' 0.7284 0.7284 3.00 1.90 . 0.104 0.057
2 '5 wavelength' 0.7284 0.7246 3.00 1.90 0.052 . .
2 '5 wavelength' 0.7284 0.7217 3.00 1.90 0.057 . .
2 '5 wavelength' 0.7246 0.7246 3.00 1.90 . 0.098 0.052
2 '5 wavelength' 0.7246 0.7217 3.00 1.90 0.054 . .
2 '5 wavelength' 0.7217 0.7284 3.00 1.90 . 0.089 0.060
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_MAD_ratio.d_res_high
_item_description.description
; The lowest value for the interplanar spacings for the
reflection data used for the comparison of Bijvoet differences.
This is called the highest resolution.
;
_item.name '_phasing_MAD_ratio.d_res_high'
_item.category_id phasing_MAD_ratio
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_ratio.d_res_low
_item_description.description
; The highest value for the interplanar spacings for the
reflection data used for the comparison of Bijvoet differences.
This is called the lowest resolution.
;
_item.name '_phasing_MAD_ratio.d_res_low'
_item.category_id phasing_MAD_ratio
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_ratio.expt_id
_item_description.description
; This data item is a pointer to _phasing_MAD_expt.id in the
PHASING_MAD_EXPT category.
;
_item.name '_phasing_MAD_ratio.expt_id'
_item.mandatory_code yes
save_
save__phasing_MAD_ratio.clust_id
_item_description.description
; This data item is a pointer to _phasing_MAD_clust.id in
the PHASING_MAD_CLUST category.
;
_item.name '_phasing_MAD_ratio.clust_id'
_item.mandatory_code yes
save_
save__phasing_MAD_ratio.ratio_one_wl
_item_description.description
; The root-mean-square Bijvoet difference at one wavelength for
all reflections.
;
_item.name '_phasing_MAD_ratio.ratio_one_wl'
_item.category_id phasing_MAD_ratio
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_ratio.ratio_one_wl_centric
_item_description.description
; The root-mean-square Bijvoet difference at one wavelength for
centric reflections. This would be equal to zero for perfect
data and thus serves as an estimate of the noise in the
anomalous signals.
;
_item.name '_phasing_MAD_ratio.ratio_one_wl_centric'
_item.category_id phasing_MAD_ratio
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_ratio.ratio_two_wl
_item_description.description
; The root-mean-square dispersive Bijvoet difference between
two wavelengths for all reflections.
;
_item.name '_phasing_MAD_ratio.ratio_two_wl'
_item.category_id phasing_MAD_ratio
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_ratio.wavelength_1
_item_description.description
; This data item is a pointer to _phasing_MAD_set.wavelength in
the PHASING_MAD_SET category.
;
_item.name '_phasing_MAD_ratio.wavelength_1'
_item.mandatory_code yes
save_
save__phasing_MAD_ratio.wavelength_2
_item_description.description
; This data item is a pointer to _phasing_MAD_set.wavelength in
the PHASING_MAD_SET category.
;
_item.name '_phasing_MAD_ratio.wavelength_2'
_item.mandatory_code yes
save_
#####################
## PHASING_MAD_SET ##
#####################
save_phasing_MAD_set
_category.description
; Data items in the PHASING_MAD_SET category record
details about the individual data sets used in a MAD phasing
experiment.
;
_category.id phasing_MAD_set
_category.mandatory_code no
loop_
_category_key.name '_phasing_MAD_set.expt_id'
'_phasing_MAD_set.clust_id'
'_phasing_MAD_set.set_id'
'_phasing_MAD_set.wavelength'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by Shapiro et al. [Nature (London)
(1995), 374, 327-337].
;
;
loop_
_phasing_MAD_set.expt_id
_phasing_MAD_set.clust_id
_phasing_MAD_set.set_id
_phasing_MAD_set.wavelength
_phasing_MAD_set.wavelength_details
_phasing_MAD_set.d_res_low
_phasing_MAD_set.d_res_high
_phasing_MAD_set.f_prime
_phasing_MAD_set.f_double_prime
1 '4 wavelength' aa 1.4013 'pre-edge' 20.00 3.00
-12.48 3.80
1 '4 wavelength' bb 1.3857 'peak' 20.00 3.00
-31.22 17.20
1 '4 wavelength' cc 1.3852 'edge' 20.00 3.00
-13.97 29.17
1 '4 wavelength' dd 1.3847 'remote' 20.00 3.00
-6.67 17.34
1 '5 wavelength' ee 1.3857 'ascending edge' 20.00 3.00
-28.33 14.84
1 '5 wavelength' ff 1.3852 'peak' 20.00 3.00
-21.50 30.23
1 '5 wavelength' gg 1.3847 'descending edge' 20.00 3.00
-10.71 20.35
1 '5 wavelength' hh 1.3784 'remote 1' 20.00 3.00
-14.45 11.84
1 '5 wavelength' ii 1.2862 'remote 2' 20.00 3.00
-9.03 9.01
2 '5 wavelength' jj 0.7263 'pre-edge' 15.00 1.90
-21.10 4.08
2 '5 wavelength' kk 0.7251 'edge' 15.00 1.90
-34.72 7.92
2 '5 wavelength' ll 0.7248 'peak' 15.00 1.90
-24.87 10.30
2 '5 wavelength' mm 0.7246 'descending edge' 15.00 1.90
-17.43 9.62
2 '5 wavelength' nn 0.7217 'remote' 15.00 1.90
-13.26 8.40
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_MAD_set.clust_id
_item_description.description
; This data item is a pointer to _phasing_MAD_clust.id in
the PHASING_MAD_CLUST category.
;
_item.name '_phasing_MAD_set.clust_id'
_item.mandatory_code yes
save_
save__phasing_MAD_set.d_res_high
_item_description.description
; The lowest value for the interplanar spacings for the
reflection data used for this set of data. This is called
the highest resolution.
;
_item.name '_phasing_MAD_set.d_res_high'
_item.category_id phasing_MAD_set
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_set.d_res_low
_item_description.description
; The highest value for the interplanar spacings for the
reflection data used for this set of data. This is called
the lowest resolution.
;
_item.name '_phasing_MAD_set.d_res_low'
_item.category_id phasing_MAD_set
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_set.expt_id
_item_description.description
; This data item is a pointer to _phasing_MAD_expt.id in the
PHASING_MAD_EXPT category.
;
_item.name '_phasing_MAD_set.expt_id'
_item.mandatory_code yes
save_
save__phasing_MAD_set.f_double_prime
_item_description.description
; The f'' component of the anomalous scattering factor for this
wavelength.
;
_item.name '_phasing_MAD_set.f_double_prime'
_item.category_id phasing_MAD_set
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_set.f_prime
_item_description.description
; The f' component of the anomalous scattering factor for this
wavelength.
;
_item.name '_phasing_MAD_set.f_prime'
_item.category_id phasing_MAD_set
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MAD_set.set_id
_item_description.description
; This data item is a pointer to _phasing_set.id in the
PHASING_SET category.
;
_item.name '_phasing_MAD_set.set_id'
_item.mandatory_code yes
save_
save__phasing_MAD_set.wavelength
_item_description.description
; The wavelength at which this data set was measured.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_phasing_MAD_set.wavelength' phasing_MAD_set yes
'_phasing_MAD_ratio.wavelength_1' phasing_MAD_ratio yes
'_phasing_MAD_ratio.wavelength_2' phasing_MAD_ratio yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_phasing_MAD_ratio.wavelength_1' '_phasing_MAD_set.wavelength'
'_phasing_MAD_ratio.wavelength_2' '_phasing_MAD_set.wavelength'
_item_type.code float
save_
save__phasing_MAD_set.wavelength_details
_item_description.description
; A descriptor for this wavelength in this cluster of data sets.
;
_item.name '_phasing_MAD_set.wavelength_details'
_item.category_id phasing_MAD_set
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'peak'
'remote'
'ascending edge'
save_
#################
## PHASING_MIR ##
#################
save_phasing_MIR
_category.description
; Data items in the PHASING_MIR category record details about
the phasing of the structure where methods involving isomorphous
replacement are involved.
All isomorphous-replacement-based techniques are covered
by this category, including single isomorphous replacement (SIR),
multiple isomorphous replacement (MIR) and single or multiple
isomorphous replacement plus anomalous scattering (SIRAS, MIRAS).
;
_category.id phasing_MIR
_category.mandatory_code no
_category_key.name '_phasing_MIR.entry_id'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738].
;
;
_phasing_MIR.method
; Standard phase refinement (Blow & Crick, 1959)
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_MIR.details
_item_description.description
; A description of special aspects of the isomorphous-replacement
phasing.
;
_item.name '_phasing_MIR.details'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_type.code text
save_
save__phasing_MIR.d_res_high
_item_description.description
; The lowest value in angstroms for the interplanar spacings
for the reflection data used for the native data set. This is
called the highest resolution.
;
_item.name '_phasing_MIR.d_res_high'
_item.category_id phasing_MIR
_item.mandatory_code yes
_item_aliases.alias_name '_phasing_MIR.ebi_d_res_high'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR.d_res_low
_item_description.description
; The highest value in angstroms for the interplanar spacings
for the reflection data used for the native data set. This is
called the lowest resolution.
;
_item.name '_phasing_MIR.d_res_low'
_item.category_id phasing_MIR
_item.mandatory_code yes
_item_aliases.alias_name '_phasing_MIR.ebi_d_res_low'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_phasing_MIR.entry_id'
_item.mandatory_code yes
save_
save__phasing_MIR.FOM
_item_description.description
; The mean value of the figure of merit m for all reflections
phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
the integral is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR.FOM'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_fom'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR.FOM_acentric
_item_description.description
; The mean value of the figure of merit m for the acentric
reflections phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
the integral is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR.FOM_acentric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_fom_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR.FOM_centric
_item_description.description
; The mean value of the figure of merit m for the centric
reflections phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
the integral is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR.FOM_centric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_fom_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR.method
_item_description.description
; A description of the MIR phasing method applied to phase this
structure.
Note that this is not the computer program used, which is
described in the SOFTWARE category, but rather the method
itself.
This data item should be used to describe significant
methodological options used within the MIR phasing program.
;
_item.name '_phasing_MIR.method'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_type.code text
save_
save__phasing_MIR.reflns
_item_description.description
; The total number of reflections phased in the native data set.
;
_item.name '_phasing_MIR.reflns'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_reflns'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR.reflns_acentric
_item_description.description
; The number of acentric reflections phased in the native data
set.
;
_item.name '_phasing_MIR.reflns_acentric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_reflns_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR.reflns_centric
_item_description.description
; The number of centric reflections phased in the native data
set.
;
_item.name '_phasing_MIR.reflns_centric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_reflns_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR.reflns_criterion
_item_description.description
; Criterion used to limit the reflections used in the phasing
calculations.
;
_item.name '_phasing_MIR.reflns_criterion'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_reflns_criteria'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code text
_item_examples.case '> 4 \s(I)'
save_
#####################
## PHASING_MIR_DER ##
#####################
save_phasing_MIR_der
_category.description
; Data items in the PHASING_MIR_DER category record details
about individual derivatives used in the phasing of the
structure when methods involving isomorphous replacement are
involved.
A derivative in this context does not necessarily equate with
a data set; for instance, the same data set could be used to
one resolution limit as an isomorphous scatterer and to a
different resolution (and with a different sigma cutoff) as an
anomalous scatterer. These would be treated as two distinct
derivatives, although both derivatives would point to the same
data sets via _phasing_MIR_der.der_set_id and
_phasing_MIR_der.native_set_id.
;
_category.id phasing_MIR_der
_category.mandatory_code no
_category_key.name '_phasing_MIR_der.id'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738].
;
;
loop_
_phasing_MIR_der.id
_phasing_MIR_der.number_of_sites
_phasing_MIR_der.details
KAu(CN)2 3
'major site interpreted in difference Patterson'
K2HgI4 6 'sites found in cross-difference Fourier'
K3IrCl6 2 'sites found in cross-difference Fourier'
All 11 'data for all three derivatives combined'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_MIR_der.d_res_high
_item_description.description
; The lowest value for the interplanar spacings for the
reflection data used for this derivative. This is called the
highest resolution.
;
_item.name '_phasing_MIR_der.d_res_high'
_item.category_id phasing_MIR_der
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR_der.d_res_low
_item_description.description
; The highest value for the interplanar spacings for the
reflection data used for this derivative. This is called the
lowest resolution.
;
_item.name '_phasing_MIR_der.d_res_low'
_item.category_id phasing_MIR_der
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR_der.der_set_id
_item_description.description
; The data set that was treated as the derivative in this
experiment.
This data item is a pointer to _phasing_set.id in the
PHASING_SET category.
;
_item.name '_phasing_MIR_der.der_set_id'
_item.mandatory_code yes
save_
save__phasing_MIR_der.details
_item_description.description
; A description of special aspects of this derivative, its data,
its solution or its use in phasing.
;
_item.name '_phasing_MIR_der.details'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code text
save_
save__phasing_MIR_der.id
_item_description.description
; The value of _phasing_MIR_der.id must uniquely identify
a record in the PHASING_MIR_DER list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_phasing_MIR_der.id' phasing_MIR_der yes
'_phasing_MIR_der_refln.der_id' phasing_MIR_der_refln yes
'_phasing_MIR_der_shell.der_id' phasing_MIR_der_shell yes
'_phasing_MIR_der_site.der_id' phasing_MIR_der_site yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_phasing_MIR_der_refln.der_id' '_phasing_MIR_der.id'
'_phasing_MIR_der_shell.der_id' '_phasing_MIR_der.id'
'_phasing_MIR_der_site.der_id' '_phasing_MIR_der.id'
_item_type.code line
loop_
_item_examples.case 'KAu(CN)2'
'K2HgI4_anom'
'K2HgI4_iso'
save_
save__phasing_MIR_der.native_set_id
_item_description.description
; The data set that was treated as the native in this
experiment.
This data item is a pointer to _phasing_set.id in the
PHASING_SET category.
;
_item.name '_phasing_MIR_der.native_set_id'
_item.mandatory_code yes
save_
save__phasing_MIR_der.number_of_sites
_item_description.description
; The number of heavy-atom sites in this derivative.
;
_item.name '_phasing_MIR_der.number_of_sites'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code int
save_
save__phasing_MIR_der.power_acentric
_item_description.description
; The mean phasing power P for acentric reflections for this
derivative.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure-factor amplitude of this
derivative
Fph~calc~ = the calculated structure-factor amplitude of this
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
;
_item.name '_phasing_MIR_der.power_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_power_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.power_centric
_item_description.description
; The mean phasing power P for centric reflections for this
derivative.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
;
_item.name '_phasing_MIR_der.power_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_power_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.R_cullis_acentric
_item_description.description
; Residual factor R~cullis,acen~ for acentric reflections for this
derivative.
The Cullis R factor was originally defined only for centric
reflections. It is, however, also a useful statistical
measure for acentric reflections, which is how it is used in
this data item.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis,acen~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
Fp~obs~ = the observed structure-factor amplitude of the native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. R. Soc. London Ser. A,
265, 15-38.
;
_item.name '_phasing_MIR_der.R_cullis_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.R_cullis_anomalous
_item_description.description
; Residual factor R~cullis,ano~ for anomalous reflections for this
derivative.
The Cullis R factor was originally defined only for centric
reflections. It is, however, also a useful statistical
measure for anomalous reflections, which is how it is used in
this data item.
This is tabulated for acentric terms. A value less than 1.0
means there is some contribution to the phasing from the
anomalous data.
sum |Fph+~obs~Fph-~obs~ - Fh+~calc~ - Fh-~calc~|
R~cullis,ano~ = ------------------------------------------------
sum|Fph+~obs~ - Fph-~obs~|
Fph+~obs~ = the observed positive Friedel structure-factor
amplitude for the derivative
Fph-~obs~ = the observed negative Friedel structure-factor
amplitude for the derivative
Fh+~calc~ = the calculated positive Friedel structure-factor
amplitude from the heavy-atom model
Fh-~calc~ = the calculated negative Friedel structure-factor
amplitude from the heavy-atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. R. Soc. London Ser. A,
265, 15-38.
;
_item.name '_phasing_MIR_der.R_cullis_anomalous'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_anomalous'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.R_cullis_centric
_item_description.description
; Residual factor R~cullis~ for centric reflections for this
derivative.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
Fp~obs~ = the observed structure-factor amplitude of the native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. R. Soc. London Ser. A,
265, 15-38.
;
_item.name '_phasing_MIR_der.R_cullis_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.reflns_acentric
_item_description.description
; The number of acentric reflections used in phasing for this
derivative.
;
_item.name '_phasing_MIR_der.reflns_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_der.reflns_anomalous
_item_description.description
; The number of anomalous reflections used in phasing for this
derivative.
;
_item.name '_phasing_MIR_der.reflns_anomalous'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_anomalous'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_der.reflns_centric
_item_description.description
; The number of centric reflections used in phasing for this
derivative.
;
_item.name '_phasing_MIR_der.reflns_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_der.reflns_criteria
_item_description.description
; Criteria used to limit the reflections used in the phasing
calculations.
;
_item.name '_phasing_MIR_der.reflns_criteria'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code text
_item_examples.case '> 4 \s(I)'
save_
###########################
## PHASING_MIR_DER_REFLN ##
###########################
save_phasing_MIR_der_refln
_category.description
; Data items in the PHASING_MIR_DER_REFLN category record details
about the calculated structure factors obtained in an MIR
phasing experiment.
This list may contain information from a number of different
derivatives; _phasing_MIR_der_refln.der_id indicates to which
derivative a given record corresponds. (A derivative in this
context does not necessarily equate with a data set; see the
definition of the PHASING_MIR_DER category for a
discussion of the meaning of derivative.)
It is not necessary for the data items describing the measured
value of F to appear in this list, as they will be
given in the PHASING_SET_REFLN category. However, these
items can also be listed here for completeness.
;
_category.id phasing_MIR_der_refln
_category.mandatory_code no
loop_
_category_key.name '_phasing_MIR_der_refln.index_h'
'_phasing_MIR_der_refln.index_k'
'_phasing_MIR_der_refln.index_l'
'_phasing_MIR_der_refln.der_id'
'_phasing_MIR_der_refln.set_id'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for the 6,1,25 reflection
of an Hg/Pt derivative of protein NS1.
;
;
_phasing_MIR_der_refln.index_h 6
_phasing_MIR_der_refln.index_k 1
_phasing_MIR_der_refln.index_l 25
_phasing_MIR_der_refln.der_id HGPT1
_phasing_MIR_der_refln.set_id 'NS1-96'
_phasing_MIR_der_refln.F_calc_au 106.66
_phasing_MIR_der_refln.F_meas_au 204.67
_phasing_MIR_der_refln.F_meas_sigma 6.21
_phasing_MIR_der_refln.HL_A_iso -3.15
_phasing_MIR_der_refln.HL_B_iso -0.76
_phasing_MIR_der_refln.HL_C_iso 0.65
_phasing_MIR_der_refln.HL_D_iso 0.23
_phasing_MIR_der_refln.phase_calc 194.48
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_MIR_der_refln.der_id
_item_description.description
; This data item is a pointer to _phasing_MIR_der.id in the
PHASING_MIR_DER category.
;
_item.name '_phasing_MIR_der_refln.der_id'
_item.mandatory_code yes
save_
save__phasing_MIR_der_refln.F_calc
_item_description.description
; The calculated value of the structure factor for this derivative,
in electrons.
;
_item.name '_phasing_MIR_der_refln.F_calc'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code no
_item_related.related_name '_phasing_MIR_der_refln.F_calc_au'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code electrons
save_
save__phasing_MIR_der_refln.F_calc_au
_item_description.description
; The calculated value of the structure factor for this derivative,
in arbitrary units.
;
_item.name '_phasing_MIR_der_refln.F_calc_au'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code no
_item_related.related_name '_phasing_MIR_der_refln.F_calc'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code arbitrary
save_
save__phasing_MIR_der_refln.F_meas
_item_description.description
; The measured value of the structure factor for this derivative,
in electrons.
;
_item.name '_phasing_MIR_der_refln.F_meas'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_phasing_MIR_der_refln.F_meas_sigma'
associated_esd
'_phasing_MIR_der_refln.F_meas_au'
conversion_arbitrary
_item_type.code float
_item_type_conditions.code esd
_item_units.code electrons
save_
save__phasing_MIR_der_refln.F_meas_au
_item_description.description
; The measured value of the structure factor for this derivative,
in arbitrary units.
;
_item.name '_phasing_MIR_der_refln.F_meas_au'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_phasing_MIR_der_refln.F_meas_sigma_au'
associated_esd
'_phasing_MIR_der_refln.F_meas'
conversion_arbitrary
_item_type.code float
_item_type_conditions.code esd
_item_units.code arbitrary
save_
save__phasing_MIR_der_refln.F_meas_sigma
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_MIR_der_refln.F_meas, in electrons.
;
_item.name '_phasing_MIR_der_refln.F_meas_sigma'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_phasing_MIR_der_refln.F_meas'
associated_value
'_phasing_MIR_der_refln.F_meas_sigma_au'
conversion_arbitrary
_item_type.code float
_item_units.code electrons
save_
save__phasing_MIR_der_refln.F_meas_sigma_au
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_MIR_der_refln.F_meas_au, in arbitrary units.
;
_item.name '_phasing_MIR_der_refln.F_meas_sigma_au'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_phasing_MIR_der_refln.F_meas_au'
associated_value
'_phasing_MIR_der_refln.F_meas_sigma'
conversion_arbitrary
_item_type.code float
_item_units.code arbitrary
save_
save__phasing_MIR_der_refln.HL_A_iso
_item_description.description
; The isomorphous Hendrickson-Lattman coefficient A~iso~ for this
reflection for this derivative.
-2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^)
* Fp~obs~ * cos(alphah~calc~)
A~iso~ = -----------------------------------------------
E^2^
E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^
for centric reflections
= [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^
for acentric reflections
Fp~obs~ = the observed structure-factor amplitude of the
native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude
from the heavy-atom model
alphah~calc~ = the calculated phase from the heavy-atom model
This coefficient appears in the expression for the phase
probability of each isomorphous derivative:
P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha)
+ C * cos(2 * alpha) + D * sin(2 * alpha)]
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
;
_item.name '_phasing_MIR_der_refln.HL_A_iso'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MIR_der_refln.HL_B_iso
_item_description.description
; The isomorphous Hendrickson-Lattman coefficient B~iso~ for this
reflection for this derivative.
-2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^)
* Fp~obs~ * sin(alphah~calc~)
B~iso~ = -----------------------------------------------
E^2^
E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^
for centric reflections
= [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^
for acentric reflections
Fp~obs~ = the observed structure-factor amplitude of the
native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude
from the heavy-atom model
alphah~calc~ = the phase calculated from the heavy-atom model
This coefficient appears in the expression for the phase
probability of each isomorphous derivative:
P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha)
+ C * cos(2 * alpha) + D * sin(2 * alpha)]
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
;
_item.name '_phasing_MIR_der_refln.HL_B_iso'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MIR_der_refln.HL_C_iso
_item_description.description
; The isomorphous Hendrickson-Lattman coefficient C~iso~ for this
reflection for this derivative.
-Fp~obs~^2^ * [sin(alphah~calc~)^2^
- cos(alphah~calc~)^2^]
C~iso~ = ------------------------------------
E^2^
E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^
for centric reflections
= [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^
for acentric reflections
Fp~obs~ = the observed structure-factor amplitude of the
native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude
from the heavy-atom model
alphah~calc~ = the phase calculated from the heavy-atom model
This coefficient appears in the expression for the phase
probability of each isomorphous derivative:
P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha)
+ C * cos(2 * alpha) + D * sin(2 * alpha)]
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
;
_item.name '_phasing_MIR_der_refln.HL_C_iso'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MIR_der_refln.HL_D_iso
_item_description.description
; The isomorphous Hendrickson-Lattman coefficient D~iso~ for this
reflection for this derivative.
-2.0 * Fp~obs~^2^ * sin(alphah~calc~)^2^
* cos(alphah~calc~)^2^
D~iso~ = ----------------------------------------
E^2^
E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^
for centric reflections
= [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^
for acentric reflections
Fp~obs~ = the observed structure-factor amplitude of the
native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude
from the heavy-atom model
alphah~calc~ = the phase calculated from the heavy-atom model
This coefficient appears in the expression for the phase
probability of each isomorphous derivative:
P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha)
+ C * cos(2 * alpha) + D * sin(2 * alpha)]
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
;
_item.name '_phasing_MIR_der_refln.HL_D_iso'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MIR_der_refln.index_h
_item_description.description
; Miller index h for this reflection for this derivative.
;
_item.name '_phasing_MIR_der_refln.index_h'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_refln.index_k'
'_phasing_MIR_der_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__phasing_MIR_der_refln.index_k
_item_description.description
; Miller index k for this reflection for this derivative.
;
_item.name '_phasing_MIR_der_refln.index_k'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_refln.index_h'
'_phasing_MIR_der_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__phasing_MIR_der_refln.index_l
_item_description.description
; Miller index l for this reflection for this derivative.
;
_item.name '_phasing_MIR_der_refln.index_l'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_refln.index_h'
'_phasing_MIR_der_refln.index_k'
_item_sub_category.id miller_index
_item_type.code int
save_
save__phasing_MIR_der_refln.phase_calc
_item_description.description
; The calculated value of the structure-factor phase based on the
heavy-atom model for this derivative in degrees.
;
_item.name '_phasing_MIR_der_refln.phase_calc'
_item.category_id phasing_MIR_der_refln
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__phasing_MIR_der_refln.set_id
_item_description.description
; This data item is a pointer to _phasing_set.id in the
PHASING_SET category.
;
_item.name '_phasing_MIR_der_refln.set_id'
_item.mandatory_code yes
save_
###########################
## PHASING_MIR_DER_SHELL ##
###########################
save_phasing_MIR_der_shell
_category.description
; Data items in the PHASING_MIR_DER_SHELL category record
statistics, broken down into shells of resolution, for an MIR
phasing experiment.
This list may contain information from a number of different
derivatives; _phasing_MIR_der_shell.der_id indicates to which
derivative a given record corresponds. (A derivative in this
context does not necessarily equate with a data set; see the
definition of the PHASING_MIR_DER category for a
discussion of the meaning of derivative.)
;
_category.id phasing_MIR_der_shell
_category.mandatory_code no
loop_
_category_key.name '_phasing_MIR_der_shell.der_id'
'_phasing_MIR_der_shell.d_res_low'
'_phasing_MIR_der_shell.d_res_high'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738]
with addition of an arbitrary low-resolution limit.
;
;
loop_
_phasing_MIR_der_shell.der_id
_phasing_MIR_der_shell.d_res_low
_phasing_MIR_der_shell.d_res_high
_phasing_MIR_der_shell.ha_ampl
_phasing_MIR_der_shell.loc
KAu(CN)2 15.0 8.3 54 26
KAu(CN)2 8.3 6.4 54 20
KAu(CN)2 6.4 5.2 50 20
KAu(CN)2 5.2 4.4 44 23
KAu(CN)2 4.4 3.8 39 23
KAu(CN)2 3.8 3.4 33 21
KAu(CN)2 3.4 3.0 28 17
KAu(CN)2 15.0 3.0 38 21
K2HgI4 15.0 8.3 149 87
K2HgI4 8.3 6.4 121 73
K2HgI4 6.4 5.2 95 61
K2HgI4 5.2 4.4 80 60
K2HgI4 4.4 3.8 73 63
K2HgI4 3.8 3.4 68 57
K2HgI4 3.4 3.0 63 46
K2HgI4 15.0 3.0 79 58
K3IrCl6 15.0 8.3 33 27
K3IrCl6 8.3 6.4 40 23
K3IrCl6 6.4 5.2 31 22
K3IrCl6 5.2 4.4 27 23
K3IrCl6 4.4 3.8 22 23
K3IrCl6 3.8 3.4 19 20
K3IrCl6 3.4 3.0 16 20
K3IrCl6 15.0 3.0 23 21
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_MIR_der_shell.d_res_high
_item_description.description
; The lowest value for the interplanar spacings for the
reflection data for this derivative in this shell. This is called
the highest resolution.
;
_item.name '_phasing_MIR_der_shell.d_res_high'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR_der_shell.d_res_low
_item_description.description
; The highest value for the interplanar spacings for the
reflection data for this derivative in this shell. This is called
the lowest resolution.
;
_item.name '_phasing_MIR_der_shell.d_res_low'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR_der_shell.der_id
_item_description.description
; This data item is a pointer to _phasing_MIR_der.id in the
PHASING_MIR_DER category.
;
_item.name '_phasing_MIR_der_shell.der_id'
_item.mandatory_code yes
save_
save__phasing_MIR_der_shell.fom
_item_description.description
; The mean value of the figure of merit m for reflections for this
derivative in this shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~alpha~ = the probability that the phase angle alpha is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR_der_shell.fom'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der_shell.ha_ampl
_item_description.description
; The mean heavy-atom amplitude for reflections for this
derivative in this shell.
;
_item.name '_phasing_MIR_der_shell.ha_ampl'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der_shell.loc
_item_description.description
; The mean lack-of-closure error loc for reflections for this
derivative in this shell.
loc = sum|Fph~obs~ - Fph~calc~|
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
sum is taken over the specified reflections
;
_item.name '_phasing_MIR_der_shell.loc'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der_shell.phase
_item_description.description
; The mean of the phase values for reflections for this
derivative in this shell.
;
_item.name '_phasing_MIR_der_shell.phase'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MIR_der_shell.power
_item_description.description
; The mean phasing power P for reflections for this derivative
in this shell.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
;
_item.name '_phasing_MIR_der_shell.power'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der_shell.R_cullis
_item_description.description
; Residual factor R~cullis~ for centric reflections for this
derivative in this shell.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
Fp~obs~ = the observed structure-factor amplitude of the native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. R. Soc. London Ser. A,
265, 15-38.
;
_item.name '_phasing_MIR_der_shell.R_cullis'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der_shell.R_kraut
_item_description.description
; Residual factor R~kraut~ for general reflections for this
derivative in this shell.
sum|Fph~obs~ - Fph~calc~|
R~kraut~ = -------------------------
sum|Fph~obs~|
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
sum is taken over the specified reflections
Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T.
(1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424.
;
_item.name '_phasing_MIR_der_shell.R_kraut'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der_shell.reflns
_item_description.description
; The number of reflections in this shell.
;
_item.name '_phasing_MIR_der_shell.reflns'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
##########################
## PHASING_MIR_DER_SITE ##
##########################
save_phasing_MIR_der_site
_category.description
; Data items in the PHASING_MIR_DER_SITE category record details
about the heavy-atom sites in an MIR phasing experiment.
This list may contain information from a number of different
derivatives; _phasing_MIR_der_site.der_id indicates to which
derivative a given record corresponds. (A derivative in this
context does not necessarily equate with a data set; see the
definition of the PHASING_MIR_DER category for a
discussion of the meaning of derivative.)
;
_category.id phasing_MIR_der_site
_category.mandatory_code no
loop_
_category_key.name '_phasing_MIR_der_site.der_id'
'_phasing_MIR_der_site.id'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738]
with occupancies converted from electrons to fractional.
;
;
loop_
_phasing_MIR_der_site.der_id
_phasing_MIR_der_site.id
_phasing_MIR_der_site.atom_type_symbol
_phasing_MIR_der_site.occupancy
_phasing_MIR_der_site.fract_x
_phasing_MIR_der_site.fract_y
_phasing_MIR_der_site.fract_z
_phasing_MIR_der_site.B_iso
KAu(CN)2 1 Au 0.40 0.082 0.266 0.615 33.0
KAu(CN)2 2 Au 0.03 0.607 0.217 0.816 25.9
KAu(CN)2 3 Au 0.02 0.263 0.782 0.906 15.7
K2HgI4 1 Hg 0.63 0.048 0.286 0.636 33.7
K2HgI4 2 Hg 0.34 0.913 0.768 0.889 36.7
K2HgI4 3 Hg 0.23 0.974 0.455 0.974 24.2
K2HgI4 4 Hg 0.28 0.903 0.836 0.859 14.7
K2HgI4 5 Hg 0.07 0.489 0.200 0.885 6.4
K2HgI4 6 Hg 0.07 0.162 0.799 0.889 32.9
K3IrCl6 1 Ir 0.26 0.209 0.739 0.758 40.8
K3IrCl6 2 Ir 0.05 0.279 0.613 0.752 24.9
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_MIR_der_site.atom_type_symbol
_item_description.description
; This data item is a pointer to _atom_type.symbol in the
ATOM_TYPE category.
The scattering factors referenced via this data item should be
those used in the refinement of the heavy-atom data; in some
cases this is the scattering factor for the single heavy
atom, in other cases these are the scattering factors for an
atomic cluster.
;
_item.name '_phasing_MIR_der_site.atom_type_symbol'
_item.mandatory_code yes
save_
save__phasing_MIR_der_site.B_iso
_item_description.description
; Isotropic displacement parameter for this heavy-atom site in this
derivative.
;
_item.name '_phasing_MIR_der_site.B_iso'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_related.related_name '_phasing_MIR_der_site.B_iso_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__phasing_MIR_der_site.B_iso_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_MIR_der_site.B_iso.
;
_item.name '_phasing_MIR_der_site.B_iso_esd'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_phasing_MIR_der_site.B_iso'
_item_related.function_code associated_value
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR_der_site.Cartn_x
_item_description.description
; The x coordinate of this heavy-atom position in this derivative
specified as orthogonal angstroms. The orthogonal Cartesian axes
are related to the cell axes as specified by the description
given in _atom_sites.Cartn_transform_axes.
;
_item.name '_phasing_MIR_der_site.Cartn_x'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.Cartn_y'
'_phasing_MIR_der_site.Cartn_z'
_item_related.related_name '_phasing_MIR_der_site.Cartn_x_esd'
_item_related.function_code associated_esd
_item_sub_category.id cartesian_coordinate
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__phasing_MIR_der_site.Cartn_x_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_MIR_der_site.Cartn_x.
;
_item.name '_phasing_MIR_der_site.Cartn_x_esd'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.Cartn_y_esd'
'_phasing_MIR_der_site.Cartn_z_esd'
_item_related.related_name '_phasing_MIR_der_site.Cartn_x'
_item_related.function_code associated_value
_item_sub_category.id cartesian_coordinate_esd
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR_der_site.Cartn_y
_item_description.description
; The y coordinate of this heavy-atom position in this derivative
specified as orthogonal angstroms. The orthogonal Cartesian axes
are related to the cell axes as specified by the description
given in _atom_sites.Cartn_transform_axes.
;
_item.name '_phasing_MIR_der_site.Cartn_y'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.Cartn_x'
'_phasing_MIR_der_site.Cartn_z'
_item_related.related_name '_phasing_MIR_der_site.Cartn_y_esd'
_item_related.function_code associated_esd
_item_sub_category.id cartesian_coordinate
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__phasing_MIR_der_site.Cartn_y_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_MIR_der_site.Cartn_y.
;
_item.name '_phasing_MIR_der_site.Cartn_y_esd'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.Cartn_x_esd'
'_phasing_MIR_der_site.Cartn_z_esd'
_item_related.related_name '_phasing_MIR_der_site.Cartn_y'
_item_related.function_code associated_value
_item_sub_category.id cartesian_coordinate_esd
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR_der_site.Cartn_z
_item_description.description
; The z coordinate of this heavy-atom position in this derivative
specified as orthogonal angstroms. The orthogonal Cartesian axes
are related to the cell axes as specified by the description
given in _atom_sites.Cartn_transform_axes.
;
_item.name '_phasing_MIR_der_site.Cartn_z'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.Cartn_x'
'_phasing_MIR_der_site.Cartn_y'
_item_related.related_name '_phasing_MIR_der_site.Cartn_z_esd'
_item_related.function_code associated_esd
_item_sub_category.id cartesian_coordinate
_item_type.code float
_item_type_conditions.code esd
_item_units.code angstroms
save_
save__phasing_MIR_der_site.Cartn_z_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_MIR_der_site.Cartn_z.
;
_item.name '_phasing_MIR_der_site.Cartn_z_esd'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.Cartn_x_esd'
'_phasing_MIR_der_site.Cartn_y_esd'
_item_related.related_name '_phasing_MIR_der_site.Cartn_z'
_item_related.function_code associated_value
_item_sub_category.id cartesian_coordinate_esd
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR_der_site.der_id
_item_description.description
; This data item is a pointer to _phasing_MIR_der.id in the
PHASING_MIR_DER category.
;
_item.name '_phasing_MIR_der_site.der_id'
_item.mandatory_code yes
save_
save__phasing_MIR_der_site.details
_item_description.description
; A description of special aspects of the derivative site.
;
_item.name '_phasing_MIR_der_site.details'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'binds to His 117'
'minor site obtained from difference Fourier'
'same as site 2 in the K2HgI4 derivative'
save_
save__phasing_MIR_der_site.fract_x
_item_description.description
; The x coordinate of this heavy-atom position in this derivative
specified as a fraction of _cell.length_a.
;
_item.name '_phasing_MIR_der_site.fract_x'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.fract_y'
'_phasing_MIR_der_site.fract_z'
_item_related.related_name '_phasing_MIR_der_site.fract_x_esd'
_item_related.function_code associated_esd
_item_sub_category.id fractional_coordinate
_item_type.code float
_item_type_conditions.code esd
save_
save__phasing_MIR_der_site.fract_x_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_MIR_der_site.fract_x.
;
_item.name '_phasing_MIR_der_site.fract_x_esd'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.fract_y_esd'
'_phasing_MIR_der_site.fract_z_esd'
_item_related.related_name '_phasing_MIR_der_site.fract_x'
_item_related.function_code associated_value
_item_sub_category.id fractional_coordinate_esd
_item_type.code float
save_
save__phasing_MIR_der_site.fract_y
_item_description.description
; The y coordinate of this heavy-atom position in this derivative
specified as a fraction of _cell.length_b.
;
_item.name '_phasing_MIR_der_site.fract_y'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.fract_x'
'_phasing_MIR_der_site.fract_z'
_item_related.related_name '_phasing_MIR_der_site.fract_y_esd'
_item_related.function_code associated_esd
_item_sub_category.id fractional_coordinate
_item_type.code float
_item_type_conditions.code esd
save_
save__phasing_MIR_der_site.fract_y_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_MIR_der_site.fract_y.
;
_item.name '_phasing_MIR_der_site.fract_y_esd'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.fract_x_esd'
'_phasing_MIR_der_site.fract_z_esd'
_item_related.related_name '_phasing_MIR_der_site.fract_y'
_item_related.function_code associated_value
_item_sub_category.id fractional_coordinate_esd
_item_type.code float
save_
save__phasing_MIR_der_site.fract_z
_item_description.description
; The z coordinate of this heavy-atom position in this derivative
specified as a fraction of _cell.length_c.
;
_item.name '_phasing_MIR_der_site.fract_z'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.fract_x'
'_phasing_MIR_der_site.fract_y'
_item_related.related_name '_phasing_MIR_der_site.fract_z_esd'
_item_related.function_code associated_esd
_item_sub_category.id fractional_coordinate
_item_type.code float
_item_type_conditions.code esd
save_
save__phasing_MIR_der_site.fract_z_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_MIR_der_site.fract_z.
;
_item.name '_phasing_MIR_der_site.fract_z_esd'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
# _item_default.value 0.0
loop_
_item_dependent.dependent_name
'_phasing_MIR_der_site.fract_x_esd'
'_phasing_MIR_der_site.fract_y_esd'
_item_related.related_name '_phasing_MIR_der_site.fract_z'
_item_related.function_code associated_value
_item_sub_category.id fractional_coordinate_esd
_item_type.code float
save_
save__phasing_MIR_der_site.id
_item_description.description
; The value of _phasing_MIR_der_site.id must uniquely identify each
site in each derivative in the PHASING_MIR_DER_SITE list.
The atom identifiers need not be unique over all sites in all
derivatives; they need only be unique for each site in each
derivative.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_phasing_MIR_der_site.id'
_item.category_id phasing_MIR_der_site
_item.mandatory_code yes
_item_type.code code
save_
save__phasing_MIR_der_site.occupancy
_item_description.description
; The fraction of the atom type present at this heavy-atom site
in a given derivative. The sum of the occupancies of all the
atom types at this site may not significantly exceed 1.0 unless
it is a dummy site.
;
_item.name '_phasing_MIR_der_site.occupancy'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_default.value 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der_site.occupancy_anom
_item_description.description
; The relative anomalous occupancy of the atom type
present at this heavy-atom site in a given derivative.
This atom occupancy will probably be on an arbitrary scale.
;
_item.name '_phasing_MIR_der_site.occupancy_anom'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_anom_su'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
save_
save__phasing_MIR_der_site.occupancy_anom_su
_item_description.description
; The standard uncertainty (estimated standard deviation) of
_phasing_MIR_der_site.occupancy_anom.
;
_item.name '_phasing_MIR_der_site.occupancy_anom_su'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom_esd'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
# _item_default.value 0.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_anom'
_item_related.function_code associated_value
_item_type.code float
save_
save__phasing_MIR_der_site.occupancy_iso
_item_description.description
; The relative real isotropic occupancy of the atom type
present at this heavy-atom site in a given derivative.
This atom occupancy will probably be on an arbitrary scale.
;
_item.name '_phasing_MIR_der_site.occupancy_iso'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_iso_su'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
save_
save__phasing_MIR_der_site.occupancy_iso_su
_item_description.description
; The standard uncertainty (estimated standard deviation) of
_phasing_MIR_der_site.occupancy_iso.
;
_item.name '_phasing_MIR_der_site.occupancy_iso_su'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso_esd'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
# _item_default.value 0.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_iso'
_item_related.function_code associated_value
_item_type.code float
save_
#######################
## PHASING_MIR_SHELL ##
#######################
save_phasing_MIR_shell
_category.description
; Data items in the PHASING_MIR_SHELL category record statistics
for an isomorphous replacement phasing experiment.broken
down into shells of resolution.
;
_category.id phasing_MIR_shell
_category.mandatory_code no
loop_
_category_key.name '_phasing_MIR_shell.d_res_low'
'_phasing_MIR_shell.d_res_high'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem.
(1993), 268, 10728-10738]
with addition of an arbitrary low-resolution limit.
;
;
loop_
_phasing_MIR_shell.d_res_low
_phasing_MIR_shell.d_res_high
_phasing_MIR_shell.reflns
_phasing_MIR_shell.FOM
15.0 8.3 80 0.69
8.3 6.4 184 0.73
6.4 5.2 288 0.72
5.2 4.4 406 0.65
4.4 3.8 554 0.54
3.8 3.4 730 0.53
3.4 3.0 939 0.50
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_MIR_shell.d_res_high
_item_description.description
; The lowest value for the interplanar spacings for the
reflection data in this shell. This is called the highest
resolution. Note that the resolution limits of shells in
the items _phasing_MIR_shell.d_res_high and
_phasing_MIR_shell.d_res_low are independent of the resolution
limits of shells in the items _reflns_shell.d_res_high and
_reflns_shell.d_res_low.
;
_item.name '_phasing_MIR_shell.d_res_high'
_item.category_id phasing_MIR_shell
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR_shell.d_res_low
_item_description.description
; The highest value for the interplanar spacings for the
reflection data in this shell. This is called the lowest
resolution. Note that the resolution limits of shells in the
items _phasing_MIR_shell.d_res_high and
_phasing_MIR_shell.d_res_low are independent of the resolution
limits of shells in the items _reflns_shell.d_res_high and
_reflns_shell.d_res_low.
;
_item.name '_phasing_MIR_shell.d_res_low'
_item.category_id phasing_MIR_shell
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR_shell.FOM
_item_description.description
; The mean value of the figure of merit m for reflections in this
shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~alpha~ = the probability that the phase angle alpha is correct
the integral is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR_shell.FOM'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_shell.FOM_acentric
_item_description.description
; The mean value of the figure of merit m for acentric reflections
in this shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
the integral is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR_shell.FOM_acentric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_shell.FOM_centric
_item_description.description
; The mean value of the figure of merit m for centric reflections
in this shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
the integral is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR_shell.FOM_centric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_shell.loc
_item_description.description
; The mean lack-of-closure error loc for reflections in this shell.
loc = sum|Fph~obs~ - Fph~calc~|
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
sum is taken over the specified reflections
;
_item.name '_phasing_MIR_shell.loc'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_shell.mean_phase
_item_description.description
; The mean of the phase values for all reflections in this shell.
;
_item.name '_phasing_MIR_shell.mean_phase'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_type.code float
save_
save__phasing_MIR_shell.power
_item_description.description
; The mean phasing power P for reflections in this shell.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
;
_item.name '_phasing_MIR_shell.power'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_shell.R_cullis
_item_description.description
; Residual factor R~cullis~ for centric reflections in this shell.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
Fp~obs~ = the observed structure-factor amplitude of the native
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fh~calc~ = the calculated structure-factor amplitude from the
heavy-atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. R. Soc. London Ser. A,
265, 15-38.
;
_item.name '_phasing_MIR_shell.R_cullis'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_shell.R_kraut
_item_description.description
; Residual factor R~kraut~ for general reflections in this shell.
sum|Fph~obs~ - Fph~calc~|
R~kraut~ = -------------------------
sum|Fph~obs~|
Fph~obs~ = the observed structure-factor amplitude of the
derivative
Fph~calc~ = the calculated structure-factor amplitude of the
derivative
sum is taken over the specified reflections
Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T.
(1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424.
;
_item.name '_phasing_MIR_shell.R_kraut'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_shell.reflns
_item_description.description
; The number of reflections in this shell.
;
_item.name '_phasing_MIR_shell.reflns'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_shell.reflns_acentric
_item_description.description
; The number of acentric reflections in this shell.
;
_item.name '_phasing_MIR_shell.reflns_acentric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_shell.reflns_anomalous
_item_description.description
; The number of anomalous reflections in this shell.
;
_item.name '_phasing_MIR_shell.reflns_anomalous'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
# _item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_anomalous'
# _item_aliases.dictionary ebi_extensions
# _item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_shell.reflns_centric
_item_description.description
; The number of centric reflections in this shell.
;
_item.name '_phasing_MIR_shell.reflns_centric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
#################
## PHASING_SET ##
#################
save_phasing_set
_category.description
; Data items in the PHASING_SET category record details about
the data sets used in a phasing experiment. A given data set
may be used in a number of different ways; for instance, a
single data set could be used both as an isomorphous derivative
and as a component of a multiple-wavelength calculation. This
category establishes identifiers for each data set and permits
the archiving of a subset of experimental information for each
data set (cell constants, wavelength, temperature etc.).
This and related categories of data items are provided so that
derivative intensity and phase information can be stored in
the same data block as the information for the refined
structure.
If all the possible experimental information for each data
set (raw data sets, crystal growth conditions etc.) is to be
archived, these data items should be recorded in a separate
data block.
;
_category.id phasing_set
_category.mandatory_code no
_category_key.name '_phasing_set.id'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for an Hg/Pt derivative of
protein NS1.
;
;
_phasing_set.id 'NS1-96'
_phasing_set.cell_angle_alpha 90.0
_phasing_set.cell_angle_beta 90.0
_phasing_set.cell_angle_gamma 90.0
_phasing_set.cell_length_a 38.63
_phasing_set.cell_length_b 38.63
_phasing_set.cell_length_c 82.88
_phasing_set.radiation_wavelength 1.5145
_phasing_set.detector_type 'image plate'
_phasing_set.detector_specific 'RXII'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_set.cell_angle_alpha
_item_description.description
; Unit-cell angle alpha for this data set in degrees.
;
_item.name '_phasing_set.cell_angle_alpha'
_item.category_id phasing_set
_item.mandatory_code no
_item_default.value 90.0
loop_
_item_dependent.dependent_name
'_phasing_set.cell_angle_beta'
'_phasing_set.cell_angle_gamma'
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 0.0
0.0 0.0
_item_sub_category.id cell_angle
_item_type.code float
_item_units.code degrees
save_
save__phasing_set.cell_angle_beta
_item_description.description
; Unit-cell angle beta for this data set in degrees.
;
_item.name '_phasing_set.cell_angle_beta'
_item.category_id phasing_set
_item.mandatory_code no
_item_default.value 90.0
loop_
_item_dependent.dependent_name
'_phasing_set.cell_angle_alpha'
'_phasing_set.cell_angle_gamma'
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 0.0
0.0 0.0
_item_sub_category.id cell_angle
_item_type.code float
_item_units.code degrees
save_
save__phasing_set.cell_angle_gamma
_item_description.description
; Unit-cell angle gamma for this data set in degrees.
;
_item.name '_phasing_set.cell_angle_gamma'
_item.category_id phasing_set
_item.mandatory_code no
_item_default.value 90.0
loop_
_item_dependent.dependent_name
'_phasing_set.cell_angle_alpha'
'_phasing_set.cell_angle_beta'
loop_
_item_range.maximum
_item_range.minimum 180.0 180.0
180.0 0.0
0.0 0.0
_item_sub_category.id cell_angle
_item_type.code float
_item_units.code degrees
save_
save__phasing_set.cell_length_a
_item_description.description
; Unit-cell length a for this data set in angstroms.
;
_item.name '_phasing_set.cell_length_a'
_item.category_id phasing_set
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_phasing_set.cell_length_b'
'_phasing_set.cell_length_c'
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_sub_category.id cell_length
_item_type.code float
_item_units.code angstroms
save_
save__phasing_set.cell_length_b
_item_description.description
; Unit-cell length b for this data set in angstroms.
;
_item.name '_phasing_set.cell_length_b'
_item.category_id phasing_set
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_phasing_set.cell_length_a'
'_phasing_set.cell_length_c'
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_sub_category.id cell_length
_item_type.code float
_item_units.code angstroms
save_
save__phasing_set.cell_length_c
_item_description.description
; Unit-cell length c for this data set in angstroms.
;
_item.name '_phasing_set.cell_length_c'
_item.category_id phasing_set
_item.mandatory_code no
loop_
_item_dependent.dependent_name
'_phasing_set.cell_length_a'
'_phasing_set.cell_length_b'
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_sub_category.id cell_length
_item_type.code float
_item_units.code angstroms
save_
save__phasing_set.detector_specific
_item_description.description
; The particular radiation detector. In general, this will be a
manufacturer, description, model number or some combination of
these.
;
_item.name '_phasing_set.detector_specific'
_item.category_id phasing_set
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'Siemens model x'
'Kodak XG'
'MAR Research model y'
save_
save__phasing_set.detector_type
_item_description.description
; The general class of the radiation detector.
;
_item.name '_phasing_set.detector_type'
_item.category_id phasing_set
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'multiwire'
'imaging plate'
'CCD'
'film'
save_
save__phasing_set.id
_item_description.description
; The value of _phasing_set.id must uniquely identify
a record in the PHASING_SET list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_phasing_set.id' phasing_set yes
'_phasing_set_refln.set_id' phasing_set_refln yes
'_phasing_MAD_set.set_id' phasing_MAD_set yes
'_phasing_MIR_der.der_set_id' phasing_MIR_der yes
'_phasing_MIR_der.native_set_id' phasing_MIR_der yes
'_phasing_MIR_der_refln.set_id' phasing_MIR_der_refln yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_phasing_set_refln.set_id' '_phasing_set.id'
'_phasing_MAD_set.set_id' '_phasing_set.id'
'_phasing_MIR_der.der_set_id' '_phasing_set.id'
'_phasing_MIR_der.native_set_id' '_phasing_set.id'
'_phasing_MIR_der_refln.set_id' '_phasing_set.id'
_item_type.code line
loop_
_item_examples.case 'KAu(CN)2'
'K2HgI4'
save_
save__phasing_set.radiation_source_specific
_item_description.description
; The particular source of radiation. In general, this will be a
manufacturer, description, or model number (or some combination
of these) for laboratory sources and an institution name and
beamline name for synchrotron sources.
;
_item.name '_phasing_set.radiation_source_specific'
_item.category_id phasing_set
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'Rigaku RU200'
'Philips fine focus Mo'
'NSLS beamline X8C'
save_
save__phasing_set.radiation_wavelength
_item_description.description
; The mean wavelength of the radiation used to measure this
data set.
;
_item.name '_phasing_set.radiation_wavelength'
_item.category_id phasing_set
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_set.temp
_item_description.description
; The temperature in kelvins at which the data set was
measured.
;
_item.name '_phasing_set.temp'
_item.category_id phasing_set
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code kelvins
save_
#######################
## PHASING_SET_REFLN ##
#######################
save_phasing_set_refln
_category.description
; Data items in the PHASING_SET_REFLN category record the values
of the measured structure factors used in a phasing experiment.
This list may contain information from a number of different
data sets; _phasing_set_refln.set_id indicates the data set
to which a given record corresponds.
;
_category.id phasing_set_refln
_category.mandatory_code no
loop_
_category_key.name '_phasing_set_refln.index_h'
'_phasing_set_refln.index_k'
'_phasing_set_refln.index_l'
'_phasing_set_refln.set_id'
loop_
_category_group.id 'inclusive_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for the 15,15,32
reflection of an Hg/Pt derivative of protein NS1.
;
;
_phasing_set_refln.set_id 'NS1-96'
_phasing_set_refln.index_h 15
_phasing_set_refln.index_k 15
_phasing_set_refln.index_l 32
_phasing_set_refln.F_meas_au 181.79
_phasing_set_refln.F_meas_sigma_au 3.72
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__phasing_set_refln.set_id
_item_description.description
; This data item is a pointer to _phasing_set.id in the
PHASING_SET category.
;
_item.name '_phasing_set_refln.set_id'
_item.mandatory_code yes
save_
save__phasing_set_refln.F_meas
_item_description.description
; The measured value of the structure factor for this reflection
in this data set in electrons.
;
_item.name '_phasing_set_refln.F_meas'
_item.category_id phasing_set_refln
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_phasing_set_refln.F_meas_sigma'
associated_esd
'_phasing_set_refln.F_meas_au'
conversion_arbitrary
_item_type.code float
_item_type_conditions.code esd
_item_units.code electrons
save_
save__phasing_set_refln.F_meas_au
_item_description.description
; The measured value of the structure factor for this reflection
in this data set in arbitrary units.
;
_item.name '_phasing_set_refln.F_meas_au'
_item.category_id phasing_set_refln
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_phasing_set_refln.F_meas_sigma_au'
associated_esd
'_phasing_set_refln.F_meas'
conversion_arbitrary
_item_type.code float
_item_type_conditions.code esd
_item_units.code arbitrary
save_
save__phasing_set_refln.F_meas_sigma
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_set_refln.F_meas in electrons.
;
_item.name '_phasing_set_refln.F_meas_sigma'
_item.category_id phasing_set_refln
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_phasing_set_refln.F_meas'
associated_value
'_phasing_set_refln.F_meas_sigma_au'
conversion_arbitrary
_item_type.code float
_item_units.code electrons
save_
save__phasing_set_refln.F_meas_sigma_au
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _phasing_set_refln.F_meas_au in arbitrary units.
;
_item.name '_phasing_set_refln.F_meas_sigma_au'
_item.category_id phasing_set_refln
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_phasing_set_refln.F_meas_au'
associated_value
'_phasing_set_refln.F_meas_sigma'
conversion_arbitrary
_item_type.code float
_item_units.code arbitrary
save_
save__phasing_set_refln.index_h
_item_description.description
; Miller index h of this reflection in this data set.
;
_item.name '_phasing_set_refln.index_h'
_item.category_id phasing_set_refln
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_phasing_set_refln.index_k'
'_phasing_set_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__phasing_set_refln.index_k
_item_description.description
; Miller index k of this reflection in this data set.
;
_item.name '_phasing_set_refln.index_k'
_item.category_id phasing_set_refln
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_phasing_set_refln.index_h'
'_phasing_set_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__phasing_set_refln.index_l
_item_description.description
; Miller index l of this reflection in this data set.
;
_item.name '_phasing_set_refln.index_l'
_item.category_id phasing_set_refln
_item.mandatory_code yes
loop_
_item_dependent.dependent_name
'_phasing_set_refln.index_h'
'_phasing_set_refln.index_k'
_item_sub_category.id miller_index
_item_type.code int
save_
##########
## PUBL ##
##########
save_publ
_category.description
; Data items in the PUBL category are used when submitting a
manuscript for publication.
;
_category.id publ
_category.mandatory_code no
_category_key.name '_publ.entry_id'
loop_
_category_group.id 'inclusive_group'
'iucr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
; _publ.section_title
; trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)-
1,3-oxazolidin-5-one
;
_publ.section_abstract
; The oxazolidinone ring is a shallow envelope
conformation with the tert-butyl and iso-butyl groups
occupying trans-positions with respect to the ring. The
angles at the N atom sum to 356.2\%, indicating a very
small degree of pyramidalization at this atom. This is
consistent with electron delocalization between the N
atom and the carbonyl centre [N-C=O = 1.374(3)\%A].
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on C~31~H~48~N~4~O~4~, reported by Coleman, Patrick,
Andersen & Rettig [Acta Cryst. (1996), C52, 1525-1527].
;
; _publ.section_title
; Hemiasterlin methyl ester
;
_publ.section_title_footnote
; IUPAC name: methyl 2,5-dimethyl-4-{2-[3-methyl-
2-methylamino-3-(N-methylbenzo[b]pyrrol-
3-yl)butanamido]-3,3-dimethyl-N-methyl-
butanamido}-2-hexenoate.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__publ.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_publ.entry_id'
_item.mandatory_code yes
save_
save__publ.contact_author
_item_description.description
; The name and address of the author submitting the manuscript and
data block. This is the person contacted by the journal
editorial staff. It is preferable to use the separate data items
_publ.contact_author_name and _publ.contact_author_address.
;
_item.name '_publ.contact_author'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_contact_author'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Professor George Ferguson
Department of Chemistry and Biochemistry
University of Guelph
Ontario
Canada
N1G 2W1
;
save_
save__publ.contact_author_address
_item_description.description
; The address of the author submitting the manuscript and data
block. This is the person contacted by the journal editorial
staff.
;
_item.name '_publ.contact_author_address'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_contact_author_address'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Department of Chemistry and Biochemistry
University of Guelph
Ontario
Canada
N1G 2W1
;
save_
save__publ.contact_author_email
_item_description.description
; E-mail address in a form recognizable to international networks.
The format of e-mail addresses is given in Section 3.4, Address
Specification, of Internet Message Format, RFC 2822, P. Resnick
(Editor), Network Standards Group, April 2001.
;
_item.name '_publ.contact_author_email'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_contact_author_email'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'name@host.domain.country'
'uur5@banjo.bitnet'
save_
save__publ.contact_author_fax
_item_description.description
; Facsimile telephone number of the author submitting the
manuscript and data block.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number with no spaces. The earlier convention of including
the international dialing prefix in parentheses is no longer
recommended.
;
_item.name '_publ.contact_author_fax'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_contact_author_fax'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case '12(34)9477330'
'12()349477330'
save_
save__publ.contact_author_name
_item_description.description
; The name of the author submitting the manuscript and data
block. This is the person contacted by the journal editorial
staff.
;
_item.name '_publ.contact_author_name'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_contact_author_name'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Professor George Ferguson
;
save_
save__publ.contact_author_phone
_item_description.description
; Telephone number of the author submitting the manuscript and
data block.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number and any extension number prefixed by 'x',
with no spaces. The earlier convention of including
the international dialing prefix in parentheses is no longer
recommended.
;
_item.name '_publ.contact_author_phone'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_contact_author_phone'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case '12(34)9477330'
'12()349477330'
'12(34)9477330x5543'
save_
save__publ.contact_letter
_item_description.description
; A letter submitted to the journal editor by the contact author.
;
_item.name '_publ.contact_letter'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_contact_letter'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.manuscript_creation
_item_description.description
; A description of the word-processor package and computer used to
create the word-processed manuscript stored as
_publ.manuscript_processed.
;
_item.name '_publ.manuscript_creation'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_creation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'Tex file created by FrameMaker on a Sun 3/280'
save_
save__publ.manuscript_processed
_item_description.description
; The full manuscript of a paper (excluding possibly the figures
and the tables) output in ASCII characters from a word processor.
Information about the generation of this data item must be
specified in the data item _publ.manuscript_creation.
;
_item.name '_publ.manuscript_processed'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_processed'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.manuscript_text
_item_description.description
; The full manuscript of a paper (excluding figures and possibly
the tables) output as standard ASCII text.
;
_item.name '_publ.manuscript_text'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_text'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.requested_category
_item_description.description
; The category of paper submitted. For submission to
Acta Crystallographica Section C or
Acta Crystallographica Section E, ONLY the codes indicated
for use with these journals should be used.
;
_item.name '_publ.requested_category'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_requested_category'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value FA
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail
FA 'Full article'
FI 'Full submission - inorganic (Acta C)'
FO 'Full submission - organic (Acta C)'
FM 'Full submission - metal-organic (Acta C)'
CI 'CIF-access paper - inorganic (Acta C) (no longer in use)'
CO 'CIF-access paper - organic (Acta C) (no longer in use)'
CM 'CIF-access paper - metal-organic (Acta C) (no longer in use)'
EI 'Electronic submission - inorganic (Acta E)'
EO 'Electronic submission - organic (Acta E)'
EM 'Electronic submission - metal-organic (Acta E)'
AD 'Addenda and Errata (Acta C, Acta E)'
SC 'Short communication'
save_
save__publ.requested_coeditor_name
_item_description.description
; The name of the co-editor whom the authors would like to
handle the submitted manuscript.
;
_item.name '_publ.requested_coeditor_name'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_requested_coeditor_name'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__publ.requested_journal
_item_description.description
; The name of the journal to which the manuscript is being
submitted.
;
_item.name '_publ.requested_journal'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_requested_journal'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
save_
save__publ.section_abstract
_item_description.description
; The abstract section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ.manuscript_processed.
;
_item.name '_publ.section_abstract'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_abstract'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_acknowledgements
_item_description.description
; The acknowledgements section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ.manuscript_processed.
;
_item.name '_publ.section_acknowledgements'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_acknowledgements'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_comment
_item_description.description
; The comment section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ.manuscript_processed.
;
_item.name '_publ.section_comment'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_comment'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_discussion
_item_description.description
; The discussion section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ.manuscript_processed.
;
_item.name '_publ.section_discussion'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_discussion'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_experimental
_item_description.description
; The experimental section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ.manuscript_processed.
The _publ.section_exptl_prep, _publ.section_exptl_solution and
_publ.section_exptl_refinement items are preferred for
separating the chemical preparation, structure solution and
refinement aspects of the description of the experiment.
;
_item.name '_publ.section_experimental'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_experimental'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_exptl_prep
_item_description.description
; The experimental preparation section of a manuscript if the
manuscript is submitted in parts. As an alternative see
_publ.manuscript_text and _publ.manuscript_processed.
;
_item.name '_publ.section_exptl_prep'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_exptl_prep'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_exptl_refinement
_item_description.description
; The experimental refinement section of a manuscript if the
manuscript is submitted in parts. As an alternative see
_publ.manuscript_text and _publ.manuscript_processed.
;
_item.name '_publ.section_exptl_refinement'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_exptl_refinement'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_exptl_solution
_item_description.description
; The experimental solution section of a manuscript if the
manuscript is submitted in parts. As an alternative see
_publ.manuscript_text and _publ.manuscript_processed.
;
_item.name '_publ.section_exptl_solution'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_exptl_solution'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_figure_captions
_item_description.description
; The figure captions section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ.manuscript_processed.
;
_item.name '_publ.section_figure_captions'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_figure_captions'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_introduction
_item_description.description
; The introduction section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ.manuscript_processed.
;
_item.name '_publ.section_introduction'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_introduction'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_references
_item_description.description
; The references section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ.manuscript_processed.
;
_item.name '_publ.section_references'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_references'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_synopsis
_item_description.description
; The synopsis section of a manuscript if the manuscript is
submitted in parts. As an alternative see _publ.manuscript_text
and _publ.manuscript_processed.
;
_item.name '_publ.section_synopsis'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_synopsis'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_table_legends
_item_description.description
; The table legends section of a manuscript if the manuscript
is submitted in parts. As an alternative see
_publ.manuscript_text and _publ.manuscript_processed.
;
_item.name '_publ.section_table_legends'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_table_legends'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_title
_item_description.description
; The title of a manuscript if the manuscript is submitted in
parts. As an alternative see _publ.manuscript_text and
_publ.manuscript_processed.
;
_item.name '_publ.section_title'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_title'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ.section_title_footnote
_item_description.description
; The footnote to the title of a manuscript if the manuscript
is submitted in parts. As an alternative see
_publ.manuscript_text and _publ.manuscript_processed.
;
_item.name '_publ.section_title_footnote'
_item.category_id publ
_item.mandatory_code no
_item_aliases.alias_name '_publ_section_title_footnote'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
#################
## PUBL_AUTHOR ##
#################
save_publ_author
_category.description
; Data items in the PUBL_AUTHOR category record details of
the authors of a manuscript submitted for publication.
;
_category.id publ_author
_category.mandatory_code no
_category_key.name '_publ_author.name'
loop_
_category_group.id 'inclusive_group'
'iucr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
loop_
_publ_author.name
_publ_author.address
'Willis, Anthony C.'
; Research School of Chemistry
Australian National University
GPO Box 4
Canberra, A.C.T.
Australia 2601
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__publ_author.address
_item_description.description
; The address of a publication author. If there is more than one
author this is looped with _publ_author.name.
;
_item.name '_publ_author.address'
_item.category_id publ_author
_item.mandatory_code no
_item_aliases.alias_name '_publ_author_address'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Department
Institute
Street
City and postcode
COUNTRY
;
save_
save__publ_author.email
_item_description.description
; The e-mail address of a publication author. If there is more
than one author, this will be looped with _publ_author.name.
The format of e-mail addresses is given in Section 3.4, Address
Specification, of Internet Message Format, RFC 2822, P. Resnick
(Editor), Network Standards Group, April 2001.
;
_item.name '_publ_author.email'
_item.category_id publ_author
_item.mandatory_code no
_item_aliases.alias_name '_publ_author_email'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.3.1
_item_type.code text
loop_
_item_examples.case
name@host.domain.country
bm@iucr.org
save_
save__publ_author.footnote
_item_description.description
; A footnote accompanying an author's name in the list of authors
of a paper. Typically indicates sabbatical address, additional
affiliations or date of decease.
;
_item.name '_publ_author.footnote'
_item.category_id publ_author
_item.mandatory_code no
_item_aliases.alias_name '_publ_author_footnote'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'On leave from U. Western Australia'
'Also at Department of Biophysics'
save_
save__publ_author.name
_item_description.description
; The name of a publication author. If there are multiple authors
this will be looped with _publ_author.address. The family
name(s), followed by a comma and including any dynastic
components, precedes the first names or initials.
;
_item.name '_publ_author.name'
_item.category_id publ_author
_item.mandatory_code yes
_item_aliases.alias_name '_publ_author_name'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'Bleary, Percival R.'
'O'Neil, F.K.'
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
save_
###############
## PUBL_BODY ##
###############
save_publ_body
_category.description
; Data items in the PUBL_BODY category permit the labelling of
different text sections within the body of a paper.
Note that these should not be used in a paper which has
a standard format with sections tagged by specific data names
(such as in Acta Crystallographica Section C). Typically,
each journal will supply a list of the specific items it
requires in its Notes for Authors.
;
_category.id publ_body
_category.mandatory_code no
loop_
_category_key.name '_publ_body.element'
'_publ_body.label'
loop_
_category_group.id 'inclusive_group'
'iucr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on a paper by R. Restori & D. Schwarzenbach
[Acta Cryst. (1996), A52, 369-378].
;
;
loop_
_publ_body.element
_publ_body.label
_publ_body.title
_publ_body.format
_publ_body.contents
section 1 Introduction cif
; X-ray diffraction from a crystalline material provides
information on the thermally and spatially averaged
electron density in the crystal...
;
section 2 Theory tex
; In the rigid-atom approximation, the dynamic electron
density of an atom is described by the convolution
product of the static atomic density and a probability
density function,
$\rho_{dyn}(\bf r) = \rho_{stat}(\bf r) * P(\bf r). \eqno(1)$
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on a paper by R. J. Papoular, Y. Vekhter & P. Coppens
[Acta Cryst. (1996), A52, 397-407].
;
;
loop_
_publ_body.element
_publ_body.label
_publ_body.title
_publ_body.contents
section 3
; The two-channel method for retrieval of the deformation
electron density
;
.
subsection 3.1 'The two-channel entropy S[\D\r(r)]'
; As the wide dynamic range involved in the total electron
density...
;
subsection 3.2
'Uniform vs informative prior model densities' .
subsubsection 3.2.1 'Use of uniform models'
; Straightforward algebra leads to expressions analogous
to...
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__publ_body.contents
_item_description.description
; A text section of a paper.
;
_item.name '_publ_body.contents'
_item.category_id publ_body
_item.mandatory_code no
_item_aliases.alias_name '_publ_body_contents'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__publ_body.element
_item_description.description
; The functional role of the associated text section.
;
_item.name '_publ_body.element'
_item.category_id publ_body
_item.mandatory_code no
_item_aliases.alias_name '_publ_body_element'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
loop_
_item_enumeration.value 'section'
'subsection'
'subsubsection'
'appendix'
'footnote'
save_
save__publ_body.format
_item_description.description
; Code indicating the appropriate typesetting conventions
for accented characters and special symbols in the text
section.
;
_item.name '_publ_body.format'
_item.category_id publ_body
_item.mandatory_code no
_item_aliases.alias_name '_publ_body_format'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail ascii 'no coding for special symbols'
cif 'CIF convention'
latex 'LaTeX'
sgml 'SGML (ISO 8879)'
tex 'TeX'
troff 'troff or nroff'
save_
save__publ_body.label
_item_description.description
; Code identifying the section of text.
;
_item.name '_publ_body.label'
_item.category_id publ_body
_item.mandatory_code no
_item_aliases.alias_name '_publ_body_label'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
loop_
_item_examples.case '1'
'1.1'
'2.1.3'
save_
save__publ_body.title
_item_description.description
; Title of the associated section of text.
;
_item.name '_publ_body.title'
_item.category_id publ_body
_item.mandatory_code no
_item_aliases.alias_name '_publ_body_title'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
##########################
## PUBL_MANUSCRIPT_INCL ##
##########################
save_publ_manuscript_incl
_category.description
; Data items in the PUBL_MANUSCRIPT_INCL category allow
the authors of a manuscript submitted for publication to list
data names that should be added to the standard request list
used by the journal printing software.
;
_category.id publ_manuscript_incl
_category.mandatory_code no
_category_key.name '_publ_manuscript_incl.entry_id'
loop_
_category_group.id 'inclusive_group'
'iucr_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - hypothetical example.
;
;
_publ_manuscript_incl.entry_id 'EXAMHYPO'
loop_
_publ_manuscript_incl.extra_item
_publ_manuscript_incl.extra_info
_publ_manuscript_incl.extra_defn
'_atom_site.symmetry_multiplicity'
'to emphasise special sites' yes
'_chemical.compound_source'
'rare material, unusual source' yes
'_reflns.d_resolution_high'
'limited data is a problem here' yes
'_crystal.magnetic_permeability'
'unusual value for this material' no
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__publ_manuscript_incl.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_publ_manuscript_incl.entry_id'
_item.mandatory_code yes
save_
save__publ_manuscript_incl.extra_defn
_item_description.description
; Flags whether the corresponding data item marked for inclusion
in a journal request list is a standard CIF definition or not.
;
_item.name '_publ_manuscript_incl.extra_defn'
_item.category_id publ_manuscript_incl
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_incl_extra_defn'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail no
'not a standard CIF data name'
n
'abbreviation for "no"'
yes
'a standard CIF data name'
y
'abbreviation for "yes"'
save_
save__publ_manuscript_incl.extra_info
_item_description.description
; A short note indicating the reason why the author wishes the
corresponding data item marked for inclusion in the journal
request list to be published.
;
_item.name '_publ_manuscript_incl.extra_info'
_item.category_id publ_manuscript_incl
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_incl_extra_info'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'to emphasise very special sites'
'rare material from unusual source'
'the limited data is a problem here'
'a new data quantity needed here'
save_
save__publ_manuscript_incl.extra_item
_item_description.description
; Specifies the inclusion of specific data into a manuscript
which are not normally requested by the journal. The values
of this item are the extra data names (which MUST be enclosed
in single quotes) that will be added to the journal request list.
;
_item.name '_publ_manuscript_incl.extra_item'
_item.category_id publ_manuscript_incl
_item.mandatory_code no
_item_aliases.alias_name '_publ_manuscript_incl_extra_item'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case '_atom_site.symmetry_multiplicity'
'_chemical.compound_source'
'_reflns.d_resolution_high'
'_crystal.magnetic_permeability'
save_
############
## REFINE ##
############
save_refine
_category.description
; Data items in the REFINE category record details about the
structure-refinement parameters.
;
_category.id refine
_category.mandatory_code no
_category_key.name '_refine.entry_id'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_refine.entry_id '5HVP'
_refine.ls_number_reflns_obs 12901
_refine.ls_number_restraints 6609
_refine.ls_number_parameters 7032
_refine.ls_R_Factor_obs 0.176
_refine.ls_weighting_scheme calc
_refine.ls_weighting_details
; Sigdel model of Konnert-Hendrickson:
Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6)
Afsig = 22.0, Bfsig = -150.0 at beginning of refinement
Afsig = 15.5, Bfsig = -50.0 at end of refinement
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_refine.details sfls:_F_calc_weight_full_matrix
_refine.ls_structure_factor_coef F
_refine.ls_matrix_type full
_refine.ls_weighting_scheme calc
_refine.ls_weighting_details 'w=1/(\s^2^(F)+0.0004F^2^)'
_refine.ls_hydrogen_treatment 'refxyz except H332B noref'
_refine.ls_extinction_method Zachariasen
_refine.ls_extinction_coef 3514
_refine.ls_extinction_expression
; Larson, A. C. (1970). "Crystallographic Computing", edited
by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.
_refine.ls_abs_structure_details
; The absolute configuration was assigned to agree with the
known chirality at C3 arising from its precursor l-leucine.
;
_refine.ls_abs_structure_Flack 0
_refine.ls_number_reflns_obs 1408
_refine.ls_number_parameters 272
_refine.ls_number_restraints 0
_refine.ls_number_constraints 0
_refine.ls_R_factor_all .038
_refine.ls_R_factor_obs .034
_refine.ls_wR_factor_all .044
_refine.ls_wR_factor_obs .042
_refine.ls_goodness_of_fit_all 1.462
_refine.ls_goodness_of_fit_obs 1.515
_refine.ls_shift_over_esd_max .535
_refine.ls_shift_over_esd_mean .044
_refine.diff_density_min -.108
_refine.diff_density_max .131
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine.aniso_B[1][1]
_item_description.description
; The [1][1] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
;
_item.name '_refine.aniso_B[1][1]'
_item.category_id refine
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__refine.aniso_B[1][2]
_item_description.description
; The [1][2] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
;
_item.name '_refine.aniso_B[1][2]'
_item.category_id refine
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__refine.aniso_B[1][3]
_item_description.description
; The [1][3] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
;
_item.name '_refine.aniso_B[1][3]'
_item.category_id refine
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__refine.aniso_B[2][2]
_item_description.description
; The [2][2] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
;
_item.name '_refine.aniso_B[2][2]'
_item.category_id refine
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__refine.aniso_B[2][3]
_item_description.description
; The [2][3] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
;
_item.name '_refine.aniso_B[2][3]'
_item.category_id refine
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__refine.aniso_B[3][3]
_item_description.description
; The [3][3] element of the matrix that defines the overall
anisotropic displacement model if one was refined for this
structure.
;
_item.name '_refine.aniso_B[3][3]'
_item.category_id refine
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
_item_units.code angstroms_squared
save_
save__refine.B_iso_max
_item_description.description
; The maximum isotropic displacement parameter (B value)
found in the coordinate set.
;
_item.name '_refine.B_iso_max'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms_squared
save_
save__refine.B_iso_mean
_item_description.description
; The mean isotropic displacement parameter (B value)
for the coordinate set.
;
_item.name '_refine.B_iso_mean'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms_squared
save_
save__refine.B_iso_min
_item_description.description
; The minimum isotropic displacement parameter (B value)
found in the coordinate set.
;
_item.name '_refine.B_iso_min'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms_squared
save_
save__refine.correlation_coeff_Fo_to_Fc
_item_description.description
; The correlation coefficient between the observed and
calculated structure factors for reflections included in
the refinement.
The correlation coefficient is scale-independent and gives
an idea of the quality of the refined model.
sum~i~(Fo~i~ Fc~i~ - )
R~corr~ = ------------------------------------------------------------
SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^}
Fo = observed structure factors
Fc = calculated structure factors
<> denotes average value
summation is over reflections included in the refinement
;
_item.name '_refine.correlation_coeff_Fo_to_Fc'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.correlation_coeff_Fo_to_Fc_free
_item_description.description
; The correlation coefficient between the observed and
calculated structure factors for reflections not included
in the refinement (free reflections).
The correlation coefficient is scale-independent and gives
an idea of the quality of the refined model.
sum~i~(Fo~i~ Fc~i~ - )
R~corr~ = ------------------------------------------------------------
SQRT{sum~i~(Fo~i~)^2^-^2^} SQRT{sum~i~(Fc~i~)^2^-^2^}
Fo = observed structure factors
Fc = calculated structure factors
<> denotes average value
summation is over reflections not included
in the refinement (free reflections)
;
_item.name '_refine.correlation_coeff_Fo_to_Fc_free'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc_free'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.details
_item_description.description
; Description of special aspects of the refinement process.
;
_item.name '_refine.details'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_special_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__refine.diff_density_max
_item_description.description
; The maximum value of the electron density in the final difference
Fourier map.
;
_item.name '_refine.diff_density_max'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_diff_density_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_refine.diff_density_max_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code electrons_per_angstroms_cubed
save_
save__refine.diff_density_max_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _refine.diff_density_max.
;
_item.name '_refine.diff_density_max_esd'
_item.category_id refine
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_refine.diff_density_max'
_item_related.function_code associated_value
_item_type.code float
_item_units.code electrons_per_angstroms_cubed
save_
save__refine.diff_density_min
_item_description.description
; The minimum value of the electron density in the final difference
Fourier map.
;
_item.name '_refine.diff_density_min'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_diff_density_min'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_refine.diff_density_min_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code electrons_per_angstroms_cubed
save_
save__refine.diff_density_min_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _refine.diff_density_min.
;
_item.name '_refine.diff_density_min_esd'
_item.category_id refine
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_refine.diff_density_min'
_item_related.function_code associated_value
_item_type.code float
_item_units.code electrons_per_angstroms_cubed
save_
save__refine.diff_density_rms
_item_description.description
; The root-mean-square-deviation of the electron density in the
final difference Fourier map. This value is measured with respect
to the arithmetic mean density and is derived from summations
over each grid point in the asymmetric unit of the cell. This
quantity is useful for assessing the significance of the values
of _refine.diff_density_min and _refine.diff_density_max, and
also for defining suitable contour levels.
;
_item.name '_refine.diff_density_rms'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_diff_density_rms'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_refine.diff_density_rms_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code electrons_per_angstroms_cubed
save_
save__refine.diff_density_rms_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _refine.diff_density_rms.
;
_item.name '_refine.diff_density_rms_esd'
_item.category_id refine
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_refine.diff_density_rms'
_item_related.function_code associated_value
_item_type.code float
_item_units.code electrons_per_angstroms_cubed
save_
save__refine.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_refine.entry_id'
_item.mandatory_code yes
save_
save__refine.ls_abs_structure_details
_item_description.description
; The nature of the absolute structure and how it was determined.
For example, this may describe the Friedel pairs used.
;
_item.name '_refine.ls_abs_structure_details'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_abs_structure_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__refine.ls_abs_structure_Flack
_item_description.description
; The measure of absolute structure (enantiomorph or polarity) as
defined by Flack (1983).
For centrosymmetric structures, the only permitted value, if the
data name is present, is 'inapplicable', represented by '.' .
For noncentrosymmetric structures the value must lie in the
99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a
standard uncertainty (estimated standard deviation) u must
be supplied. The item range of [0.0:1.0] is correctly
interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881.
;
_item.name '_refine.ls_abs_structure_Flack'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_abs_structure_Flack'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 0.0
0.0 0.0
_item_related.related_name '_refine.ls_abs_structure_Flack_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
save_
save__refine.ls_abs_structure_Flack_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _refine.ls_abs_structure_Flack.
;
_item.name '_refine.ls_abs_structure_Flack_esd'
_item.category_id refine
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_refine.ls_abs_structure_Flack'
_item_related.function_code associated_value
_item_type.code float
save_
save__refine.ls_abs_structure_Rogers
_item_description.description
; The measure of absolute structure (enantiomorph or polarity) as
defined by Rogers.
The value must lie in the 99.97% Gaussian confidence interval
-1 -3u =< \h =< 1 + 3u and a standard uncertainty (estimated
standard deviation) u must be supplied. The item range of
[-1.0, 1.0] is correctly interpreted as meaning
(-1.0 - 3u) =< \h =< (1.0 + 3u).
Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741.
;
_item.name '_refine.ls_abs_structure_Rogers'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_abs_structure_Rogers'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_related.related_name '_refine.ls_abs_structure_Rogers_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
save_
save__refine.ls_abs_structure_Rogers_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _refine.ls_abs_structure_Rogers.
;
_item.name '_refine.ls_abs_structure_Rogers_esd'
_item.category_id refine
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_refine.ls_abs_structure_Rogers'
_item_related.function_code associated_value
_item_type.code float
save_
save__refine.ls_d_res_high
_item_description.description
; The smallest value for the interplanar spacings for the
reflection data used in the refinement in angstroms. This is
called the highest resolution.
;
_item.name '_refine.ls_d_res_high'
_item.category_id refine
_item.mandatory_code yes
_item_aliases.alias_name '_refine_ls_d_res_high'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine.ls_d_res_low
_item_description.description
; The largest value for the interplanar spacings for
the reflection data used in the refinement in angstroms.
This is called the lowest resolution.
;
_item.name '_refine.ls_d_res_low'
_item.category_id refine
_item.mandatory_code yes
_item_aliases.alias_name '_refine_ls_d_res_low'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine.ls_extinction_coef
_item_description.description
; The extinction coefficient used to calculate the correction
factor applied to the structure-factor data. The nature of the
extinction coefficient is given in the definitions of
_refine.ls_extinction_expression and
_refine.ls_extinction_method.
For the 'Zachariasen' method it is the r* value; for the
'Becker-Coppens type 1 isotropic' method it is the 'g' value,
and for 'Becker-Coppens type 2 isotropic' corrections it is
the 'rho' value. Note that the magnitude of these values is
usually of the order of 10000.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-47, 148-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
_item.name '_refine.ls_extinction_coef'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_extinction_coef'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_refine.ls_extinction_coef_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_examples.case 3472
_item_examples.detail 'Zachariasen coefficient r* = 0.347 E04'
save_
save__refine.ls_extinction_coef_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _refine.ls_extinction_coef.
;
_item.name '_refine.ls_extinction_coef_esd'
_item.category_id refine
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_refine.ls_extinction_coef'
_item_related.function_code associated_value
_item_type.code float
save_
save__refine.ls_extinction_expression
_item_description.description
; A description of or reference to the extinction-correction
equation used to apply the data item
_refine.ls_extinction_coef. This information must be sufficient
to reproduce the extinction-correction factors applied to the
structure factors.
;
_item.name '_refine.ls_extinction_expression'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_extinction_expression'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Larson, A. C. (1970). "Crystallographic Computing", edited by
F. R. Ahmed. Eq. (22), p.292. Copenhagen: Munksgaard.
;
save_
save__refine.ls_extinction_method
_item_description.description
; A description of the extinction-correction method applied.
This description should
include information about the correction method, either
'Becker-Coppens' or 'Zachariasen'. The latter is sometimes
referred to as the 'Larson' method even though it employs
Zachariasen's formula.
The Becker-Coppens procedure is referred to as 'type 1' when
correcting secondary extinction dominated by the mosaic spread;
as 'type 2' when secondary extinction is dominated by particle
size and includes a primary extinction component; and as 'mixed'
when there is a mixture of types 1 and 2.
For the Becker-Coppens method, it is also necessary to set the
mosaic distribution as either 'Gaussian' or 'Lorentzian' and the
nature of the extinction as 'isotropic' or 'anisotropic'. Note
that if either the 'mixed' or 'anisotropic' corrections are
applied, the multiple coefficients cannot be contained in
*_extinction_coef and must be listed in _refine.details.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-147, 148-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558- 564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
_item.name '_refine.ls_extinction_method'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_extinction_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value Zachariasen
_item_type.code text
_item_examples.case 'B-C type 2 Gaussian isotropic'
save_
save__refine.ls_goodness_of_fit_all
_item_description.description
; The least-squares goodness-of-fit parameter S for all data
after the final cycle of refinement. Ideally, account should be
taken of parameters restrained in the least-squares refinement.
See also the definition of _refine.ls_restrained_S_all.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
S = ( ---------------------------- )
( N~ref~ - N~param~ )
Y~obs~ = the observed coefficients
(see _refine.ls_structure_factor_coef)
Y~calc~ = the calculated coefficients
(see _refine.ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(e.s.d. squared)]
N~ref~ = the number of reflections used in the refinement
N~param~ = the number of refined parameters
sum is taken over the specified reflections
;
_item.name '_refine.ls_goodness_of_fit_all'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_goodness_of_fit_all'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine.ls_goodness_of_fit_all_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
save_
save__refine.ls_goodness_of_fit_all_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _refine.ls_goodness_of_fit_all.
;
_item.name '_refine.ls_goodness_of_fit_all_esd'
_item.category_id refine
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_refine.ls_goodness_of_fit_all'
_item_related.function_code associated_value
_item_type.code float
save_
save__refine.ls_goodness_of_fit_obs
_item_description.description
; The least-squares goodness-of-fit parameter S for reflection data
classified as 'observed' (see _reflns.observed_criterion) after
the final cycle of refinement. Ideally, account should be taken
of parameters restrained in the least-squares refinement.
See also the definition of _refine.ls_restrained_S_obs.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
S = ( ---------------------------- )
( N~ref~ - N~param~ )
Y~obs~ = the observed coefficients
(see _refine.ls_structure_factor_coef)
Y~calc~ = the calculated coefficients
(see _refine.ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(e.s.d. squared)]
N~ref~ = the number of reflections used in the refinement
N~param~ = the number of refined parameters
sum is taken over the specified reflections
;
_item.name '_refine.ls_goodness_of_fit_obs'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_goodness_of_fit_obs'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine.ls_goodness_of_fit_obs_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
save_
save__refine.ls_goodness_of_fit_obs_esd
_item_description.description
; The standard uncertainty (estimated standard deviation)
of _refine.ls_goodness_of_fit_obs.
;
_item.name '_refine.ls_goodness_of_fit_obs_esd'
_item.category_id refine
_item.mandatory_code no
# _item_default.value 0.0
_item_related.related_name '_refine.ls_goodness_of_fit_obs'
_item_related.function_code associated_value
_item_type.code float
save_
save__refine.ls_hydrogen_treatment
_item_description.description
; Treatment of hydrogen atoms in the least-squares refinement.
;
_item.name '_refine.ls_hydrogen_treatment'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_hydrogen_treatment'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value undef
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail refall 'refined all H-atom parameters'
refxyz 'refined H-atom coordinates only'
refU 'refined H-atom U's only'
noref 'no refinement of H-atom parameters'
constr 'H-atom parameters constrained'
mixed 'some constrained, some independent'
undef 'H-atom parameters not defined'
save_
save__refine.ls_matrix_type
_item_description.description
; Type of matrix used to accumulate the least-squares derivatives.
;
_item.name '_refine.ls_matrix_type'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_matrix_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value full
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail full 'full'
fullcycle
'full with fixed elements per cycle'
atomblock 'block diagonal per atom'
userblock 'user-defined blocks'
diagonal 'diagonal elements only'
sparse 'selected elements only'
save_
save__refine.ls_number_constraints
_item_description.description
; The number of constrained (non-refined or dependent) parameters
in the least-squares process. These may be due to symmetry or any
other constraint process (e.g. rigid-body refinement). See also
_atom_site.constraints and _atom_site.refinement_flags. A general
description of constraints may appear in _refine.details.
;
_item.name '_refine.ls_number_constraints'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_number_constraints'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value 0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine.ls_number_parameters
_item_description.description
; The number of parameters refined in the least-squares process.
If possible, this number should include some contribution from
the restrained parameters. The restrained parameters are
distinct from the constrained parameters (where one or more
parameters are linearly dependent on the refined value of
another). Least-squares restraints often depend on geometry or
energy considerations and this makes their direct contribution
to this number, and to the goodness-of-fit calculation,
difficult to assess.
;
_item.name '_refine.ls_number_parameters'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_number_parameters'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine.ls_number_reflns_all
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low.
;
_item.name '_refine.ls_number_reflns_all'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine.ls_number_reflns_obs
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low
and the observation limit established by
_reflns.observed_criterion.
;
_item.name '_refine.ls_number_reflns_obs'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_number_reflns'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine.ls_number_reflns_R_free
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low
and the observation limit established by
_reflns.observed_criterion, and that were used as the test
reflections (i.e. were excluded from the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in _reflns.R_free_details.
;
_item.name '_refine.ls_number_reflns_R_free'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine.ls_number_reflns_R_work
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low
and the observation limit established by
_reflns.observed_criterion, and that were used as the working
reflections (i.e. were included in the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in _reflns.R_free_details.
;
_item.name '_refine.ls_number_reflns_R_work'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine.ls_number_restraints
_item_description.description
; The number of restrained parameters. These are parameters which
are not directly dependent on another refined parameter.
Restrained parameters often involve geometry or energy
dependencies.
See also _atom_site.constraints and _atom_site.refinement_flags.
A general description of refinement constraints may appear in
_refine.details.
;
_item.name '_refine.ls_number_restraints'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_number_restraints'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine.ls_percent_reflns_obs
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low
and the observation limit established by
_reflns.observed_criterion, expressed as a percentage of the
number of geometrically observable reflections that satisfy
the resolution limits.
;
_item.name '_refine.ls_percent_reflns_obs'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
save_
save__refine.ls_percent_reflns_R_free
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine.ls_d_res_high and _refine.ls_d_res_low
and the observation limit established by
_reflns.observed_criterion, and that were used as the test
reflections (i.e. were excluded from the refinement) when the
refinement included the calculation of a 'free' R factor,
expressed as a percentage of the number of geometrically
observable reflections that satisfy the resolution limits.
;
_item.name '_refine.ls_percent_reflns_R_free'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
save_
save__refine.ls_R_factor_all
_item_description.description
; Residual factor R for all reflections that satisfy the resolution
limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine.ls_R_factor_all'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_R_factor_all'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine.ls_wR_factor_all'
_item_related.function_code alternate
_item_type.code float
save_
save__refine.ls_R_factor_obs
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low and the observation limit established by
_reflns.observed_criterion.
_refine.ls_R_factor_obs should not be confused with
_refine.ls_R_factor_R_work; the former reports the results of a
refinement in which all observed reflections were used, the
latter a refinement in which a subset of the observed
reflections were excluded from refinement for the calculation
of a 'free' R factor. However, it would be meaningful to quote
both values if a 'free' R factor were calculated for most of
the refinement, but all of the observed reflections were used
in the final rounds of refinement; such a protocol should be
explained in _refine.details.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine.ls_R_factor_obs'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_R_factor_obs'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine.ls_wR_factor_obs'
_item_related.function_code alternate
_item_type.code float
save_
save__refine.ls_R_factor_R_free
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low and the observation limit established by
_reflns.observed_criterion, and that were used as the test
reflections (i.e. were excluded from the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in _reflns.R_free_details.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine.ls_R_factor_R_free'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
loop_
_item_related.related_name
_item_related.function_code '_refine.ls_wR_factor_R_free'
alternate
'_refine.ls_R_factor_R_free_error'
associated_error
_item_type.code float
save_
save__refine.ls_R_factor_R_free_error
_item_description.description
; The estimated error in _refine.ls_R_factor_R_free.
The method used to estimate the error is described in the
item _refine.ls_R_factor_R_free_error_details.
;
_item.name '_refine.ls_R_factor_R_free_error'
_item.category_id refine
_item.mandatory_code no
_item_related.related_name '_refine.ls_R_factor_R_free'
_item_related.function_code associated_value
_item_type.code float
save_
save__refine.ls_R_factor_R_free_error_details
_item_description.description
; Special aspects of the method used to estimated the error in
_refine.ls_R_factor_R_free.
;
_item.name '_refine.ls_R_factor_R_free_error_details'
_item.category_id refine
_item.mandatory_code no
_item_type.code text
save_
save__refine.ls_R_factor_R_work
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low and the observation limit established by
_reflns.observed_criterion, and that were used as the working
reflections (i.e. were included in the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in _reflns.R_free_details.
_refine.ls_R_factor_obs should not be confused with
_refine.ls_R_factor_R_work; the former reports the results of a
refinement in which all observed reflections were used, the
latter a refinement in which a subset of the observed
reflections were excluded from refinement for the calculation
of a 'free' R factor. However, it would be meaningful to quote
both values if a 'free' R factor were calculated for most of
the refinement, but all of the observed reflections were used
in the final rounds of refinement; such a protocol should be
explained in _refine.details.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine.ls_R_factor_R_work'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine.ls_wR_factor_R_work'
_item_related.function_code alternate
_item_type.code float
save_
save__refine.ls_R_Fsqd_factor_obs
_item_description.description
; Residual factor R(Fsqd) for reflections that satisfy the
resolution limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low and the observation limit established by
_reflns.observed_criterion, calculated on the squares of the
observed and calculated structure-factor amplitudes.
sum|F~obs~^2^ - F~calc~^2^|
R(Fsqd) = ---------------------------
sum|F~obs~^2^|
F~obs~^2^ = squares of the observed structure-factor amplitudes
F~calc~^2^ = squares of the calculated structure-factor
amplitudes
sum is taken over the specified reflections
;
_item.name '_refine.ls_R_Fsqd_factor_obs'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_R_Fsqd_factor'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine.ls_R_I_factor_obs
_item_description.description
; Residual factor R(I) for reflections that satisfy the
resolution limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low and the observation limit established by
_reflns.observed_criterion, calculated on the estimated
reflection intensities.
This is most often calculated in Rietveld refinements against
powder data, where it is referred to as R~B~ or R~Bragg~.
sum|I~obs~ - I~calc~|
R(I) = ---------------------
sum|I~obs~|
I~obs~ = the net observed intensities
I~calc~ = the net calculated intensities
sum is taken over the specified reflections
;
_item.name '_refine.ls_R_I_factor_obs'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_R_I_factor'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine.ls_redundancy_reflns_all
_item_description.description
; The ratio of the total number of observations of the
reflections that satisfy the resolution limits established by
_refine.ls_d_res_high and _refine.ls_d_res_low to the number
of crystallographically unique reflections that satisfy the
same limits.
;
_item.name '_refine.ls_redundancy_reflns_all'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
save_
save__refine.ls_redundancy_reflns_obs
_item_description.description
; The ratio of the total number of observations of the
reflections that satisfy the resolution limits established by
_refine.ls_d_res_high and _refine.ls_d_res_low and the
observation limit established by _reflns.observed_criterion to
the number of crystallographically unique reflections that
satisfy the same limits.
;
_item.name '_refine.ls_redundancy_reflns_obs'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
save_
save__refine.ls_restrained_S_all
_item_description.description
; The least-squares goodness-of-fit parameter S' for all
reflections after the final cycle of least-squares refinement.
This parameter explicitly includes the restraints applied
in the least-squares process. See also the definition of
_refine.ls_goodness_of_fit_all.
( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^
( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| )
S' = ( ------------------------------------- )
( N~ref~ + N~restr~ - N~param~ )
Y~obs~ = the observed coefficients
(see _refine.ls_structure_factor_coef)
Y~calc~ = the calculated coefficients
(see _refine.ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(e.s.d. squared)]
P~calc~ = the calculated restraint values
P~targ~ = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see _refine.ls_number_reflns_obs)
N~restr~ = the number of restraints
(see _refine.ls_number_restraints)
N~param~ = the number of refined parameters
(see _refine.ls_number_parameters)
sum is taken over the specified reflections
sumr is taken over the restraints
;
_item.name '_refine.ls_restrained_S_all'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_restrained_S_all'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine.ls_restrained_S_obs
_item_description.description
; The least-squares goodness-of-fit parameter S' for reflection
data classified as observed (see _reflns.observed_criterion)
after the final cycle of least-squares refinement. This
parameter explicitly includes the restraints applied in
the least-squares process. See also the definition of
_refine.ls_goodness_of_fit_obs.
( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^
( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| )
S' = ( ------------------------------------- )
( N~ref~ + N~restr~ - N~param~ )
Y~obs~ = the observed coefficients
(see _refine.ls_structure_factor_coef)
Y~calc~ = the calculated coefficients
(see _refine.ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(e.s.d. squared)]
P~calc~ = the calculated restraint values
P~targ~ = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see _refine.ls_number_reflns_obs)
N~restr~ = the number of restraints
(see _refine.ls_number_restraints)
N~param~ = the number of refined parameters
(see _refine.ls_number_parameters)
sum is taken over the specified reflections
sumr is taken over the restraints
;
_item.name '_refine.ls_restrained_S_obs'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_restrained_S_obs'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine.ls_shift_over_esd_max
_item_description.description
; The largest ratio of the final least-squares parameter shift
to the final standard uncertainty (estimated standard
deviation).
;
_item.name '_refine.ls_shift_over_esd_max'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_shift/esd_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine.ls_shift_over_esd_mean
_item_description.description
; The average ratio of the final least-squares parameter shift
to the final standard uncertainty (estimated standard
deviation).
;
_item.name '_refine.ls_shift_over_esd_mean'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_shift/esd_mean'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine.ls_structure_factor_coef
_item_description.description
; Structure-factor coefficient |F|, F^2^ or I used in the least-
squares refinement process.
;
_item.name '_refine.ls_structure_factor_coef'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_structure_factor_coef'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value F
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail F 'structure-factor magnitude'
Fsqd 'structure factor squared'
Inet 'net intensity'
save_
save__refine.ls_weighting_details
_item_description.description
; A description of special aspects of the weighting scheme used
in least-squares refinement. Used to describe the weighting
when the value of _refine.ls_weighting_scheme is specified
as 'calc'.
;
_item.name '_refine.ls_weighting_details'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_weighting_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Sigdel model of Konnert-Hendrickson:
Sigdel =
Afsig + Bfsig*(sin(theta)/lambda-1/6)
Afsig = 22.0, Bfsig = 150.0
at the beginning of refinement.
Afsig = 16.0, Bfsig = 60.0
at the end of refinement.
;
save_
save__refine.ls_weighting_scheme
_item_description.description
; The weighting scheme applied in the least-squares process. The
standard code may be followed by a description of the weight
(but see _refine.ls_weighting_details for a preferred approach).
;
_item.name '_refine.ls_weighting_scheme'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_weighting_scheme'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value sigma
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail sigma 'based on measured e.s.d.'s'
unit 'unit or no weights applied'
calc 'calculated weights applied'
save_
save__refine.ls_wR_factor_all
_item_description.description
; Weighted residual factor wR for all reflections that satisfy the
resolution limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
_refine.ls_structure_factor_coef
Y~calc~ = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
sum is taken over the specified reflections
;
_item.name '_refine.ls_wR_factor_all'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_wR_factor_all'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine.ls_R_factor_all'
_item_related.function_code alternate
_item_type.code float
save_
save__refine.ls_wR_factor_obs
_item_description.description
; Weighted residual factor wR for reflections that satisfy the
resolution limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low and the observation limit established by
_reflns.observed_criterion.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
_refine.ls_structure_factor_coef
Y~calc~ = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
sum is taken over the specified reflections
;
_item.name '_refine.ls_wR_factor_obs'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_ls_wR_factor_obs'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine.ls_R_factor_obs'
_item_related.function_code alternate
_item_type.code float
save_
save__refine.ls_wR_factor_R_free
_item_description.description
; Weighted residual factor wR for reflections that satisfy the
resolution limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low and the observation limit established by
_reflns.observed_criterion, and that were used as the test
reflections (i.e. were excluded from the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in _reflns.R_free_details.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
_refine.ls_structure_factor_coef
Y~calc~ = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
sum is taken over the specified reflections
;
_item.name '_refine.ls_wR_factor_R_free'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine.ls_R_factor_R_free'
_item_related.function_code alternate
_item_type.code float
save_
save__refine.ls_wR_factor_R_work
_item_description.description
; Weighted residual factor wR for reflections that satisfy the
resolution limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low and the observation limit established by
_reflns.observed_criterion, and that were used as the working
reflections (i.e. were included in the refinement) when the
refinement included the calculation of a 'free' R factor.
Details of how reflections were assigned to the working and
test sets are given in _reflns.R_free_details.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
_refine.ls_structure_factor_coef
Y~calc~ = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
sum is taken over the specified reflections
;
_item.name '_refine.ls_wR_factor_R_work'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine.ls_R_factor_R_work'
_item_related.function_code alternate
_item_type.code float
save_
save__refine.occupancy_max
_item_description.description
; The maximum value for occupancy found in the coordinate set.
;
_item.name '_refine.occupancy_max'
_item.category_id refine
_item.mandatory_code no
# _item_default.value 1.0
loop_
_item_range.maximum
_item_range.minimum
. 0.0
0.0 0.0
_item_type.code float
save_
save__refine.occupancy_min
_item_description.description
; The minimum value for occupancy found in the coordinate set.
;
_item.name '_refine.occupancy_min'
_item.category_id refine
_item.mandatory_code no
# _item_default.value 1.0
loop_
_item_range.maximum
_item_range.minimum
. 0.0
0.0 0.0
_item_type.code float
save_
save__refine.overall_SU_B
_item_description.description
; The overall standard uncertainty (estimated standard deviation)
of the displacement parameters based on a maximum-likelihood
residual.
The overall standard uncertainty (sigma~B~)^2 gives an idea
of the uncertainty in the B values of averagely defined
atoms (atoms with B values equal to the average B value).
N_a
(sigma~B~)^2 = 8 ----------------------------------------------
sum~i~ {[1/Sigma - (E_o)^2 (1-m^2)](SUM_AS)s^4}
SUM_AS = (sigma_A)^2/Sigma^2
N_a = number of atoms
Sigma = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2]
E_o = normalized structure factors
sigma_{E;exp} = experimental uncertainties of normalized
structure factors
sigma_A = SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = form factor of atoms
delta_x = expected error
m = figure of merit of phases of reflections
included in the summation
s = reciprocal-space vector
epsilon = multiplicity of diffracting plane
summation is over all reflections included in refinement
Ref: (sigma_A estimation) "Refinement of macromolecular
structures by the maximum-likelihood method",
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
(SU ML estimation) Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
;
_item.name '_refine.overall_SU_B'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_B'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_SU_ML
_item_description.description
; The overall standard uncertainty (estimated standard deviation)
of the positional parameters based on a maximum likelihood
residual.
The overall standard uncertainty (sigma~X~)^2 gives an
idea of the uncertainty in the position of averagely
defined atoms (atoms with B values equal to average B value)
3 N_a
(sigma~X~)^2 = -----------------------------------------------------
8 pi^2 sum~i~ {[1/Sigma - (E_o)^2 (1-m^2)](SUM_AS)s^2}
SUM_AS = (sigma_A)^2/Sigma^2)
N_a = number of atoms
Sigma = (sigma_{E;exp})^2 + epsilon [1-{sigma_A)^2]
E_o = normalized structure factors
sigma_{E;exp} = experimental uncertainties of normalized
structure factors
sigma_A = SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = form factor of atoms
delta_x = expected error
m = figure of merit of phases of reflections
included in the summation
s = reciprocal-space vector
epsilon = multiplicity of the diffracting plane
summation is over all reflections included in refinement
Ref: (sigma_A estimation) "Refinement of macromolecular
structures by the maximum-likelihood method",
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
(SU ML estimation) Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
;
_item.name '_refine.overall_SU_ML'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_ML'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_SU_R_Cruickshank_DPI
_item_description.description
; The overall standard uncertainty (estimated standard deviation)
of the displacement parameters based on the crystallographic
R value, expressed in a formalism known as the dispersion
precision indicator (DPI).
The overall standard uncertainty (sigma~B~) gives an idea
of the uncertainty in the B values of averagely defined
atoms (atoms with B values equal to the average B value).
N_a
(sigma_B)^2 = 0.65 --------- (R_value)^2 (D_min)^2 C^(-2/3)
(N_o-N_p)
N_a = number of atoms
N_o = number of reflections included in refinement
N_p = number of refined parameters
R_value = conventional crystallographic R value
D_min = maximum resolution
C = completeness of data
Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
;
_item.name '_refine.overall_SU_R_Cruickshank_DPI'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_R_Cruickshanks_DPI'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_SU_R_free
_item_description.description
; The overall standard uncertainty (estimated standard deviation)
of the displacement parameters based on the free R value.
The overall standard uncertainty gives an idea of the
uncertainty in the B values of averagely defined atoms
(atoms with B values equal to the average B value).
N_a
(sigma_B)^2 = 0.65 ----- (R_free)^2 (D_min)^2 C^(-2/3)
N_o
N_a = number of atoms
N_o = number of reflections included in refinement
R_free = conventional free crystallographic R value calculated
using reflections not included in refinement
D_min = maximum resolution
C = completeness of data
Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
;
_item.name '_refine.overall_SU_R_free'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_Rfree'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_FOM_free_R_set
_item_description.description
; Average figure of merit of phases of reflections not included
in the refinement.
This value is derived from the likelihood function.
FOM = I_1(X)/I_0(X)
I_0, I_1 = zero- and first-order modified Bessel functions
of the first kind
X = sigma_A |E_o| |E_c|/SIGMA
E_o, E_c = normalized observed and calculated structure
factors
sigma_A = SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = form factor of atoms
delta_x = expected error
SIGMA = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2]
sigma_{E;exp} = uncertainties of normalized observed
structure factors
epsilon = multiplicity of the diffracting plane
Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
;
_item.name '_refine.overall_FOM_free_R_set'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_overall_FOM_free_Rset'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_FOM_work_R_set
_item_description.description
; Average figure of merit of phases of reflections included in
the refinement.
This value is derived from the likelihood function
FOM = I_1(X)/I_0(X)
I_0, I_1 = zero- and first-order modified Bessel functions
of the first kind
X = sigma_A |E_o| |E_c|/SIGMA
E_o, E_c = normalized observed and calculated structure
factors
sigma_A = SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = form factor of atoms
delta_x = expected error
SIGMA = (sigma_{E;exp})^2 + epsilon [1-(sigma_A)^2]
sigma_{E;exp} = uncertainties of normalized observed
structure factors
epsilon = multiplicity of diffracting plane
Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
;
_item.name '_refine.overall_FOM_work_R_set'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_overall_FOM_work_Rset'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.solvent_model_details
_item_description.description
; Special aspects of the solvent model used during refinement.
;
_item.name '_refine.solvent_model_details'
_item.category_id refine
_item.mandatory_code no
_item_type.code text
save_
save__refine.solvent_model_param_bsol
_item_description.description
; The value of the BSOL solvent-model parameter describing
the average isotropic displacement parameter of disordered
solvent atoms.
This is one of the two parameters (the other is
_refine.solvent_model_param_ksol) in Tronrud's method of
modelling the contribution of bulk solvent to the
scattering. The standard scale factor is modified according
to the expression
k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]
where k0 and B0 are the scale factors for the protein.
Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
;
_item.name '_refine.solvent_model_param_bsol'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
save_
save__refine.solvent_model_param_ksol
_item_description.description
; The value of the KSOL solvent-model parameter describing
the ratio of the electron density in the bulk solvent to the
electron density in the molecular solute.
This is one of the two parameters (the other is
_refine.solvent_model_param_bsol) in Tronrud's method of
modelling the contribution of bulk solvent to the
scattering. The standard scale factor is modified according
to the expression
k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]
where k0 and B0 are the scale factors for the protein.
Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
;
_item.name '_refine.solvent_model_param_ksol'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
save_
####################
## REFINE_ANALYZE ##
####################
save_refine_analyze
_category.description
; Data items in the REFINE_ANALYZE category record details
about the refined structure that are often used to analyze the
refinement and assess its quality. A given computer program
may or may not produce values corresponding to these data
names.
;
_category.id refine_analyze
_category.mandatory_code no
_category_key.name '_refine_analyze.entry_id'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_refine_analyze.entry_id
_refine_analyze.Luzzati_coordinate_error_obs
_refine_analyze.Luzzati_d_res_low_obs
5HVP 0.056 2.51
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_analyze.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_refine_analyze.entry_id'
_item.category_id refine_analyze
_item.mandatory_code yes
save_
save__refine_analyze.Luzzati_coordinate_error_free
_item_description.description
; The estimated coordinate error obtained from the plot of
the R value versus sin(theta)/lambda for the reflections
treated as a test set during refinement.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
;
_item.name '_refine_analyze.Luzzati_coordinate_error_free'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.Luzzati_coordinate_error_obs
_item_description.description
; The estimated coordinate error obtained from the plot of
the R value versus sin(theta)/lambda for reflections classified
as observed.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
;
_item.name '_refine_analyze.Luzzati_coordinate_error_obs'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.Luzzati_d_res_low_free
_item_description.description
; The value of the low-resolution cutoff used in constructing the
Luzzati plot for reflections treated as a test set during
refinement.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
;
_item.name '_refine_analyze.Luzzati_d_res_low_free'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.Luzzati_d_res_low_obs
_item_description.description
; The value of the low-resolution cutoff used in
constructing the Luzzati plot for reflections classified as
observed.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
;
_item.name '_refine_analyze.Luzzati_d_res_low_obs'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.Luzzati_sigma_a_free
_item_description.description
; The value of sigma~a~ used in constructing the Luzzati plot for
the reflections treated as a test set during refinement.
Details of the estimation of sigma~a~ can be specified
in _refine_analyze.Luzzati_sigma_a_free_details.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
;
_item.name '_refine_analyze.Luzzati_sigma_a_free'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.Luzzati_sigma_a_free_details
_item_description.description
; Details of the estimation of sigma~a~ for the reflections
treated as a test set during refinement.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
;
_item.name '_refine_analyze.Luzzati_sigma_a_free_details'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code text
save_
save__refine_analyze.Luzzati_sigma_a_obs
_item_description.description
; The value of sigma~a~ used in constructing the Luzzati plot for
reflections classified as observed. Details of the
estimation of sigma~a~ can be specified in
_refine_analyze.Luzzati_sigma_a_obs_details.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
;
_item.name '_refine_analyze.Luzzati_sigma_a_obs'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.Luzzati_sigma_a_obs_details
_item_description.description
; Special aspects of the estimation of sigma~a~ for the
reflections classified as observed.
Ref: Luzzati, V. (1952). Traitement statistique des erreurs
dans la determination des structures cristallines. Acta
Cryst. 5, 802-810.
;
_item.name '_refine_analyze.Luzzati_sigma_a_obs_details'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code text
save_
save__refine_analyze.number_disordered_residues
_item_description.description
; The number of discretely disordered residues in the refined
model.
;
_item.name '_refine_analyze.number_disordered_residues'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code float
save_
save__refine_analyze.occupancy_sum_hydrogen
_item_description.description
; The sum of the occupancies of the hydrogen atoms in the refined
model.
;
_item.name '_refine_analyze.occupancy_sum_hydrogen'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code float
save_
save__refine_analyze.occupancy_sum_non_hydrogen
_item_description.description
; The sum of the occupancies of the non-hydrogen atoms in the
refined model.
;
_item.name '_refine_analyze.occupancy_sum_non_hydrogen'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code float
save_
save__refine_analyze.RG_d_res_high
_item_description.description
; The value of the high-resolution cutoff in angstroms
used in the calculation of the Hamilton generalized
R factor (RG) stored in _refine_analyze.RG_work and
_refine_analyze.RG_free.
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
_item.name '_refine_analyze.RG_d_res_high'
_item.category_id refine_analyze
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_high'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.RG_d_res_low
_item_description.description
; The value of the low-resolution cutoff in angstroms
used in the calculation of the Hamilton generalized
R factor (RG) stored in _refine_analyze.RG_work and
_refine_analyze.RG_free.
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
_item.name '_refine_analyze.RG_d_res_low'
_item.category_id refine_analyze
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_low'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.RG_free
_item_description.description
; The Hamilton generalized R factor for all reflections that
satisfy the resolution limits established by
_refine_analyze.RG_d_res_high and
_refine_analyze.RG_d_res_low for the free R set of
reflections that were excluded from the refinement.
sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)
RG = Sqrt( ----------------------------------------------------------------- )
sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j
where
|Fobs| = the observed structure-factor amplitudes
|Fcalc| = the calculated structure-factor amplitudes
G = the scale factor which puts |Fcalc| on the
same scale as |Fobs|
w_{i,j} = the weight for the combination of the reflections
i and j.
sum_i and sum_j are taken over the specified reflections
When the covariance of the amplitudes of reflection i and
reflection j is zero (i.e. the reflections are independent)
w{i,i} can be redefined as w_i and the nested sums collapsed
into one sum.
sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2
RG = Sqrt( ----------------------------------- )
sum_i w_i |Fobs|_i^2
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
_item.name '_refine_analyze.RG_free'
_item.category_id refine_analyze
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_free'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_analyze.RG_work
_item_description.description
; The Hamilton generalized R factor for all reflections
that satisfy the resolution limits established by
_refine_analyze.RG_d_res_high and
_refine_analyze.RG_d_res_low and for those
reflections included in the working set when a free R set
of reflections is omitted from the refinement.
sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)
RG = Sqrt( ----------------------------------------------------------------- )
sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j
where
|Fobs| = the observed structure-factor amplitudes
|Fcalc| = the calculated structure-factor amplitudes
G = the scale factor which puts |Fcalc| on the
same scale as |Fobs|
w_{i,j} = the weight for the combination of the reflections
i and j.
sum_i and sum_j are taken over the specified reflections
When the covariance of the amplitudes of reflection i and
reflection j is zero (i.e. the reflections are independent)
w{i,i} can be redefined as w_i and the nested sums collapsed
into one sum.
sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2
RG = Sqrt( ----------------------------------- )
sum_i w_i |Fobs|_i^2
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
_item.name '_refine_analyze.RG_work'
_item.category_id refine_analyze
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_work'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_analyze.RG_free_work_ratio
_item_description.description
; The observed ratio of RGfree to RGwork. The expected RG ratio
is the value that should be achievable at the end of a structure
refinement when only random uncorrelated errors exist in the data
and the model provided that the observations are properly
weighted. When compared with the observed RG ratio it may
indicate that a structure has not reached convergence or a
model has been over-refined with no corresponding improvement
in the model.
In an unrestrained refinement, the ratio of RGfree to RGwork with
only random uncorrelated errors at convergence depends only
on the number of reflections and the number of parameters
according to
sqrt[(f + m) / (f - m) ]
where f = the number of included structure amplitudes and
target distances, and
m = the number of parameters being refined.
In the restrained case, RGfree is calculated from a random
selection of residuals including both structure amplitudes
and restraints. When restraints are included in the refinement,
the RG ratio requires a term for the contribution to the
minimized residual at convergence, D~restr~, due to those
restraints:
D~restr~ = r - sum [w_i . (a_i)^t . (H)^-1 a_i]
where
r is the number of geometrical, displacement-parameter and
other restraints
H is the (m,m) normal matrix given by A^t.W.A
W is the (n,n) symmetric weight matrix of the included
observations
A is the least-squares design matrix of derivatives of
order (n,m)
a_i is the ith row of A
Then the expected RGratio becomes
sqrt [ (f + (m - r + D~restr~))/ (f - (m - r + D~restr~)) ]
There is no data name for the expected value of RGfree/RGwork yet.
Ref: Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998).
Acta Cryst. D54, 547-557.
;
_item.name '_refine_analyze.RG_free_work_ratio'
_item.category_id refine_analyze
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_work_free_ratio'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
##################
## REFINE_B_ISO ##
##################
save_refine_B_iso
_category.description
; Data items in the REFINE_B_ISO category record details about
the treatment of isotropic B factors (displacement parameters)
during refinement.
;
_category.id refine_B_iso
_category.mandatory_code no
_category_key.name '_refine_B_iso.class'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_refine_B_iso.class
_refine_B_iso.treatment
'protein' isotropic
'solvent' isotropic
'inhibitor' isotropic
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_B_iso.class
_item_description.description
; A class of atoms treated similarly for isotropic B-factor
(displacement-parameter) refinement.
;
_item.name '_refine_B_iso.class'
_item.category_id refine_B_iso
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'all'
'protein'
'solvent'
'sugar-phosphate backbone'
save_
save__refine_B_iso.details
_item_description.description
; A description of special aspects of the isotropic B-factor
(displacement-parameter) refinement for the class of atoms
described in _refine_B_iso.class.
;
_item.name '_refine_B_iso.details'
_item.category_id refine_B_iso
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The temperature factors of atoms in the side
chain of Arg 92 were held fixed due to
unstable behavior in refinement.
;
save_
save__refine_B_iso.treatment
_item_description.description
; The treatment of isotropic B-factor (displacement-parameter)
refinement for a class of atoms defined in _refine_B_iso.class.
;
_item.name '_refine_B_iso.treatment'
_item.category_id refine_B_iso
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value fixed
isotropic
anisotropic
save_
save__refine_B_iso.value
_item_description.description
; The value of the isotropic B factor (displacement parameter)
assigned to a class of atoms defined in _refine_B_iso.class.
Meaningful only for atoms with fixed isotropic B factors.
;
_item.name '_refine_B_iso.value'
_item.category_id refine_B_iso
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms_squared
save_
###############################
## REFINE_FUNCTION_MINIMIZED ##
###############################
save_refine_funct_minimized
_category.description
; Data items in the REFINE_FUNCT_MINIMIZED category record
details about the individual terms of the function minimized
during refinement.
;
_category.id refine_funct_minimized
_category.mandatory_code no
_category_key.name '_refine_funct_minimized.type'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on RESTRAIN refinement for the CCP4 test data set
toxd.
;
;
loop_
_refine_funct_minimized.type
_refine_funct_minimized.number_terms
_refine_funct_minimized.residual
'sum(W*Delta(Amplitude)^2' 3009 1621.3
'sum(W*Delta(Plane+Rigid)^2' 85 56.68
'sum(W*Delta(Distance)^2' 1219 163.59
'sum(W*Delta(U-tempfactors)^2' 1192 69.338
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_funct_minimized.number_terms
_item_description.description
; The number of observations in this term. For example, if the
term is a residual of the X-ray intensities, this item would
contain the number of reflections used in the refinement.
;
_item.name '_refine_funct_minimized.number_terms'
_item.category_id refine_funct_minimized
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refine_funct_minimized.NumTerms'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_funct_minimized.residual
_item_description.description
; The residual for this term of the function that was minimized
during the refinement.
;
_item.name '_refine_funct_minimized.residual'
_item.category_id refine_funct_minimized
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refine_funct_minimized.Residual'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_funct_minimized.type
_item_description.description
; The type of the function being minimized.
;
_item.name '_refine_funct_minimized.type'
_item.category_id refine_funct_minimized
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refine_funct_minimized.type'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code line
save_
save__refine_funct_minimized.weight
_item_description.description
; The weight applied to this term of the function that was
minimized during the refinement.
;
_item.name '_refine_funct_minimized.weight'
_item.category_id refine_funct_minimized
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refine_funct_minimized.weight'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
#################
## REFINE_HIST ##
#################
save_refine_hist
_category.description
; Data items in the REFINE_HIST category record details about the
steps during the refinement of the structure.
These data items are not meant to be as thorough a description
of the refinement as is provided for the final model in other
categories; rather, these data items provide a mechanism for
sketching out the progress of the refinement, supported by a
small set of representative statistics.
;
_category.id refine_hist
_category.mandatory_code no
_category_key.name '_refine_hist.cycle_id'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for the collagen-like
peptide [(POG)4 EKG (POG)5]3.
;
;
_refine_hist.cycle_id C134
_refine_hist.d_res_high 1.85
_refine_hist.d_res_low 20.0
_refine_hist.number_atoms_solvent 217
_refine_hist.number_atoms_total 808
_refine_hist.number_reflns_all 6174
_refine_hist.number_reflns_obs 4886
_refine_hist.number_reflns_R_free 476
_refine_hist.number_reflns_R_work 4410
_refine_hist.R_factor_all .265
_refine_hist.R_factor_obs .195
_refine_hist.R_factor_R_free .274
_refine_hist.R_factor_R_work .160
_refine_hist.details
; Add majority of solvent molecules. B factors refined by
group. Continued to remove misplaced water molecules.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_hist.cycle_id
_item_description.description
; The value of _refine_hist.cycle_id must uniquely identify a
record in the REFINE_HIST list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_refine_hist.cycle_id'
_item.category_id refine_hist
_item.mandatory_code yes
_item_type.code code
save_
save__refine_hist.details
_item_description.description
; A description of special aspects of this cycle of the refinement
process.
;
_item.name '_refine_hist.details'
_item.category_id refine_hist
_item.mandatory_code no
_item_type.code text
_item_examples.case
; Residues 13-17 fit and added to model;
substantial rebuilding of loop containing
residues 43-48; addition of first atoms to
solvent model; ten cycles of Prolsq
refinement.
;
save_
save__refine_hist.d_res_high
_item_description.description
; The lowest value for the interplanar spacings for the
reflection data for this cycle of refinement. This is called
the highest resolution.
;
_item.name '_refine_hist.d_res_high'
_item.category_id refine_hist
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_hist.d_res_low
_item_description.description
; The highest value for the interplanar spacings for the
reflection data for this cycle of refinement. This is
called the lowest resolution.
;
_item.name '_refine_hist.d_res_low'
_item.category_id refine_hist
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_hist.number_atoms_solvent
_item_description.description
; The number of solvent atoms that were included in the model at
this cycle of the refinement.
;
_item.name '_refine_hist.number_atoms_solvent'
_item.category_id refine_hist
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_hist.number_atoms_total
_item_description.description
; The total number of atoms that were included in the model at
this cycle of the refinement.
;
_item.name '_refine_hist.number_atoms_total'
_item.category_id refine_hist
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_hist.number_reflns_all
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine_hist.d_res_high and
_refine_hist.d_res_low.
;
_item.name '_refine_hist.number_reflns_all'
_item.category_id refine_hist
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_hist.number_reflns_obs
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine_hist.d_res_high and
_refine_hist.d_res_low and the observation criterion
established by _reflns.observed_criterion.
;
_item.name '_refine_hist.number_reflns_obs'
_item.category_id refine_hist
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_hist.number_reflns_R_free
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine_hist.d_res_high and
_refine_hist.d_res_low and the observation limit
established by _reflns.observed_criterion, and that were used
as the test reflections (i.e. were excluded from the refinement)
when the refinement included the calculation of a 'free'
R factor. Details of how reflections were assigned to the
working and test sets are given in _reflns.R_free_details.
;
_item.name '_refine_hist.number_reflns_R_free'
_item.category_id refine_hist
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_hist.number_reflns_R_work
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine_hist.d_res_high and
_refine_hist.d_res_low and the observation limit
established by _reflns.observed_criterion, and that were used
as the working reflections (i.e. were included in the
refinement) when the refinement included the calculation
of a 'free' R factor. Details of how reflections were
assigned to the working and test sets are given in
_reflns.R_free_details.
;
_item.name '_refine_hist.number_reflns_R_work'
_item.category_id refine_hist
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_hist.R_factor_all
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine_hist.d_res_high and
_refine_hist.d_res_low.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine_hist.R_factor_all'
_item.category_id refine_hist
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_hist.R_factor_obs
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine_hist.d_res_high and
_refine_hist.d_res_low and the observation criterion
established by _reflns.observed_criterion.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine_hist.R_factor_obs'
_item.category_id refine_hist
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_hist.R_factor_R_free
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine_hist.d_res_high and
_refine_hist.d_res_low and the observation limit
established by _reflns.observed_criterion, and that were used
as the test reflections (i.e. were excluded from the refinement)
when the refinement included the calculation of a 'free'
R factor. Details of how reflections were assigned to the
working and test sets are given in _reflns.R_free_details.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine_hist.R_factor_R_free'
_item.category_id refine_hist
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_hist.R_factor_R_work
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine_hist.d_res_high and
_refine_hist.d_res_low and the observation limit
established by _reflns.observed_criterion, and that were used
as the working reflections (i.e. were included in the refinement)
when the refinement included the calculation of a 'free'
R factor. Details of how reflections were assigned to the
working and test sets are given in _reflns.R_free_details.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine_hist.R_factor_R_work'
_item.category_id refine_hist
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
#####################
## REFINE_LS_RESTR ##
#####################
save_refine_ls_restr
_category.description
; Data items in the REFINE_LS_RESTR category record details about
the restraints applied to various classes of parameters during
the least-squares refinement.
;
_category.id refine_ls_restr
_category.mandatory_code no
_category_key.name '_refine_ls_restr.type'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_refine_ls_restr.type
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.dev_ideal
_refine_ls_restr.number
_refine_ls_restr.criterion
_refine_ls_restr.rejects
'bond_d' 0.020 0.018 1654 '> 2\s' 22
'angle_d' 0.030 0.038 2246 '> 2\s' 139
'planar_d' 0.040 0.043 498 '> 2\s' 21
'planar' 0.020 0.015 270 '> 2\s' 1
'chiral' 0.150 0.177 278 '> 2\s' 2
'singtor_nbd' 0.500 0.216 582 '> 2\s' 0
'multtor_nbd' 0.500 0.207 419 '> 2\s' 0
'xyhbond_nbd' 0.500 0.245 149 '> 2\s' 0
'planar_tor' 3.0 2.6 203 '> 2\s' 9
'staggered_tor' 15.0 17.4 298 '> 2\s' 31
'orthonormal_tor' 20.0 18.1 12 '> 2\s' 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_ls_restr.criterion
_item_description.description
; A criterion used to define a parameter value that deviates
significantly from its ideal value in the model obtained by
restrained least-squares refinement.
;
_item.name '_refine_ls_restr.criterion'
_item.category_id refine_ls_restr
_item.mandatory_code no
_item_type.code text
_item_examples.case '> 3\s'
save_
save__refine_ls_restr.dev_ideal
_item_description.description
; For the given parameter type, the root-mean-square deviation
between the ideal values used as restraints in the least-squares
refinement and the values obtained by refinement. For instance,
bond distances may deviate by 0.018 \%A (r.m.s.) from ideal
values in the current model.
;
_item.name '_refine_ls_restr.dev_ideal'
_item.category_id refine_ls_restr
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_ls_restr.dev_ideal_target
_item_description.description
; For the given parameter type, the target root-mean-square
deviation between the ideal values used as restraints in the
least-squares refinement and the values obtained by refinement.
;
_item.name '_refine_ls_restr.dev_ideal_target'
_item.category_id refine_ls_restr
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_ls_restr.number
_item_description.description
; The number of parameters of this type subjected to restraint in
least-squares refinement.
;
_item.name '_refine_ls_restr.number'
_item.category_id refine_ls_restr
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_ls_restr.rejects
_item_description.description
; The number of parameters of this type that deviate from ideal
values by more than the amount defined in
_refine_ls_restr.criterion in the model obtained by restrained
least-squares refinement.
;
_item.name '_refine_ls_restr.rejects'
_item.category_id refine_ls_restr
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_ls_restr.type
_item_description.description
; The type of the parameter being restrained.
Explicit sets of data values are provided for the programs
PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with
RESTRAIN_). As computer programs change, these data values
are given as examples, not as an enumeration list. Computer
programs that convert a data block to a refinement table will
expect the exact form of the data values given here to be used.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_refine_ls_restr.type' refine_ls_restr yes
'_refine_ls_restr_type.type' refine_ls_restr_type yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_refine_ls_restr_type.type' '_refine_ls_restr.type'
_item_type.code line
loop_
_item_examples.case
_item_examples.detail
'p_bond_d' 'bond distance'
'p_angle_d' 'bond angle expressed as a distance'
'p_planar_d' 'planar 1,4 distance'
'p_xhbond_d' 'X-H bond distance'
'p_xhangle_d' 'X-H bond angle expressed as a distance'
'p_hydrog_d' 'hydrogen distance'
'p_special_d' 'special distance'
'p_planar' 'planes'
'p_chiral' 'chiral centres'
'p_singtor_nbd' 'single-torsion non-bonded contact'
'p_multtor_nbd' 'multiple-torsion non-bonded contact'
'p_xyhbond_nbd' 'possible (X...Y) hydrogen bond'
'p_xhyhbond_nbd' 'possible (X-H...Y) hydrogen bond'
'p_special_tor' 'special torsion angle'
'p_planar_tor' 'planar torsion angle'
'p_staggered_tor' 'staggered torsion angle'
'p_orthonormal_tor' 'orthonormal torsion angle'
'p_mcbond_it' 'main-chain bond isotropic displacement parameter'
'p_mcangle_it' 'main-chain angle isotropic displacement parameter'
'p_scbond_it' 'side-chain bond isotropic displacement parameter'
'p_scangle_it' 'side-chain angle isotropic displacement parameter'
'p_xhbond_it' 'X-H bond isotropic displacement parameter'
'p_xhangle_it' 'X-H angle isotropic displacement parameter'
'p_special_it' 'special isotropic displacement parameter'
'RESTRAIN_Distances < 2.12'
; The root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range less than 2.12 Angstroms.
;
'RESTRAIN_Distances 2.12 < D < 2.625'
; The root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range 2.12 - 2.625 Angstroms.
;
'RESTRAIN_Distances > 2.625'
; The root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range greater than 2.625 Angstroms.
;
'RESTRAIN_Peptide Planes'
; The root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves for peptide planes.
;
'RESTRAIN_Ring and other planes'
; The root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves for rings and planes other than peptide planes.
;
'RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4' .
'RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6' .
'RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0' .
'RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2' .
'RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4' .
'RESTRAIN_rms diffs for Uiso atoms at dist >2.4' .
save_
save__refine_ls_restr.weight
_item_description.description
; The weighting value applied to this type of restraint in
the least-squares refinement.
;
_item.name '_refine_ls_restr.weight'
_item.category_id refine_ls_restr
_item.mandatory_code no
_item_type.code float
save_
#########################
## REFINE_LS_RESTR_NCS ##
#########################
save_refine_ls_restr_ncs
_category.description
; Data items in the REFINE_LS_RESTR_NCS category record details
about the restraints applied to atom positions in domains
related by noncrystallographic symmetry during least-squares
refinement, and also about the deviation of the restrained
atomic parameters at the end of the refinement. It is
expected that these values will only be reported once for each
set of restrained domains.
;
_category.id refine_ls_restr_ncs
_category.mandatory_code no
_category_key.name '_refine_ls_restr_ncs.dom_id'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
;
;
_refine_ls_restr_ncs.dom_id d2
_refine_ls_restr_ncs.weight_position 300.0
_refine_ls_restr_ncs.weight_B_iso 2.0
_refine_ls_restr_ncs.rms_dev_position 0.09
_refine_ls_restr_ncs.rms_dev_B_iso 0.16
_refine_ls_restr_ncs.ncs_model_details
;
NCS restraint for pseudo-twofold symmetry between domains
d1 and d2. Position weight coefficient given in
Kcal/(mol \%A^2^) and isotropic B weight coefficient given
in \%A^2^.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_ls_restr_ncs.dom_id
_item_description.description
; This data item is a pointer to _struct_ncs_dom.id in the
STRUCT_NCS_DOM category.
;
_item.name '_refine_ls_restr_ncs.dom_id'
_item.category_id refine_ls_restr_ncs
_item.mandatory_code yes
_item_type.code code
save_
save__refine_ls_restr_ncs.ncs_model_details
_item_description.description
; Special aspects of the manner in which noncrystallographic
restraints were applied to atomic parameters in the domain
specified by _refine_ls_restr_ncs.dom_id and equivalent
atomic parameters in the domains against which it was restrained.
;
_item.name '_refine_ls_restr_ncs.ncs_model_details'
_item.category_id refine_ls_restr_ncs
_item.mandatory_code no
_item_type.code text
save_
save__refine_ls_restr_ncs.rms_dev_B_iso
_item_description.description
; The root-mean-square deviation in equivalent isotropic
displacement parameters in the domain specified by
_refine_ls_restr_ncs.dom_id
and in the domains against which it was restrained.
;
_item.name '_refine_ls_restr_ncs.rms_dev_B_iso'
_item.category_id refine_ls_restr_ncs
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms_squared
save_
save__refine_ls_restr_ncs.rms_dev_position
_item_description.description
; The root-mean-square deviation in equivalent atom positions in
the domain specified by _refine_ls_restr_ncs.dom_id and in the
domains against which it was restrained.
;
_item.name '_refine_ls_restr_ncs.rms_dev_position'
_item.category_id refine_ls_restr_ncs
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_ls_restr_ncs.weight_B_iso
_item_description.description
; The value of the weighting coefficient used in
noncrystallographic symmetry restraint of isotropic displacement
parameters in the domain specified by
_refine_ls_restr_ncs.dom_id to equivalent isotropic
displacement parameters in the domains against
which it was restrained.
;
_item.name '_refine_ls_restr_ncs.weight_B_iso'
_item.category_id refine_ls_restr_ncs
_item.mandatory_code no
_item_type.code float
save_
save__refine_ls_restr_ncs.weight_position
_item_description.description
; The value of the weighting coefficient used in
noncrystallographic symmetry restraint of atom positions in the
domain specified by _refine_ls_restr_ncs.dom_id to equivalent
atom positions in the domains against which it was restrained.
;
_item.name '_refine_ls_restr_ncs.weight_position'
_item.category_id refine_ls_restr_ncs
_item.mandatory_code no
_item_type.code float
save_
##########################
## REFINE_LS_RESTR_TYPE ##
##########################
save_refine_ls_restr_type
_category.description
; Data items in the REFINE_LS_RESTR_TYPE category record details
about the restraint types used in the least-squares refinement.
;
_category.id refine_ls_restr_type
_category.mandatory_code no
_category_key.name '_refine_ls_restr_type.type'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on RESTRAIN refinement for the CCP4 test data set
toxd.
;
;
loop_
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
'RESTRAIN_Distances < 2.12' 509 0.005 0.022
'RESTRAIN_Distances 2.12 < D < 2.625' 671 0.016 0.037
'RESTRAIN_Distances > 2.625' 39 0.034 0.043
'RESTRAIN_Peptide Planes' 59 0.002 0.010
'RESTRAIN_Ring and other planes' 26 0.014 0.010
'RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4'
212 0.106 .
'RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6'
288 0.101 .
'RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0'
6 0.077 .
'RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2'
10 0.114 .
'RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4'
215 0.119 .
'RESTRAIN_rms diffs for Uiso atoms at dist >2.4'
461 0.106 .
loop_
_refine_ls_restr_type.type
_refine_ls_restr_type.distance_cutoff_low
_refine_ls_restr_type.distance_cutoff_high
'RESTRAIN_Distances < 2.12' . 2.12
'RESTRAIN_Distances 2.12 < D < 2.625' 2.12 2.625
'RESTRAIN_Distances > 2.625' 2.625 .
'RESTRAIN_Peptide Planes' . .
'RESTRAIN_Ring and other planes' . .
'RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4'
1.2 1.4
'RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6'
1.4 1.6
'RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0'
1.8 2.0
'RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2'
2.0 2.2
'RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4'
2.2 2.4
'RESTRAIN_rms diffs for Uiso atoms at dist >2.4'
2.4 .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_ls_restr_type.distance_cutoff_high
_item_description.description
; The upper limit in angstroms of the distance range applied to
the current restraint type.
;
_item.name '_refine_ls_restr_type.distance_cutoff_high'
_item.category_id refine_ls_restr_type
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_ls_restr_type.distance_cutoff_low
_item_description.description
; The lower limit in angstroms of the distance range applied to
the current restraint type.
;
_item.name '_refine_ls_restr_type.distance_cutoff_low'
_item.category_id refine_ls_restr_type
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_ls_restr_type.type
_item_description.description
; This data item is a pointer to _refine_ls_restr.type in the
REFINE_LS_RESTR category.
;
_item.name '_refine_ls_restr_type.type'
_item.category_id refine_ls_restr_type
_item.mandatory_code yes
_item_type.code line
save_
#####################
## REFINE_LS_SHELL ##
#####################
save_refine_ls_shell
_category.description
; Data items in the REFINE_LS_SHELL category record details about
the results of the least-squares refinement broken down into
shells of resolution.
;
_category.id refine_ls_shell
_category.mandatory_code no
loop_
_category_key.name '_refine_ls_shell.d_res_low'
'_refine_ls_shell.d_res_high'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_refine_ls_shell.d_res_low
_refine_ls_shell.d_res_high
_refine_ls_shell.number_reflns_obs
_refine_ls_shell.R_factor_obs
8.00 4.51 1226 0.196
4.51 3.48 1679 0.146
3.48 2.94 2014 0.160
2.94 2.59 2147 0.182
2.59 2.34 2127 0.193
2.34 2.15 2061 0.203
2.15 2.00 1647 0.188
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_ls_shell.d_res_high
_item_description.description
; The lowest value for the interplanar spacings for the
reflection data in this shell. This is called
the highest resolution.
;
_item.name '_refine_ls_shell.d_res_high'
_item.category_id refine_ls_shell
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_ls_shell.d_res_low
_item_description.description
; The highest value for the interplanar spacings for the
reflection data in this shell. This is called the lowest
resolution.
;
_item.name '_refine_ls_shell.d_res_low'
_item.category_id refine_ls_shell
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_ls_shell.number_reflns_all
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine_ls_shell.d_res_high and
_refine_ls_shell.d_res_low.
;
_item.name '_refine_ls_shell.number_reflns_all'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_ls_shell.number_reflns_obs
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine_ls_shell.d_res_high and
_refine_ls_shell.d_res_low and the observation criterion
established by _reflns.observed_criterion.
;
_item.name '_refine_ls_shell.number_reflns_obs'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_ls_shell.number_reflns_R_free
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine_ls_shell.d_res_high and
_refine_ls_shell.d_res_low and the observation limit
established by _reflns.observed_criterion, and that were used
as the test reflections (i.e. were excluded from the refinement)
when the refinement included the calculation of a 'free'
R factor. Details of how reflections were assigned to the
working and test sets are given in _reflns.R_free_details.
;
_item.name '_refine_ls_shell.number_reflns_R_free'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_ls_shell.number_reflns_R_work
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine_ls_shell.d_res_high and
_refine_ls_shell.d_res_low and the observation limit
established by _reflns.observed_criterion, and that were used
as the working reflections (i.e. were included in the
refinement) when the refinement included the calculation of
a 'free' R factor. Details of how reflections were assigned
to the working and test sets are given in _reflns.R_free_details.
;
_item.name '_refine_ls_shell.number_reflns_R_work'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_ls_shell.percent_reflns_obs
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine_ls_shell.d_res_high and
_refine_ls_shell.d_res_low and the observation criterion
established by _reflns.observed_criterion, expressed as a
percentage of the number of geometrically observable
reflections that satisfy the resolution limits.
;
_item.name '_refine_ls_shell.percent_reflns_obs'
_item.category_id refine_ls_shell
_item.mandatory_code no
_item_type.code float
save_
save__refine_ls_shell.percent_reflns_R_free
_item_description.description
; The number of reflections that satisfy the resolution limits
established by _refine_ls_shell.d_res_high and
_refine_ls_shell.d_res_low and the observation limit
established by _reflns.observed_criterion, and that were used
as the test reflections (i.e. were excluded from the refinement)
when the refinement included the calculation of a 'free'
R factor, expressed as a percentage of the number of
geometrically observable reflections that satisfy the
reflection limits.
;
_item.name '_refine_ls_shell.percent_reflns_R_free'
_item.category_id refine_ls_shell
_item.mandatory_code no
_item_type.code float
save_
save__refine_ls_shell.R_factor_all
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine_ls_shell.d_res_high and
_refine_ls_shell.d_res_low.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine_ls_shell.R_factor_all'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine_ls_shell.wR_factor_all'
_item_related.function_code alternate
_item_type.code float
save_
save__refine_ls_shell.R_factor_obs
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine_ls_shell.d_res_high and
_refine_ls_shell.d_res_low and the observation criterion
established by _reflns.observed_criterion.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine_ls_shell.R_factor_obs'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine_ls_shell.wR_factor_obs'
_item_related.function_code alternate
_item_type.code float
save_
save__refine_ls_shell.R_factor_R_free
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine_ls_shell.d_res_high and
_refine_ls_shell.d_res_low and the observation limit
established by _reflns.observed_criterion, and that were
used as the test reflections (i.e. were excluded from the
refinement) when the refinement included the calculation
of a 'free' R factor. Details of how reflections were assigned
to the working and test sets are given in _reflns.R_free_details.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine_ls_shell.R_factor_R_free'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
loop_
_item_related.related_name
_item_related.function_code '_refine_ls_shell.wR_factor_R_free'
alternate
'_refine_ls_shell.R_factor_R_free_error'
associated_error
_item_type.code float
save_
save__refine_ls_shell.R_factor_R_free_error
_item_description.description
; The estimated error in _refine_ls_shell.R_factor_R_free.
The method used to estimate the error is described in the
item _refine.ls_R_factor_R_free_error_details.
;
_item.name '_refine_ls_shell.R_factor_R_free_error'
_item.category_id refine_ls_shell
_item.mandatory_code no
_item_related.related_name '_refine_ls_shell.R_factor_R_free'
_item_related.function_code associated_value
_item_type.code float
save_
save__refine_ls_shell.R_factor_R_work
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine_ls_shell.d_res_high and
_refine_ls_shell.d_res_low and the observation limit
established by _reflns.observed_criterion, and that were used
as the working reflections (i.e. were included in the
refinement) when the refinement included the calculation of
a 'free' R factor. Details of how reflections were assigned
to the working and test sets are given in _reflns.R_free_details.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|F~obs~|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine_ls_shell.R_factor_R_work'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine_ls_shell.wR_factor_R_work'
_item_related.function_code alternate
_item_type.code float
save_
save__refine_ls_shell.redundancy_reflns_all
_item_description.description
; The ratio of the total number of observations of the reflections
that satisfy the resolution limits established by
_refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low
to the number of crystallographically unique reflections that
satisfy the same limits.
;
_item.name '_refine_ls_shell.redundancy_reflns_all'
_item.category_id refine_ls_shell
_item.mandatory_code no
_item_type.code float
save_
save__refine_ls_shell.redundancy_reflns_obs
_item_description.description
; The ratio of the total number of observations of the
reflections that satisfy the resolution limits established by
_refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and
the observation criterion established by
_reflns.observed_criterion to the number of crystallographically
unique reflections that satisfy the same limits.
;
_item.name '_refine_ls_shell.redundancy_reflns_obs'
_item.category_id refine_ls_shell
_item.mandatory_code no
_item_type.code float
save_
save__refine_ls_shell.wR_factor_all
_item_description.description
; Weighted residual factor wR for reflections that satisfy the
resolution limits established by _refine_ls_shell.d_res_high
and _refine_ls_shell.d_res_low.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
_refine.ls_structure_factor_coef
Y~calc~ = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
sum is taken over the specified reflections
;
_item.name '_refine_ls_shell.wR_factor_all'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine_ls_shell.R_factor_all'
_item_related.function_code alternate
_item_type.code float
save_
save__refine_ls_shell.wR_factor_obs
_item_description.description
; Weighted residual factor wR for reflections that satisfy the
resolution limits established by _refine_ls_shell.d_res_high
and _refine_ls_shell.d_res_low and the observation criterion
established by _reflns.observed_criterion.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
_refine.ls_structure_factor_coef
Y~calc~ = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
sum is taken over the specified reflections
;
_item.name '_refine_ls_shell.wR_factor_obs'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine_ls_shell.R_factor_obs'
_item_related.function_code alternate
_item_type.code float
save_
save__refine_ls_shell.wR_factor_R_free
_item_description.description
; Weighted residual factor wR for reflections that satisfy the
resolution limits established by _refine_ls_shell.d_res_high
and _refine_ls_shell.d_res_low and the observation limit
established by _reflns.observed_criterion, and that were used
as the test reflections (i.e. were excluded from the refinement)
when the refinement included the calculation of a 'free'
R factor. Details of how reflections were assigned to the
working and test sets are given in _reflns.R_free_details.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
_refine.ls_structure_factor_coef
Y~calc~ = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
sum is taken over the specified reflections
;
_item.name '_refine_ls_shell.wR_factor_R_free'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine_ls_shell.R_factor_R_free'
_item_related.function_code alternate
_item_type.code float
save_
save__refine_ls_shell.wR_factor_R_work
_item_description.description
; Weighted residual factor wR for reflections that satisfy the
resolution limits established by _refine_ls_shell.d_res_high
and _refine_ls_shell.d_res_low and the observation limit
established by _reflns.observed_criterion, and that were used
as the working reflections (i.e. were included in the
refinement) when the refinement included the calculation of
a 'free' R factor. Details of how reflections were assigned
to the working and test sets are given in _reflns.R_free_details.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Y~obs~^2^| )
Y~obs~ = the observed amplitude specified by
_refine.ls_structure_factor_coef
Y~calc~ = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
sum is taken over the specified reflections
;
_item.name '_refine_ls_shell.wR_factor_R_work'
_item.category_id refine_ls_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_related.related_name '_refine_ls_shell.R_factor_R_work'
_item_related.function_code alternate
_item_type.code float
save_
######################
## REFINE_OCCUPANCY ##
######################
save_refine_occupancy
_category.description
; Data items in the REFINE_OCCUPANCY category record details
about the treatment of atom occupancies during refinement.
;
_category.id refine_occupancy
_category.mandatory_code no
_category_key.name '_refine_occupancy.class'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_refine_occupancy.class
_refine_occupancy.treatment
_refine_occupancy.value
_refine_occupancy.details
'protein' fix 1.00 .
'solvent' fix 1.00 .
'inhibitor orientation 1' fix 0.65 .
'inhibitor orientation 2' fix 0.35
; The inhibitor binds to the enzyme in two alternative
conformations. The occupancy of each conformation was
adjusted so as to result in approximately equal mean
thermal factors for the atoms in each conformation.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_occupancy.class
_item_description.description
; The class of atoms treated similarly for occupancy refinement.
;
_item.name '_refine_occupancy.class'
_item.category_id refine_occupancy
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'all'
'protein'
'solvent'
'sugar-phosphate backbone'
save_
save__refine_occupancy.details
_item_description.description
; A description of special aspects of the occupancy refinement for
a class of atoms described in _refine_occupancy.class.
;
_item.name '_refine_occupancy.details'
_item.category_id refine_occupancy
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The inhibitor binds to the enzyme in two
alternative conformations. The occupancy of
each conformation was adjusted so as to result
in approximately equal mean thermal factors
for the atoms in each conformation.
;
save_
save__refine_occupancy.treatment
_item_description.description
; The treatment of occupancies for a class of atoms
described in _refine_occupancy.class.
;
_item.name '_refine_occupancy.treatment'
_item.category_id refine_occupancy
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail fix 'fixed'
ref 'refined'
save_
save__refine_occupancy.value
_item_description.description
; The value of occupancy assigned to a class of atoms defined in
_refine_occupancy.class. Meaningful only for atoms with fixed
occupancy.
;
_item.name '_refine_occupancy.value'
_item.category_id refine_occupancy
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 0.0
0.0 0.0
_item_type.code float
loop_
_item_examples.case 1.0
0.41
save_
###########
## REFLN ##
###########
save_refln
_category.description
; Data items in the REFLN category record details about the
reflection data used to determine the ATOM_SITE data items.
The REFLN data items refer to individual reflections and must
be included in looped lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
;
_category.id refln
_category.mandatory_code no
loop_
_category_key.name '_refln.index_h'
'_refln.index_k'
'_refln.index_l'
loop_
_category_group.id 'inclusive_group'
'refln_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov
[Acta Cryst. (1993), C49, 1352-1354].
;
;
loop_
_refln.index_h
_refln.index_k
_refln.index_l
_refln.F_squared_calc
_refln.F_squared_meas
_refln.F_squared_sigma
_refln.status
2 0 0 85.57 58.90 1.45 o
3 0 0 15718.18 15631.06 30.40 o
4 0 0 55613.11 49840.09 61.86 o
5 0 0 246.85 241.86 10.02 o
6 0 0 82.16 69.97 1.93 o
7 0 0 1133.62 947.79 11.78 o
8 0 0 2558.04 2453.33 20.44 o
9 0 0 283.88 393.66 7.79 o
10 0 0 283.70 171.98 4.26 o
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refln.A_calc
_item_description.description
; The calculated value of structure-factor component A in
electrons.
A = |F|cos(phase)
;
_item.name '_refln.A_calc'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_A_calc'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_refln.A_calc_au'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code electrons
save_
save__refln.A_calc_au
_item_description.description
; The calculated value of structure-factor component A in
arbitrary units.
A = |F|cos(phase)
;
_item.name '_refln.A_calc_au'
_item.category_id refln
_item.mandatory_code no
_item_related.related_name '_refln.A_calc'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code arbitrary
save_
save__refln.A_meas
_item_description.description
; The measured value of structure-factor component A in electrons.
A = |F|cos(phase)
;
_item.name '_refln.A_meas'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_A_meas'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_refln.A_meas_au'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code electrons
save_
save__refln.A_meas_au
_item_description.description
; The measured value of structure-factor component A in
arbitrary units.
A = |F|cos(phase)
;
_item.name '_refln.A_meas_au'
_item.category_id refln
_item.mandatory_code no
_item_related.related_name '_refln.A_meas'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code arbitrary
save_
save__refln.B_calc
_item_description.description
; The calculated value of structure-factor component B in
electrons.
B = |F|sin(phase)
;
_item.name '_refln.B_calc'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_B_calc'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_refln.B_calc_au'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code electrons
save_
save__refln.B_calc_au
_item_description.description
; The calculated value of structure-factor component B in
arbitrary units.
B = |F|sin(phase)
;
_item.name '_refln.B_calc_au'
_item.category_id refln
_item.mandatory_code no
_item_related.related_name '_refln.B_calc'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code arbitrary
save_
save__refln.B_meas
_item_description.description
; The measured value of structure-factor component B in electrons.
B = |F|sin(phase)
;
_item.name '_refln.B_meas'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_B_meas'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_refln.B_meas_au'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code electrons
save_
save__refln.B_meas_au
_item_description.description
; The measured value of structure-factor component B in
arbitrary units.
B = |F|sin(phase)
;
_item.name '_refln.B_meas_au'
_item.category_id refln
_item.mandatory_code no
_item_related.related_name '_refln.B_meas'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code arbitrary
save_
save__refln.crystal_id
_item_description.description
; This data item is a pointer to _exptl_crystal.id in the
EXPTL_CRYSTAL category.
;
_item.name '_refln.crystal_id'
_item.mandatory_code yes
_item_aliases.alias_name '_refln_crystal_id'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__refln.F_calc
_item_description.description
; The calculated value of the structure factor in electrons.
;
_item.name '_refln.F_calc'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_F_calc'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_related.related_name '_refln.F_calc_au'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code electrons
save_
save__refln.F_calc_au
_item_description.description
; The calculated value of the structure factor in arbitrary
units.
;
_item.name '_refln.F_calc_au'
_item.category_id refln
_item.mandatory_code no
_item_related.related_name '_refln.F_calc'
_item_related.function_code conversion_arbitrary
_item_type.code float
_item_units.code arbitrary
save_
save__refln.F_meas
_item_description.description
; The measured value of the structure factor in electrons.
;
_item.name '_refln.F_meas'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_F_meas'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_refln.F_meas_sigma'
associated_esd
'_refln.F_meas_au'
conversion_arbitrary
_item_type.code float
_item_type_conditions.code esd
_item_units.code electrons
save_
save__refln.F_meas_au
_item_description.description
; The measured value of the structure factor in arbitrary units.
;
_item.name '_refln.F_meas_au'
_item.category_id refln
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_refln.F_meas_sigma_au'
associated_esd
'_refln.F_meas'
conversion_arbitrary
_item_type.code float
_item_type_conditions.code esd
_item_units.code arbitrary
save_
save__refln.F_meas_sigma
_item_description.description
; The standard uncertainty (estimated standard deviation) of
_refln.F_meas in electrons.
;
_item.name '_refln.F_meas_sigma'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_F_sigma'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_refln.F_meas'
associated_value
'_refln.F_meas_sigma_au'
conversion_arbitrary
_item_type.code float
_item_units.code electrons
save_
save__refln.F_meas_sigma_au
_item_description.description
; The standard uncertainty (estimated standard deviation) of
_refln.F_meas_au in arbitrary units.
;
_item.name '_refln.F_meas_sigma_au'
_item.category_id refln
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_refln.F_meas_au'
associated_value
'_refln.F_meas_sigma'
conversion_arbitrary
_item_type.code float
_item_units.code arbitrary
save_
save__refln.F_squared_calc
_item_description.description
; The calculated value of the squared structure factor in
electrons squared.
;
_item.name '_refln.F_squared_calc'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_F_squared_calc'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code electrons_squared
save_
save__refln.F_squared_meas
_item_description.description
; The measured value of the squared structure factor in electrons
squared.
;
_item.name '_refln.F_squared_meas'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_F_squared_meas'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code electrons_squared
save_
save__refln.F_squared_sigma
_item_description.description
; The standard uncertainty (derived from measurement) of the
squared structure factor in electrons squared.
;
_item.name '_refln.F_squared_sigma'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_F_squared_sigma'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code electrons_squared
save_
save__refln.fom
_item_description.description
; The figure of merit m for this reflection.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that the phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_refln.fom'
_item.category_id refln
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refln.index_h
_item_description.description
; Miller index h of the reflection. The values of the Miller
indices in the REFLN category must correspond to the cell
defined by cell lengths and cell angles in the CELL category.
;
_item.name '_refln.index_h'
_item.category_id refln
_item.mandatory_code yes
_item_aliases.alias_name '_refln_index_h'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_refln.index_k'
'_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln.index_k
_item_description.description
; Miller index k of the reflection. The values of the Miller
indices in the REFLN category must correspond to the cell
defined by cell lengths and cell angles in the CELL category.
;
_item.name '_refln.index_k'
_item.category_id refln
_item.mandatory_code yes
_item_aliases.alias_name '_refln_index_k'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_refln.index_h'
'_refln.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln.index_l
_item_description.description
; Miller index l of the reflection. The values of the Miller
indices in the REFLN category must correspond to the cell
defined by cell lengths and cell angles in the CELL category.
;
_item.name '_refln.index_l'
_item.category_id refln
_item.mandatory_code yes
_item_aliases.alias_name '_refln_index_l'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_dependent.dependent_name
'_refln.index_h'
'_refln.index_k'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln.intensity_calc
_item_description.description
; The calculated value of the intensity in the same units as
_refln.intensity_meas.
;
_item.name '_refln.intensity_calc'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_intensity_calc'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
save_
save__refln.intensity_meas
_item_description.description
; The measured value of the intensity.
;
_item.name '_refln.intensity_meas'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_intensity_meas'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
save_
save__refln.intensity_sigma
_item_description.description
; The standard uncertainty (derived from measurement) of the
intensity in the same units as _refln.intensity_meas.
;
_item.name '_refln.intensity_sigma'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_intensity_sigma'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
save_
#save__refln.mean_path_length_tbar
# _item_description.description
#; Mean path length in millimetres through the crystal for this
# reflection.
#;
# _item.name '_refln.mean_path_length_tbar'
# _item.category_id refln
# _item.mandatory_code no
# _item_aliases.alias_name '_refln_mean_path_length_tbar'
# _item_aliases.dictionary cif_core.dic
# _item_aliases.version 2.0.1
# _item_type.code float
# _item_units.code millimetres
# save_
save__refln.status
_item_description.description
; Classification of a reflection so as to indicate its status with
respect to inclusion in the refinement and the calculation of
R factors.
;
_item.name '_refln.status'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_observed_status'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
# _item_default.value o
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail o
; satisfies _refine.ls_d_res_high,
satisfies _refine.ls_d_res_low,
observed by _reflns.observed_criterion,
not flagged as systematically absent,
not flagged as unreliable
;
<
; satisfies _refine.ls_d_res_high,
satisfies _refine.ls_d_res_low,
unobserved by _reflns.observed_criterion,
not flagged as systematically absent,
not flagged as unreliable
;
- 'systematically absent reflection'
x 'unreliable measurement -- not used'
h 'does not satisfy _refine.ls_d_res_high'
l 'does not satisfy _refine.ls_d_res_low'
f
; satisfies _refine.ls_d_res_high,
satisfies _refine.ls_d_res_low,
observed by _reflns.observed_criterion,
not flagged as systematically absent,
not flagged as unreliable,
excluded from refinement so as to be
included in the calculation of a 'free' R
factor
;
save_
save__refln.phase_calc
_item_description.description
; The calculated structure-factor phase in degrees.
;
_item.name '_refln.phase_calc'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_phase_calc'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__refln.phase_meas
_item_description.description
; The measured structure-factor phase in degrees.
;
_item.name '_refln.phase_meas'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_phase_meas'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
_item_units.code degrees
save_
save__refln.refinement_status
_item_description.description
; Status of a reflection in the structure-refinement process.
;
_item.name '_refln.refinement_status'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_refinement_status'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_default.value incl
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail incl 'included in ls process'
excl 'excluded from ls process'
extn 'excluded due to extinction'
save_
save__refln.scale_group_code
_item_description.description
; This data item is a pointer to _reflns_scale.group_code in the
REFLNS_SCALE category.
;
_item.name '_refln.scale_group_code'
_item.mandatory_code yes
_item_aliases.alias_name '_refln_scale_group_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
save__refln.sint_over_lambda
_item_description.description
; The (sin theta)/lambda value in reciprocal angstroms for this
reflection.
;
_item.name '_refln.sint_over_lambda'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_sint/lambda'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code reciprocal_angstroms
save_
save__refln.symmetry_epsilon
_item_description.description
; The symmetry reinforcement factor corresponding to the number of
times the reflection indices are generated identically from the
space-group symmetry operations.
;
_item.name '_refln.symmetry_epsilon'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_symmetry_epsilon'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 48 48
48 1
1 1
_item_type.code int
save_
save__refln.symmetry_multiplicity
_item_description.description
; The number of symmetry-equivalent reflections. The equivalent
reflections have the same structure-factor magnitudes because
of the space-group symmetry and the Friedel relationship.
;
_item.name '_refln.symmetry_multiplicity'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_symmetry_multiplicity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 48 48
48 1
1 1
_item_type.code int
save_
save__refln.wavelength
_item_description.description
; The mean wavelength in angstroms of radiation used to measure
this reflection. This is an important parameter for data
collected using energy-dispersive detectors or the Laue
method.
;
_item.name '_refln.wavelength'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln_wavelength'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refln.wavelength_id
_item_description.description
; This data item is a pointer to _diffrn_radiation.wavelength_id in
the DIFFRN_RADIATION category.
;
_item.name '_refln.wavelength_id'
_item.mandatory_code yes
_item_aliases.alias_name '_refln_wavelength_id'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
save_
###################
## REFLN_SYS_ABS ##
###################
save_refln_sys_abs
_category.description
; Data items in the REFLN_SYS_ABS category record details about
the reflection data that should be systematically absent,
given the designated space group.
;
_category.id refln_sys_abs
_category.mandatory_code no
loop_
_category_key.name '_refln_sys_abs.index_h'
'_refln_sys_abs.index_k'
'_refln_sys_abs.index_l'
loop_
_category_group.id 'inclusive_group'
'refln_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - hypothetical example.
;
;
loop_
_refln_sys_abs.index_h
_refln_sys_abs.index_k
_refln_sys_abs.index_l
_refln_sys_abs.I
_refln_sys_abs.sigmaI
_refln_sys_abs.I_over_sigmaI
0 3 0 28.32 22.95 1.23
0 5 0 14.11 16.38 0.86
0 7 0 114.81 20.22 5.67
0 9 0 32.99 24.51 1.35
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refln_sys_abs.I
_item_description.description
; The measured value of the intensity in arbitrary units.
;
_item.name '_refln_sys_abs.I'
_item.category_id refln_sys_abs
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refln_sys_abs.I'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_related.related_name
_item_related.function_code '_refln_sys_abs.sigmaI'
associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code arbitrary
save_
save__refln_sys_abs.I_over_sigmaI
_item_description.description
; The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI. Used
to evaluate whether a reflection that should be systematically
absent according to the designated space group is in fact
absent.
;
_item.name '_refln_sys_abs.I_over_sigmaI'
_item.category_id refln_sys_abs
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refln_sys_abs.I_over_sigma'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refln_sys_abs.index_h
_item_description.description
; Miller index h of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to
the cell defined by cell lengths and cell angles in the CELL
category.
;
_item.name '_refln_sys_abs.index_h'
_item.category_id refln_sys_abs
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refln_sys_abs.h'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_dependent.dependent_name
'_refln_sys_abs.index_k'
'_refln_sys_abs.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln_sys_abs.index_k
_item_description.description
; Miller index k of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to the
cell defined by cell lengths and cell angles in the CELL
category.
;
_item.name '_refln_sys_abs.index_k'
_item.category_id refln_sys_abs
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refln_sys_abs.k'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_dependent.dependent_name
'_refln_sys_abs.index_h'
'_refln_sys_abs.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln_sys_abs.index_l
_item_description.description
; Miller index l of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to the
cell defined by cell lengths and cell angles in the CELL
category.
;
_item.name '_refln_sys_abs.index_l'
_item.category_id refln_sys_abs
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refln_sys_abs.l'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_dependent.dependent_name
'_refln_sys_abs.index_h'
'_refln_sys_abs.index_k'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln_sys_abs.sigmaI
_item_description.description
; The standard uncertainty (estimated standard deviation) of
_refln_sys_abs.I in arbitrary units.
;
_item.name '_refln_sys_abs.sigmaI'
_item.category_id refln_sys_abs
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refln_sys_abs.sigmaI'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_related.related_name
_item_related.function_code '_refln_sys_abs.I'
associated_value
_item_type.code float
_item_units.code arbitrary
save_
############
## REFLNS ##
############
save_reflns
_category.description
; Data items in the REFLNS category record details about the
reflection data used to determine the ATOM_SITE data items.
The REFLN data items refer to individual reflections and must
be included in looped lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
;
_category.id reflns
_category.mandatory_code no
_category_key.name '_reflns.entry_id'
loop_
_category_group.id 'inclusive_group'
'refln_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_reflns.entry_id '5HVP'
_reflns.data_reduction_method
; Xengen program scalei. Anomalous pairs were merged. Scaling
proceeded in several passes, beginning with 1-parameter
fit and ending with 3-parameter fit.
;
_reflns.data_reduction_details
; Merging and scaling based on only those reflections
with I > \s(I).
;
_reflns.d_resolution_high 2.00
_reflns.d_resolution_low 8.00
_reflns.limit_h_max 22
_reflns.limit_h_min 0
_reflns.limit_k_max 46
_reflns.limit_k_min 0
_reflns.limit_l_max 57
_reflns.limit_l_min 0
_reflns.number_obs 7228
_reflns.observed_criterion '> 1 \s(I)'
_reflns.details none
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_reflns.limit_h_min 0
_reflns.limit_h_max 6
_reflns.limit_k_min 0
_reflns.limit_k_max 17
_reflns.limit_l_min 0
_reflns.limit_l_max 22
_reflns.number_all 1592
_reflns.number_obs 1408
_reflns.observed_criterion F_>_6.0_\s(F)
_reflns.d_resolution_high 0.8733
_reflns.d_resolution_low 11.9202
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__reflns.B_iso_Wilson_estimate
_item_description.description
; The value of the overall isotropic displacement parameter
estimated from the slope of the Wilson plot.
;
_item.name '_reflns.B_iso_Wilson_estimate'
_item.category_id reflns
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms_squared
save_
save__reflns.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_reflns.entry_id'
_item.mandatory_code yes
save_
save__reflns.data_reduction_details
_item_description.description
; A description of special aspects of the data-reduction
procedures.
;
_item.name '_reflns.data_reduction_details'
_item.category_id reflns
_item.mandatory_code no
_item_type.code text
_item_examples.case
; Merging and scaling based on only those
reflections with I > sig(I).
;
save_
save__reflns.data_reduction_method
_item_description.description
; The method used for data reduction.
Note that this is not the computer program used, which is
described in the SOFTWARE category, but the method
itself.
This data item should be used to describe significant
methodological options used within the data-reduction programs.
;
_item.name '_reflns.data_reduction_method'
_item.category_id reflns
_item.mandatory_code no
_item_type.code text
_item_examples.case
; Profile fitting by method of Kabsch (1987).
Scaling used spherical harmonic coefficients.
;
save_
save__reflns.d_resolution_high
_item_description.description
; The smallest value for the interplanar spacings for
the reflection data. This is called the highest resolution.
;
_item.name '_reflns.d_resolution_high'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_d_resolution_high'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__reflns.d_resolution_low
_item_description.description
; The largest value for the interplanar spacings for the
reflection data. This is called the lowest resolution.
;
_item.name '_reflns.d_resolution_low'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_d_resolution_low'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__reflns.details
_item_description.description
; A description of reflection data not covered by other data
names. This should include details of the Friedel pairs.
;
_item.name '_reflns.details'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_special_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__reflns.limit_h_max
_item_description.description
; Maximum value of the Miller index h for the reflection data. This
need not have the same value as _diffrn_reflns.limit_h_max.
;
_item.name '_reflns.limit_h_max'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_h_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__reflns.limit_h_min
_item_description.description
; Minimum value of the Miller index h for the reflection data. This
need not have the same value as _diffrn_reflns.limit_h_min.
;
_item.name '_reflns.limit_h_min'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_h_min'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__reflns.limit_k_max
_item_description.description
; Maximum value of the Miller index k for the reflection data. This
need not have the same value as _diffrn_reflns.limit_k_max.
;
_item.name '_reflns.limit_k_max'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_k_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__reflns.limit_k_min
_item_description.description
; Minimum value of the Miller index k for the reflection data. This
need not have the same value as _diffrn_reflns.limit_k_min.
;
_item.name '_reflns.limit_k_min'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_k_min'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__reflns.limit_l_max
_item_description.description
; Maximum value of the Miller index l for the reflection data. This
need not have the same value as _diffrn_reflns.limit_l_max.
;
_item.name '_reflns.limit_l_max'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_l_max'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__reflns.limit_l_min
_item_description.description
; Minimum value of the Miller index l for the reflection data. This
need not have the same value as _diffrn_reflns.limit_l_min.
;
_item.name '_reflns.limit_l_min'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_limit_l_min'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__reflns.number_all
_item_description.description
; The total number of reflections in the REFLN list (not the
DIFFRN_REFLN list). This number may contain Friedel-equivalent
reflections according to the nature of the structure and the
procedures used. The item _reflns.details describes the
reflection data.
;
_item.name '_reflns.number_all'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_number_total'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__reflns.number_obs
_item_description.description
; The number of reflections in the REFLN list (not the DIFFRN_REFLN
list) classified as observed (see _reflns.observed_criterion).
This number may contain Friedel-equivalent reflections according
to the nature of the structure and the procedures used.
;
_item.name '_reflns.number_obs'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_number_observed'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__reflns.observed_criterion
_item_description.description
; The criterion used to classify a reflection as 'observed'. This
criterion is usually expressed in terms of a sigma(I) or
sigma(F) threshold.
;
_item.name '_reflns.observed_criterion'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_observed_criterion'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_related.related_name
_item_related.function_code '_reflns.observed_criterion_sigma_F'
alternate
'_reflns.observed_criterion_sigma_I'
alternate
'_reflns.observed_criterion_I_min'
alternate
'_reflns.observed_criterion_I_max'
alternate
'_reflns.observed_criterion_F_min'
alternate
'_reflns.observed_criterion_F_max'
alternate
_item_type.code text
_item_examples.case '>2sigma(I)'
save_
save__reflns.observed_criterion_F_max
_item_description.description
; The criterion used to classify a reflection as 'observed'
expressed as an upper limit for the value of F.
;
_item.name '_reflns.observed_criterion_F_max'
_item.category_id reflns
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_reflns.observed_criterion'
alternate
'_reflns.observed_criterion_I_max'
convention
_item_type.code float
save_
save__reflns.observed_criterion_F_min
_item_description.description
; The criterion used to classify a reflection as 'observed'
expressed as a lower limit for the value of F.
;
_item.name '_reflns.observed_criterion_F_min'
_item.category_id reflns
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_reflns.observed_criterion'
alternate
'_reflns.observed_criterion_I_min'
convention
_item_type.code float
save_
save__reflns.observed_criterion_I_max
_item_description.description
; The criterion used to classify a reflection as 'observed'
expressed as an upper limit for the value of I.
;
_item.name '_reflns.observed_criterion_I_max'
_item.category_id reflns
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_reflns.observed_criterion'
alternate
'_reflns.observed_criterion_F_max'
convention
_item_type.code float
save_
save__reflns.observed_criterion_I_min
_item_description.description
; The criterion used to classify a reflection as 'observed'
expressed as a lower limit for the value of I.
;
_item.name '_reflns.observed_criterion_I_min'
_item.category_id reflns
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_reflns.observed_criterion'
alternate
'_reflns.observed_criterion_F_min'
convention
_item_type.code float
save_
save__reflns.observed_criterion_sigma_F
_item_description.description
; The criterion used to classify a reflection as 'observed'
expressed as a multiple of the value of sigma(F).
;
_item.name '_reflns.observed_criterion_sigma_F'
_item.category_id reflns
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_reflns.observed_criterion'
alternate
'_reflns.observed_criterion_sigma_I'
convention
_item_type.code float
save_
save__reflns.observed_criterion_sigma_I
_item_description.description
; The criterion used to classify a reflection as 'observed'
expressed as a multiple of the value of sigma(I).
;
_item.name '_reflns.observed_criterion_sigma_I'
_item.category_id reflns
_item.mandatory_code no
loop_
_item_related.related_name
_item_related.function_code '_reflns.observed_criterion'
alternate
'_reflns.observed_criterion_sigma_F'
convention
_item_type.code float
save_
save__reflns.percent_possible_obs
_item_description.description
; The percentage of geometrically possible reflections represented
by reflections that satisfy the resolution limits established
by _reflns.d_resolution_high and _reflns.d_resolution_low and
the observation limit established by
_reflns.observed_criterion.
;
_item.name '_reflns.percent_possible_obs'
_item.category_id reflns
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__reflns.R_free_details
_item_description.description
; A description of the method by which a subset of reflections was
selected for exclusion from refinement so as to be used in the
calculation of a 'free' R factor.
;
_item.name '_reflns.R_free_details'
_item.category_id reflns
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The data set was sorted with l varying most
rapidly and h varying least rapidly. Every
10th reflection in this sorted list was
excluded from refinement and included in the
calculation of a 'free' R factor.
;
save_
save__reflns.Rmerge_F_all
_item_description.description
; Residual factor Rmerge for all reflections that satisfy the
resolution limits established by _reflns.d_resolution_high
and _reflns.d_resolution_low.
sum~i~(sum~j~|F~j~ - |)
Rmerge(F) = --------------------------
sum~i~(sum~j~)
F~j~ = the amplitude of the jth observation of reflection i
= the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
;
_item.name '_reflns.Rmerge_F_all'
_item.category_id reflns
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__reflns.Rmerge_F_obs
_item_description.description
; Residual factor Rmerge for reflections that satisfy the
resolution limits established by _reflns.d_resolution_high
and _reflns.d_resolution_low and the observation limit
established by _reflns.observed_criterion.
sum~i~(sum~j~|F~j~ - |)
Rmerge(F) = --------------------------
sum~i~(sum~j~)
F~j~ = the amplitude of the jth observation of reflection i
= the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
;
_item.name '_reflns.Rmerge_F_obs'
_item.category_id reflns
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
##################
## REFLNS_SCALE ##
##################
save_reflns_scale
_category.description
; Data items in the REFLNS_SCALE category record details about
the structure-factor scales. They are referenced from within
the REFLN list through _refln.scale_group_code.
;
_category.id reflns_scale
_category.mandatory_code no
_category_key.name '_reflns_scale.group_code'
loop_
_category_group.id 'inclusive_group'
'refln_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for the collagen-like
peptide [(POG)4 EKG (POG)5]3.
;
;
_reflns_scale.group_code SG1
_reflns_scale.meas_F 4.0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__reflns_scale.group_code
_item_description.description
; The code identifying a scale _reflns_scale.meas_F,
_reflns_scale.meas_F_squared or _reflns_scale.meas_intensity.
These are linked to the REFLN list by the
_refln.scale_group_code. These codes
need not correspond to those in the DIFFRN_SCALE list.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_reflns_scale.group_code' reflns_scale yes
'_refln.scale_group_code' refln yes
_item_aliases.alias_name '_reflns_scale_group_code'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_linked.child_name
_item_linked.parent_name
'_refln.scale_group_code' '_reflns_scale.group_code'
_item_type.code line
loop_
_item_examples.case '1'
'2'
'c1'
'c2'
save_
save__reflns_scale.meas_F
_item_description.description
; A scale associated with _reflns_scale.group_code.
;
_item.name '_reflns_scale.meas_F'
_item.category_id reflns_scale
_item.mandatory_code no
_item_aliases.alias_name '_reflns_scale_meas_F'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__reflns_scale.meas_F_squared
_item_description.description
; A scale associated with _reflns_scale.group_code.
;
_item.name '_reflns_scale.meas_F_squared'
_item.category_id reflns_scale
_item.mandatory_code no
_item_aliases.alias_name '_reflns_scale_meas_F_squared'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__reflns_scale.meas_intensity
_item_description.description
; A scale associated with _reflns_scale.group_code.
;
_item.name '_reflns_scale.meas_intensity'
_item.category_id reflns_scale
_item.mandatory_code no
_item_aliases.alias_name '_reflns_scale_meas_intensity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
##################
## REFLNS_SHELL ##
##################
save_reflns_shell
_category.description
; Data items in the REFLNS_SHELL category record details about
the reflection data used to determine the ATOM_SITE data items
broken down into shells of resolution.
;
_category.id reflns_shell
_category.mandatory_code no
loop_
_category_key.name '_reflns_shell.d_res_high'
'_reflns_shell.d_res_low'
loop_
_category_group.id 'inclusive_group'
'refln_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_reflns_shell.d_res_high
_reflns_shell.d_res_low
_reflns_shell.meanI_over_sigI_obs
_reflns_shell.number_measured_obs
_reflns_shell.number_unique_obs
_reflns_shell.percent_possible_obs
_reflns_shell.Rmerge_F_obs
31.38 3.82 69.8 9024 2540 96.8 1.98
3.82 3.03 26.1 7413 2364 95.1 3.85
3.03 2.65 10.5 5640 2123 86.2 6.37
2.65 2.41 6.4 4322 1882 76.8 8.01
2.41 2.23 4.3 3247 1714 70.4 9.86
2.23 2.10 3.1 1140 812 33.3 13.99
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__reflns_shell.d_res_high
_item_description.description
; The smallest value in angstroms for the interplanar spacings
for the reflections in this shell. This is called the highest
resolution.
;
_item.name '_reflns_shell.d_res_high'
_item.category_id reflns_shell
_item.mandatory_code yes
_item_aliases.alias_name '_reflns_shell_d_res_high'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__reflns_shell.d_res_low
_item_description.description
; The highest value in angstroms for the interplanar spacings
for the reflections in this shell. This is called the lowest
resolution.
;
_item.name '_reflns_shell.d_res_low'
_item.category_id reflns_shell
_item.mandatory_code yes
_item_aliases.alias_name '_reflns_shell_d_res_low'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__reflns_shell.meanI_over_sigI_all
_item_description.description
; The ratio of the mean of the intensities of all reflections
in this shell to the mean of the standard uncertainties of the
intensities of all reflections in this shell.
;
_item.name '_reflns_shell.meanI_over_sigI_all'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_meanI_over_sigI_all'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
save_
save__reflns_shell.meanI_over_sigI_obs
_item_description.description
; The ratio of the mean of the intensities of the reflections
classified as 'observed' (see _reflns.observed_criterion) in
this shell to the mean of the standard uncertainties of the
intensities of the 'observed' reflections in this
shell.
;
_item.name '_reflns_shell.meanI_over_sigI_obs'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_meanI_over_sigI_obs'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code float
save_
save__reflns_shell.number_measured_all
_item_description.description
; The total number of reflections measured for this
shell.
;
_item.name '_reflns_shell.number_measured_all'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_number_measured_all'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__reflns_shell.number_measured_obs
_item_description.description
; The number of reflections classified as 'observed'
(see _reflns.observed_criterion) for this
shell.
;
_item.name '_reflns_shell.number_measured_obs'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_number_measured_obs'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__reflns_shell.number_possible
_item_description.description
; The number of unique reflections it is possible to measure in
this shell.
;
_item.name '_reflns_shell.number_possible'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_number_possible'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__reflns_shell.number_unique_all
_item_description.description
; The total number of measured reflections which are symmetry-
unique after merging for this shell.
;
_item.name '_reflns_shell.number_unique_all'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_number_unique_all'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__reflns_shell.number_unique_obs
_item_description.description
; The total number of measured reflections classified as 'observed'
(see _reflns.observed_criterion) which are symmetry-unique
after merging for this shell.
;
_item.name '_reflns_shell.number_unique_obs'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_number_unique_obs'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__reflns_shell.percent_possible_all
_item_description.description
; The percentage of geometrically possible reflections represented
by all reflections measured for this shell.
;
_item.name '_reflns_shell.percent_possible_all'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_percent_possible_all'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__reflns_shell.percent_possible_obs
_item_description.description
; The percentage of geometrically possible reflections represented
by reflections classified as 'observed' (see
_reflns.observed_criterion) for this shell.
;
_item.name '_reflns_shell.percent_possible_obs'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_percent_possible_obs'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__reflns_shell.Rmerge_F_all
_item_description.description
; Residual factor Rmerge for all reflections that satisfy the
resolution limits established by _reflns_shell.d_res_high and
_reflns_shell.d_res_low.
sum~i~(sum~j~|F~j~ - |)
Rmerge(F) = --------------------------
sum~i~(sum~j~)
F~j~ = the amplitude of the jth observation of reflection i
= the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
;
_item.name '_reflns_shell.Rmerge_F_all'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_Rmerge_F_all'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__reflns_shell.Rmerge_F_obs
_item_description.description
; Residual factor Rmerge for reflections that satisfy the
resolution limits established by _reflns_shell.d_res_high and
_reflns_shell.d_res_low and the observation criterion
established by _reflns.observed_criterion.
sum~i~(sum~j~|F~j~ - |)
Rmerge(F) = --------------------------
sum~i~(sum~j~)
F~j~ = the amplitude of the jth observation of reflection i
= the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
;
_item.name '_reflns_shell.Rmerge_F_obs'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_Rmerge_F_obs'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__reflns_shell.Rmerge_I_all
_item_description.description
; The value of Rmerge(I) for all reflections in a given shell.
sum~i~(sum~j~|I~j~ - |)
Rmerge(I) = --------------------------
sum~i~(sum~j~)
I~j~ = the intensity of the jth observation of reflection i
= the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
;
_item.name '_reflns_shell.Rmerge_I_all'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_Rmerge_I_all'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__reflns_shell.Rmerge_I_obs
_item_description.description
; The value of Rmerge(I) for reflections classified as 'observed'
(see _reflns.observed_criterion) in a given shell.
sum~i~(sum~j~|I~j~ - |)
Rmerge(I) = --------------------------
sum~i~(sum~j~)
I~j~ = the intensity of the jth observation of reflection i
= the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection
;
_item.name '_reflns_shell.Rmerge_I_obs'
_item.category_id reflns_shell
_item.mandatory_code no
_item_aliases.alias_name '_reflns_shell_Rmerge_I_obs'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
##############
## SOFTWARE ##
##############
save_software
_category.description
; Data items in the SOFTWARE category record details about
the software used in the structure analysis, which implies
any software used in the generation of any data items
associated with the structure determination and
structure representation.
These data items allow computer programs to be referenced
in more detail than data items in the COMPUTING category do.
;
_category.id software
_category.mandatory_code no
loop_
_category_key.name '_software.name'
'_software.version'
loop_
_category_group.id 'inclusive_group'
'computing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_software.name
_software.version
_software.date
_software.type
_software.contact_author
_software.contact_author_email
_software.location
_software.classification
_software.citation_id
_software.language
_software.compiler_name
_software.compiler_version
_software.hardware
_software.os
_software.os_version
_software.dependencies
_software.mods
_software.description
Prolsq unknown . program 'Wayne A. Hendrickson' ?
'ftp://rosebud.sdsc.edu/pub/sdsc/xtal/CCP4/ccp4/'
refinement ref5 Fortran
'Convex Fortran' v8.0 'Convex C220' ConvexOS v10.1
'Requires that Protin be run first' optimized
'restrained least-squares refinement'
;
save_
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save__software.citation_id
_item_description.description
; This data item is a pointer to _citation.id in the CITATION
category.
;
_item.name '_software.citation_id'
_item.mandatory_code no
save_
save__software.classification
_item_description.description
; The classification of the program according to its
major function.
;
_item.name '_software.classification'
_item.category_id software
_item.mandatory_code no
_item_type.code uline
loop_
_item_examples.case 'data collection'
'data reduction'
'phasing'
'model building'
'refinement'
'validation'
'other'
save_
save__software.compiler_name
_item_description.description
; The compiler used to compile the software.
;
_item.name '_software.compiler_name'
_item.category_id software
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'Convex Fortran'
'gcc'
'DEC C'
save_
save__software.compiler_version
_item_description.description
; The version of the compiler used to compile the software.
;
_item.name '_software.compiler_version'
_item.category_id software
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case '3.1'
'2.1 alpha'
save_
save__software.contact_author
_item_description.description
; The recognized contact author of the software. This could be
the original author, someone who has modified the code or
someone who maintains the code. It should be the person
most commonly associated with the code.
;
_item.name '_software.contact_author'
_item.category_id software
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'T. Alwyn Jones'
'Axel Brunger'
save_
save__software.contact_author_email
_item_description.description
; The e-mail address of the person specified in
_software.contact_author.
;
_item.name '_software.contact_author_email'
_item.category_id software
_item.mandatory_code no
_item_type.code line
_item_examples.case 'bourne@sdsc.edu'
save_
save__software.date
_item_description.description
; The date the software was released.
;
_item.name '_software.date'
_item.category_id software
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 1991-10-01
1990-04-30
save_
save__software.description
_item_description.description
; Description of the software.
;
_item.name '_software.description'
_item.category_id software
_item.mandatory_code no
_item_type.code line
_item_examples.case 'Uses method of restrained least squares'
save_
save__software.dependencies
_item_description.description
; Any prerequisite software required to run _software.name.
;
_item.name '_software.dependencies'
_item.category_id software
_item.mandatory_code no
_item_type.code line
_item_examples.case 'PDBlib class library'
save_
save__software.hardware
_item_description.description
; The hardware upon which the software was run.
;
_item.name '_software.hardware'
_item.category_id software
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'Sun Sparc 10 model 41'
'Dec Alpha 3000 model 500S'
'Silicon Graphics Elan'
'Compaq PC 486/66'
save_
save__software.language
_item_description.description
; The major computing language in which the software is
coded.
;
_item.name '_software.language'
_item.category_id software
_item.mandatory_code no
_item_type.code uline
loop_
_item_enumeration.value Ada
assembler
Awk
Basic
'C++'
'C/C++'
C
csh
Fortran
Fortran_77
'Fortran 77'
'Fortran 90'
Java
ksh
Pascal
Perl
Python
sh
Tcl
Other
save_
save__software.location
_item_description.description
; The URL for an Internet address at which
details of the software can be found.
;
_item.name '_software.location'
_item.category_id software
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'http://rosebud.sdsc.edu/projects/pb/IUCr/software.html'
'ftp://ftp.sdsc.edu/pub/sdsc/biology/'
save_
save__software.mods
_item_description.description
; Any noteworthy modifications to the base software, if applicable.
;
_item.name '_software.mods'
_item.category_id software
_item.mandatory_code no
_item_type.code line
_item_examples.case 'Added support for space group F432'
save_
save__software.name
_item_description.description
; The name of the software.
;
_item.name '_software.name'
_item.category_id software
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'Merlot'
'O'
'Xengen'
'X-plor'
save_
save__software.os
_item_description.description
; The name of the operating system under which the software
runs.
;
_item.name '_software.os'
_item.category_id software
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'Ultrix'
'OpenVMS'
'DOS'
'Windows 95'
'Windows NT'
'Irix'
'HPUX'
'DEC Unix'
save_
save__software.os_version
_item_description.description
; The version of the operating system under which the software
runs.
;
_item.name '_software.os_version'
_item.category_id software
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case '3.1'
'4.2.1'
save_
save__software.type
_item_description.description
; The classification of the software according to the most
common types.
;
_item.name '_software.type'
_item.category_id software
_item.mandatory_code no
_item_type.code uline
loop_
_item_enumeration.value
_item_enumeration.detail program
; individual program with limited
functionality
;
library
; used by a program at load time
;
package
; collections of programs with multiple
functionality
;
filter
; filters input and output streams
;
jiffy
; short, simple program
;
other
; all other kinds of software
;
save_
save__software.version
_item_description.description
; The version of the software.
;
_item.name '_software.version'
_item.category_id software
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case 'v1.0'
'beta'
'3.1-2'
'unknown'
save_
############
## STRUCT ##
############
save_struct
_category.description
; Data items in the STRUCT category record details about the
description of the crystallographic structure.
;
_category.id struct
_category.mandatory_code no
_category_key.name '_struct.entry_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_struct.entry_id '5HVP'
_struct.title
; HIV-1 protease complex with acetyl-pepstatin
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_struct.entry_id'
_item.mandatory_code yes
save_
save__struct.title
_item_description.description
; A title for the data block. The author should attempt to convey
the essence of the structure archived in the CIF in the title,
and to distinguish this structural result from others.
;
_item.name '_struct.title'
_item.category_id struct
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case '5'-D(*(I)CP*CP*GP*G)-3'
'T4 lysozyme mutant - S32A'
'hen egg white lysozyme at -30 degrees C'
'quail egg white lysozyme at 2 atmospheres'
save_
#################
## STRUCT_ASYM ##
#################
save_struct_asym
_category.description
; Data items in the STRUCT_ASYM category record details about the
structural elements in the asymmetric unit.
;
_category.id struct_asym
_category.mandatory_code no
_category_key.name '_struct_asym.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_asym.id
_struct_asym.entity_id
_struct_asym.details
A 1 'one monomer of the dimeric enzyme'
B 1 'one monomer of the dimeric enzyme'
C 2 'one partially occupied position for the inhibitor'
D 2 'one partially occupied position for the inhibitor'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_asym.details
_item_description.description
; A description of special aspects of this portion of the contents
of the asymmetric unit.
;
_item.name '_struct_asym.details'
_item.category_id struct_asym
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The drug binds to this enzyme in two roughly
twofold symmetric modes. Hence this
biological unit (3) is roughly twofold
symmetric to biological unit (2). Disorder in
the protein chain indicated with alternative
ID 2 should be used with this biological unit.
;
save_
save__struct_asym.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_struct_asym.entity_id'
_item.mandatory_code yes
save_
save__struct_asym.id
_item_description.description
; The value of _struct_asym.id must uniquely identify a record in
the STRUCT_ASYM list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_asym.id' struct_asym yes
'_atom_site.label_asym_id' atom_site no
'_geom_angle.atom_site_label_asym_id_1' geom_angle no
'_geom_angle.atom_site_label_asym_id_2' geom_angle no
'_geom_angle.atom_site_label_asym_id_3' geom_angle no
'_geom_bond.atom_site_label_asym_id_1' geom_bond no
'_geom_bond.atom_site_label_asym_id_2' geom_bond no
'_geom_contact.atom_site_label_asym_id_1' geom_contact no
'_geom_contact.atom_site_label_asym_id_2' geom_contact no
'_geom_hbond.atom_site_label_asym_id_A' geom_hbond no
'_geom_hbond.atom_site_label_asym_id_D' geom_hbond no
'_geom_hbond.atom_site_label_asym_id_H' geom_hbond no
'_geom_torsion.atom_site_label_asym_id_1' geom_torsion no
'_geom_torsion.atom_site_label_asym_id_2' geom_torsion no
'_geom_torsion.atom_site_label_asym_id_3' geom_torsion no
'_geom_torsion.atom_site_label_asym_id_4' geom_torsion no
'_struct_biol_gen.asym_id' struct_biol_gen yes
'_struct_conf.beg_label_asym_id' struct_conf yes
'_struct_conf.end_label_asym_id' struct_conf yes
'_struct_conn.ptnr1_label_asym_id' struct_conn yes
'_struct_conn.ptnr2_label_asym_id' struct_conn yes
'_struct_mon_nucl.label_asym_id' struct_mon_nucl yes
'_struct_mon_prot.label_asym_id' struct_mon_prot yes
'_struct_mon_prot_cis.label_asym_id' struct_mon_prot_cis yes
'_struct_ncs_dom_lim.beg_label_asym_id' struct_ncs_dom_lim yes
'_struct_ncs_dom_lim.end_label_asym_id' struct_ncs_dom_lim yes
'_struct_sheet_range.beg_label_asym_id' struct_sheet_range yes
'_struct_sheet_range.end_label_asym_id' struct_sheet_range yes
'_struct_site_gen.label_asym_id' struct_site_gen yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_atom_site.label_asym_id' '_struct_asym.id'
'_struct_biol_gen.asym_id' '_struct_asym.id'
'_geom_angle.atom_site_label_asym_id_1' '_atom_site.label_asym_id'
'_geom_angle.atom_site_label_asym_id_2' '_atom_site.label_asym_id'
'_geom_angle.atom_site_label_asym_id_3' '_atom_site.label_asym_id'
'_geom_bond.atom_site_label_asym_id_1' '_atom_site.label_asym_id'
'_geom_bond.atom_site_label_asym_id_2' '_atom_site.label_asym_id'
'_geom_contact.atom_site_label_asym_id_1' '_atom_site.label_asym_id'
'_geom_contact.atom_site_label_asym_id_2' '_atom_site.label_asym_id'
'_geom_hbond.atom_site_label_asym_id_A' '_atom_site.label_asym_id'
'_geom_hbond.atom_site_label_asym_id_D' '_atom_site.label_asym_id'
'_geom_hbond.atom_site_label_asym_id_H' '_atom_site.label_asym_id'
'_geom_torsion.atom_site_label_asym_id_1' '_atom_site.label_asym_id'
'_geom_torsion.atom_site_label_asym_id_2' '_atom_site.label_asym_id'
'_geom_torsion.atom_site_label_asym_id_3' '_atom_site.label_asym_id'
'_geom_torsion.atom_site_label_asym_id_4' '_atom_site.label_asym_id'
'_struct_conf.beg_label_asym_id' '_atom_site.label_asym_id'
'_struct_conf.end_label_asym_id' '_atom_site.label_asym_id'
'_struct_conn.ptnr1_label_asym_id' '_atom_site.label_asym_id'
'_struct_conn.ptnr2_label_asym_id' '_atom_site.label_asym_id'
'_struct_mon_nucl.label_asym_id' '_atom_site.label_asym_id'
'_struct_mon_prot.label_asym_id' '_atom_site.label_asym_id'
'_struct_mon_prot_cis.label_asym_id' '_atom_site.label_asym_id'
'_struct_ncs_dom_lim.beg_label_asym_id' '_atom_site.label_asym_id'
'_struct_ncs_dom_lim.end_label_asym_id' '_atom_site.label_asym_id'
'_struct_sheet_range.beg_label_asym_id' '_atom_site.label_asym_id'
'_struct_sheet_range.end_label_asym_id' '_atom_site.label_asym_id'
'_struct_site_gen.label_asym_id' '_atom_site.label_asym_id'
_item_type.code code
loop_
_item_examples.case '1'
'A'
'2B3'
save_
#################
## STRUCT_BIOL ##
#################
save_struct_biol
_category.description
; Data items in the STRUCT_BIOL category record details about
the structural elements that form each structure of biological
significance.
A given crystal structure may contain many different biological
structures. A given structural component in the asymmetric
unit may be part of more than one biological unit. A given
biological structure may involve crystallographic symmetry.
For instance, in a structure of a lysozyme-FAB structure, the
light- and heavy-chain components of the FAB could be one
biological unit, while the two chains of the FAB and the lysozyme
could constitute a second biological unit.
;
_category.id struct_biol
_category.mandatory_code no
_category_key.name '_struct_biol.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_biol.id
_struct_biol.details
1
; significant deviations from twofold symmetry exist in this
dimeric enzyme
;
2
; The drug binds to this enzyme in two roughly twofold
symmetric modes. Hence this biological unit (2) is roughly
twofold symmetric to biological unit (3). Disorder in the
protein chain indicated with alternative ID 1 should be
used with this biological unit.
;
3
; The drug binds to this enzyme in two roughly twofold
symmetric modes. Hence this biological unit (3) is roughly
twofold symmetric to biological unit (2). Disorder in the
protein chain indicated with alternative ID 2 should be
used with this biological unit.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_biol.details
_item_description.description
; A description of special aspects of the biological unit.
;
_item.name '_struct_biol.details'
_item.category_id struct_biol
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The drug binds to this enzyme in two roughly
twofold symmetric modes. Hence this
biological unit (3) is roughly twofold
symmetric to biological unit (2). Disorder in
the protein chain indicated with alternative
ID 2 should be used with this biological unit.
;
save_
save__struct_biol.id
_item_description.description
; The value of _struct_biol.id must uniquely identify a record in
the STRUCT_BIOL list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_biol.id' struct_biol yes
'_struct_biol_gen.biol_id' struct_biol_gen yes
'_struct_biol_keywords.biol_id' struct_biol_keywords yes
'_struct_biol_view.biol_id' struct_biol_view yes
'_struct_ref.biol_id' struct_ref no
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_biol_gen.biol_id' '_struct_biol.id'
'_struct_biol_keywords.biol_id' '_struct_biol.id'
'_struct_biol_view.biol_id' '_struct_biol.id'
'_struct_ref.biol_id' '_struct_biol.id'
_item_type.code line
save_
#####################
## STRUCT_BIOL_GEN ##
#####################
save_struct_biol_gen
_category.description
; Data items in the STRUCT_BIOL_GEN category record details about
the generation of each biological unit. The STRUCT_BIOL_GEN
data items provide the specifications of the components that
constitute that biological unit, which may include symmetry
elements.
;
_category.id struct_biol_gen
_category.mandatory_code no
loop_
_category_key.name '_struct_biol_gen.biol_id'
'_struct_biol_gen.asym_id'
'_struct_biol_gen.symmetry'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_biol_gen.biol_id
_struct_biol_gen.asym_id
_struct_biol_gen.symmetry
1 A 1_555
1 B 1_555
2 A 1_555
2 B 1_555
2 C 1_555
3 A 1_555
3 B 1_555
3 D 1_555
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_biol_gen.asym_id
_item_description.description
; This data item is a pointer to _struct_asym.id in the STRUCT_ASYM
category.
;
_item.name '_struct_biol_gen.asym_id'
_item.mandatory_code yes
save_
save__struct_biol_gen.biol_id
_item_description.description
; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL
category.
;
_item.name '_struct_biol_gen.biol_id'
_item.mandatory_code yes
save_
save__struct_biol_gen.details
_item_description.description
; A description of special aspects of the symmetry generation of
this portion of the biological structure.
;
_item.name '_struct_biol_gen.details'
_item.category_id struct_biol_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The zinc atom lies on a special position;
application of symmetry elements to generate
the insulin hexamer will generate excess zinc
atoms, which must be removed by hand.
;
save_
save__struct_biol_gen.symmetry
_item_description.description
; Describes the symmetry operation that should be applied to the
atom set specified by _struct_biol_gen.asym_id to generate a
portion of the biological structure.
;
_item.name '_struct_biol_gen.symmetry'
_item.category_id struct_biol_gen
_item.mandatory_code yes
# _item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
##########################
## STRUCT_BIOL_KEYWORDS ##
##########################
save_struct_biol_keywords
_category.description
; Data items in the STRUCT_BIOL_KEYWORDS category record
keywords that describe each biological unit.
;
_category.id struct_biol_keywords
_category.mandatory_code no
loop_
_category_key.name '_struct_biol_keywords.biol_id'
'_struct_biol_keywords.text'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_biol_keywords.biol_id
_struct_biol_keywords.text
1 'aspartyl-protease'
1 'aspartic-protease'
1 'acid-protease'
1 'aspartyl-proteinase'
1 'aspartic-proteinase'
1 'acid-proteinase'
1 'enzyme'
1 'protease'
1 'proteinase'
1 'dimer'
2 'drug-enzyme complex'
2 'inhibitor-enzyme complex'
2 'drug-protease complex'
2 'inhibitor-protease complex'
3 'drug-enzyme complex'
3 'inhibitor-enzyme complex'
3 'drug-protease complex'
3 'inhibitor-protease complex'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_biol_keywords.biol_id
_item_description.description
; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL
category.
;
_item.name '_struct_biol_keywords.biol_id'
_item.mandatory_code yes
save_
save__struct_biol_keywords.text
_item_description.description
; Keywords describing this biological entity.
;
_item.name '_struct_biol_keywords.text'
_item.category_id struct_biol_keywords
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'antibody'
'antigen'
'enzyme'
'cytokine'
'tRNA'
save_
######################
## STRUCT_BIOL_VIEW ##
######################
save_struct_biol_view
_category.description
; Data items in the STRUCT_BIOL_VIEW category record details
about how to draw and annotate an informative view of the
biological structure.
;
_category.id struct_biol_view
_category.mandatory_code no
loop_
_category_key.name '_struct_biol_view.biol_id'
'_struct_biol_view.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on NDB structure GDL001 by Coll, Aymami,
Van Der Marel, Van Boom, Rich & Wang
[Biochemistry, (1989), 28, 310-320].
;
;
_struct_biol_view.biol_id c1
_struct_biol_view.id 1
_struct_biol_view.rot_matrix[1][1] 0.132
_struct_biol_view.rot_matrix[1][2] 0.922
_struct_biol_view.rot_matrix[1][3] -0.363
_struct_biol_view.rot_matrix[2][1] 0.131
_struct_biol_view.rot_matrix[2][2] -0.380
_struct_biol_view.rot_matrix[2][3] -0.916
_struct_biol_view.rot_matrix[3][1] -0.982
_struct_biol_view.rot_matrix[3][2] 0.073
_struct_biol_view.rot_matrix[3][3] -0.172
_struct_biol_view.details
; This view highlights the ATAT-Netropsin interaction in the
DNA-drug complex.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_biol_view.biol_id
_item_description.description
; This data item is a pointer to _struct_biol.id in the STRUCT_BIOL
category.
;
_item.name '_struct_biol_view.biol_id'
_item.mandatory_code yes
save_
save__struct_biol_view.details
_item_description.description
; A description of special aspects of this view of the biological
structure.
This data item can be used as a figure legend.
;
_item.name '_struct_biol_view.details'
_item.category_id struct_biol_view
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The enzyme has been oriented with the
molecular twofold axis aligned with the
horizontal axis of the figure.
;
save_
save__struct_biol_view.id
_item_description.description
; The value of _struct_biol_view.id must uniquely identify a
record in the STRUCT_BIOL_VIEW list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_struct_biol_view.id'
_item.category_id struct_biol_view
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case 'Figure 1'
'unliganded enzyme'
'view down enzyme active site'
save_
save__struct_biol_view.rot_matrix[1][1]
_item_description.description
; The [1][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
_struct_biol_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_biol_view.rot_matrix[1][1]'
_item.category_id struct_biol_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_biol_view.rot_matrix[1][2]
_item_description.description
; The [1][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
_struct_biol_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_biol_view.rot_matrix[1][2]'
_item.category_id struct_biol_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_biol_view.rot_matrix[1][3]
_item_description.description
; The [1][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
_struct_biol_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_biol_view.rot_matrix[1][3]'
_item.category_id struct_biol_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_biol_view.rot_matrix[2][1]
_item_description.description
; The [2][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
_struct_biol_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_biol_view.rot_matrix[2][1]'
_item.category_id struct_biol_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_biol_view.rot_matrix[2][2]
_item_description.description
; The [2][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
_struct_biol_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_biol_view.rot_matrix[2][2]'
_item.category_id struct_biol_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_biol_view.rot_matrix[2][3]
_item_description.description
; The [2][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
_struct_biol_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_biol_view.rot_matrix[2][3]'
_item.category_id struct_biol_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_biol_view.rot_matrix[3][1]
_item_description.description
; The [3][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
_struct_biol_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_biol_view.rot_matrix[3][1]'
_item.category_id struct_biol_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_biol_view.rot_matrix[3][2]
_item_description.description
; The [3][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
_struct_biol_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_biol_view.rot_matrix[3][2]'
_item.category_id struct_biol_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_biol_view.rot_matrix[3][3]
_item_description.description
; The [3][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_BIOL_GEN category to give a view useful for describing the
structure. The conventions used in the rotation are described in
_struct_biol_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_biol_view.rot_matrix[3][3]'
_item.category_id struct_biol_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
#################
## STRUCT_CONF ##
#################
save_struct_conf
_category.description
; Data items in the STRUCT_CONF category record details about
the backbone conformation of a segment of polymer.
Data items in the STRUCT_CONF_TYPE category define the
criteria used to identify the backbone conformations.
;
_category.id struct_conf
_category.mandatory_code no
_category_key.name '_struct_conf.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_conf.id
_struct_conf.conf_type_id
_struct_conf.beg_label_comp_id
_struct_conf.beg_label_asym_id
_struct_conf.beg_label_seq_id
_struct_conf.end_label_comp_id
_struct_conf.end_label_asym_id
_struct_conf.end_label_seq_id
_struct_conf.details
HELX1 HELX_RH_AL_P ARG A 87 GLN A 92 .
HELX2 HELX_RH_AL_P ARG B 287 GLN B 292 .
STRN1 STRN_P PRO A 1 LEU A 5 .
STRN2 STRN_P CYS B 295 PHE B 299 .
STRN3 STRN_P CYS A 95 PHE A 299 .
STRN4 STRN_P PRO B 201 LEU B 205 .
# - - - - data truncated for brevity - - - -
TURN1 TURN_TY1P_P ILE A 15 GLN A 18 .
TURN2 TURN_TY2_P GLY A 49 GLY A 52 .
TURN3 TURN_TY1P_P ILE A 55 HIS A 69 .
TURN4 TURN_TY1_P THR A 91 GLY A 94 .
# - - - - data truncated for brevity - - - -
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_conf.beg_label_asym_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_conf.beg_label_asym_id'
_item.mandatory_code yes
save_
save__struct_conf.beg_label_comp_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to _atom_site.label_comp_id in
the ATOM_SITE category.
;
_item.name '_struct_conf.beg_label_comp_id'
_item.mandatory_code yes
save_
save__struct_conf.beg_label_seq_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_conf.beg_label_seq_id'
_item.mandatory_code yes
save_
save__struct_conf.beg_auth_asym_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_conf.beg_auth_asym_id'
_item.mandatory_code no
save_
save__struct_conf.beg_auth_comp_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to _atom_site.auth_comp_id in
the ATOM_SITE category.
;
_item.name '_struct_conf.beg_auth_comp_id'
_item.mandatory_code no
save_
save__struct_conf.beg_auth_seq_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment begins.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_conf.beg_auth_seq_id'
_item.mandatory_code no
save_
save__struct_conf.conf_type_id
_item_description.description
; This data item is a pointer to _struct_conf_type.id in the
STRUCT_CONF_TYPE category.
;
_item.name '_struct_conf.conf_type_id'
_item.mandatory_code yes
save_
save__struct_conf.details
_item_description.description
; A description of special aspects of the conformation assignment.
;
_item.name '_struct_conf.details'
_item.category_id struct_conf
_item.mandatory_code no
_item_type.code text
save_
save__struct_conf.end_label_asym_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_conf.end_label_asym_id'
_item.mandatory_code yes
save_
save__struct_conf.end_label_comp_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_conf.end_label_comp_id'
_item.mandatory_code yes
save_
save__struct_conf.end_label_seq_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_conf.end_label_seq_id'
_item.mandatory_code yes
save_
save__struct_conf.end_auth_asym_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_conf.end_auth_asym_id'
_item.mandatory_code no
save_
save__struct_conf.end_auth_comp_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_conf.end_auth_comp_id'
_item.mandatory_code no
save_
save__struct_conf.end_auth_seq_id
_item_description.description
; A component of the identifier for the residue at which the
conformation segment ends.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_conf.end_auth_seq_id'
_item.mandatory_code no
save_
save__struct_conf.id
_item_description.description
; The value of _struct_conf.id must uniquely identify a record in
the STRUCT_CONF list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_struct_conf.id'
_item.category_id struct_conf
_item.mandatory_code yes
_item_type.code code
save_
######################
## STRUCT_CONF_TYPE ##
######################
save_struct_conf_type
_category.description
; Data items in the STRUCT_CONF_TYPE category record details
about the criteria used to identify backbone conformations of a
segment of polymer.
;
_category.id struct_conf_type
_category.mandatory_code no
_category_key.name '_struct_conf_type.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_conf_type.id
_struct_conf_type.criteria
_struct_conf_type.reference
HELX_RH_AL_P 'author judgement' .
STRN_P 'author judgement' .
TURN_TY1_P 'author judgement' .
TURN_TY1P_P 'author judgement' .
TURN_TY2_P 'author judgement' .
TURN_TY2P_P 'author judgement' .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_conf_type.criteria
_item_description.description
; The criteria used to assign this conformation type.
;
_item.name '_struct_conf_type.criteria'
_item.category_id struct_conf_type
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'author judgement'
'phi=54-74, psi=30-50'
save_
save__struct_conf_type.id
_item_description.description
; The descriptor that categorizes the type of the conformation
of the backbone of the polymer (whether protein or nucleic acid).
Explicit values for the torsion angles that define each
conformation are not given here, but it is expected that the
author would provide such information in either the
_struct_conf_type.criteria or _struct_conf_type.reference data
items, or both.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_conf_type.id' struct_conf_type yes
'_struct_conf.conf_type_id' struct_conf yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_conf.conf_type_id' '_struct_conf_type.id'
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail HELX_P
; helix with handedness and type not specified
(protein)
;
HELX_OT_P
; helix with handedness and type that do not
conform to an accepted category (protein)
;
#
HELX_RH_P
; right-handed helix with type not specified
(protein)
;
HELX_RH_OT_P
; right-handed helix with type that does not
conform to an accepted category (protein)
;
HELX_RH_AL_P
'right-handed alpha helix (protein)'
HELX_RH_GA_P
'right-handed gamma helix (protein)'
HELX_RH_OM_P
'right-handed omega helix (protein)'
HELX_RH_PI_P
'right-handed pi helix (protein)'
HELX_RH_27_P
'right-handed 2-7 helix (protein)'
HELX_RH_3T_P
'right-handed 3-10 helix (protein)'
HELX_RH_PP_P
'right-handed polyproline helix (protein)'
#
HELX_LH_P
; left-handed helix with type not specified
(protein)
;
HELX_LH_OT_P
; left-handed helix with type that does not
conform to an accepted category (protein)
;
HELX_LH_AL_P
'left-handed alpha helix (protein)'
HELX_LH_GA_P
'left-handed gamma helix (protein)'
HELX_LH_OM_P
'left-handed omega helix (protein)'
HELX_LH_PI_P
'left-handed pi helix (protein)'
HELX_LH_27_P
'left-handed 2-7 helix (protein)'
HELX_LH_3T_P
'left-handed 3-10 helix (protein)'
HELX_LH_PP_P
'left-handed polyproline helix (protein)'
#
HELX_N
; helix with handedness and type not specified
(nucleic acid)
;
HELX_OT_N
; helix with handedness and type that do not
conform to an accepted category (nucleic
acid)
;
#
HELX_RH_N
; right-handed helix with type not specified
(nucleic acid)
;
HELX_RH_OT_N
; right-handed helix with type that does not
conform to an accepted category (nucleic
acid)
;
HELX_RH_A_N
'right-handed A helix (nucleic acid)'
HELX_RH_B_N
'right-handed B helix (nucleic acid)'
HELX_RH_Z_N
'right-handed Z helix (nucleic acid)'
#
HELX_LH_N
; left-handed helix with type not specified
(nucleic acid)
;
HELX_LH_OT_N
; left-handed helix with type that does not
conform to an accepted category (nucleic
acid)
;
HELX_LH_A_N
'left-handed A helix (nucleic acid)'
HELX_LH_B_N
'left-handed B helix (nucleic acid)'
HELX_LH_Z_N
'left-handed Z helix (nucleic acid)'
#
TURN_P
'turn with type not specified (protein)'
TURN_OT_P
; turn with type that does not conform to an
accepted category (protein)
;
TURN_TY1_P
'type I turn (protein)'
TURN_TY1P_P
'type I prime turn (protein)'
TURN_TY2_P
'type II turn (protein)'
TURN_TY2P_P
'type II prime turn (protein)'
TURN_TY3_P
'type III turn (protein)'
TURN_TY3P_P
'type III prime turn (protein)'
#
STRN
'beta strand (protein)'
save_
save__struct_conf_type.reference
_item_description.description
; A literature reference that defines the criteria used to assign
this conformation type and subtype.
;
_item.name '_struct_conf_type.reference'
_item.category_id struct_conf_type
_item.mandatory_code no
_item_type.code text
save_
#################
## STRUCT_CONN ##
#################
save_struct_conn
_category.description
; Data items in the STRUCT_CONN category record details about
the connections between portions of the structure. These can be
hydrogen bonds, salt bridges, disulfide bridges and so on.
The STRUCT_CONN_TYPE records define the criteria used to
identify these connections.
;
_category.id struct_conn
_category.mandatory_code no
_category_key.name '_struct_conn.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_role
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_role
_struct_conn.ptnr2_symmetry
_struct_conn.details
C1 saltbr ARG A 87 NZ1 positive 1_555 GLU A 92 OE1
negative 1_555 .
C2 hydrog ARG B 287 N donor 1_555 GLY B 292 O
acceptor 1_555 .
# - - - - data truncated for brevity - - - -
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_conn.conn_type_id
_item_description.description
; This data item is a pointer to _struct_conn_type.id in the
STRUCT_CONN_TYPE category.
;
_item.name '_struct_conn.conn_type_id'
_item.mandatory_code yes
save_
save__struct_conn.details
_item_description.description
; A description of special aspects of the connection.
;
_item.name '_struct_conn.details'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code text
_item_examples.case 'disulfide bridge C-S-S-C is highly distorted'
save_
save__struct_conn.id
_item_description.description
; The value of _struct_conn.id must uniquely identify a record in
the STRUCT_CONN list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_struct_conn.id'
_item.category_id struct_conn
_item.mandatory_code yes
_item_type.code code
save_
save__struct_conn.ptnr1_label_alt_id
_item_description.description
; A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_struct_conn.ptnr1_label_alt_id'
_item.mandatory_code no
save_
save__struct_conn.ptnr1_label_asym_id
_item_description.description
; A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr1_label_asym_id'
_item.mandatory_code yes
save_
save__struct_conn.ptnr1_label_atom_id
_item_description.description
; A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_struct_conn.ptnr1_label_atom_id'
_item.mandatory_code yes
save_
save__struct_conn.ptnr1_label_comp_id
_item_description.description
; A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr1_label_comp_id'
_item.mandatory_code yes
save_
save__struct_conn.ptnr1_label_seq_id
_item_description.description
; A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr1_label_seq_id'
_item.mandatory_code yes
save_
save__struct_conn.ptnr1_auth_asym_id
_item_description.description
; A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr1_auth_asym_id'
_item.mandatory_code no
save_
save__struct_conn.ptnr1_auth_atom_id
_item_description.description
; A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr1_auth_atom_id'
_item.mandatory_code no
save_
save__struct_conn.ptnr1_auth_comp_id
_item_description.description
; A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr1_auth_comp_id'
_item.mandatory_code no
save_
save__struct_conn.ptnr1_auth_seq_id
_item_description.description
; A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr1_auth_seq_id'
_item.mandatory_code no
save_
save__struct_conn.ptnr1_role
_item_description.description
; The chemical or structural role of the first partner in
the structure connection.
;
_item.name '_struct_conn.ptnr1_role'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code uline
loop_
_item_examples.case 'donor'
'acceptor'
'negative'
'positive'
'metal'
'metal coordination'
save_
save__struct_conn.ptnr1_symmetry
_item_description.description
; Describes the symmetry operation that should be applied to the
atom set specified by _struct_conn.ptnr1_label* to generate the
first partner in the structure connection.
;
_item.name '_struct_conn.ptnr1_symmetry'
_item.category_id struct_conn
_item.mandatory_code no
# _item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__struct_conn.ptnr2_label_alt_id
_item_description.description
; A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_struct_conn.ptnr2_label_alt_id'
_item.mandatory_code no
save_
save__struct_conn.ptnr2_label_asym_id
_item_description.description
; A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr2_label_asym_id'
_item.mandatory_code yes
save_
save__struct_conn.ptnr2_label_atom_id
_item_description.description
; A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_struct_conn.ptnr2_label_atom_id'
_item.mandatory_code yes
save_
save__struct_conn.ptnr2_label_comp_id
_item_description.description
; A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr2_label_comp_id'
_item.mandatory_code yes
save_
save__struct_conn.ptnr2_label_seq_id
_item_description.description
; A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr2_label_seq_id'
_item.mandatory_code yes
save_
save__struct_conn.ptnr2_auth_asym_id
_item_description.description
; A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr2_auth_asym_id'
_item.mandatory_code no
save_
save__struct_conn.ptnr2_auth_atom_id
_item_description.description
; A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr2_auth_atom_id'
_item.mandatory_code no
save_
save__struct_conn.ptnr2_auth_comp_id
_item_description.description
; A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr2_auth_comp_id'
_item.mandatory_code no
save_
save__struct_conn.ptnr2_auth_seq_id
_item_description.description
; A component of the identifier for partner 2 of the structure
connection.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_conn.ptnr2_auth_seq_id'
_item.mandatory_code no
save_
save__struct_conn.ptnr2_role
_item_description.description
; The chemical or structural role of the second partner in
the structure connection.
;
_item.name '_struct_conn.ptnr2_role'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code uline
loop_
_item_examples.case 'donor'
'acceptor'
'negative'
'positive'
'metal'
'metal coordination'
save_
save__struct_conn.ptnr2_symmetry
_item_description.description
; Describes the symmetry operation that should be applied to the
atom set specified by _struct_conn.ptnr2_label* to generate the
second partner in the structure connection.
;
_item.name '_struct_conn.ptnr2_symmetry'
_item.category_id struct_conn
_item.mandatory_code no
# _item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
######################
## STRUCT_CONN_TYPE ##
######################
save_struct_conn_type
_category.description
; Data items in the STRUCT_CONN_TYPE category record details
about the criteria used to identify interactions between
portions of the structure.
;
_category.id struct_conn_type
_category.mandatory_code no
_category_key.name '_struct_conn_type.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_conn_type.id
_struct_conn_type.criteria
_struct_conn_type.reference
saltbr
'negative to positive distance > 2.5 \%A, < 3.2 \%A' .
hydrog
'NO distance > 2.5\%A, < 3.5\%A, NOC angle < 120 degrees' .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_conn_type.criteria
_item_description.description
; The criteria used to define the interaction.
;
_item.name '_struct_conn_type.criteria'
_item.category_id struct_conn_type
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'O to N distance > 2.5 \%A, < 3.2 \%A'
'authors judgement'
save_
save__struct_conn_type.id
_item_description.description
; The chemical or structural type of the interaction.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_conn_type.id' struct_conn_type yes
'_struct_conn.conn_type_id' struct_conn yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_conn.conn_type_id' '_struct_conn_type.id'
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail covale 'covalent bond'
disulf 'disulfide bridge'
hydrog 'hydrogen bond'
metalc 'metal coordination'
mismat 'mismatched base pairs'
saltbr 'ionic interaction'
modres 'covalent residue modification'
covale_base 'covalent modification of a nucleotide base'
covale_sugar 'covalent modification of a nucleotide sugar'
covale_phosphate 'covalent modification of a nucleotide phosphate'
save_
save__struct_conn_type.reference
_item_description.description
; A reference that specifies the criteria used to define the
interaction.
;
_item.name '_struct_conn_type.reference'
_item.category_id struct_conn_type
_item.mandatory_code no
_item_type.code text
save_
#####################
## STRUCT_KEYWORDS ##
#####################
save_struct_keywords
_category.description
; Data items in the STRUCT_KEYWORDS category specify keywords
that describe the chemical structure in this entry.
;
_category.id struct_keywords
_category.mandatory_code no
_category_key.name '_struct_keywords.entry_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_keywords.entry_id
_struct_keywords.text
'5HVP' 'enzyme-inhibitor complex, aspartyl protease, static disorder'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_keywords.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_struct_keywords.entry_id'
_item.mandatory_code yes
save_
save__struct_keywords.text
_item_description.description
; Keywords describing this structure.
;
_item.name '_struct_keywords.text'
_item.category_id struct_keywords
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'serine protease'
'inhibited complex'
'high-resolution refinement'
save_
########################
## STRUCT_MON_DETAILS ##
########################
save_struct_mon_details
_category.description
; Data items in the STRUCT_MON_DETAILS category record details
about specifics of calculations summarized in data items in the
STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can
include the coefficients used in map calculations,
the radii used for including points in a calculation and so on.
;
_category.id struct_mon_details
_category.mandatory_code no
_category_key.name '_struct_mon_details.entry_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
save_
save__struct_mon_details.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_struct_mon_details.entry_id'
_item.mandatory_code yes
save_
save__struct_mon_details.prot_cis
_item_description.description
; An ideal cis peptide bond would have an omega torsion angle of
zero. This data item gives the value in degrees by which the
observed torsion angle can differ from 0.0 and still be
considered cis.
;
_item.name '_struct_mon_details.prot_cis'
_item.category_id struct_mon_details
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_examples.case 30.0
save_
save__struct_mon_details.RSCC
_item_description.description
; This data item describes the specifics of the calculations that
generated the values given in _struct_mon_prot.RSCC_all,
_struct_mon_prot.RSCC_main and _struct_mon_prot.RSCC_side. The
coefficients used to calculate the p(o) and p(c) maps should be
given as well as the criterion for the inclusion of map grid
points in the calculation.
;
_item.name '_struct_mon_details.RSCC'
_item.category_id struct_mon_details
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
; The map p(o) was calculated with coefficients
2F(o) - F(c) and with phase alpha(c). F(o)
are the observed structure-factor amplitudes,
F(c) are the amplitudes calculated from the
current model and alpha(c) are the phases
calculated from the current model.
The map p(c) was calculated in program O using
a Gaussian distribution function around the
atoms in the current model.
Map grid points within 1.5 A of the
designated atoms were included in the
calculation.
;
; The map p(o) was calculated with coefficients
F(o) and with phase alpha(c). F(o) are the
observed structure-factor amplitudes, and
alpha(c) are the phases calculated from the
current model.
The map p(c) was calculated with coefficients
F(c) and with phases alpha(c). F(c) and
alpha(c) are the structure-factor amplitudes
and phases, respectively, calculated from the
current model.
Map grid points within a van der Waals radius
of the designated atoms were included in the
calculation.
;
save_
save__struct_mon_details.RSR
_item_description.description
; This data item describes the specifics of the calculations that
generated the values given in _struct_mon_prot.RSR_all,
_struct_mon_prot.RSR_main and _struct_mon_prot.RSR_side. The
coefficients used to calculate the p(o) and p(c) maps should be
given as well as the criterion for the inclusion of map grid
points in the calculation.
;
_item.name '_struct_mon_details.RSR'
_item.category_id struct_mon_details
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
; The map p(o) was calculated with coefficients
2F(o) - F(c) and with phase alpha(c). F(o)
are the observed structure-factor amplitudes,
F(c) are the amplitudes calculated from the
current model and alpha(c) are the phases
calculated from the current model.
The map p(c) was calculated in program O using
a Gaussian distribution function around the
atoms in the current model.
Map grid points within 1.5 A of the
designated atoms were included in the
calculation.
;
; The map p(o) was calculated with coefficients
F(o) and with phase alpha(c). F(o) are the
observed structure-factor amplitudes, and
alpha(c) are the phases calculated from the
current model.
The map p(c) was calculated with coefficients
F(c) and with phases alpha(c). F(c) and
alpha(c) are the structure-factor amplitudes
and phases, respectively, calculated from the
current model.
Map grid points within a van der Waals radius
of the designated atoms were included in the
calculation.
;
save_
#####################
## STRUCT_MON_NUCL ##
#####################
save_struct_mon_nucl
_category.description
; Data items in the STRUCT_MON_NUCL category record details about
structural properties of a nucleic acid when analyzed at the
monomer level. Analogous data items for proteins are given in
the STRUCT_MON_PROT category. For items where the value of the
property depends on the method employed to calculate it,
details of the method of calculation are given using data items
in the STRUCT_MON_DETAILS category.
;
_category.id struct_mon_nucl
_category.mandatory_code no
loop_
_category_key.name '_struct_mon_nucl.label_alt_id'
'_struct_mon_nucl.label_asym_id'
'_struct_mon_nucl.label_comp_id'
'_struct_mon_nucl.label_seq_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on NDB structure BDL028.
;
;
loop_
_struct_mon_nucl.label_comp_id
_struct_mon_nucl.label_seq_id
_struct_mon_nucl.label_asym_id
_struct_mon_nucl.label_alt_id
_struct_mon_nucl.alpha
_struct_mon_nucl.beta
_struct_mon_nucl.gamma
_struct_mon_nucl.delta
_struct_mon_nucl.epsilon
_struct_mon_nucl.zeta
C 1 A . . . 29.9 131.9 222.1 174.2
G 2 A . 334.0 130.6 33.1 125.6 167.6 270.9
T 3 A . 258.2 178.7 101.0 114.6 216.6 259.3
# ---- abbreviated list -----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_mon_nucl.alpha
_item_description.description
; The value in degrees of the backbone torsion angle alpha
(O3'-P-O5'-C5').
;
_item.name '_struct_mon_nucl.alpha'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.auth_asym_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_nucl.auth_asym_id'
_item.mandatory_code no
save_
save__struct_mon_nucl.auth_comp_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_nucl.auth_comp_id'
_item.mandatory_code no
save_
save__struct_mon_nucl.auth_seq_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_nucl.auth_seq_id'
_item.mandatory_code no
save_
save__struct_mon_nucl.beta
_item_description.description
; The value in degrees of the backbone torsion angle beta
(P-O5'-C5'-C4').
;
_item.name '_struct_mon_nucl.beta'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.chi1
_item_description.description
; The value in degrees of the sugar-base torsion angle chi1
(O4'-C1'-N1-C2).
;
_item.name '_struct_mon_nucl.chi1'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.chi2
_item_description.description
; The value in degrees of the sugar-base torsion angle chi2
(O4'-C1'-N9-C4).
;
_item.name '_struct_mon_nucl.chi2'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.delta
_item_description.description
; The value in degrees of the backbone torsion angle delta
(C5'-C4'-C3'-O3').
;
_item.name '_struct_mon_nucl.delta'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.details
_item_description.description
; A description of special aspects of the residue, its
conformation, behaviour in refinement, or any other aspect
that requires annotation.
;
_item.name '_struct_mon_nucl.details'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_examples.case
; Part of the phosphodiester backbone not in
density.
;
save_
save__struct_mon_nucl.epsilon
_item_description.description
; The value in degrees of the backbone torsion angle epsilon
(C4'-C3'-O3'-P).
;
_item.name '_struct_mon_nucl.epsilon'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.gamma
_item_description.description
; The value in degrees of the backbone torsion angle gamma
(O5'-C5'-C4'-C3').
;
_item.name '_struct_mon_nucl.gamma'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.label_alt_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_struct_mon_nucl.label_alt_id'
_item.mandatory_code yes
save_
save__struct_mon_nucl.label_asym_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_nucl.label_asym_id'
_item.mandatory_code yes
save_
save__struct_mon_nucl.label_comp_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_nucl.label_comp_id'
_item.mandatory_code yes
save_
save__struct_mon_nucl.label_seq_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_nucl.label_seq_id'
_item.mandatory_code yes
save_
save__struct_mon_nucl.mean_B_all
_item_description.description
; The mean value of the isotropic displacement parameter
for all atoms in the monomer.
;
_item.name '_struct_mon_nucl.mean_B_all'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.mean_B_base
_item_description.description
; The mean value of the isotropic displacement parameter
for atoms in the base moiety of the nucleic acid monomer.
;
_item.name '_struct_mon_nucl.mean_B_base'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.mean_B_phos
_item_description.description
; The mean value of the isotropic displacement parameter
for atoms in the phosphate moiety of the nucleic acid monomer.
;
_item.name '_struct_mon_nucl.mean_B_phos'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.mean_B_sugar
_item_description.description
; The mean value of the isotropic displacement parameter
for atoms in the sugar moiety of the nucleic acid monomer.
;
_item.name '_struct_mon_nucl.mean_B_sugar'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.nu0
_item_description.description
; The value in degrees of the sugar torsion angle nu0
(C4'-O4'-C1'-C2').
;
_item.name '_struct_mon_nucl.nu0'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.nu1
_item_description.description
; The value in degrees of the sugar torsion angle nu1
(O4'-C1'-C2'-C3').
;
_item.name '_struct_mon_nucl.nu1'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.nu2
_item_description.description
; The value in degrees of the sugar torsion angle nu2
(C1'-C2'-C3'-C4').
;
_item.name '_struct_mon_nucl.nu2'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.nu3
_item_description.description
; The value in degrees of the sugar torsion angle nu3
(C2'-C3'-C4'-O4').
;
_item.name '_struct_mon_nucl.nu3'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.nu4
_item_description.description
; The value in degrees of the sugar torsion angle nu4
(C3'-C4'-O4'-C1').
;
_item.name '_struct_mon_nucl.nu4'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.P
_item_description.description
; P is the phase angle of pseudorotation for five-membered rings.
For ribose and deoxyribose sugars in nucleic
acids
(tau4 +tau1)-(tau3+tau0)
P = ATAN (-------------------------)
2tau2 (sin 36+sin 72)
If tau2 is <0, then P=P+180 degree (Altona & Sundaralingam,
1972).
Ref: Altona, C. & Sundaralingam, M. (1972).
J. Am. Chem. Soc. 94, 8205-8212.
;
_item.name '_struct_mon_nucl.P'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.RSCC_all
_item_description.description
; The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms in the
nucleic acid monomer.
sum|p~obs~ - | * sum|p~calc~ - |
RSCC = -------------------------------------------------
[ sum|p~obs~ - |^2^
* sum|p~calc~ - |^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSCC. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in _struct_mon_details.RSCC.
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
;
_item.name '_struct_mon_nucl.RSCC_all'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.RSCC_base
_item_description.description
; The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms in the
base moiety of the nucleic acid monomer.
sum|p~obs~ - | * sum|p~calc~ - |
RSCC = -------------------------------------------------
[ sum|p~obs~ - |^2^
* sum|p~calc~ - |^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSCC. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in _struct_mon_details.RSCC.
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
;
_item.name '_struct_mon_nucl.RSCC_base'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.RSCC_phos
_item_description.description
; The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms in the
phosphate moiety of the nucleic acid monomer.
sum|p~obs~ - | * sum|p~calc~ - |
RSCC = -------------------------------------------------
[ sum|p~obs~ - |^2^
* sum|p~calc~ - |^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSCC. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in _struct_mon_details.RSCC.
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
;
_item.name '_struct_mon_nucl.RSCC_phos'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.RSCC_sugar
_item_description.description
; The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms in the
sugar moiety of the nucleic acid monomer.
sum|p~obs~ - | * sum|p~calc~ - |
RSCC = -------------------------------------------------
[ sum|p~obs~ - |^2^
* sum|p~calc~ - |^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSCC. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in _struct_mon_details.RSCC.
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
;
_item.name '_struct_mon_nucl.RSCC_sugar'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.RSR_all
_item_description.description
; The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the nucleic acid monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSR. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
_struct_mon_details.RSR.
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
;
_item.name '_struct_mon_nucl.RSR_all'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.RSR_base
_item_description.description
; The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the base moiety of the
nucleic acid monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSR. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
_struct_mon_details.RSR.
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
;
_item.name '_struct_mon_nucl.RSR_base'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.RSR_phos
_item_description.description
; The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the phosphate moiety of the
nucleic acid monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSR. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
_struct_mon_details.RSR.
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
;
_item.name '_struct_mon_nucl.RSR_phos'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.RSR_sugar
_item_description.description
; The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the sugar moiety of the
nucleic acid monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSR. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
_struct_mon_details.RSR.
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
;
_item.name '_struct_mon_nucl.RSR_sugar'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_nucl.tau0
_item_description.description
; The value in degrees of the sugar torsion angle tau0
(C4'-O4'-C1'-C2').
;
_item.name '_struct_mon_nucl.tau0'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.tau1
_item_description.description
; The value in degrees of the sugar torsion angle tau1
(O4'-C1'-C2'-C3').
;
_item.name '_struct_mon_nucl.tau1'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.tau2
_item_description.description
; The value in degrees of the sugar torsion angle tau2
(C1'-C2'-C3'-C4').
;
_item.name '_struct_mon_nucl.tau2'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.tau3
_item_description.description
; The value in degrees of the sugar torsion angle tau3
(C2'-C3'-C4'-O4').
;
_item.name '_struct_mon_nucl.tau3'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.tau4
_item_description.description
; The value in degrees of the sugar torsion angle tau4
(C3'-C4'-O4'-C1').
;
_item.name '_struct_mon_nucl.tau4'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.taum
_item_description.description
; The maximum amplitude of puckering. This is derived from the
pseudorotation value P and the torsion angles in the ribose
ring.
Tau2= Taum cosP
Tau3= Taum cos(P+144)
Tau4= Taum cos(P+288)
Tau0= Taum cos(P+ 72)
Tau1= Taum cos(P+216)
;
_item.name '_struct_mon_nucl.taum'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_nucl.zeta
_item_description.description
; The value in degrees of the backbone torsion angle zeta
(C3'-O3'-P-O5').
;
_item.name '_struct_mon_nucl.zeta'
_item.category_id struct_mon_nucl
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
#####################
## STRUCT_MON_PROT ##
#####################
save_struct_mon_prot
_category.description
; Data items in the STRUCT_MON_PROT category record details about
structural properties of a protein when analyzed at the monomer
level. Analogous data items for nucleic acids are given in the
STRUCT_MON_NUCL category. For items where the value of the
property depends on the method employed to calculate it,
details of the method of calculation are given using data items
in the STRUCT_MON_DETAILS category.
;
_category.id struct_mon_prot
_category.mandatory_code no
loop_
_category_key.name '_struct_mon_prot.label_alt_id'
'_struct_mon_prot.label_asym_id'
'_struct_mon_prot.label_comp_id'
'_struct_mon_prot.label_seq_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for protein NS1.
This example provides details for residue ARG 35.
;
;
_struct_mon_prot.label_comp_id ARG
_struct_mon_prot.label_seq_id 35
_struct_mon_prot.label_asym_id A
_struct_mon_prot.label_alt_id .
_struct_mon_prot.chi1 -67.9
_struct_mon_prot.chi2 -174.7
_struct_mon_prot.chi3 -67.7
_struct_mon_prot.chi4 -86.3
_struct_mon_prot.chi5 4.2
_struct_mon_prot.RSCC_all 0.90
_struct_mon_prot.RSR_all 0.18
_struct_mon_prot.mean_B_all 30.0
_struct_mon_prot.mean_B_main 25.0
_struct_mon_prot.mean_B_side 35.1
_struct_mon_prot.omega 180.1
_struct_mon_prot.phi -60.3
_struct_mon_prot.psi -46.0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_mon_prot.chi1
_item_description.description
; The value in degrees of the side-chain torsion angle chi1, for
those residues containing such an angle.
;
_item.name '_struct_mon_prot.chi1'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_prot.chi2
_item_description.description
; The value in degrees of the side-chain torsion angle chi2, for
those residues containing such an angle.
;
_item.name '_struct_mon_prot.chi2'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_prot.chi3
_item_description.description
; The value in degrees of the side-chain torsion angle chi3, for
those residues containing such an angle.
;
_item.name '_struct_mon_prot.chi3'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_prot.chi4
_item_description.description
; The value in degrees of the side-chain torsion angle chi4, for
those residues containing such an angle.
;
_item.name '_struct_mon_prot.chi4'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_prot.chi5
_item_description.description
; The value in degrees of the side-chain torsion angle chi5, for
those residues containing such an angle.
;
_item.name '_struct_mon_prot.chi5'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_prot.details
_item_description.description
; A description of special aspects of the residue, its
conformation, behaviour in refinement, or any other aspect that
requires annotation.
;
_item.name '_struct_mon_prot.details'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case 'very poor density'
; The side chain of this density may occupy
alternative conformations, but alternative
conformations were not fit in this model.
;
; This residue has a close contact with the
bound inhibitor, which may account for
the nonstandard conformation of the side
chain.
;
save_
save__struct_mon_prot.label_alt_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_struct_mon_prot.label_alt_id'
_item.mandatory_code yes
save_
save__struct_mon_prot.label_asym_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot.label_asym_id'
_item.mandatory_code yes
save_
save__struct_mon_prot.label_comp_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot.label_comp_id'
_item.mandatory_code yes
save_
save__struct_mon_prot.label_seq_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot.label_seq_id'
_item.mandatory_code yes
save_
save__struct_mon_prot.auth_asym_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot.auth_asym_id'
_item.mandatory_code no
save_
save__struct_mon_prot.auth_comp_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot.auth_comp_id'
_item.mandatory_code no
save_
save__struct_mon_prot.auth_seq_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot.auth_seq_id'
_item.mandatory_code no
save_
save__struct_mon_prot.RSCC_all
_item_description.description
; The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms
in the monomer.
sum|p~obs~ - | * sum|p~calc~ - |
RSCC = -------------------------------------------------
[ sum|p~obs~ - |^2^
* sum|p~calc~ - |^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSCC. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in _struct_mon_details.RSCC.
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
;
_item.name '_struct_mon_prot.RSCC_all'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_prot.RSCC_main
_item_description.description
; The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms
in the main chain of the monomer.
sum|p~obs~ - | * sum|p~calc~ - |
RSCC = -------------------------------------------------
[ sum|p~obs~ - |^2^
* sum|p~calc~ - |^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSCC. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in _struct_mon_details.RSCC.
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
;
_item.name '_struct_mon_prot.RSCC_main'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_prot.RSCC_side
_item_description.description
; The real-space (linear) correlation coefficient RSCC, as
described by Jones et al. (1991), evaluated over all atoms
in the side chain of the monomer.
sum|p~obs~ - | * sum|p~calc~ - |
RSCC = -------------------------------------------------
[ sum|p~obs~ - |^2^
* sum|p~calc~ - |^2^ ]^1/2^
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSCC. < > indicates an average and the
sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should
also be given in _struct_mon_details.RSCC.
Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M.
(1991). Acta Cryst. A47, 110-119.
;
_item.name '_struct_mon_prot.RSCC_side'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_prot.RSR_all
_item_description.description
; The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSR. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
_struct_mon_details.RSR.
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
;
_item.name '_struct_mon_prot.RSR_all'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_prot.RSR_main
_item_description.description
; The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the main chain of the
monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSR. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
_struct_mon_details.RSR.
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
;
_item.name '_struct_mon_prot.RSR_main'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_prot.RSR_side
_item_description.description
; The real-space residual RSR, as described by Branden & Jones
(1990), evaluated over all atoms in the side chain of the
monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an 'experimental' map
p~calc~ = the density in a 'calculated' map
sum is taken over the specified grid points
Details of how these maps were calculated should be given
in _struct_mon_details.RSR. The sums are taken over all map grid
points near the relevant atoms. The radius for including grid
points in the calculation should also be given in
_struct_mon_details.RSR.
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343,
687-689.
;
_item.name '_struct_mon_prot.RSR_side'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_prot.mean_B_all
_item_description.description
; The mean value of the isotropic displacement parameter for all
atoms in the monomer.
;
_item.name '_struct_mon_prot.mean_B_all'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_prot.mean_B_main
_item_description.description
; The mean value of the isotropic displacement parameter for atoms
in the main chain of the monomer.
;
_item.name '_struct_mon_prot.mean_B_main'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_prot.mean_B_side
_item_description.description
; The mean value of the isotropic displacement parameter for atoms
in the side chain of the monomer.
;
_item.name '_struct_mon_prot.mean_B_side'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
save_
save__struct_mon_prot.omega
_item_description.description
; The value in degrees of the main-chain torsion angle omega.
;
_item.name '_struct_mon_prot.omega'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_prot.phi
_item_description.description
; The value in degrees of the main-chain torsion angle phi.
;
_item.name '_struct_mon_prot.phi'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__struct_mon_prot.psi
_item_description.description
; The value in degrees of the main-chain torsion angle psi.
;
_item.name '_struct_mon_prot.psi'
_item.category_id struct_mon_prot
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
#########################
## STRUCT_MON_PROT_CIS ##
#########################
save_struct_mon_prot_cis
_category.description
; Data items in the STRUCT_MON_PROT_CIS category identify
monomers that have been found to have the peptide bond in the cis
conformation. The criterion used to select residues to be
designated as containing cis peptide bonds is given in
_struct_mon_details.prot_cis.
;
_category.id struct_mon_prot_cis
_category.mandatory_code no
loop_
_category_key.name '_struct_mon_prot_cis.label_alt_id'
'_struct_mon_prot_cis.label_asym_id'
'_struct_mon_prot_cis.label_comp_id'
'_struct_mon_prot_cis.label_seq_id'
'_struct_mon_prot_cis.pdbx_PDB_model_num'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB structure 1ACY of Ghiara, Stura, Stanfield,
Profy & Wilson [Science (1994), 264, 82-85].
;
;
loop_
_struct_mon_prot_cis.label_comp_id
_struct_mon_prot_cis.label_seq_id
_struct_mon_prot_cis.label_asym_id
_struct_mon_prot_cis.label_alt_id
_struct_mon_prot_cis.pdbx_PDB_model_num
PRO 8 L . 1
PRO 77 L . 1
PRO 95 L . 1
PRO 141 L . 1
# ----- abbreviated -----
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_mon_prot_cis.label_alt_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_struct_mon_prot_cis.label_alt_id'
_item.mandatory_code yes
save_
save__struct_mon_prot_cis.label_asym_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot_cis.label_asym_id'
_item.mandatory_code yes
save_
save__struct_mon_prot_cis.label_comp_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot_cis.label_comp_id'
_item.mandatory_code yes
save_
save__struct_mon_prot_cis.label_seq_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot_cis.label_seq_id'
_item.mandatory_code yes
save_
save__struct_mon_prot_cis.auth_asym_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot_cis.auth_asym_id'
_item.mandatory_code no
save_
save__struct_mon_prot_cis.auth_comp_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot_cis.auth_comp_id'
_item.mandatory_code no
save_
save__struct_mon_prot_cis.auth_seq_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_mon_prot_cis.auth_seq_id'
_item.mandatory_code no
save_
####################
## STRUCT_NCS_DOM ##
####################
save_struct_ncs_dom
_category.description
; Data items in the STRUCT_NCS_DOM category record information
about the domains in an ensemble of domains related by one or
more noncrystallographic symmetry operators.
A domain need not correspond to a complete polypeptide chain;
it can be composed of one or more segments in a single chain,
or by segments from more than one chain.
;
_category.id struct_ncs_dom
_category.mandatory_code no
_category_key.name '_struct_ncs_dom.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
;
;
loop_
_struct_ncs_dom.id
_struct_ncs_dom.details
d1 'Chains A, B, and C'
d2 'Chains D, E, and F'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_ncs_dom.details
_item_description.description
; A description of special aspects of the structural elements that
comprise a domain in an ensemble of domains related by
noncrystallographic symmetry.
;
_item.name '_struct_ncs_dom.details'
_item.category_id struct_ncs_dom
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The loop between residues 18 and 23 in this
domain interacts with a symmetry-related
molecule, and thus deviates significantly from
the noncrystallographic threefold.
;
save_
save__struct_ncs_dom.id
_item_description.description
; The value of _struct_ncs_dom.id must uniquely identify a
record in the STRUCT_NCS_DOM list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_ncs_dom.id' struct_ncs_dom yes
'_struct_ncs_dom_lim.dom_id' struct_ncs_dom_lim yes
'_struct_ncs_ens_gen.dom_id_1' struct_ncs_ens_gen yes
'_struct_ncs_ens_gen.dom_id_2' struct_ncs_ens_gen yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_ncs_dom_lim.dom_id' '_struct_ncs_dom.id'
'_struct_ncs_ens_gen.dom_id_1' '_struct_ncs_dom.id'
'_struct_ncs_ens_gen.dom_id_2' '_struct_ncs_dom.id'
_item_type.code code
save_
########################
## STRUCT_NCS_DOM_LIM ##
########################
save_struct_ncs_dom_lim
_category.description
; Data items in the STRUCT_NCS_DOM_LIM category identify the
start and end points of polypeptide chain segments
that form all or part of a domain in an ensemble of domains
related by noncrystallographic symmetry.
;
_category.id struct_ncs_dom_lim
_category.mandatory_code no
loop_
_category_key.name '_struct_ncs_dom_lim.dom_id'
'_struct_ncs_dom_lim.beg_label_alt_id'
'_struct_ncs_dom_lim.beg_label_asym_id'
'_struct_ncs_dom_lim.beg_label_comp_id'
'_struct_ncs_dom_lim.beg_label_seq_id'
'_struct_ncs_dom_lim.end_label_alt_id'
'_struct_ncs_dom_lim.end_label_asym_id'
'_struct_ncs_dom_lim.end_label_comp_id'
'_struct_ncs_dom_lim.end_label_seq_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
;
;
loop_
_struct_ncs_dom_lim.dom_id
_struct_ncs_dom_lim.beg_label_alt_id
_struct_ncs_dom_lim.beg_label_asym_id
_struct_ncs_dom_lim.beg_label_comp_id
_struct_ncs_dom_lim.beg_label_seq_id
_struct_ncs_dom_lim.end_label_alt_id
_struct_ncs_dom_lim.end_label_asym_id
_struct_ncs_dom_lim.end_label_comp_id
_struct_ncs_dom_lim.end_label_seq_id
d1 . A PRO 1 . A GLY 29
d1 . B PRO 31 . B GLY 59
d1 . C PRO 61 . B GLY 89
d2 . D PRO 91 . D GLY 119
d2 . E PRO 121 . E GLY 149
d2 . F PRO 151 . F GLY 179
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_ncs_dom_lim.beg_label_alt_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_struct_ncs_dom_lim.beg_label_alt_id'
_item.mandatory_code yes
save_
save__struct_ncs_dom_lim.beg_label_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.beg_label_asym_id'
_item.mandatory_code yes
save_
save__struct_ncs_dom_lim.beg_label_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.beg_label_comp_id'
_item.mandatory_code yes
save_
save__struct_ncs_dom_lim.beg_label_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.beg_label_seq_id'
_item.mandatory_code yes
save_
save__struct_ncs_dom_lim.beg_auth_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.beg_auth_asym_id'
_item.mandatory_code no
save_
save__struct_ncs_dom_lim.beg_auth_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.beg_auth_comp_id'
_item.mandatory_code no
save_
save__struct_ncs_dom_lim.beg_auth_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.beg_auth_seq_id'
_item.mandatory_code no
save_
save__struct_ncs_dom_lim.dom_id
_item_description.description
; This data item is a pointer to _struct_ncs_dom.id in the
STRUCT_NCS_DOM category.
;
_item.name '_struct_ncs_dom_lim.dom_id'
_item.mandatory_code yes
save_
save__struct_ncs_dom_lim.end_label_alt_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_struct_ncs_dom_lim.end_label_alt_id'
_item.mandatory_code yes
save_
save__struct_ncs_dom_lim.end_label_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.end_label_asym_id'
_item.mandatory_code yes
save_
save__struct_ncs_dom_lim.end_label_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.end_label_comp_id'
_item.mandatory_code yes
save_
save__struct_ncs_dom_lim.end_label_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.end_label_seq_id'
_item.mandatory_code yes
save_
save__struct_ncs_dom_lim.end_auth_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.end_auth_asym_id'
_item.mandatory_code no
save_
save__struct_ncs_dom_lim.end_auth_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.end_auth_comp_id'
_item.mandatory_code no
save_
save__struct_ncs_dom_lim.end_auth_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_ncs_dom_lim.end_auth_seq_id'
_item.mandatory_code no
save_
####################
## STRUCT_NCS_ENS ##
####################
save_struct_ncs_ens
_category.description
; Data items in the STRUCT_NCS_ENS category record information
about ensembles of domains related by noncrystallographic
symmetry. The point group of the ensemble when taken as a
whole may be specified, as well as any special aspects of the
ensemble that require description.
;
_category.id struct_ncs_ens
_category.mandatory_code no
_category_key.name '_struct_ncs_ens.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
;
;
_struct_ncs_ens.id en1
_struct_ncs_ens.details
; The ensemble represents the pseudo-twofold symmetry
between domains d1 and d2.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_ncs_ens.details
_item_description.description
; A description of special aspects of the ensemble.
;
_item.name '_struct_ncs_ens.details'
_item.category_id struct_ncs_ens
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The ensemble has a slight translation between
domains 1 and 4, but overall it can accurately
be described as point group 222
;
save_
save__struct_ncs_ens.id
_item_description.description
; The value of _struct_ncs_ens.id must uniquely identify a
record in the STRUCT_NCS_ENS list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_ncs_ens.id' struct_ncs_ens yes
'_struct_ncs_ens_gen.ens_id' struct_ncs_ens_gen yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_ncs_ens_gen.ens_id' '_struct_ncs_ens.id'
_item_type.code code
save_
save__struct_ncs_ens.point_group
_item_description.description
; The point group of the ensemble of structural elements related by
one or more noncrystallographic symmetry operations. The
relationships need not be precise; this data item is intended
to give a rough description of the noncrystallographic symmetry
relationships.
;
_item.name '_struct_ncs_ens.point_group'
_item.category_id struct_ncs_ens
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case '3'
'422'
'non-proper'
save_
########################
## STRUCT_NCS_ENS_GEN ##
########################
save_struct_ncs_ens_gen
_category.description
; Data items in the STRUCT_NCS_ENS_GEN category list domains
related by a noncrystallographic symmetry operation and
identify the operator.
;
_category.id struct_ncs_ens_gen
_category.mandatory_code no
loop_
_category_key.name '_struct_ncs_ens_gen.ens_id'
'_struct_ncs_ens_gen.dom_id_1'
'_struct_ncs_ens_gen.dom_id_2'
'_struct_ncs_ens_gen.oper_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for the collagen-like
peptide, HYP-.
;
;
_struct_ncs_ens_gen.dom_id_1 d1
_struct_ncs_ens_gen.dom_id_2 d2
_struct_ncs_ens_gen.ens_id en1
_struct_ncs_ens_gen.oper_id ncsop1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_ncs_ens_gen.dom_id_1
_item_description.description
; The identifier for the domain that will remain unchanged by the
transformation operator.
This data item is a pointer to _struct_ncs_dom.id in the
STRUCT_NCS_DOM category.
;
_item.name '_struct_ncs_ens_gen.dom_id_1'
_item.mandatory_code yes
save_
save__struct_ncs_ens_gen.dom_id_2
_item_description.description
; The identifier for the domain that will be transformed by
application of the transformation operator.
This data item is a pointer to _struct_ncs_dom.id in the
STRUCT_NCS_DOM category.
;
_item.name '_struct_ncs_ens_gen.dom_id_2'
_item.mandatory_code yes
save_
save__struct_ncs_ens_gen.ens_id
_item_description.description
; This data item is a pointer to _struct_ncs_ens.id in the
STRUCT_NCS_ENS category.
;
_item.name '_struct_ncs_ens_gen.ens_id'
_item.mandatory_code yes
save_
save__struct_ncs_ens_gen.oper_id
_item_description.description
; This data item is a pointer to _struct_ncs_oper.id in the
STRUCT_NCS_OPER category.
;
_item.name '_struct_ncs_ens_gen.oper_id'
_item.mandatory_code yes
save_
#####################
## STRUCT_NCS_OPER ##
#####################
save_struct_ncs_oper
_category.description
; Data items in the STRUCT_NCS_OPER category describe the
noncrystallographic symmetry operations.
Each operator is specified as a matrix and a subsequent
translation vector. Operators need not represent proper
rotations.
;
_category.id struct_ncs_oper
_category.mandatory_code no
_category_key.name '_struct_ncs_oper.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for the protein NS1.
;
;
_struct_ncs_oper.id ncsop1
_struct_ncs_oper.code given
_struct_ncs_oper.matrix[1][1] 0.247
_struct_ncs_oper.matrix[1][2] 0.935
_struct_ncs_oper.matrix[1][3] 0.256
_struct_ncs_oper.matrix[2][1] 0.929
_struct_ncs_oper.matrix[2][2] 0.153
_struct_ncs_oper.matrix[2][3] 0.337
_struct_ncs_oper.matrix[3][1] 0.276
_struct_ncs_oper.matrix[3][2] 0.321
_struct_ncs_oper.matrix[3][3] -0.906
_struct_ncs_oper.vector[1] -8.253
_struct_ncs_oper.vector[2] -11.743
_struct_ncs_oper.vector[3] -1.782
_struct_ncs_oper.details
; Matrix and translation vector for pseudo-twofold operation.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_ncs_oper.code
_item_description.description
; A code to indicate whether this operator describes a
relationship between coordinates all of which are given in the
data block (in which case the value of code is 'given'), or
whether the operator is used to generate new coordinates from
those that are given in the data block (in which case the value
of code is 'generate').
;
_item.name '_struct_ncs_oper.code'
_item.category_id struct_ncs_oper
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail given
; operator relates coordinates given in the
data block
;
generate
; operator generates new coordinates from
those given in the data block
;
save_
save__struct_ncs_oper.details
_item_description.description
; A description of special aspects of the noncrystallographic
symmetry operator.
;
_item.name '_struct_ncs_oper.details'
_item.category_id struct_ncs_oper
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The operation is given as a precise threefold
rotation, despite the fact the best rms
fit between domain 1 and domain 2 yields a
rotation of 119.7 degrees and a translation
of 0.13 angstroms.
;
save_
save__struct_ncs_oper.id
_item_description.description
; The value of _struct_ncs_oper.id must uniquely identify a
record in the STRUCT_NCS_OPER list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_ncs_oper.id' struct_ncs_oper yes
'_struct_ncs_ens_gen.oper_id' struct_ncs_ens_gen yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_ncs_ens_gen.oper_id' '_struct_ncs_oper.id'
_item_type.code code
save_
save__struct_ncs_oper.matrix[1][1]
_item_description.description
; The [1][1] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.matrix[1][1]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_ncs_oper.matrix[1][2]
_item_description.description
; The [1][2] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.matrix[1][2]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_ncs_oper.matrix[1][3]
_item_description.description
; The [1][3] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.matrix[1][3]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_ncs_oper.matrix[2][1]
_item_description.description
; The [2][1] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.matrix[2][1]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_ncs_oper.matrix[2][2]
_item_description.description
; The [2][2] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.matrix[2][2]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_ncs_oper.matrix[2][3]
_item_description.description
; The [2][3] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.matrix[2][3]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_ncs_oper.matrix[3][1]
_item_description.description
; The [3][1] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.matrix[3][1]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_ncs_oper.matrix[3][2]
_item_description.description
; The [3][2] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.matrix[3][2]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_ncs_oper.matrix[3][3]
_item_description.description
; The [3][3] element of the 3x3 matrix component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.matrix[3][3]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_ncs_oper.vector[1]
_item_description.description
; The [1] element of the three-element vector component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.vector[1]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
# _item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__struct_ncs_oper.vector[2]
_item_description.description
; The [2] element of the three-element vector component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.vector[2]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
# _item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__struct_ncs_oper.vector[3]
_item_description.description
; The [3] element of the three-element vector component of a
noncrystallographic symmetry operation.
;
_item.name '_struct_ncs_oper.vector[3]'
_item.category_id struct_ncs_oper
_item.mandatory_code no
# _item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
################
## STRUCT_REF ##
################
save_struct_ref
_category.description
; Data items in the STRUCT_REF category allow the author of a
data block to relate the entities or biological units
described in the data block to information archived in external
databases.
For references to the sequence of a polymer, the value of
the data item _struct_ref.seq_align is used to indicate
whether the correspondence between the sequence of the entity
or biological unit in the data block and the sequence in the
referenced database entry is 'complete' or 'partial'. If
this value is 'partial', the region (or regions) of the
alignment may be delimited using data items in the
STRUCT_REF_SEQ category.
Similarly, the value of _struct_ref.seq_dif is used to indicate
whether the two sequences contain point differences. If the
value is 'yes', the differences may be identified and annotated
using data items in the STRUCT_REF_SEQ_DIF category.
;
_category.id struct_ref
_category.mandatory_code no
_category_key.name '_struct_ref.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_ref.id
_struct_ref.entity_id
_struct_ref.biol_id
_struct_ref.db_name
_struct_ref.db_code
_struct_ref.seq_align
_struct_ref.seq_dif
_struct_ref.details
1 1 . 'Genbank' '12345' 'entire' 'yes' .
2 . 2 'PDB' '1ABC' . .
; The structure of the closely related compound,
isobutyryl-pepstatin (pepstatin A) in complex with
rhizopuspepsin
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_ref.biol_id
_item_description.description
; This data item is a pointer to _struct_biol.id in the
STRUCT_BIOL category.
;
_item.name '_struct_ref.biol_id'
_item.mandatory_code no
save_
save__struct_ref.db_code
_item_description.description
; The code for this entity or biological unit or for a closely
related entity or biological unit in the named database.
;
_item.name '_struct_ref.db_code'
_item.category_id struct_ref
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case '1ABC'
'ABCDEF'
save_
save__struct_ref.db_name
_item_description.description
; The name of the database containing reference information about
this entity or biological unit.
;
_item.name '_struct_ref.db_name'
_item.category_id struct_ref
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case 'PDB'
'CSD'
'Genbank'
save_
save__struct_ref.details
_item_description.description
; A description of special aspects of the relationship between
the entity or biological unit described in the data block and
that in the referenced database entry.
;
_item.name '_struct_ref.details'
_item.category_id struct_ref
_item.mandatory_code no
_item_type.code text
save_
save__struct_ref.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_struct_ref.entity_id'
_item.mandatory_code yes
save_
save__struct_ref.id
_item_description.description
; The value of _struct_ref.id must uniquely identify a record
in the STRUCT_REF list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_ref.id' struct_ref yes
'_struct_ref_seq.ref_id' struct_ref_seq yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_ref_seq.ref_id' '_struct_ref.id'
_item_type.code code
save_
save__struct_ref.seq_align
_item_description.description
; A flag to indicate the scope of the alignment between the
sequence of the entity or biological unit described in the data
block and that in the referenced database entry. 'entire'
indicates that alignment spans the entire length of both
sequences (although point differences may occur and can be
annotated using the data items in the STRUCT_REF_SEQ_DIF
category). 'partial' indicates a partial alignment. The region
(or regions) of the alignment may be delimited using data items
in the STRUCT_REF_SEQ category. This data item may also take
the value '.', indicating that the reference is not to a
sequence.
;
_item.name '_struct_ref.seq_align'
_item.category_id struct_ref
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail complete 'alignment is complete'
partial 'alignment is partial'
. 'reference is not to a sequence'
save_
save__struct_ref.seq_dif
_item_description.description
; A flag to indicate the presence ('yes') or absence ('no') of
point differences between the sequence of the entity or
biological unit described in the data block and that in
the referenced database entry. This data item may also
take the value '.', indicating that the reference is not to a
sequence.
;
_item.name '_struct_ref.seq_dif'
_item.category_id struct_ref
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail no 'there are no point differences'
n 'abbreviation for "no"'
yes 'there are point difference'
y 'abbreviation for "yes"'
. 'reference is not to a sequence'
save_
####################
## STRUCT_REF_SEQ ##
####################
save_struct_ref_seq
_category.description
; Data items in the STRUCT_REF_SEQ category provide a mechanism
for indicating and annotating a region (or regions) of alignment
between the sequence of an entity or biological unit described
in the data block and the sequence in the referenced database
entry.
;
_category.id struct_ref_seq
_category.mandatory_code no
_category_key.name '_struct_ref_seq.align_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on the sequence alignment of CHER from M. xantus
(36 to 288) and CHER from S. typhimurium (18 to 276).
;
;
_struct_ref_seq.align_id alg1
_struct_ref_seq.ref_id seqdb1
_struct_ref_seq.seq_align_beg 36
_struct_ref_seq.seq_align_end 288
_struct_ref_seq.db_align_beg 18
_struct_ref_seq.db_align_end 276
_struct_ref_seq.details
; The alignment contains 3 gaps larger than 2 residues
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_ref_seq.align_id
_item_description.description
; The value of _struct_ref_seq.align_id must uniquely identify a
record in the STRUCT_REF_SEQ list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_ref_seq.align_id' struct_ref_seq yes
'_struct_ref_seq_dif.align_id' struct_ref_seq_dif yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_ref_seq_dif.align_id' '_struct_ref_seq.align_id'
_item_type.code code
save_
save__struct_ref_seq.db_align_beg
_item_description.description
; The sequence position in the referenced database entry
at which the alignment begins.
;
_item.name '_struct_ref_seq.db_align_beg'
_item.mandatory_code yes
# loop_
# _item_range.maximum
# _item_range.minimum . 1
# 1 1
_item_type.code int
save_
save__struct_ref_seq.db_align_end
_item_description.description
; The sequence position in the referenced database entry
at which the alignment ends.
;
_item.name '_struct_ref_seq.db_align_end'
_item.mandatory_code yes
# loop_
# _item_range.maximum
# _item_range.minimum . 1
# 1 1
_item_type.code int
save_
save__struct_ref_seq.details
_item_description.description
; A description of special aspects of the sequence alignment.
;
_item.name '_struct_ref_seq.details'
_item.category_id struct_ref_seq
_item.mandatory_code no
_item_type.code text
save_
save__struct_ref_seq.ref_id
_item_description.description
; This data item is a pointer to _struct_ref.id in the
STRUCT_REF category.
;
_item.name '_struct_ref_seq.ref_id'
_item.mandatory_code yes
save_
save__struct_ref_seq.seq_align_beg
_item_description.description
; The sequence position in the entity or biological unit described
in the data block at which the alignment begins.
This data item is a pointer to _entity_poly_seq.num in the
ENTITY_POLY_SEQ category.
;
_item.name '_struct_ref_seq.seq_align_beg'
_item.mandatory_code yes
save_
save__struct_ref_seq.seq_align_end
_item_description.description
; The sequence position in the entity or biological unit described
in the data block at which the alignment ends.
This data item is a pointer to _entity_poly_seq.num in the
ENTITY_POLY_SEQ category.
;
_item.name '_struct_ref_seq.seq_align_end'
_item.mandatory_code yes
save_
########################
## STRUCT_REF_SEQ_DIF ##
########################
save_struct_ref_seq_dif
_category.description
; Data items in the STRUCT_REF_SEQ_DIF category provide a
mechanism for indicating and annotating point differences
between the sequence of the entity or biological unit described
in the data block and the sequence of the referenced database
entry.
;
_category.id struct_ref_seq_dif
_category.mandatory_code no
_category_key.name '_struct_ref_seq_dif.pdbx_ordinal'
#
# loop_
# _category_key.name '_struct_ref_seq_dif.align_id'
# '_struct_ref_seq_dif.seq_num'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on laboratory records for CAP-DNA complex.
;
;
_struct_ref_seq_dif.pdbx_ordinal 1
_struct_ref_seq_dif.align_id algn2
_struct_ref_seq_dif.seq_num 181
_struct_ref_seq_dif.db_mon_id GLU
_struct_ref_seq_dif.mon_id PHE
_struct_ref_seq_dif.details
; A point mutation was introduced in the CAP at position 181
substituting PHE for GLU.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_ref_seq_dif.align_id
_item_description.description
; This data item is a pointer to _struct_ref_seq.align_id in
the STRUCT_REF_SEQ category.
;
_item.name '_struct_ref_seq_dif.align_id'
_item.mandatory_code yes
save_
save__struct_ref_seq_dif.db_mon_id
_item_description.description
; The monomer type found at this position in the referenced
database entry.
This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_struct_ref_seq_dif.db_mon_id'
_item.mandatory_code yes
save_
save__struct_ref_seq_dif.details
_item_description.description
; A description of special aspects of the point differences
between the sequence of the entity or biological unit described
in the data block and that in the referenced database entry.
;
_item.name '_struct_ref_seq_dif.details'
_item.category_id struct_ref_seq_dif
_item.mandatory_code no
_item_type.code text
save_
save__struct_ref_seq_dif.mon_id
_item_description.description
; The monomer type found at this position in the sequence of
the entity or biological unit described in this data block.
This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_struct_ref_seq_dif.mon_id'
_item.mandatory_code yes
save_
save__struct_ref_seq_dif.seq_num
_item_description.description
; This data item is a pointer to _entity_poly_seq.num in the
ENTITY_POLY_SEQ category.
;
_item.name '_struct_ref_seq_dif.seq_num'
_item.mandatory_code yes
save_
##################
## STRUCT_SHEET ##
##################
save_struct_sheet
_category.description
; Data items in the STRUCT_SHEET category record details about
the beta-sheets.
;
_category.id struct_sheet
_category.mandatory_code no
_category_key.name '_struct_sheet.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - simple beta-barrel.
N O N O N O N O N O N O
10--11--12--13--14--15--16--17--18--19--20 strand_a
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
30--31--32--33--34--35--36--37--38--39--40 strand_b
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
50--51--52--53--54--55--56--57--58--59--60 strand_c
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
70--71--72--73--74--75--76--77--78--79--80 strand_d
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
90--91--92--93--94--95--96--97--98--99-100 strand_e
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
110-111-112-113-114-115-116-117-118-119-120 strand_f
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
130-131-132-133-134-135-136-137-138-139-140 strand_g
N O N O N O N O N O
/ \ / \ / \ / \ / \
N O N O N O N O N O N O
150-151-152-153-154-155-156-157-158-159-160 strand_h
N O N O N O N O N O
/ \ / \ / \ / \ / \
;
;
_struct_sheet.id sheet_1
_struct_sheet.type 'beta-barrel'
_struct_sheet.number_strands 8
_struct_sheet.details .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
N O N O N O N O
-10--11--12--13--14--15--16--17--18-> strand_a
N O N O N O N O N O
| | | | | | | | | |
O N O N O N O N O N
<-119-118-117-116-115-114-113-112-111-110- strand_b
O N O N O N O N O N
\ / \ / \ / \ / \
O N O N O N O N O N O N
<-41--40--39--38--37--36--35--34--33--32--31--30- strand_c
O N O N O N O N O N O N
| | | | | | | | | | | |
N O N O N O N O N O N O
strand_d1 -50--51--52-> -90--91--92--93--95--95--96--97-> strand_d2
N O N O N O N O N O
| | | | | | | | | | | |
O N O N O N O N O N O N
<-80--79--78--77--76--75--74--73--72--71--70- strand_e
O N O N O N O N O N
;
;
_struct_sheet.id sheet_2
_struct_sheet.type 'five stranded, mixed-sense'
_struct_sheet.number_strands 5
_struct_sheet.details 'strand_d is in two pieces'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_sheet.details
_item_description.description
; A description of special aspects of the beta-sheet.
;
_item.name '_struct_sheet.details'
_item.category_id struct_sheet
_item.mandatory_code no
_item_type.code text
save_
save__struct_sheet.id
_item_description.description
; The value of _struct_sheet.id must uniquely identify a record in
the STRUCT_SHEET list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_sheet.id' struct_sheet yes
'_struct_sheet_hbond.sheet_id' struct_sheet_hbond yes
'_struct_sheet_order.sheet_id' struct_sheet_order yes
'_struct_sheet_range.sheet_id' struct_sheet_range yes
'_struct_sheet_topology.sheet_id' struct_sheet_topology yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_sheet_hbond.sheet_id' '_struct_sheet.id'
'_struct_sheet_order.sheet_id' '_struct_sheet.id'
'_struct_sheet_range.sheet_id' '_struct_sheet.id'
'_struct_sheet_topology.sheet_id' '_struct_sheet.id'
_item_type.code code
save_
save__struct_sheet.number_strands
_item_description.description
; The number of strands in the sheet. If a given range of residues
bulges out from the strands, it is still counted as one strand.
If a strand is composed of two different regions of polypeptide,
it is still counted as one strand, as long as the proper hydrogen-
bonding connections are made to adjacent strands.
;
_item.name '_struct_sheet.number_strands'
_item.category_id struct_sheet
_item.mandatory_code no
_item_type.code int
save_
save__struct_sheet.type
_item_description.description
; A simple descriptor for the type of the sheet.
;
_item.name '_struct_sheet.type'
_item.category_id struct_sheet
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'jelly-roll'
'Rossmann fold'
'beta barrel'
save_
########################
## STRUCT_SHEET_HBOND ##
########################
save_struct_sheet_hbond
_category.description
; Data items in the STRUCT_SHEET_HBOND category record details
about the hydrogen bonding between residue ranges in a beta-
sheet. It is necessary to treat hydrogen bonding independently
of the designation of ranges, because the hydrogen bonding may
begin in different places for the interactions of a given strand
with the one preceding it and the one following it in the sheet.
;
_category.id struct_sheet_hbond
_category.mandatory_code no
loop_
_category_key.name '_struct_sheet_hbond.sheet_id'
'_struct_sheet_hbond.range_id_1'
'_struct_sheet_hbond.range_id_2'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - simple beta-barrel.
;
;
loop_
_struct_sheet_hbond.sheet_id
_struct_sheet_hbond.range_id_1
_struct_sheet_hbond.range_id_2
_struct_sheet_hbond.range_1_beg_label_seq_id
_struct_sheet_hbond.range_1_beg_label_atom_id
_struct_sheet_hbond.range_2_beg_label_seq_id
_struct_sheet_hbond.range_2_beg_label_atom_id
_struct_sheet_hbond.range_1_end_label_seq_id
_struct_sheet_hbond.range_1_end_label_atom_id
_struct_sheet_hbond.range_2_end_label_seq_id
_struct_sheet_hbond.range_2_end_label_atom_id
sheet_1 strand_a strand_b 11 N 30 O 19 O 40 N
sheet_1 strand_b strand_c 31 N 50 O 39 O 60 N
sheet_1 strand_c strand_d 51 N 70 O 59 O 80 N
sheet_1 strand_d strand_e 71 N 90 O 89 O 100 N
sheet_1 strand_e strand_f 91 N 110 O 99 O 120 N
sheet_1 strand_f strand_g 111 N 130 O 119 O 140 N
sheet_1 strand_g strand_h 131 N 150 O 139 O 160 N
sheet_1 strand_h strand_a 151 N 10 O 159 O 180 N
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
;
;
loop_
_struct_sheet_hbond.sheet_id
_struct_sheet_hbond.range_id_1
_struct_sheet_hbond.range_id_2
_struct_sheet_hbond.range_1_beg_label_seq_id
_struct_sheet_hbond.range_1_beg_label_atom_id
_struct_sheet_hbond.range_2_beg_label_seq_id
_struct_sheet_hbond.range_2_beg_label_atom_id
_struct_sheet_hbond.range_1_end_label_seq_id
_struct_sheet_hbond.range_1_end_label_atom_id
_struct_sheet_hbond.range_2_end_label_seq_id
_struct_sheet_hbond.range_2_end_label_atom_id
sheet_2 strand_a strand_b 20 N 119 O 18 O 111 N
sheet_2 strand_b strand_c 110 N 33 O 118 N 41 O
sheet_2 strand_c strand_d1 38 N 52 O 40 O 50 N
sheet_2 strand_c strand_d2 30 N 96 O 36 O 90 N
sheet_2 strand_d1 strand_e 51 N 80 O 51 O 80 N
sheet_2 strand_d2 strand_e 91 N 76 O 97 O 70 N
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_sheet_hbond.range_1_beg_label_atom_id
_item_description.description
; A component of the identifier for the residue for the first
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_1_beg_label_atom_id'
_item.mandatory_code yes
save_
save__struct_sheet_hbond.range_1_beg_label_seq_id
_item_description.description
; A component of the identifier for the residue for the first
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_1_beg_label_seq_id'
_item.mandatory_code yes
save_
save__struct_sheet_hbond.range_1_end_label_atom_id
_item_description.description
; A component of the identifier for the residue for the first
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_1_end_label_atom_id'
_item.mandatory_code yes
save_
save__struct_sheet_hbond.range_1_end_label_seq_id
_item_description.description
; A component of the identifier for the residue for the first
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_1_end_label_seq_id'
_item.mandatory_code yes
save_
save__struct_sheet_hbond.range_2_beg_label_atom_id
_item_description.description
; A component of the identifier for the residue for the second
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_2_beg_label_atom_id'
_item.mandatory_code yes
save_
save__struct_sheet_hbond.range_2_beg_label_seq_id
_item_description.description
; A component of the identifier for the residue for the second
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_2_beg_label_seq_id'
_item.mandatory_code yes
save_
save__struct_sheet_hbond.range_2_end_label_atom_id
_item_description.description
; A component of the identifier for the residue for the second
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_2_end_label_atom_id'
_item.mandatory_code yes
save_
save__struct_sheet_hbond.range_2_end_label_seq_id
_item_description.description
; A component of the identifier for the residue for the second
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_2_end_label_seq_id'
_item.mandatory_code yes
save_
save__struct_sheet_hbond.range_1_beg_auth_atom_id
_item_description.description
; A component of the identifier for the residue for the first
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_1_beg_auth_atom_id'
_item.mandatory_code no
save_
save__struct_sheet_hbond.range_1_beg_auth_seq_id
_item_description.description
; A component of the identifier for the residue for the first
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_1_beg_auth_seq_id'
_item.mandatory_code no
save_
save__struct_sheet_hbond.range_1_end_auth_atom_id
_item_description.description
; A component of the identifier for the residue for the first
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_1_end_auth_atom_id'
_item.mandatory_code no
save_
save__struct_sheet_hbond.range_1_end_auth_seq_id
_item_description.description
; A component of the identifier for the residue for the first
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_1_end_auth_seq_id'
_item.mandatory_code no
save_
save__struct_sheet_hbond.range_2_beg_auth_atom_id
_item_description.description
; A component of the identifier for the residue for the second
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_2_beg_auth_atom_id'
_item.mandatory_code no
save_
save__struct_sheet_hbond.range_2_beg_auth_seq_id
_item_description.description
; A component of the identifier for the residue for the second
partner of the first hydrogen bond between two residue ranges
in a sheet.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_2_beg_auth_seq_id'
_item.mandatory_code no
save_
save__struct_sheet_hbond.range_2_end_auth_atom_id
_item_description.description
; A component of the identifier for the residue for the second
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_2_end_auth_atom_id'
_item.mandatory_code no
save_
save__struct_sheet_hbond.range_2_end_auth_seq_id
_item_description.description
; A component of the identifier for the residue for the second
partner of the last hydrogen bond between two residue ranges in
a sheet.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_hbond.range_2_end_auth_seq_id'
_item.mandatory_code no
save_
save__struct_sheet_hbond.range_id_1
_item_description.description
; This data item is a pointer to _struct_sheet_range.id in
the STRUCT_SHEET_RANGE category.
;
_item.name '_struct_sheet_hbond.range_id_1'
_item.mandatory_code yes
save_
save__struct_sheet_hbond.range_id_2
_item_description.description
; This data item is a pointer to _struct_sheet_range.id in
the STRUCT_SHEET_RANGE category.
;
_item.name '_struct_sheet_hbond.range_id_2'
_item.mandatory_code yes
save_
save__struct_sheet_hbond.sheet_id
_item_description.description
; This data item is a pointer to _struct_sheet.id in the
STRUCT_SHEET category.
;
_item.name '_struct_sheet_hbond.sheet_id'
_item.mandatory_code yes
save_
########################
## STRUCT_SHEET_ORDER ##
########################
save_struct_sheet_order
_category.description
; Data items in the STRUCT_SHEET_ORDER category record details
about the order of the residue ranges that form a beta-sheet.
All order links are pairwise and the specified pairs are
assumed to be adjacent to one another in the sheet. These data
items are an alternative to the STRUCT_SHEET_TOPOLOGY data
items and they allow all manner of sheets to be described.
;
_category.id struct_sheet_order
_category.mandatory_code no
loop_
_category_key.name '_struct_sheet_order.sheet_id'
'_struct_sheet_order.range_id_1'
'_struct_sheet_order.range_id_2'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - simple beta-barrel.
;
;
loop_
_struct_sheet_order.sheet_id
_struct_sheet_order.range_id_1
_struct_sheet_order.range_id_2
_struct_sheet_order.offset
_struct_sheet_order.sense
sheet_1 strand_a strand_b +1 parallel
sheet_1 strand_b strand_c +1 parallel
sheet_1 strand_c strand_d +1 parallel
sheet_1 strand_d strand_e +1 parallel
sheet_1 strand_e strand_f +1 parallel
sheet_1 strand_f strand_g +1 parallel
sheet_1 strand_g strand_h +1 parallel
sheet_1 strand_h strand_a +1 parallel
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
;
;
loop_
_struct_sheet_order.sheet_id
_struct_sheet_order.range_id_1
_struct_sheet_order.range_id_2
_struct_sheet_order.offset
_struct_sheet_order.sense
sheet_2 strand_a strand_b +1 anti-parallel
sheet_2 strand_b strand_c +1 parallel
sheet_2 strand_c strand_d1 +1 anti-parallel
sheet_2 strand_c strand_d2 +1 anti-parallel
sheet_2 strand_d1 strand_e +1 anti-parallel
sheet_2 strand_d2 strand_e +1 anti-parallel
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_sheet_order.offset
_item_description.description
; Designates the relative position in the sheet, plus or minus, of
the second residue range to the first.
;
_item.name '_struct_sheet_order.offset'
_item.category_id struct_sheet_order
_item.mandatory_code no
_item_type.code int
save_
save__struct_sheet_order.range_id_1
_item_description.description
; This data item is a pointer to _struct_sheet_range.id in
the STRUCT_SHEET_RANGE category.
;
_item.name '_struct_sheet_order.range_id_1'
_item.mandatory_code yes
save_
save__struct_sheet_order.range_id_2
_item_description.description
; This data item is a pointer to _struct_sheet_range.id in
the STRUCT_SHEET_RANGE category.
;
_item.name '_struct_sheet_order.range_id_2'
_item.mandatory_code yes
save_
save__struct_sheet_order.sense
_item_description.description
; A flag to indicate whether the two designated residue ranges are
parallel or antiparallel to one another.
;
_item.name '_struct_sheet_order.sense'
_item.category_id struct_sheet_order
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value 'parallel'
'anti-parallel'
save_
save__struct_sheet_order.sheet_id
_item_description.description
; This data item is a pointer to _struct_sheet.id in the
STRUCT_SHEET category.
;
_item.name '_struct_sheet_order.sheet_id'
_item.mandatory_code yes
save_
########################
## STRUCT_SHEET_RANGE ##
########################
save_struct_sheet_range
_category.description
; Data items in the STRUCT_SHEET_RANGE category record details
about the residue ranges that form a beta-sheet. Residues are
included in a range if they made beta-sheet-type hydrogen-bonding
interactions with at least one adjacent strand and if there are
at least two residues in the range.
;
_category.id struct_sheet_range
_category.mandatory_code no
loop_
_category_key.name '_struct_sheet_range.sheet_id'
'_struct_sheet_range.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - simple beta-barrel.
;
;
loop_
_struct_sheet_range.sheet_id
_struct_sheet_range.id
_struct_sheet_range.beg_label_comp_id
_struct_sheet_range.beg_label_asym_id
_struct_sheet_range.beg_label_seq_id
_struct_sheet_range.end_label_comp_id
_struct_sheet_range.end_label_asym_id
_struct_sheet_range.end_label_seq_id
_struct_sheet_range.symmetry
sheet_1 strand_a ala A 20 ala A 30 1_555
sheet_1 strand_b ala A 40 ala A 50 1_555
sheet_1 strand_c ala A 60 ala A 70 1_555
sheet_1 strand_d ala A 80 ala A 90 1_555
sheet_1 strand_e ala A 100 ala A 110 1_555
sheet_1 strand_f ala A 120 ala A 130 1_555
sheet_1 strand_g ala A 140 ala A 150 1_555
sheet_1 strand_h ala A 160 ala A 170 1_555
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
;
;
loop_
_struct_sheet_range.sheet_id
_struct_sheet_range.id
_struct_sheet_range.beg_label_comp_id
_struct_sheet_range.beg_label_asym_id
_struct_sheet_range.beg_label_seq_id
_struct_sheet_range.end_label_comp_id
_struct_sheet_range.end_label_asym_id
_struct_sheet_range.end_label_seq_id
_struct_sheet_range.symmetry
sheet_2 strand_a ala A 10 ala A 18 1_555
sheet_2 strand_b ala A 110 ala A 119 1_555
sheet_2 strand_c ala A 30 ala A 41 1_555
sheet_2 strand_d1 ala A 50 ala A 52 1_555
sheet_2 strand_d2 ala A 90 ala A 97 1_555
sheet_2 strand_e ala A 70 ala A 80 1_555
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_sheet_range.beg_label_asym_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
_item.name '_struct_sheet_range.beg_label_asym_id'
_item.mandatory_code yes
save_
save__struct_sheet_range.beg_label_comp_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_struct_sheet_range.beg_label_comp_id'
_item.mandatory_code yes
save_
save__struct_sheet_range.beg_label_seq_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_range.beg_label_seq_id'
_item.mandatory_code yes
save_
save__struct_sheet_range.end_label_asym_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
_item.name '_struct_sheet_range.end_label_asym_id'
_item.mandatory_code yes
save_
save__struct_sheet_range.end_label_comp_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to _chem_comp.id in the CHEM_COMP
category.
;
_item.name '_struct_sheet_range.end_label_comp_id'
_item.mandatory_code yes
save_
save__struct_sheet_range.end_label_seq_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_range.end_label_seq_id'
_item.mandatory_code yes
save_
save__struct_sheet_range.beg_auth_asym_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_range.beg_auth_asym_id'
_item.mandatory_code no
save_
save__struct_sheet_range.beg_auth_comp_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to _atom_site.auth_comp_id in
the ATOM_SITE category.
;
_item.name '_struct_sheet_range.beg_auth_comp_id'
_item.mandatory_code no
save_
save__struct_sheet_range.beg_auth_seq_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range begins.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_range.beg_auth_seq_id'
_item.mandatory_code no
save_
save__struct_sheet_range.end_auth_asym_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_range.end_auth_asym_id'
_item.mandatory_code no
save_
save__struct_sheet_range.end_auth_comp_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_range.end_auth_comp_id'
_item.mandatory_code no
save_
save__struct_sheet_range.end_auth_seq_id
_item_description.description
; A component of the identifier for the residue at which the
beta-sheet range ends.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_sheet_range.end_auth_seq_id'
_item.mandatory_code no
save_
save__struct_sheet_range.id
_item_description.description
; The value of _struct_sheet_range.id must uniquely identify a
range in a given sheet in the STRUCT_SHEET_RANGE list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_sheet_range.id' struct_sheet_range yes
'_struct_sheet_hbond.range_id_1' struct_sheet_hbond yes
'_struct_sheet_hbond.range_id_2' struct_sheet_hbond yes
'_struct_sheet_order.range_id_1' struct_sheet_order yes
'_struct_sheet_order.range_id_2' struct_sheet_order yes
'_struct_sheet_topology.range_id_1' struct_sheet_topology yes
'_struct_sheet_topology.range_id_2' struct_sheet_topology yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_sheet_hbond.range_id_1' '_struct_sheet_range.id'
'_struct_sheet_hbond.range_id_2' '_struct_sheet_range.id'
'_struct_sheet_order.range_id_1' '_struct_sheet_range.id'
'_struct_sheet_order.range_id_2' '_struct_sheet_range.id'
'_struct_sheet_topology.range_id_1' '_struct_sheet_range.id'
'_struct_sheet_topology.range_id_2' '_struct_sheet_range.id'
_item_type.code code
save_
save__struct_sheet_range.sheet_id
_item_description.description
; This data item is a pointer to _struct_sheet.id in the
STRUCT_SHEET category.
;
_item.name '_struct_sheet_range.sheet_id'
_item.mandatory_code yes
save_
save__struct_sheet_range.symmetry
_item_description.description
; Describes the symmetry operation that should be applied to the
residues delimited by the start and end designators in
order to generate the appropriate strand in this sheet.
;
_item.name '_struct_sheet_range.symmetry'
_item.category_id struct_sheet_range
_item.mandatory_code no
# _item_default.value 1_555
_item_type.code symop
save_
###########################
## STRUCT_SHEET_TOPOLOGY ##
###########################
save_struct_sheet_topology
_category.description
; Data items in the STRUCT_SHEET_TOPOLOGY category record details
about the topology of the residue ranges that form a beta-sheet.
All topology links are pairwise and the specified pairs are
assumed to be successive in the amino-acid sequence. These
data items are useful in describing various simple and complex
folds, but they become inadequate when the strands in the sheet
come from more than one chain. The
STRUCT_SHEET_ORDER data items can be used to describe
single- and multiple-chain-containing sheets.
;
_category.id struct_sheet_topology
_category.mandatory_code no
loop_
_category_key.name '_struct_sheet_topology.sheet_id'
'_struct_sheet_topology.range_id_1'
'_struct_sheet_topology.range_id_2'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - simple beta-barrel.
;
;
loop_
_struct_sheet_topology.sheet_id
_struct_sheet_topology.range_id_1
_struct_sheet_topology.range_id_2
_struct_sheet_topology.offset
_struct_sheet_topology.sense
sheet_1 strand_a strand_b +1 parallel
sheet_1 strand_b strand_c +1 parallel
sheet_1 strand_c strand_d +1 parallel
sheet_1 strand_d strand_e +1 parallel
sheet_1 strand_e strand_f +1 parallel
sheet_1 strand_f strand_g +1 parallel
sheet_1 strand_g strand_h +1 parallel
sheet_1 strand_h strand_a +1 parallel
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - five stranded mixed-sense sheet with one two-piece strand.
;
;
loop_
_struct_sheet_topology.sheet_id
_struct_sheet_topology.range_id_1
_struct_sheet_topology.range_id_2
_struct_sheet_topology.offset
_struct_sheet_topology.sense
sheet_2 strand_a strand_c +2 anti-parallel
sheet_2 strand_c strand_d1 +1 anti-parallel
sheet_2 strand_d1 strand_e +1 anti-parallel
sheet_2 strand_e strand_d2 -1 anti-parallel
sheet_2 strand_d2 strand_b -2 anti-parallel
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_sheet_topology.offset
_item_description.description
; Designates the relative position in the sheet, plus or minus, of
the second residue range to the first.
;
_item.name '_struct_sheet_topology.offset'
_item.category_id struct_sheet_topology
_item.mandatory_code no
_item_type.code int
save_
save__struct_sheet_topology.range_id_1
_item_description.description
; This data item is a pointer to _struct_sheet_range.id in
the STRUCT_SHEET_RANGE category.
;
_item.name '_struct_sheet_topology.range_id_1'
_item.mandatory_code yes
save_
save__struct_sheet_topology.range_id_2
_item_description.description
; This data item is a pointer to _struct_sheet_range.id in
the STRUCT_SHEET_RANGE category.
;
_item.name '_struct_sheet_topology.range_id_2'
_item.mandatory_code yes
save_
save__struct_sheet_topology.sense
_item_description.description
; A flag to indicate whether the two designated residue ranges are
parallel or antiparallel to one another.
;
_item.name '_struct_sheet_topology.sense'
_item.category_id struct_sheet_topology
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value 'parallel'
'anti-parallel'
save_
save__struct_sheet_topology.sheet_id
_item_description.description
; This data item is a pointer to _struct_sheet.id in the
STRUCT_SHEET category.
;
_item.name '_struct_sheet_topology.sheet_id'
_item.mandatory_code yes
save_
#################
## STRUCT_SITE ##
#################
save_struct_site
_category.description
; Data items in the STRUCT_SITE category record details about
portions of the structure that contribute to structurally
relevant sites (e.g. active sites, substrate-binding subsites,
metal-coordination sites).
;
_category.id struct_site
_category.mandatory_code no
_category_key.name '_struct_site.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_site.id
_struct_site.details
'P2 site C'
; residues with a contact < 3.7 \%A to an atom in the P2
moiety of the inhibitor in the conformation with
_struct_asym.id = C
;
'P2 site D'
; residues with a contact < 3.7 \%A to an atom in the P1
moiety of the inhibitor in the conformation with
_struct_asym.id = D)
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_site.details
_item_description.description
; A description of special aspects of the site.
;
_item.name '_struct_site.details'
_item.category_id struct_site
_item.mandatory_code no
_item_type.code text
save_
save__struct_site.id
_item_description.description
; The value of _struct_site.id must uniquely identify a record in
the STRUCT_SITE list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_struct_site.id' struct_site yes
'_struct_site_gen.site_id' struct_site_gen yes
'_struct_site_keywords.site_id' struct_site_keywords yes
'_struct_site_view.site_id' struct_site_view yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_struct_site_gen.site_id' '_struct_site.id'
'_struct_site_keywords.site_id' '_struct_site.id'
'_struct_site_view.site_id' '_struct_site.id'
_item_type.code line
save_
#####################
## STRUCT_SITE_GEN ##
#####################
save_struct_site_gen
_category.description
; Data items in the STRUCT_SITE_GEN category record details about
the generation of portions of the structure that contribute to
structurally relevant sites.
;
_category.id struct_site_gen
_category.mandatory_code no
loop_
_category_key.name '_struct_site_gen.id'
'_struct_site_gen.site_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 1 VAL A 32 1_555 .
2 1 ILE A 47 1_555 .
3 1 VAL A 82 1_555 .
4 1 ILE A 84 1_555 .
5 2 VAL B 232 1_555 .
6 2 ILE B 247 1_555 .
7 2 VAL B 282 1_555 .
8 2 ILE B 284 1_555 .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_site_gen.details
_item_description.description
; A description of special aspects of the symmetry generation of
this portion of the structural site.
;
_item.name '_struct_site_gen.details'
_item.category_id struct_site_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The zinc atom lies on a special position;
application of symmetry elements to generate
the insulin hexamer will generate excess zinc
atoms, which must be removed by hand.
;
save_
save__struct_site_gen.id
_item_description.description
; The value of _struct_site_gen.id must uniquely identify a record
in the STRUCT_SITE_GEN list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_struct_site_gen.id'
_item.category_id struct_site_gen
_item.mandatory_code yes
_item_type.code line
save_
save__struct_site_gen.label_alt_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_struct_site_gen.label_alt_id'
_item.mandatory_code yes
save_
save__struct_site_gen.label_asym_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_site_gen.label_asym_id'
_item.mandatory_code yes
save_
save__struct_site_gen.label_atom_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _chem_comp_atom.atom_id in the
CHEM_COMP_ATOM category.
;
_item.name '_struct_site_gen.label_atom_id'
_item.mandatory_code yes
save_
save__struct_site_gen.label_comp_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_site_gen.label_comp_id'
_item.mandatory_code yes
save_
save__struct_site_gen.label_seq_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_site_gen.label_seq_id'
_item.mandatory_code yes
save_
save__struct_site_gen.auth_asym_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_struct_site_gen.auth_asym_id'
_item.mandatory_code no
save_
save__struct_site_gen.auth_atom_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_struct_site_gen.auth_atom_id'
_item.mandatory_code no
save_
save__struct_site_gen.auth_comp_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_struct_site_gen.auth_comp_id'
_item.mandatory_code no
save_
save__struct_site_gen.auth_seq_id
_item_description.description
; A component of the identifier for participants in the site.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_struct_site_gen.auth_seq_id'
_item.mandatory_code no
save_
save__struct_site_gen.site_id
_item_description.description
; This data item is a pointer to _struct_site.id in the STRUCT_SITE
category.
;
_item.name '_struct_site_gen.site_id'
_item.mandatory_code yes
save_
save__struct_site_gen.symmetry
_item_description.description
; Describes the symmetry operation that should be applied to the
atom set specified by _struct_site_gen.label* to generate a
portion of the site.
;
_item.name '_struct_site_gen.symmetry'
_item.category_id struct_site_gen
_item.mandatory_code no
# _item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
##########################
## STRUCT_SITE_KEYWORDS ##
##########################
save_struct_site_keywords
_category.description
; Data items in the STRUCT_SITE_KEYWORDS category record
keywords describing the site.
;
_category.id struct_site_keywords
_category.mandatory_code no
loop_
_category_key.name '_struct_site_keywords.site_id'
'_struct_site_keywords.text'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_struct_site_keywords.site_id
_struct_site_keywords.text
'P2 site C' 'binding site'
'P2 site C' 'binding pocket'
'P2 site C' 'P2 site'
'P2 site C' 'P2 pocket'
'P2 site D' 'binding site'
'P2 site D' 'binding pocket'
'P2 site D' 'P2 site'
'P2 site D' 'P2 pocket'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_site_keywords.site_id
_item_description.description
; This data item is a pointer to _struct_site.id in the STRUCT_SITE
category.
;
_item.name '_struct_site_keywords.site_id'
_item.mandatory_code yes
save_
save__struct_site_keywords.text
_item_description.description
; Keywords describing this site.
;
_item.name '_struct_site_keywords.text'
_item.category_id struct_site_keywords
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'active site'
'binding pocket'
'Ca coordination'
save_
######################
## STRUCT_SITE_VIEW ##
######################
save_struct_site_view
_category.description
; Data items in the STRUCT_SITE_VIEW category record details
about how to draw and annotate an informative view of the
site.
;
_category.id struct_site_view
_category.mandatory_code no
_category_key.name '_struct_site_view.id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on NDB structure GDL001 by Coll, Aymami,
Van Der Marel, Van Boom, Rich & Wang
[Biochemistry (1989), 28, 310-320].
;
;
_struct_site_view.id 1
_struct_site_view.rot_matrix[1][1] 0.132
_struct_site_view.rot_matrix[1][2] 0.922
_struct_site_view.rot_matrix[1][3] -0.363
_struct_site_view.rot_matrix[2][1] 0.131
_struct_site_view.rot_matrix[2][2] -0.380
_struct_site_view.rot_matrix[2][3] -0.916
_struct_site_view.rot_matrix[3][1] -0.982
_struct_site_view.rot_matrix[3][2] 0.073
_struct_site_view.rot_matrix[3][3] -0.172
_struct_site_view.details
; This view highlights the site of ATAT-Netropsin
interaction.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__struct_site_view.details
_item_description.description
; A description of special aspects of this view of the
site. This data item can be used as a figure legend.
;
_item.name '_struct_site_view.details'
_item.category_id struct_site_view
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The active site has been oriented with the
specificity pocket on the right and the active
site machinery on the left.
;
save_
save__struct_site_view.id
_item_description.description
; The value of _struct_site_view.id must uniquely identify a
record in the STRUCT_SITE_VIEW list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_struct_site_view.id'
_item.category_id struct_site_view
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case 'Figure 1'
'unliganded enzyme'
'view down enzyme active site'
save_
save__struct_site_view.rot_matrix[1][1]
_item_description.description
; The [1][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in _struct_site_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_site_view.rot_matrix[1][1]'
_item.category_id struct_site_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_site_view.rot_matrix[1][2]
_item_description.description
; The [1][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in _struct_site_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_site_view.rot_matrix[1][2]'
_item.category_id struct_site_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_site_view.rot_matrix[1][3]
_item_description.description
; The [1][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in _struct_site_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_site_view.rot_matrix[1][3]'
_item.category_id struct_site_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_site_view.rot_matrix[2][1]
_item_description.description
; The [2][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in _struct_site_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_site_view.rot_matrix[2][1]'
_item.category_id struct_site_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_site_view.rot_matrix[2][2]
_item_description.description
; The [2][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in _struct_site_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_site_view.rot_matrix[2][2]'
_item.category_id struct_site_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_site_view.rot_matrix[2][3]
_item_description.description
; The [2][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in _struct_site_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_site_view.rot_matrix[2][3]'
_item.category_id struct_site_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_site_view.rot_matrix[3][1]
_item_description.description
; The [3][1] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in _struct_site_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_site_view.rot_matrix[3][1]'
_item.category_id struct_site_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_site_view.rot_matrix[3][2]
_item_description.description
; The [3][2] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category to an orientation useful for
visualizing the site. The conventions used in the rotation are
described in _struct_site_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_site_view.rot_matrix[3][2]'
_item.category_id struct_site_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_site_view.rot_matrix[3][3]
_item_description.description
; The [3][3] element of the matrix used to rotate the subset of the
Cartesian coordinates in the ATOM_SITE category identified in the
STRUCT_SITE_GEN category an orientation useful for visualizing
the site. The conventions used in the rotation are
described in _struct_site_view.details.
|x'| |11 12 13| |x|
|y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~
|z'| |31 32 33| |z|
;
_item.name '_struct_site_view.rot_matrix[3][3]'
_item.category_id struct_site_view
_item.mandatory_code no
_item_sub_category.id matrix
_item_type.code float
save_
save__struct_site_view.site_id
_item_description.description
; This data item is a pointer to _struct_site.id in the STRUCT_SITE
category.
;
_item.name '_struct_site_view.site_id'
_item.mandatory_code yes
save_
##############
## SYMMETRY ##
##############
save_symmetry
_category.description
; Data items in the SYMMETRY category record details about the
space-group symmetry.
;
_category.id symmetry
_category.mandatory_code no
_category_key.name '_symmetry.entry_id'
loop_
_category_group.id 'inclusive_group'
'symmetry_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_symmetry.entry_id '5HVP'
_symmetry.cell_setting orthorhombic
_symmetry.Int_Tables_number 18
_symmetry.space_group_name_H-M 'P 21 21 2'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__symmetry.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_symmetry.entry_id'
_item.mandatory_code yes
save_
save__symmetry.cell_setting
_item_description.description
; The cell settings for this space-group symmetry.
;
_item.name '_symmetry.cell_setting'
_item.category_id symmetry
_item.mandatory_code no
_item_aliases.alias_name '_symmetry_cell_setting'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code ucode
loop_
_item_enumeration.value triclinic
monoclinic
orthorhombic
tetragonal
rhombohedral
trigonal
hexagonal
cubic
save_
save__symmetry.Int_Tables_number
_item_description.description
; Space-group number from International Tables for Crystallography
Vol. A (2002).
;
_item.name '_symmetry.Int_Tables_number'
_item.category_id symmetry
_item.mandatory_code no
_item_aliases.alias_name '_symmetry_Int_Tables_number'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code int
save_
save__symmetry.space_group_name_Hall
_item_description.description
; Space-group symbol as described by Hall (1981). This symbol
gives the space-group setting explicitly. Leave spaces between
the separate components of the symbol.
Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
(1981) A37, 921.
;
_item.name '_symmetry.space_group_name_Hall'
_item.category_id symmetry
_item.mandatory_code no
_item_aliases.alias_name '_symmetry_space_group_name_Hall'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case '-P 2ac 2n'
'-R 3 2"'
'P 61 2 2 (0 0 -1)'
save_
save__symmetry.space_group_name_H-M
_item_description.description
; Hermann-Mauguin space-group symbol. Note that the
Hermann-Mauguin symbol does not necessarily contain complete
information about the symmetry and the space-group origin. If
used, always supply the FULL symbol from International Tables
for Crystallography Vol. A (2002) and indicate the origin and
the setting if it is not implicit. If there is any doubt that
the equivalent positions can be uniquely deduced from this
symbol, specify the _symmetry_equiv.pos_as_xyz or
_symmetry.space_group_name_Hall data items as well. Leave
spaces between symbols referring to
different axes.
;
_item.name '_symmetry.space_group_name_H-M'
_item.category_id symmetry
_item.mandatory_code no
_item_aliases.alias_name '_symmetry_space_group_name_H-M'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'P 1 21/m 1'
'P 2/n 2/n 2/n (origin at -1)'
'R -3 2/m'
save_
####################
## SYMMETRY_EQUIV ##
####################
save_symmetry_equiv
_category.description
; Data items in the SYMMETRY_EQUIV category list the
symmetry-equivalent positions for the space group.
;
_category.id symmetry_equiv
_category.mandatory_code no
_category_key.name '_symmetry_equiv.id'
loop_
_category_group.id 'inclusive_group'
'symmetry_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
loop_
_symmetry_equiv.id
_symmetry_equiv.pos_as_xyz
1 '+x,+y,+z'
2 '-x,-y,z'
3 '1/2+x,1/2-y,-z'
4 '1/2-x,1/2+y,-z'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__symmetry_equiv.id
_item_description.description
; The value of _symmetry_equiv.id must uniquely identify
a record in the SYMMETRY_EQUIV category.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_symmetry_equiv.id'
_item.category_id symmetry_equiv
_item.mandatory_code yes
_item_aliases.alias_name '_symmetry_equiv_pos_site_id'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code code
save_
save__symmetry_equiv.pos_as_xyz
_item_description.description
; Symmetry-equivalent position in the 'xyz' representation. Except
for the space group P1, these data will be repeated in a loop.
The format of the data item is as per International Tables for
Crystallography Vol. A (2002). All equivalent positions should
be entered, including those for lattice centring and a centre of
symmetry, if present.
;
_item.name '_symmetry_equiv.pos_as_xyz'
_item.category_id symmetry_equiv
_item.mandatory_code no
_item_aliases.alias_name '_symmetry_equiv_pos_as_xyz'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
_item_examples.case '-y+x,-y,1/3+z'
save_
### EOF mmcif_std-def-1.dic
###########################################################################
#
# File: mmcif_std-def-2.dic
#
# mmCIF Data Dictionary
#
# This data dictionary contains the standard mmCIF data definitions.
#
# Defintion Section 2
#
# Section 2 contains definitions added to maintain correspondence
# with the Core CIF dictionary V2.3
#
#
#
###########################################################################
save__atom_site.adp_type
_item_description.description
; A standard code used to describe the type of atomic displacement
parameters used for the site.
;
_item.name '_atom_site.adp_type'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
_item_related.related_name '_atom_site.thermal_displace_type'
_item_related.function_code alternate
loop_
_item_enumeration.value
_item_enumeration.detail
Uani 'anisotropic Uij'
Uiso 'isotropic U'
Uovl 'overall U'
Umpe 'multipole expansion U'
Bani 'anisotropic Bij'
Biso 'isotropic B'
Bovl 'overall B'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_atom_site_adp_type' cif_core.dic 2.3
save_
save__atom_site.refinement_flags
_item_description.description
; A concatenated series of single-letter codes which indicate the
refinement restraints or constraints applied to this site. This
item should not be used. It has been replaced by
_atom_site.refinement_flags_posn, *_adp and *_occupancy. It is
retained in this dictionary only to provide compatibility with
old CIFs.
;
_item.name '_atom_site.refinement_flags'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
loop_
_item_related.related_name
_item_related.function_code
'_atom_site.refinement_flags_posn' replaces
'_atom_site.refinement_flags_adp' replaces
'_atom_site.refinement_flags_occupancy' replaces
loop_
_item_enumeration.value
_item_enumeration.detail
. 'no refinement constraints'
S 'special-position constraint on site'
G 'rigid-group refinement of site'
R 'riding-atom site attached to non-riding atom'
D 'distance or angle restraint on site'
T 'thermal displacement constraints'
U 'Uiso or Uij restraint (rigid bond)'
P 'partial occupancy constraint'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_atom_site_refinement_flags' cif_core.dic 2.3
save_
save__atom_site.refinement_flags_adp
_item_description.description
; A code which indicates the refinement restraints or constraints
applied to the atomic displacement parameters of this site.
;
_item.name '_atom_site.refinement_flags_adp'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
_item_related.related_name '_atom_site.refinement_flags_posn'
_item_related.function_code alternate
loop_
_item_enumeration.value
_item_enumeration.detail
. 'no constraints on atomic displacement parameters'
T 'special-position constraints on atomic displacement parameters'
U 'Uiso or Uij restraint (rigid bond)'
TU 'both constraints applied'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_atom_site_refinement_flags_adp' cif_core.dic 2.3
save_
save__atom_site.refinement_flags_occupancy
_item_description.description
; A code which indicates that refinement restraints or
constraints were applied to the occupancy of this site.
;
_item.name '_atom_site.refinement_flags_occupancy'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
_item_related.related_name '_atom_site.refinement_flags_posn'
_item_related.function_code alternate
loop_
_item_enumeration.value
_item_enumeration.detail
. 'no constraints on site-occupancy parameters'
P 'site-occupancy constraint'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_atom_site_refinement_flags_occupancy' cif_core.dic 2.3
save_
save__atom_site.refinement_flags_posn
_item_description.description
; A code which indicates the refinement restraints or constraints
applied to the positional coordinates of this site.
;
_item.name '_atom_site.refinement_flags_posn'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
_item_related.related_name '_atom_site.refinement_flags_posn'
_item_related.function_code alternate
loop_
_item_enumeration.value
_item_enumeration.detail
. 'no constraints on positional coordinates'
D 'distance or angle restraint on positional coordinates'
G 'rigid-group refinement of positional coordinates'
R 'riding-atom site attached to non-riding atom'
S 'special-position constraint on positional coordinates'
DG 'combination of the above constraints'
DR 'combination of the above constraints'
DS 'combination of the above constraints'
GR 'combination of the above constraints'
GS 'combination of the above constraints'
RS 'combination of the above constraints'
DGR 'combination of the above constraints'
DGS 'combination of the above constraints'
DRS 'combination of the above constraints'
GRS 'combination of the above constraints'
DGRS 'combination of the above constraints'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_atom_site_refinement_flags_posn' cif_core.dic 2.3
save_
save__atom_sites.special_details
_item_description.description
; Additional information about the atomic coordinates not coded
elsewhere in the CIF.
;
_item.name '_atom_sites.special_details'
_item.category_id atom_sites
_item.mandatory_code no
_item_type.code text
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_atom_sites_special_details' cif_core.dic 2.3
save_
save__atom_type.scat_dispersion_source
_item_description.description
; Reference to the source of the real and imaginary dispersion
corrections for scattering factors used for this atom type.
;
_item.name '_atom_type.scat_dispersion_source'
_item.category_id atom_type
_item.mandatory_code no
_item_type.code text
_item_examples.case 'International Tables Vol. IV Table 2.3.1'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_atom_type_scat_dispersion_source' cif_core.dic 2.3
save_
################
## AUDIT_LINK ##
################
save_audit_link
_category.description
; Data items in the AUDIT_LINK category record details about the
relationships between data blocks in the current CIF.
;
_category.id 'audit_link'
_category.mandatory_code no
loop_
_category_key.name
'_audit_link.block_code'
'_audit_link.block_description'
loop_
_category_examples.case
_category_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_audit_link.block_code
_audit_link.block_description
. 'discursive text of paper with two structures'
morA_(1) 'structure 1 of 2'
morA_(2) 'structure 2 of 2'
;
;
Example 1 - multiple structure paper, as illustrated
in A Guide to CIF for Authors (1995). IUCr: Chester.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_audit_link.block_code
_audit_link.block_description
. 'publication details'
KSE_COM 'experimental data common to ref./mod. structures'
KSE_REF 'reference structure'
KSE_MOD 'modulated structure'
;
;
Example 2 - example file for the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__audit_link.block_code
_item_description.description
; The value of _audit_block.code associated with a data block
in the current file related to the current data block. The
special value '.' may be used to refer to the current data
block for completeness.
;
_item.name '_audit_link.block_code'
_item.category_id audit_link
_item.mandatory_code yes
_item_type.code code
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_audit_link_block_code' cif_core.dic 2.3
save_
save__audit_link.block_description
_item_description.description
; A textual description of the relationship of the referenced
data block to the current one.
;
_item.name '_audit_link.block_description'
_item.category_id audit_link
_item.mandatory_code yes
_item_type.code text
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_audit_link_block_description' cif_core.dic 2.3
save_
##
save__cell.reciprocal_angle_alpha
_item_description.description
; The angle (recip-alpha) defining the reciprocal cell in degrees.
(recip-alpha), (recip-alpha) and (recip-alpha) related to the
angles in the real cell by:
cos(recip-alpha)
= [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)]
cos(recip-beta)
= [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)]
cos(recip-gamma)
= [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)]
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
_item.name '_cell.reciprocal_angle_alpha'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 180.0
180.0 180.0
_item_default.value 90.0
_item_type_conditions.code esd
_item_units.code 'degrees'
_item_related.related_name '_cell.reciprocal_angle_alpha_esd'
_item_related.function_code associated_esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_cell_reciprocal_angle_alpha' cif_core.dic 2.3
save_
save__cell.reciprocal_angle_beta
_item_description.description
; The angle (recip-beta) defining the reciprocal cell in degrees.
(recip-alpha), (recip-alpha) and (recip-alpha) related to the
angles in the real cell by:
cos(recip-alpha)
= [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)]
cos(recip-beta)
= [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)]
cos(recip-gamma)
= [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)]
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
_item.name '_cell.reciprocal_angle_beta'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 180.0
180.0 180.0
_item_default.value 90.0
_item_type_conditions.code esd
_item_units.code 'degrees'
_item_related.related_name '_cell.reciprocal_angle_beta_esd'
_item_related.function_code associated_esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_cell_reciprocal_angle_beta' cif_core.dic 2.3
save_
#
save__cell.reciprocal_angle_gamma
_item_description.description
; The angle (recip-gamma) defining the reciprocal cell in degrees.
(recip-alpha), (recip-alpha) and (recip-alpha) related to the
angles in the real cell by:
cos(recip-alpha)
= [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)]
cos(recip-beta)
= [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)]
cos(recip-gamma)
= [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)]
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
_item.name '_cell.reciprocal_angle_gamma'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 180.0
180.0 180.0
_item_default.value 90.0
_item_type_conditions.code esd
_item_units.code 'degrees'
_item_related.related_name '_cell.reciprocal_angle_gamma_esd'
_item_related.function_code associated_esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_cell_reciprocal_angle_gamma' cif_core.dic 2.3
save_
#
save__cell.reciprocal_angle_alpha_esd
_item_description.description
; The estimated standard deviation of _cell.reciprocal_angle_alpha.
;
_item.name '_cell.reciprocal_angle_alpha_esd'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_related.related_name '_cell.reciprocal_angle_alpha'
_item_related.function_code associated_value
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_cell_reciprocal_angle_alpha_esd' cif_core.dic 2.3
save_
#
save__cell.reciprocal_angle_beta_esd
_item_description.description
; The estimated standard deviation of _cell.reciprocal_angle_beta.
;
_item.name '_cell.reciprocal_angle_beta_esd'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_related.related_name '_cell.reciprocal_angle_beta'
_item_related.function_code associated_value
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_cell_reciprocal_angle_beta_esd' cif_core.dic 2.3
save_
#
save__cell.reciprocal_angle_gamma_esd
_item_description.description
; The estimated standard deviation of _cell.reciprocal_angle_gamma.
;
_item.name '_cell.reciprocal_angle_gamma_esd'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
_item_units.code 'degrees'
_item_related.related_name '_cell.reciprocal_angle_gamma'
_item_related.function_code associated_value
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_cell_reciprocal_angle_gamma_esd' cif_core.dic 2.3
save_
#
save__cell.reciprocal_length_a
_item_description.description
; The reciprocal cell length (recip-a) in inverse Angstroms.
(recip-a), (recip-b) and (recip-c) are related to the real cell
by the following equation:
recip-a = b*c*sin(alpha)/V
recip-b = c*a*sin(beta)/V
recip-c = a*b*sin(gamma)/V
where V is the cell volume.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
_item.name '_cell.reciprocal_length_a'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'reciprocal_angstroms'
_item_type_conditions.code esd
_item_related.related_name '_cell.reciprocal_length_a_esd'
_item_related.function_code associated_esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_cell_reciprocal_length_a' cif_core.dic 2.3
save_
save__cell.reciprocal_length_b
_item_description.description
; The reciprocal cell length (recip-b) in inverse Angstroms.
(recip-a), (recip-b) and (recip-c) are related to the real cell
by the following equation:
recip-a = b*c*sin(alpha)/V
recip-b = c*a*sin(beta)/V
recip-c = a*b*sin(gamma)/V
where V is the cell volume.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
_item.name '_cell.reciprocal_length_b'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'reciprocal_angstroms'
_item_type_conditions.code esd
_item_related.related_name '_cell.reciprocal_length_b_esd'
_item_related.function_code associated_esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_cell_reciprocal_length_b' cif_core.dic 2.3
save_
save__cell.reciprocal_length_c
_item_description.description
; The reciprocal cell length (recip-c) in inverse Angstroms.
(recip-a), (recip-b) and (recip-c) are related to the real cell
by the following equation:
recip-a = b*c*sin(alpha)/V
recip-b = c*a*sin(beta)/V
recip-c = a*b*sin(gamma)/V
where V is the cell volume.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
_item.name '_cell.reciprocal_length_c'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'reciprocal_angstroms'
_item_type_conditions.code esd
_item_related.related_name '_cell.reciprocal_length_c_esd'
_item_related.function_code associated_esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_cell_reciprocal_length_c' cif_core.dic 2.3
save_
save__cell.reciprocal_length_a_esd
_item_description.description
; The estimated standard deviation of _cell.reciprocal_length_a.
;
_item.name '_cell.reciprocal_length_a_esd'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
_item_units.code 'reciprocal_angstroms'
_item_related.related_name '_cell.reciprocal_length_a'
_item_related.function_code associated_value
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_cell_reciprocal_length_a_esd' cif_core.dic 2.3
save_
save__cell.reciprocal_length_b_esd
_item_description.description
; The estimated standard deviation of _cell.reciprocal_length_b.
;
_item.name '_cell.reciprocal_length_b_esd'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
_item_units.code 'reciprocal_angstroms'
_item_related.related_name '_cell.reciprocal_length_b'
_item_related.function_code associated_value
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_cell_reciprocal_length_b_esd' cif_core.dic 2.3
save_
save__cell.reciprocal_length_c_esd
_item_description.description
; The estimated standard deviation of _cell.reciprocal_length_c.
;
_item.name '_cell.reciprocal_length_c_esd'
_item.category_id cell
_item.mandatory_code no
_item_type.code float
_item_units.code 'reciprocal_angstroms'
_item_related.related_name '_cell.reciprocal_length_c'
_item_related.function_code associated_value
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_cell_reciprocal_length_c_esd' cif_core.dic 2.3
save_
# save__cell.special_details
# _item_description.description
# ; A description of special aspects of the cell choice, noting
# possible alternative settings.
# ;
# _item.name '_cell.special_details'
# _item.category_id cell
# _item.mandatory_code no
# _item_type.code text
# loop_
# _item_examples.case
# 'pseudo-orthorhombic'
# 'standard setting from 45 deg rotation around c'
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_cell_special_details' cif_core.dic 2.3
# save_
# #
save__chemical.absolute_configuration
_item_description.description
; Necessary conditions for the assignment of
_chemical.absolute_configuration are given by H. D. Flack and
G. Bernardinelli (1999, 2000).
Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55,
908-915. (http://www.iucr.org/paper?sh0129)
Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst.
33, 1143-1148. (http://www.iucr.org/paper?ks0021)
;
_item.name '_chemical.absolute_configuration'
_item.category_id chemical
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
rm
; absolute configuration established by
the structure determination of a
compound containing a chiral reference
molecule of known absolute
configuration
;
ad
; absolute configuration established by
anomalous-dispersion effects in
diffraction measurements on the
crystal
;
rmad
; absolute configuration established by
the structure determination of a
compound containing a chiral reference
molecule of known absolute
configuration and confirmed by
anomalous-dispersion effects in
diffraction measurements on the
crystal
;
syn
; absolute configuration has not been
established by anomalous-dispersion
effects in diffraction measurements on
the crystal. The enantiomer has been
assigned by reference to an unchanging
chiral centre in the synthetic
procedure
;
unk
; absolute configuration is unknown,
there being no firm chemical evidence
for its assignment to hand and it
having not been established by
anomalous-dispersion effects in
diffraction measurements on the
crystal. An arbitrary choice of
enantiomer has been made
;
. 'inapplicable'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_absolute_configuration' cif_core.dic 2.3
save_
save__chemical.melting_point_gt
_item_description.description
; A temperature in kelvins above
which the melting point (the temperature at which the
crystalline solid changes to a liquid) lies.
_chemical.melting_point_gt and _chemical.melting_point_lt
allow a range of temperatures to be given.
_chemical.melting_point should always be used in preference
to these two items whenever possible.
;
_item.name '_chemical.melting_point_gt'
_item.category_id chemical
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_chemical.melting_point'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_melting_point_gt' cif_core.dic 2.3
save_
save__chemical.melting_point_lt
_item_description.description
; A temperature in kelvins below which the melting point (the
temperature at which the crystalline solid changes to a liquid)
lies. _chemical.melting_point_gt and _chemical.melting_point_lt
allow a range of temperatures to be given.
_chemical.melting_point should always be used in preference
to these two items whenever possible.
;
_item.name '_chemical.melting_point_lt'
_item.category_id chemical
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_chemical.melting_point'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_melting_point_lt' cif_core.dic 2.3
save_
save__chemical.optical_rotation
_item_description.description
; The optical rotation in solution of the compound is
specified in the following format:
'[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)'
where:
TEMP is the temperature of the measurement in degrees
Celsius,
WAVE is an indication of the wavelength of the light
used for the measurement,
CONC is the concentration of the solution given as the
mass of the substance in g in 100 ml of solution,
SORT is the signed value (preceded by a + or a - sign)
of 100.\a/(l.c), where \a is the signed optical
rotation in degrees measured in a cell of length l in
dm and c is the value of CONC as defined above, and
SOLV is the chemical formula of the solvent.
;
_item.name '_chemical.optical_rotation'
_item.category_id chemical
_item.mandatory_code no
_item_type.code line
_item_examples.case '[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_optical_rotation' cif_core.dic 2.3
save_
save__chemical.properties_biological
_item_description.description
; A free-text description of the biological properties of the
material.
;
_item.name '_chemical.properties_biological'
_item.category_id chemical
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
; diverse biological activities including use as a
laxative and strong antibacterial activity against
S. aureus and weak activity against
cyclooxygenase-1 (COX-1)
;
; antibiotic activity against Bacillus subtilis
(ATCC 6051) but no significant activity against
Candida albicans (ATCC 14053), Aspergillus flavus
(NRRL 6541) and Fusarium verticillioides (NRRL
25457)
;
; weakly potent lipoxygenase nonredox inhibitor
;
; no influenza A virus sialidase inhibitory and
plaque reduction activities
;
; low toxicity against Drosophila melanogaster
;
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_properties_biological' cif_core.dic 2.3
save_
save__chemical.properties_physical
_item_description.description
; A free-text description of the physical properties of the material.
;
_item.name '_chemical.properties_physical'
_item.category_id chemical
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
air-sensitive
moisture-sensitive
hygroscopic
deliquescent
oxygen-sensitive
photo-sensitive
pyrophoric
semiconductor
'ferromagnetic at low temperature'
'paramagnetic and thermochromic'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_properties_physical' cif_core.dic 2.3
save_
save__chemical.temperature_decomposition
_item_description.description
; The temperature in kelvins at which the solid decomposes.
;
_item.name '_chemical.temperature_decomposition'
_item.category_id chemical
_item.mandatory_code no
_item_type.code float
_item_type_conditions.code esd
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
_item_examples.case 350
_item_related.related_name '_chemical.temperature_decomposition_esd'
_item_related.function_code associated_esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_temperature_decomposition' cif_core.dic 2.3
save_
save__chemical.temperature_decomposition_esd
_item_description.description
; The estimated standard deviation of
_chemical.temperature_decomposition.
;
_item.name '_chemical.temperature_decomposition_esd'
_item.category_id chemical
_item.mandatory_code no
_item_type.code float
_item_units.code kelvins
_item_related.related_name '_chemical.temperature_decomposition'
_item_related.function_code associated_value
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_chemical_temperature_decomposition_esd' cif_core.dic 2.3
save_
save__chemical.temperature_decomposition_gt
_item_description.description
; A temperature in kelvins above which the solid is known to
decompose. _chemical.temperature_decomposition_gt and
_chemical.temperature_decomposition_lt allow
a range of temperatures to be given.
_chemical.temperature_decomposition should always be used in
preference to these two items whenever possible.
;
_item.name '_chemical.temperature_decomposition_gt'
_item.category_id chemical
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
_item_related.related_name '_chemical.temperature_decomposition'
_item_related.function_code alternate
_item_examples.case 350
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_temperature_decomposition_gt' cif_core.dic 2.3
save_
save__chemical.temperature_decomposition_lt
_item_description.description
; A temperature in kelvins below which the solid is known to
decompose. _chemical.temperature_decomposition_gt and
_chemical.temperature_decomposition_lt allow
a range of temperatures to be given.
_chemical.temperature_decomposition should always be used in
preference to these two items whenever possible.
;
_item.name '_chemical.temperature_decomposition_lt'
_item.category_id chemical
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
_item_related.related_name '_chemical.temperature_decomposition'
_item_related.function_code alternate
_item_examples.case 350
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_temperature_decomposition_lt' cif_core.dic 2.3
save_
save__chemical.temperature_sublimation
_item_description.description
; The temperature in kelvins at which the solid sublimes.
;
_item.name '_chemical.temperature_sublimation'
_item.category_id chemical
_item.mandatory_code no
_item_type.code float
_item_type_conditions.code esd
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
_item_examples.case 350
_item_related.related_name '_chemical.temperature_sublimation_esd'
_item_related.function_code associated_esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_temperature_sublimation' cif_core.dic 2.3
save_
save__chemical.temperature_sublimation_esd
_item_description.description
; The estimated standard deviation of
_chemical.temperature_sublimation.
;
_item.name '_chemical.temperature_sublimation_esd'
_item.category_id chemical
_item.mandatory_code no
_item_type.code float
_item_units.code kelvins
_item_related.related_name '_chemical.temperature_sublimation'
_item_related.function_code associated_value
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_chemical_temperature_sublimation_esd' cif_core.dic 2.3
save_
save__chemical.temperature_sublimation_gt
_item_description.description
; A temperature in kelvins above which the solid is known to
sublime. _chemical.temperature_sublimation_gt and
_chemical.temperature_sublimation_lt allow a
range of temperatures to be given.
_chemical.temperature_sublimation should always be used in
preference to these two items whenever possible.
;
_item.name '_chemical.temperature_sublimation_gt'
_item.category_id chemical
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
_item_related.related_name '_chemical.temperature_sublimation'
_item_related.function_code alternate
_item_examples.case 350
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_temperature_sublimation_gt' cif_core.dic 2.3
save_
save__chemical.temperature_sublimation_lt
_item_description.description
; A temperature in kelvins below which the solid is known to
sublime. _chemical.temperature_sublimation_gt and
_chemical.temperature_sublimation_lt allow a
range of temperatures to be given.
_chemical.temperature_sublimation should always be used in
preference to these two items whenever possible.
;
_item.name '_chemical.temperature_sublimation_lt'
_item.category_id chemical
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
_item_related.related_name '_chemical.temperature_sublimation'
_item_related.function_code alternate
_item_examples.case 350
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_chemical_temperature_sublimation_lt' cif_core.dic 2.3
save_
#
save__citation.database_id_CSD
_item_description.description
; Identifier ('refcode') of the database record in the Cambridge
Structural Database that contains details of the cited structure.
;
_item.name '_citation.database_id_CSD'
_item.category_id citation
_item.mandatory_code no
_item_type.code code
_item_examples.case LEKKUH
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_citation_database_id_CSD' cif_core.dic 2.3
save_
save__database.CSD_history
_item_description.description
; A history of changes made by the Cambridge Crystallographic Data
Centre and incorporated into the Cambridge Structural Database
(CSD).
;
_item.name '_database.CSD_history'
_item.category_id database
_item.mandatory_code no
_item_type.code text
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_database_CSD_history' cif_core.dic 2.3
save_
save__database.code_CAS
_item_description.description
; The code assigned by Chemical Abstracts.
;
_item.name '_database.code_CAS'
_item.category_id database
_item.mandatory_code no
_item_type.code line
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_database_code_CAS' cif_core.dic 2.3
save_
save__database.code_CSD
_item_description.description
; The code assigned by the Cambridge Structural Database.
;
_item.name '_database.code_CSD'
_item.category_id database
_item.mandatory_code no
_item_type.code line
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_database_code_CSD' cif_core.dic 2.3
save_
save__database.code_ICSD
_item_description.description
; The code assigned by the Inorganic Crystal Structure
Database.
;
_item.name '_database.code_ICSD'
_item.category_id database
_item.mandatory_code no
_item_type.code line
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_database_code_ICSD' cif_core.dic 2.3
save_
save__database.code_MDF
_item_description.description
; The code assigned by the Metals Data File.
;
_item.name '_database.code_MDF'
_item.category_id database
_item.mandatory_code no
_item_type.code line
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_database_code_MDF' cif_core.dic 2.3
save_
save__database.code_NBS
_item_description.description
; The code assigned by the NBS (NIST) Crystal Data Database.
;
_item.name '_database.code_NBS'
_item.category_id database
_item.mandatory_code no
_item_type.code line
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_database_code_NBS' cif_core.dic 2.3
save_
save__database.code_PDB
_item_description.description
; The code assigned by the Protein Data Bank.
;
_item.name '_database.code_PDB'
_item.category_id database
_item.mandatory_code no
_item_type.code line
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_database_code_PDB' cif_core.dic 2.3
save_
save__database.code_PDF
_item_description.description
; The code assigned by the Powder Diffraction File (JCPDS/ICDD).
;
_item.name '_database.code_PDF'
_item.category_id database
_item.mandatory_code no
_item_type.code line
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_database_code_PDF' cif_core.dic 2.3
save_
save__database.code_depnum_ccdc_fiz
_item_description.description
; Deposition numbers assigned by the Fachinformationszentrum
Karlsruhe (FIZ) to files containing structural information
archived by the Cambridge Crystallographic Data Centre (CCDC).
;
_item.name '_database.code_depnum_ccdc_fiz'
_item.category_id database
_item.mandatory_code no
_item_type.code line
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_database_code_depnum_ccdc_fiz' cif_core.dic 2.3
save_
save__database.code_depnum_ccdc_journal
_item_description.description
; Deposition numbers assigned by various journals to files
containing structural information archived by the Cambridge
Crystallographic Data Centre (CCDC).
;
_item.name '_database.code_depnum_ccdc_journal'
_item.category_id database
_item.mandatory_code no
_item_type.code line
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_database_code_depnum_ccdc_journal' cif_core.dic 2.3
save_
save__database.code_depnum_ccdc_archive
_item_description.description
; Deposition numbers assigned by the Cambridge Crystallographic
Data Centre (CCDC) to files containing structural information
archived by the CCDC.
;
_item.name '_database.code_depnum_ccdc_archive'
_item.category_id database
_item.mandatory_code no
_item_type.code line
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_database_code_depnum_ccdc_archive' cif_core.dic 2.3
save_
save__diffrn.ambient_pressure
_item_description.description
; The mean hydrostatic pressure in kilopascals at which the
intensities were measured.
;
_item.name '_diffrn.ambient_pressure'
_item.category_id diffrn
_item.mandatory_code no
_item_type.code float
_item_type_conditions.code esd
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'kilopascals'
_item_related.related_name '_diffrn.ambient_pressure_esd'
_item_related.function_code associated_esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_ambient_pressure' cif_core.dic 2.3
save_
save__diffrn.ambient_pressure_esd
_item_description.description
; The estimated standard deviation of _diffrn.ambient_pressure.
;
_item.name '_diffrn.ambient_pressure_esd'
_item.category_id diffrn
_item.mandatory_code no
_item_type.code float
_item_units.code 'kilopascals'
_item_related.related_name '_diffrn.ambient_pressure'
_item_related.function_code associated_value
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_diffrn_ambient_pressure' cif_core.dic 2.3
save_
save__diffrn.ambient_pressure_gt
_item_description.description
; The mean hydrostatic pressure in kilopascals above which
the intensities were measured. _diffrn.ambient_pressure_gt and
_diffrn.ambient_pressure_lt allow a pressure range to be given.
_diffrn.ambient_pressure should always be used in
preference to these two items whenever possible.
;
_item.name '_diffrn.ambient_pressure_gt'
_item.category_id diffrn
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_diffrn.ambient_pressure'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'kilopascals'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_ambient_pressure_gt' cif_core.dic 2.3
save_
save__diffrn.ambient_pressure_lt
_item_description.description
; The mean hydrostatic pressure in kilopascals below which
the intensities were measured. _diffrn.ambient_pressure_gt and
_diffrn.ambient_pressure_lt allow a pressure range to be given.
_diffrn.ambient_pressure should always be used in
preference to these two items whenever possible.
;
_item.name '_diffrn.ambient_pressure_lt'
_item.category_id diffrn
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_diffrn.ambient_pressure'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'kilopascals'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_ambient_pressure_lt' cif_core.dic 2.3
save_
# save__diffrn.ambient_temperature
# _item_description.description
# ; The mean temperature in kelvins at which the intensities
# were measured.
# ;
# _item.name '_diffrn.ambient_temperature'
# _item.category_id diffrn
# _item.mandatory_code no
# _item_type.code float
# _item_type_conditions.code esd
# loop_
# _item_range.minimum
# _item_range.maximum
# 0.0 0.0
# 0.0 .
# _item_units.code kelvins
# _item_related.related_name '_diffrn.ambient_temperature_esd'
# _item_related.function_code associated_esd
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_diffrn_ambient_temperature' cif_core.dic 2.3
# save_
#save__diffrn.ambient_temperature_esd
# _item_description.description
#; The estimated standard deviation of _diffrn.ambient_temp.
#;
# _item.name '_diffrn.ambient_temperature_esd'
# _item.category_id diffrn
# _item.mandatory_code no
# _item_type.code float
# _item_units.code kelvins
# _item_related.related_name '_diffrn.ambient_temp'
# _item_related.function_code associated_value
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_diffrn_ambient_temperature_esd' cif_core.dic 2.3
# save_
save__diffrn.ambient_temp_gt
_item_description.description
; The mean temperature in kelvins above which the intensities were
measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt
allow a range of temperatures to be given.
_diffrn.ambient_temp should always be used in preference
to these two items whenever possible.
;
_item.name '_diffrn.ambient_temp_gt'
_item.category_id diffrn
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_diffrn.ambient_temp'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_ambient_temperature_gt' cif_core.dic 2.3
save_
save__diffrn.ambient_temp_lt
_item_description.description
; The mean temperature in kelvins below which the intensities were
measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt
allow a range of temperatures to be given.
_diffrn.ambient_temp should always be used in preference
to these two items whenever possible.
;
_item.name '_diffrn.ambient_temp_lt'
_item.category_id diffrn
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_diffrn.ambient_temp'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_ambient_temperature_lt' cif_core.dic 2.3
save_
save__diffrn_attenuator.material
_item_description.description
; Material from which the attenuator is made.
;
_item.name '_diffrn_attenuator.material'
_item.category_id diffrn_attenuator
_item.mandatory_code no
_item_type.code text
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_attenuator_material' cif_core.dic 2.3
save_
save__diffrn_detector.area_resol_mean
_item_description.description
; The resolution of an area detector, in pixels/mm.
;
_item.name '_diffrn_detector.area_resol_mean'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'pixels_per_millimetre'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_detector_area_resol_mean' cif_core.dic 2.3
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detector used to measure
the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
# _item_related.related_name '_diffrn_radiation_detector.dtime'
# _item_related.function_code alternate
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_detector_dtime' cif_core.dic 2.3
save_
save__diffrn_refln.class_code
_item_description.description
; The code identifying the class to which this reflection has
been assigned. This code must match a value of
_diffrn_reflns_class.code. Reflections may be grouped into
classes for a variety of purposes. For example, for modulated
structures each reflection class may be defined by the
number m=sum|m~i~|, where the m~i~ are the integer coefficients
that, in addition to h,k,l, index the corresponding diffraction
vector in the basis defined for the reciprocal lattice.
;
_item.name '_diffrn_refln.class_code'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_type.code code
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_refln_class_code' cif_core.dic 2.3
save_
save__diffrn_refln.intensity_u
_item_description.description
; Standard uncertainty of the net intensity calculated from
the diffraction counts after the attenuator and standard
scales have been applied.
;
_item.name '_diffrn_refln.intensity_u'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_diffrn_refln.intensity_sigma'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_refln_intensity_u' cif_core.dic 2.3
save_
save__diffrn_reflns.av_unetI/netI
_item_description.description
; Measure [sum u(net I)|/sum|net I|] for all measured reflections.
;
_item.name '_diffrn_reflns.av_unetI/netI'
_item.category_id diffrn_reflns
_item.mandatory_code no
_item_type.code float
# _item_related.related_name '_diffrn_reflns.av_sigmaI/netI'
# _item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_reflns_av_unetI/netI' cif_core.dic 2.3
save_
#########################
## DIFFRN_REFLNS_CLASS ##
#########################
save_diffrn_reflns_class
_category.description
; Data items in the DIFFRN_REFLNS_CLASS category record details
about the classes of reflections measured in the diffraction
experiment.
;
_category.id 'diffrn_reflns_class'
_category.mandatory_code no
_category_key.name '_diffrn_reflns_class.code'
loop_
_category_examples.case
_category_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_reflns_class.number
_diffrn_reflns_class.d_res_high
_diffrn_reflns_class.d_res_low
_diffrn_reflns_class.av_R_eq
_diffrn_reflns_class.code
_diffrn_reflns_class.description
1580 0.551 6.136 0.015 'Main' 'm=0; main reflections'
1045 0.551 6.136 0.010 'Sat1' 'm=1; first-order satellites'
;
;
Example 1 - example corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~. Each reflection class is
defined by the number m=sum|m~i~|, where the m~i~ are the
integer coefficients that, in addition to h,k,l, index the
corresponding diffraction vector in the basis defined for
the reciprocal lattice.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_reflns_class.av_R_eq
_item_description.description
; For each reflection class, the residual
[sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections
used to calculate the average intensity av(I). The av|del(I)|
term is the average absolute difference between av(I) and the
individual intensities.
;
_item.name '_diffrn_reflns_class.av_R_eq'
_item.category_id diffrn_reflns_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_reflns_class_av_R_eq' cif_core.dic 2.3
save_
save__diffrn_reflns_class.av_sgI/I
_item_description.description
; Measure [sum|sigma(net I)|/sum|net I|] for all measured intensities
in a reflection class.
;
_item.name '_diffrn_reflns_class.av_sgI/I'
_item.category_id diffrn_reflns_class
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_diffrn_reflns_class.av_uI/I'
_item_related.function_code replaces
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_reflns_class_av_sgI/I' cif_core.dic 2.3
save_
save__diffrn_reflns_class.av_uI/I
_item_description.description
; Measure [sum|u(net I)|/sum|net I|] for all measured intensities
in a reflection class.
;
_item.name '_diffrn_reflns_class.av_uI/I'
_item.category_id diffrn_reflns_class
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_diffrn_reflns_class.av_sgI/I'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_reflns_class_av_uI/I' cif_core.dic 2.3
save_
save__diffrn_reflns_class.code
_item_description.description
; The code identifying a certain reflection class.
;
_item.name '_diffrn_reflns_class.code'
_item.category_id diffrn_reflns_class
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case '1'
'm1'
's2'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_reflns_class_code' cif_core.dic 2.3
save_
save__diffrn_reflns_class.description
_item_description.description
; Description of each reflection class.
;
_item.name '_diffrn_reflns_class.description'
_item.category_id diffrn_reflns_class
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'm=1 first order satellites'
'H0L0 common projection reflections'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_reflns_class_description' cif_core.dic 2.3
save_
save__diffrn_reflns_class.d_res_high
_item_description.description
; The smallest value in angstroms for the interplanar
spacings for the reflections in each measured reflection class.
This is called the highest resolution for this reflection class.
;
_item.name '_diffrn_reflns_class.d_res_high'
_item.category_id diffrn_reflns_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'angstroms'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_reflns_class_d_res_high' cif_core.dic 2.3
save_
save__diffrn_reflns_class.d_res_low
_item_description.description
; The largest value in angstroms of the interplanar
spacings for the reflections for each measured reflection class.
This is called the lowest resolution for this reflection class.
;
_item.name '_diffrn_reflns_class.d_res_low'
_item.category_id diffrn_reflns_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'angstroms'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_reflns_class_d_res_low' cif_core.dic 2.3
save_
save__diffrn_reflns_class.number
_item_description.description
; The total number of measured intensities for each reflection
class, excluding the systematic absences arising from
centring translations.
;
_item.name '_diffrn_reflns_class.number'
_item.category_id diffrn_reflns_class
_item.mandatory_code no
_item_type.code int
loop_
_item_range.minimum
_item_range.maximum
0 0
0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_reflns_class_number' cif_core.dic 2.3
save_
save__diffrn_source.take-off_angle
_item_description.description
; The complement of the angle in degrees between the normal
to the surface of the X-ray tube target and the primary
X-ray beam for beams generated by traditional X-ray tubes.
;
_item.name '_diffrn_source.take-off_angle'
_item.category_id diffrn_source
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.00 0.00
0.00 90.0
90.0 90.0
_item_examples.case 1.5
_item_units.code 'degrees'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_source_take-off_angle' cif_core.dic 2.3
save_
save__diffrn_standards.scale_u
_item_description.description
; The standard uncertainty of the individual mean
standard scales applied to the intensity data.
;
_item.name '_diffrn_standards.scale_u'
_item.category_id diffrn_standards
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_diffrn_standards.scale_sigma'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_diffrn_standards_scale_u' cif_core.dic 2.3
save_
save__exptl_crystal.colour_lustre
_item_description.description
; The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal.colour_modifier with
_exptl_crystal.colour_primary, as in 'dark-green' or
'bluish-violet', if necessary combined with
_exptl_crystal.colour_lustre, as in 'metallic-green'.
;
_item.name '_exptl_crystal.colour_lustre'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
metallic
dull
clear
_item_related.related_name '_exptl_crystal.colour'
_item_related.function_code alternate
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_exptl_crystal_colour_lustre' cif_core.dic 2.3
save_
save__exptl_crystal.colour_modifier
_item_description.description
; The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal.colour_modifier with
_exptl_crystal.colour_primary, as in 'dark-green' or
'bluish-violet', if necessary combined with
_exptl_crystal.colour_lustre, as in 'metallic-green'.
;
_item.name '_exptl_crystal.colour_modifier'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
light
dark
whitish
blackish
grayish
brownish
reddish
pinkish
orangish
yellowish
greenish
bluish
_item_related.related_name '_exptl_crystal.colour'
_item_related.function_code alternate
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_exptl_crystal_colour_modifier' cif_core.dic 2.3
save_
save__exptl_crystal.colour_primary
_item_description.description
; The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal.colour_modifier with
_exptl_crystal.colour_primary, as in 'dark-green' or
'bluish-violet', if necessary combined with
_exptl_crystal.colour_lustre, as in 'metallic-green'.
;
_item.name '_exptl_crystal.colour_primary'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
colourless
white
black
gray
brown
red
pink
orange
yellow
green
blue
violet
_item_related.related_name '_exptl_crystal.colour'
_item_related.function_code alternate
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_exptl_crystal_colour_primary' cif_core.dic 2.3
save_
save__exptl_crystal.density_meas
_item_description.description
; Density values measured using standard chemical and physical
methods. The units are megagrams per cubic metre (grams per
cubic centimetre).
;
_item.name '_exptl_crystal.density_meas'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code float
_item_type_conditions.code esd
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'megagrams_per_cubic_metre'
_item_related.related_name '_exptl_crystal.density_meas_esd'
_item_related.function_code associated_esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_exptl_crystal_density_meas' cif_core.dic 2.3
save_
save__exptl_crystal.density_meas_esd
_item_description.description
; The estimated standard deviation of _exptl_crystal.density_meas.
;
_item.name '_exptl_crystal.density_meas_esd'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code float
_item_units.code 'megagrams_per_cubic_metre'
_item_related.related_name '_exptl_crystal.density_meas'
_item_related.function_code associated_value
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_exptl_crystal_density_meas_esd' cif_core.dic 2.3
save_
save__exptl_crystal.density_meas_gt
_item_description.description
; The value above which the density measured using standard
chemical and physical methods lies. The units are megagrams
per cubic metre (grams per cubic centimetre).
_exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt
should not be used to report new experimental work, for which
_exptl_crystal.density_meas should be used. These items are
intended for use in reporting information in existing databases
and archives which would be misleading if reported under
_exptl_crystal.density_meas.
;
_item.name '_exptl_crystal.density_meas_gt'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'megagrams_per_cubic_metre'
_item_related.related_name '_exptl_crystal.density_meas'
_item_related.function_code alternate
loop_
_item_examples.case
_item_examples.detail
2.5
; lower limit for the density (only the range
within which the density lies was given in the
original paper)
;
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_exptl_crystal_density_meas_gt' cif_core.dic 2.3
save_
save__exptl_crystal.density_meas_lt
_item_description.description
; The value below which the density measured using standard
chemical and physical methods lies. The units are megagrams
per cubic metre (grams per cubic centimetre).
_exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt
should not be used to report new experimental work, for which
_exptl_crystal.density_meas should be used. These items are
intended for use in reporting information in existing databases
and archives which would be misleading if reported under
_exptl_crystal.density_meas.
;
_item.name '_exptl_crystal.density_meas_lt'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'megagrams_per_cubic_metre'
_item_related.related_name '_exptl_crystal.density_meas'
_item_related.function_code alternate
loop_
_item_examples.case
_item_examples.detail
1.0
'specimen floats in water'
5.0
; upper limit for the density (only the range
within which the density lies was given in the
original paper)
;
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_exptl_crystal_density_meas_lt' cif_core.dic 2.3
save_
save__exptl_crystal.density_meas_temp
_item_description.description
; Temperature in kelvins at which _exptl_crystal.density_meas
was determined.
;
_item.name '_exptl_crystal.density_meas_temp'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code float
_item_type_conditions.code esd
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_exptl_crystal_density_meas_temp' cif_core.dic 2.3
save_
save__exptl_crystal.density_meas_temp_esd
_item_description.description
; The estimated standard deviation of
_exptl_crystal.density_meas_temp.
;
_item.name '_exptl_crystal.density_meas_temp_esd'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code float
_item_units.code kelvins
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_exptl_crystal_density_meas_temp_esd' cif_core.dic 2.3
save_
save__exptl_crystal.density_meas_temp_gt
_item_description.description
; Temperature in kelvins above which _exptl_crystal.density_meas
was determined. _exptl_crystal.density_meas_temp_gt and
_exptl_crystal.density_meas_temp_lt should not be used for
reporting new work, for which the correct temperature of
measurement should be given. These items are intended for
use in reporting information stored in databases or archives
which would be misleading if reported under
_exptl_crystal.density_meas_temp.
;
_item.name '_exptl_crystal.density_meas_temp_gt'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
_item_related.related_name '_exptl_crystal.density_meas_temp'
_item_related.function_code alternate
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_exptl_crystal_density_meas_temp_gt' cif_core.dic 2.3
save_
save__exptl_crystal.density_meas_temp_lt
_item_description.description
; Temperature in kelvins below which _exptl_crystal.density_meas
was determined. _exptl_crystal.density_meas_temp_gt and
_exptl_crystal.density_meas_temp_lt should not be used for
reporting new work, for which the correct temperature of
measurement should be given. These items are intended for
use in reporting information stored in databases or archives
which would be misleading if reported under
_exptl_crystal.density_meas_temp.
;
_item.name '_exptl_crystal.density_meas_temp_lt'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code kelvins
_item_related.related_name '_exptl_crystal.density_meas_temp'
_item_related.function_code alternate
loop_
_item_examples.case
_item_examples.detail
300
; The density was measured at some unspecified
temperature below room temperature.
;
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_exptl_crystal_density_meas_temp_lt' cif_core.dic 2.3
save_
save__geom_bond.valence
_item_description.description
; The bond valence calculated from _geom_bond.dist.
;
_item.name '_geom_bond.valence'
_item.category_id geom_bond
_item.mandatory_code no
_item_type.code int
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_geom_bond_valence' cif_core.dic 2.3
save_
save__publ_author.id_iucr
_item_description.description
; Identifier in the IUCr contact database of a publication
author. This identifier may be available from the World
Directory of Crystallographers (http://wdc.iucr.org).
;
_item.name '_publ_author.id_iucr'
_item.category_id publ_author
_item.mandatory_code no
_item_type.code code
_item_examples.case 2985
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_publ_author_id_iucr' cif_core.dic 2.3
save_
save__refine.ls_R_factor_gt
_item_description.description
; Residual factor for the reflections (with number given by
_reflns.number_gt) judged significantly intense (i.e. satisfying
the threshold specified by _reflns.threshold_expression)
and included in the refinement. The reflections also satisfy
the resolution limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low. This is the conventional R
factor. See also _refine.ls_wR_factor_ definitions.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
;
_item.name '_refine.ls_R_factor_gt'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_refine.ls_R_factor_obs'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_R_factor_gt' cif_core.dic 2.3
save_
save__refine.ls_goodness_of_fit_gt
_item_description.description
; The least-squares goodness-of-fit parameter S for
significantly intense reflections (see
_reflns.threshold_expression) after the final cycle of
refinement. Ideally, account should be taken of parameters
restrained in the least-squares refinement. See also
_refine.ls_restrained_S_ definitions.
{ sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
_item.name '_refine.ls_goodness_of_fit_gt'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_refine.ls_goodness_of_fit_obs'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_goodness_of_fit_gt' cif_core.dic 2.3
save_
save__refine.ls_goodness_of_fit_ref
_item_description.description
; The least-squares goodness-of-fit parameter S for all
reflections included in the refinement after the final cycle
of refinement. Ideally, account should be taken of parameters
restrained in the least-squares refinement. See also
_refine_ls_restrained_S_ definitions.
{ sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
_item.name '_refine.ls_goodness_of_fit_ref'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_goodness_of_fit_ref' cif_core.dic 2.3
save_
# save__refine.ls_shift/esd_max
# _item_description.description
# ; The largest ratio of the final least-squares parameter
# shift to the final standard uncertainty (s.u.,
# formerly described as estimated standard deviation, e.s.d.).
# ;
# _item.name '_refine.ls_shift/esd_max'
# _item.category_id refine
# _item.mandatory_code no
# _item_type.code float
# _item_related.related_name '_refine.ls_shift/su_max'
# _item_related.function_code replaces
# loop_
# _item_range.minimum
# _item_range.maximum
# 0.0 0.0
# 0.0 .
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_refine_ls_shift/esd_max' cif_core.dic 2.3
# save_
#
# save__refine.ls_shift/esd_mean
# _item_description.description
# ; The average ratio of the final least-squares parameter
# shift to the final standard uncertainty (s.u.,
# formerly described as estimated standard deviation, e.s.d.).
# ;
#
# _item.name '_refine.ls_shift/esd_mean'
# _item.category_id refine
# _item.mandatory_code no
# _item_type.code float
# _item_related.related_name '_refine.ls_shift/su_mean'
# _item_related.function_code replaces
# loop_
# _item_range.minimum
# _item_range.maximum
# 0.0 0.0
# 0.0 .
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_refine_ls_shift/esd_mean' cif_core.dic 2.3
# save_
save__refine.ls_shift_over_su_max
_item_description.description
; The largest ratio of the final least-squares parameter
shift to the final standard uncertainty.
;
_item.name '_refine.ls_shift_over_su_max'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_refine.ls_shift_over_esd_max'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_shift/su_max' cif_core.dic 2.3
save_
save__refine.ls_shift_over_su_max_lt
_item_description.description
; An upper limit for the largest ratio of the final
least-squares parameter shift to the final
standard uncertainty. This item is used when the largest
value of the shift divided by the final standard uncertainty
is too small to measure.
;
_item.name '_refine.ls_shift_over_su_max_lt'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_refine.ls_shift_over_su_max'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_shift/su_max_lt' cif_core.dic 2.3
save_
save__refine.ls_shift_over_su_mean
_item_description.description
; The average ratio of the final least-squares parameter
shift to the final standard uncertainty.
;
_item.name '_refine.ls_shift_over_su_mean'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_refine.ls_shift_over_esd_mean'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_shift/su_mean' cif_core.dic 2.3
save_
save__refine.ls_shift_over_su_mean_lt
_item_description.description
; An upper limit for the average ratio of the final
least-squares parameter shift to the
final standard uncertainty. This
item is used when the average value of the shift divided by
the final standard uncertainty is too small to measure.
;
_item.name '_refine.ls_shift_over_su_mean_lt'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_refine.ls_shift_over_su_mean'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_shift/su_mean_lt' cif_core.dic 2.3
save_
#####################
## REFINE_LS_CLASS ##
#####################
save_refine_ls_class
_category.description
; Data items in the REFINE_LS_CLASS category record details
about the reflections used for the structure refinement
for each reflection class separately.
;
_category.id 'refine_ls_class'
_category.mandatory_code no
_category_key.name '_refine_ls_class.code'
loop_
_category_examples.case
_category_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_refine_ls_class.R_factor_gt
_refine_ls_class.code
0.057 'Main'
0.074 'Com'
0.064 'NbRefls'
0.046 'LaRefls'
0.112 'Sat1'
0.177 'Sat2'
;
;
Example 1 - data for a modulated structure from van Smaalen
[J. Phys. Condens. Matter (1991), 3, 1247-1263].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_ls_class.code
_item_description.description
; The code identifying a certain reflection class. This code must
match a _reflns_class.code.
;
_item.name '_refine_ls_class.code'
_item.category_id refine_ls_class
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case
'1'
'm1'
's2'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_class_code' cif_core.dic 2.3
save_
save__refine_ls_class.d_res_high
_item_description.description
; For each reflection class, the lowest value in angstroms
for the interplanar spacings for the reflections used in the
refinement. This is called the highest resolution.
;
_item.name '_refine_ls_class.d_res_high'
_item.category_id refine_ls_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'angstroms'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_class_d_res_high' cif_core.dic 2.3
save_
save__refine_ls_class.d_res_low
_item_description.description
; For each reflection class, the highest value in angstroms
for the interplanar spacings for the reflections used in the
refinement. This is called the lowest resolution.
;
_item.name '_refine_ls_class.d_res_low'
_item.category_id refine_ls_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'angstroms'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_class_d_res_low' cif_core.dic 2.3
save_
save__refine_ls_class.R_factor_gt
_item_description.description
; For each reflection class, the residual factor for significantly
intense reflections (see _reflns.threshold_expression) included
in the refinement.
The reflections also satisfy the resolution limits established by
_refine_ls_class.d_res_high and _refine_ls_class.d_res_low.
This is the conventional R factor. See also the definition of
_refine_ls_class.wR_factor_all.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class.
;
_item.name '_refine_ls_class.R_factor_gt'
_item.category_id refine_ls_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_class_R_factor_gt' cif_core.dic 2.3
save_
save__refine_ls_class.R_factor_all
_item_description.description
; For each reflection class, the residual factor for all
reflections satisfying the resolution limits established by
_refine_ls_class.d_res_high and _refine_ls_class.d_res_low.
This is the conventional R factor. See also the
definition of _refine_ls_class.wR_factor_all.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class.
;
_item.name '_refine_ls_class.R_factor_all'
_item.category_id refine_ls_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_class_R_factor_all' cif_core.dic 2.3
save_
save__refine_ls_class.R_Fsqd_factor
_item_description.description
; For each reflection class, the residual factor R(F^2^) calculated
on the squared amplitudes of the observed and calculated
structure factors, for the reflections judged significantly
intense (i.e. satisfying the threshold specified by
_reflns.threshold_expression) and included in the refinement.
The reflections also satisfy the resolution limits established
by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low.
sum | F(obs)^2^ - F(calc)^2^ |
R(Fsqd) = -------------------------------
sum F(obs)^2^
F(obs)^2^ = squares of the observed structure-factor amplitudes
F(calc)^2^ = squares of the calculated structure-factor
amplitudes
and the sum is taken over the reflections of this class.
;
_item.name '_refine_ls_class.R_Fsqd_factor'
_item.category_id refine_ls_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_class_R_Fsqd_factor' cif_core.dic 2.3
save_
save__refine_ls_class.R_I_factor
_item_description.description
; For each reflection class, the residual factor R(I) for the
reflections judged significantly intense (i.e. satisfying the
threshold specified by _reflns.threshold_expression) and
included in the refinement.
This is most often calculated in Rietveld refinements
against powder data, where it is referred to as R~B~ or R~Bragg~
sum | I(obs) - I(calc) |
R(I) = ------------------------
sum | I(obs) |
I(obs) = the net observed intensities
I(calc) = the net calculated intensities
and the sum is taken over the reflections of this class.
;
_item.name '_refine_ls_class.R_I_factor'
_item.category_id refine_ls_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_class_R_I_factor' cif_core.dic 2.3
save_
save__refine_ls_class.wR_factor_all
_item_description.description
; For each reflection class, the weighted residual factor for all
reflections included in the refinement. The reflections also
satisfy the resolution limits established by
_refine_ls_class.d_res_high and _refine_ls_class.d_res_low.
See also the _refine_ls_class.R_factor_ definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
_refine.ls_structure_factor_coef
Y(calc) = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
and the sum is taken over the reflections of this class.
;
_item.name '_refine_ls_class.wR_factor_all'
_item.category_id refine_ls_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine_ls_class_wR_factor_all' cif_core.dic 2.3
save_
save__refln.class_code
_item_description.description
; The code identifying the class to which this reflection has been
assigned. This code must match a value of _reflns_class.code.
Reflections may be grouped into classes for a variety of
purposes. For example, for modulated structures each reflection
class may be defined by the number m=sum|m~i~|, where the m~i~
are the integer coefficients that, in addition to h,k,l, index
the corresponding diffraction vector in the basis defined
for the reciprocal lattice.
;
_item.name '_refln.class_code'
_item.category_id refln
_item.mandatory_code no
_item_type.code code
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refln_class_code' cif_core.dic 2.3
save_
save__refln.d_spacing
_item_description.description
; The d spacing in angstroms for this reflection. This is related
to the (sin theta)/lambda value by the expression
_refln.d_spacing = 2/(_refln.sint/lambda).
;
_item.name '_refln.d_spacing'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'angstroms'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refln_d_spacing' cif_core.dic 2.3
save_
save__refln.include_status
_item_description.description
; Classification of a reflection so as to indicate its status with
respect to inclusion in the refinement and the calculation of
R factors.
;
_item.name '_refln.include_status'
_item.category_id refln
_item.mandatory_code no
_item_type.code code
_item_related.related_name '_refln.status'
_item_related.function_code alternate
loop_
_item_enumeration.value
_item_enumeration.detail
o
; (lower-case letter o for 'observed')
satisfies _refine.ls_d_res_high
satisfies _refine.ls_d_res_low
exceeds _reflns.threshold_expression
;
<
; satisfies _refine.ls_d_res_high
satisfies _refine.ls_d_res_low
does not exceed
_reflns.threshold_expression
;
- 'systematically absent reflection'
x 'unreliable measurement -- not used'
h 'does not satisfy _refine.ls_d_res_high'
l 'does not satisfy _refine.ls_d_res_low'
# _item_default.value o
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refln_include_status' cif_core.dic 2.3
save_
save__refln.mean_path_length_tbar
_item_description.description
; Mean path length in millimetres through the crystal for this
reflection.
;
_item.name '_refln.mean_path_length_tbar'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'millimetres'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refln_mean_path_length_tbar' cif_core.dic 2.3
save_
# save__refln.observed_status
# _item_description.description
# ; Classification of a reflection so as to indicate its status
# with respect to inclusion in refinement and calculation of
# R factors.
# ;
#
# _item.name '_refln.observed_status'
# _item.category_id refln
# _item.mandatory_code no
# _item_type.code code
# _item_related.related_name '_refln.include_status'
# _item_related.function_code replaces
# loop_
# _item_enumeration.value
# _item_enumeration.detail
# o
# ; satisfies _refine.ls_d_res_high
# satisfies _refine.ls_d_res_low
# observed by _reflns_observed_criterion
# ;
# <
# ; satisfies _refine.ls_d_res_high
# satisfies _refine.ls_d_res_low
# unobserved by _reflns.observed_criterion
# ;
# - 'systematically absent reflection'
# x 'unreliable measurement -- not used'
# h 'does not satisfy _refine.ls_d_res_high'
# l 'does not satisfy _refine.ls_d_res_low'
#
# # _item_default.value o
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_refln_observed_status' cif_core.dic 2.3
# save_
# save__refln.sint/lambda
# _item_description.description
# ; The (sin theta)/lambda value in reciprocal angstroms for this
# reflection.
# ;
# _item.name '_refln.sint/lambda'
# _item.category_id refln
# _item.mandatory_code no
# _item_type.code float
# loop_
# _item_range.minimum
# _item_range.maximum
# 0.0 0.0
# 0.0 .
# _item_units.code 'reciprocal_angstroms'
# loop_
# _item_aliases.alias_name
# _item_aliases.dictionary
# _item_aliases.version
# '_refln_sint/lambda' cif_core.dic 2.3
# save_
save__reflns.Friedel_coverage
_item_description.description
; The proportion of Friedel-related reflections present in
the number of 'independent' reflections specified by
the item _reflns.number_all.
This proportion is calculated as the ratio:
[N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry)
where, working from the DIFFRN_REFLN list,
N(Crystal class) is the number of reflections obtained on
averaging under the symmetry of the crystal class
N(Laue symmetry) is the number of reflections obtained on
averaging under the Laue symmetry.
Examples:
(a) For centrosymmetric structures, the value of
_reflns.Friedel_coverage is
necessarily equal to 0.0, as the crystal class
is identical to the Laue symmetry.
(b) For whole-sphere data for a crystal in the space
group P1, _reflns.Friedel_coverage is equal to 1.0,
as no reflection h k l is equivalent to -h -k -l
in the crystal class and all Friedel pairs
{h k l; -h -k -l} have been measured.
(c) For whole-sphere data in space group Pmm2,
_reflns.Friedel_coverage
will be < 1.0 because although reflections h k l and
-h -k -l are not equivalent when h k l indices are
nonzero, they are when l=0.
(d) For a crystal in space group Pmm2, measurements of the
two inequivalent octants h >= 0, k >=0, l lead to the
same value as in (c), whereas measurements of the
two equivalent octants h >= 0, k, l >= 0 will lead to
a zero value for _reflns.Friedel_coverage.
;
_item.name '_reflns.Friedel_coverage'
_item.category_id reflns
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 1.0
1.0 1.0
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_Friedel_coverage' cif_core.dic 2.3
save_
save__reflns.number_gt
_item_description.description
; The number of reflections in the REFLN list (not the
DIFFRN_REFLN list) that are significantly intense, satisfying
the criterion specified by _reflns.threshold_expression. This may
include Friedel-equivalent reflections (i.e. those which are
symmetry-equivalent under the Laue symmetry but inequivalent
under the crystal class) according to the nature of the
structure and the procedures used. Any special characteristics
of the reflections included in the REFLN list should be
described using the item _reflns.details.
;
_item.name '_reflns.number_gt'
_item.category_id reflns
_item.mandatory_code no
_item_type.code int
# _item_related.related_name '_reflns.number_observed'
# _item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0 0
0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_number_gt' cif_core.dic 2.3
save_
save__reflns.threshold_expression
_item_description.description
; The threshold, usually based on multiples of u(I), u(F^2^)
or u(F), that serves to identify significantly intense
reflections, the number of which is given by _reflns.number_gt.
These reflections are used in the calculation of
_refine.ls_R_factor_gt.
;
_item.name '_reflns.threshold_expression'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns_threshold_expression'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.3
loop_
_item_related.related_name
_item_related.function_code '_reflns.observed_criterion'
alternate
_item_type.code text
_item_examples.case 'I>2u(I)'
save_
##################
## REFLNS_CLASS ##
##################
save_reflns_class
_category.description
; Data items in the REFLNS_CLASS category record details
of the reflections used to determine the structural
parameters for each reflection class.
;
_category.id 'reflns_class'
_category.mandatory_code no
_category_key.name '_reflns_class.code'
loop_
_category_examples.case
_category_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_reflns_class.number_gt
_reflns_class.code
584 'Main'
226 'Sat1'
50 'Sat2'
;
;
Example 1 - example corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__reflns_class.code
_item_description.description
; The code identifying a certain reflection class.
;
_item.name '_reflns_class.code'
_item.category_id reflns_class
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case
'1'
'm1'
's2'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_class_code' cif_core.dic 2.3
save_
save__reflns_class.description
_item_description.description
; Description of each reflection class.
;
_item.name '_reflns_class.description'
_item.category_id reflns_class
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'm=1 first order satellites'
'H0L0 common projection reflections'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_class_description' cif_core.dic 2.3
save_
save__reflns_class.d_res_high
_item_description.description
; For each reflection class, the smallest value in angstroms
for the interplanar spacings for the reflections used in the
refinement. This is called the highest resolution.
;
_item.name '_reflns_class.d_res_high'
_item.category_id reflns_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'angstroms'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_class_d_res_high' cif_core.dic 2.3
save_
save__reflns_class.d_res_low
_item_description.description
; For each reflection class, the largest value in angstroms
for the interplanar spacings for the reflections used in the
refinement. This is called the lowest resolution.
;
_item.name '_reflns_class.d_res_low'
_item.category_id reflns_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
_item_units.code 'angstroms'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_class_d_res_low' cif_core.dic 2.3
save_
save__reflns_class.number_gt
_item_description.description
; For each reflection class, the number of significantly intense
reflections (see _reflns.threshold_expression) in the REFLN
list (not the DIFFRN_REFLN list). This may include Friedel-
equivalent reflections (i.e. those which are symmetry-equivalent
under the Laue symmetry but inequivalent under the crystal
class) according to the nature of the structure and the
procedures used. Any special characteristics of the reflections
included in the REFLN list should be described using the item
_reflns.details.
;
_item.name '_reflns_class.number_gt'
_item.category_id reflns_class
_item.mandatory_code no
_item_type.code int
loop_
_item_range.minimum
_item_range.maximum
0 0
0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_class_number_gt' cif_core.dic 2.3
save_
save__reflns_class.number_total
_item_description.description
; For each reflection class, the total number of reflections
in the REFLN list (not the DIFFRN_REFLN list). This may
include Friedel-equivalent reflections (i.e. those which are
symmetry-equivalent under the Laue symmetry but inequivalent
under the crystal class) according to the nature of the
structure and the procedures used. Any special characteristics
of the reflections included in the REFLN list should be
described using the item _reflns.details.
;
_item.name '_reflns_class.number_total'
_item.category_id reflns_class
_item.mandatory_code no
_item_type.code int
loop_
_item_range.minimum
_item_range.maximum
0 0
0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_class_number_total' cif_core.dic 2.3
save_
save__reflns_class.R_factor_all
_item_description.description
; For each reflection class, the residual factor for all
reflections included in the refinement.
The reflections also satisfy the resolution limits established by
_reflns_class.d_res_high and _reflns_class.d_res_low.
This is the conventional R factor. See also the
definition of _reflns_class.wR_factor_all.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class.
;
_item.name '_reflns_class.R_factor_all'
_item.category_id reflns_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_class_R_factor_all' cif_core.dic 2.3
save_
save__reflns_class.R_factor_gt
_item_description.description
; For each reflection class, the residual factor for significantly
intense reflections (see _reflns.threshold_expression) included
in the refinement.
The reflections also satisfy the resolution limits established by
_reflns_class.d_res_high and _reflns_class.d_res_low.
This is the conventional R factor. See also the
definition of _reflns_class.wR_factor_all.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class.
;
_item.name '_reflns_class.R_factor_gt'
_item.category_id reflns_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_class_R_factor_gt' cif_core.dic 2.3
save_
save__reflns_class.R_Fsqd_factor
_item_description.description
; For each reflection class, the residual factor R(F^2^) calculated
on the squared amplitudes of the observed and calculated
structure factors for the reflections judged significantly
intense (i.e. satisfying the threshold specified by
_reflns.threshold_expression) and included in the refinement.
The reflections also satisfy the resolution limits established
by _reflns_class.d_res_high and _reflns_class.d_res_low.
sum | F(obs)^2^ - F(calc)^2^ |
R(Fsqd) = -------------------------------
sum F(obs)^2^
F(obs)^2^ = squares of the observed structure-factor amplitudes
F(calc)^2^ = squares of the calculated structure-factor
amplitudes
and the sum is taken over the reflections of this class.
;
_item.name '_reflns_class.R_Fsqd_factor'
_item.category_id reflns_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_class_R_Fsqd_factor' cif_core.dic 2.3
save_
save__reflns_class.R_I_factor
_item_description.description
; For each reflection class, the residual factor R(I) for the
reflections judged significantly intense (i.e. satisfying the
threshold specified by _reflns.threshold_expression) and
included in the refinement.
This is most often calculated in Rietveld refinements
against powder data, where it is referred to as R~B~ or R~Bragg~.
sum | I(obs) - I(calc) |
R(I) = ------------------------
sum | I(obs) |
I(obs) = the net observed intensities
I(calc) = the net calculated intensities
and the sum is taken over the reflections of this class.
;
_item.name '_reflns_class.R_I_factor'
_item.category_id reflns_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_class_R_I_factor' cif_core.dic 2.3
save_
save__reflns_class.wR_factor_all
_item_description.description
; For each reflection class, the weighted residual factors for all
reflections included in the refinement. The reflections also
satisfy the resolution limits established by
_reflns_class.d_res_high and _reflns_class.d_res_low.
See also _reflns_class.R_factor_ definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
_refine.ls_structure_factor_coef
Y(calc) = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
and the sum is taken over the reflections of this class.
;
_item.name '_reflns_class.wR_factor_all'
_item.category_id reflns_class
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_class_wR_factor_all' cif_core.dic 2.3
save_
save__reflns_shell.meanI_over_sigI_gt
_item_description.description
; The ratio of the mean of the intensities of the significantly
intense reflections (see _reflns.threshold_expression) in
this shell to the mean of the standard uncertainties of the
intensities of the significantly intense reflections in this
shell.
;
_item.name '_reflns_shell.meanI_over_sigI_gt'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_reflns_shell.meanI_over_uI_gt'
_item_related.function_code replaces
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_shell_meanI_over_sigI_gt' cif_core.dic 2.3
save_
save__reflns_shell.meanI_over_uI_all
_item_description.description
; The ratio of the mean of the intensities of all reflections
in this shell to the mean of the standard uncertainties of the
intensities of all reflections in this shell.
;
_item.name '_reflns_shell.meanI_over_uI_all'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_reflns_shell.meanI_over_sigI_all'
_item_related.function_code alternate
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_shell_meanI_over_uI_all' cif_core.dic 2.3
save_
save__reflns_shell.meanI_over_uI_gt
_item_description.description
; The ratio of the mean of the intensities of the significantly
intense reflections (see _reflns.threshold_expression) in
this shell to the mean of the standard uncertainties of the
intensities of the significantly intense reflections in this
shell.
;
_item.name '_reflns_shell.meanI_over_uI_gt'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code
'_reflns_shell.meanI_over_sigI_gt' alternate
'_reflns_shell.meanI_over_sigI_obs' alternate
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_shell_meanI_over_uI_gt' cif_core.dic 2.3
save_
save__reflns_shell.number_measured_gt
_item_description.description
; The number of significantly intense reflections
(see _reflns.threshold_expression) measured for this
shell.
;
_item.name '_reflns_shell.number_measured_gt'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code int
_item_related.related_name '_reflns_shell.number_measured_obs'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0 0
0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_shell_number_measured_gt' cif_core.dic 2.3
save_
save__reflns_shell.number_unique_gt
_item_description.description
; The total number of significantly intense reflections
(see _reflns.threshold_expression) resulting from merging
measured symmetry-equivalent reflections for this resolution
shell.
;
_item.name '_reflns_shell.number_unique_gt'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code int
_item_related.related_name '_reflns_shell.number_unique_obs'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0 0
0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_shell_number_unique_gt' cif_core.dic 2.3
save_
save__reflns_shell.percent_possible_gt
_item_description.description
; The percentage of geometrically possible reflections
represented by significantly intense reflections
(see _reflns.threshold_expression) measured for this
shell.
;
_item.name '_reflns_shell.percent_possible_gt'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_reflns_shell.percent_possible_obs'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 100.0
100.0 100.0
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_shell_percent_possible_gt' cif_core.dic 2.3
save_
save__reflns_shell.Rmerge_F_gt
_item_description.description
; The value of Rmerge(F) for significantly intense reflections
(see _reflns.threshold_expression) in a given shell.
sum~i~ ( sum~j~ | F~j~ - | )
Rmerge(F) = --------------------------------
sum~i~ ( sum~j~ )
F~j~ = the amplitude of the jth observation of reflection i
= the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
_item.name '_reflns_shell.Rmerge_F_gt'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_reflns_shell.Rmerge_F_obs'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_shell_Rmerge_F_gt' cif_core.dic 2.3
save_
save__reflns_shell.Rmerge_I_gt
_item_description.description
; The value of Rmerge(I) for significantly intense reflections
(see _reflns.threshold_expression) in a given shell.
sum~i~ ( sum~j~ | I~j~ - | )
Rmerge(I) = --------------------------------
sum~i~ ( sum~j~ )
I~j~ = the intensity of the jth observation of reflection i
= the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
_item.name '_reflns_shell.Rmerge_I_gt'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code float
_item_related.related_name '_reflns_shell.Rmerge_I_obs'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 .
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_reflns_shell_Rmerge_I_gt' cif_core.dic 2.3
save_
#################
## SPACE_GROUP ##
#################
save_space_group
_category.description
; Contains all the data items that refer to the space group as a
whole, such as its name or crystal system. They may be looped,
for example, in a list of space groups and their properties.
Only a subset of the SPACE_GROUP category items appear in
this dictionary. The remainder are found in the symmetry CIF
dictionary.
Space-group types are identified by their number as given in
International Tables for Crystallography Vol. A. Specific
settings of the space groups can be identified either by their
Hall symbol or by specifying their symmetry operations.
The commonly used Hermann-Mauguin symbol determines the
space-group type uniquely but several different Hermann-Mauguin
symbols may refer to the same space-group type. A Hermann-Mauguin
symbol contains information on the choice of the basis, but not
on the choice of origin. Different formats for the
Hermann-Mauguin symbol are found in the symmetry CIF dictionary.
;
_category.id 'space_group'
_category.mandatory_code no
_category_key.name '_space_group.id'
loop_
_category_examples.case
_category_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_space_group.id 1
_space_group.name_H-M_alt 'C 2/c'
_space_group.IT_number 15
_space_group.name_Hall '-C 2yc'
_space_group.crystal_system monoclinic
;
;
Example 1 - the monoclinic space group No. 15 with unique axis b.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__space_group.crystal_system
_item_description.description
; The name of the system of geometric crystal classes of space
groups (crystal system) to which the space group belongs.
Note that rhombohedral space groups belong to the
trigonal system.
;
_item.name '_space_group.crystal_system'
_item.category_id space_group
_item.mandatory_code no
_item_type.code code
_item_related.related_name '_symmetry.cell_setting'
_item_related.function_code alternate
loop_
_item_enumeration.value triclinic
monoclinic
orthorhombic
tetragonal
trigonal
hexagonal
cubic
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_space_group_crystal_system' cif_core.dic 2.3
save_
save__space_group.id
_item_description.description
; This is the unique identifier for the SPACE_GROUP category.
;
_item.name '_space_group.id'
_item.category_id space_group
_item.mandatory_code yes
_item_type.code code
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_space_group_id' cif_core.dic 2.3
save_
save__space_group.IT_number
_item_description.description
; The number as assigned in International Tables for
Crystallography Vol. A, specifying the proper affine class (i.e.
the orientation-preserving affine class) of space groups
(crystallographic space-group type) to which the space group
belongs. This number defines the space-group type but not
the coordinate system in which it is expressed.
;
_item.name '_space_group.IT_number'
_item.category_id space_group
_item.mandatory_code no
_item_type.code int
_item_related.related_name '_symmetry.Int_Tables_number'
_item_related.function_code alternate
loop_
_item_range.minimum
_item_range.maximum
1 1
1 230
230 230
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_space_group_IT_number' cif_core.dic 2.3
save_
save__space_group.name_Hall
_item_description.description
; Space-group symbol defined by Hall.
Each component of the space-group name is separated by a
space or an underscore. The use of a space is strongly
recommended. The underscore is only retained because it
was used in old CIFs. It should not be
used in new CIFs.
_space_group.name_Hall uniquely defines the space group and
its reference to a particular coordinate system.
Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
(1981), A37, 921.
[See also International Tables for Crystallography
Vol. B (2001), Chapter 1.4, Appendix 1.4.2.]
;
_item.name '_space_group.name_Hall'
_item.category_id space_group
_item.mandatory_code no
_item_type.code line
_item_related.related_name '_symmetry.space_group_name_Hall'
_item_related.function_code alternate
loop_
_item_examples.case
_item_examples.detail
'P 2c -2ac' 'equivalent to Pca21'
'-I 4bd 2ab 3' 'equivalent to Ia3d'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_space_group_name_Hall' cif_core.dic 2.3
save_
save__space_group.name_H-M_alt
_item_description.description
; _space_group.name_H-M_alt allows any Hermann-Mauguin symbol
to be given. The way in which this item is used is determined
by the user and in general is not intended to be interpreted by
computer. It may, for example, be used to give one of the
extended Hermann-Mauguin symbols given in Table 4.3.2.1 of
International Tables for Crystallography Vol. A (2002) or
a Hermann-Mauguin symbol for a conventional or unconventional
setting.
Each component of the space-group name is separated by a
space or an underscore. The use of a space is strongly
recommended. The underscore is only retained because it
was used in old CIFs. It should not be
used in new CIFs. Subscripts should appear without special
symbols. Bars should be given as negative signs before the
numbers to which they apply.
The commonly used Hermann-Mauguin symbol determines the space-
group type uniquely but a given space-group type may be
described by more than one Hermann-Mauguin symbol. The space-
group type is best described using _space_group.IT_number.
The Hermann-Mauguin symbol may contain information on the
choice of basis, but not on the choice of origin. To
define the setting uniquely, use _space_group.name_Hall or
list the symmetry operations.
;
_item.name '_space_group.name_H-M_alt'
_item.category_id space_group
_item.mandatory_code no
_item_type.code line
_item_related.related_name '_symmetry.space_group_name_H-M'
_item_related.function_code alternate
loop_
_item_examples.case
_item_examples.detail
; loop_
_space_group.name_H-M_alt
'C m c m'
'C 2/c 2/m 21/m'
'A m a m'
;
'three examples for space group No. 63'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_space_group_name_H-M_alt' cif_core.dic 2.3
save_
#######################
## SPACE_GROUP_SYMOP ##
#######################
save_space_group_symop
_category.description
; Contains information about the symmetry operations of the
space group.
;
_category.id 'space_group_symop'
_category.mandatory_code no
_category_key.name '_space_group_symop.id'
loop_
_category_examples.case
_category_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; loop_
_space_group_symop.id
_space_group_symop.operation_xyz
1 x,y,z
2 -x,-y,-z
3 -x,1/2+y,1/2-z
4 x,1/2-y,1/2+z
;
;
Example 1 - The symmetry operations for the space group P21/c.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__space_group_symop.id
_item_description.description
; An arbitrary identifier that uniquely labels each symmetry
operation in the list.
;
_item.name '_space_group_symop.id'
_item.category_id space_group_symop
_item.mandatory_code yes
_item_type.code code
_item_related.related_name '_symmetry_equiv.id'
_item_related.function_code alternate
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_space_group_symop_id' cif_core.dic 2.3
save_
save__space_group_symop.operation_xyz
_item_description.description
; A parsable string giving one of the symmetry operations of the
space group in algebraic form. If W is a matrix representation
of the rotational part of the symmetry operation defined by the
positions and signs of x, y and z, and w is a column of
translations defined by the fractions, an equivalent position
X' is generated from a given position X by the equation
X' = WX + w
(Note: X is used to represent bold_italics_x in International
Tables for Crystallography Vol. A, Part 5)
When a list of symmetry operations is given, it must contain
a complete set of coordinate representatives which generates
all the operations of the space group by the addition of
all primitive translations of the space group. Such
representatives are to be found as the coordinates of
the general-equivalent position in International Tables for
Crystallography Vol. A (2002), to which it is necessary to
add any centring translations shown above the
general-equivalent position.
That is to say, it is necessary to list explicity all the
symmetry operations required to generate all the atoms in
the unit cell defined by the setting used.
;
_item.name '_space_group_symop.operation_xyz'
_item.category_id space_group_symop
_item.mandatory_code no
_item_type.code line
# _item_default.value 'x,y,z'
_item_related.related_name '_symmetry_equiv.pos_as_xyz'
_item_related.function_code alternate
loop_
_item_examples.case
_item_examples.detail
'x,1/2-y,1/2+z'
; glide reflection through the plane (x,1/4,z),
with glide vector 1/2 c
;
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_space_group_symop_operation_xyz' cif_core.dic 2.3
save_
save__space_group_symop.sg_id
_item_description.description
; This must match a particular value of _space_group.id, allowing
the symmetry operation to be identified with a particular space
group.
;
_item.name '_space_group_symop.sg_id'
_item.category_id space_group_symop
_item.mandatory_code no
_item_type.code code
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_space_group_symop_sg_id' cif_core.dic 2.3
save_
###################
## VALENCE_PARAM ##
###################
save_valence_param
_category.description
; Data items in the VALENCE_PARAM category define the
parameters used for calculating bond valences from bond
lengths. In addition to the parameters, a pointer
is given to the reference (in VALENCE_REF) from which
the bond-valence parameters were taken.
;
_category.id 'valence_param'
_category.mandatory_code no
loop_
_category_key.name
'_valence_param.atom_1'
'_valence_param.atom_1_valence'
'_valence_param.atom_2'
'_valence_param.atom_2_valence'
loop_
_category_examples.case
_category_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_valence_param.atom_1
_valence_param.atom_1_valence
_valence_param.atom_2
_valence_param.atom_2_valence
_valence_param.Ro
_valence_param.B
_valence_param.ref_id
_valence_param.details
Cu 2 O -2 1.679 0.37 a .
Cu 2 O -2 1.649 0.37 j .
Cu 2 N -3 1.64 0.37 m '2-coordinate N'
Cu 2 N -3 1.76 0.37 m '3-coordinate N'
loop_
_valence_ref.id
_valence_ref.reference
a 'Brown & Altermatt (1985), Acta Cryst. B41, 244-247'
j 'Liu & Thorp (1993), Inorg. Chem. 32, 4102-4205'
m 'See, Krause & Strub (1998), Inorg. Chem. 37, 5369-5375'
;
;
Example 1 - a bond-valence parameter list with accompanying references.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__valence_param.atom_1
_item_description.description
; The element symbol of the first atom forming the bond whose
bond-valence parameters are given in this category.
;
_item.name '_valence_param.atom_1'
_item.category_id valence_param
_item.mandatory_code yes
_item_type.code code
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_valence_param_atom_1' cif_core.dic 2.3
save_
save__valence_param.atom_1_valence
_item_description.description
; The valence (formal charge) of the first atom whose
bond-valence parameters are given in this category.
;
_item.name '_valence_param.atom_1_valence'
_item.category_id valence_param
_item.mandatory_code yes
_item_type.code int
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_valence_param_atom_1_valence' cif_core.dic 2.3
save_
save__valence_param.atom_2
_item_description.description
; The element symbol of the second atom forming the bond whose
bond-valence parameters are given in this category.
;
_item.name '_valence_param.atom_2'
_item.category_id valence_param
_item.mandatory_code yes
_item_type.code code
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_valence_param_atom_2' cif_core.dic 2.3
save_
save__valence_param.atom_2_valence
_item_description.description
; The valence (formal charge) of the second atom whose
bond-valence parameters are given in this category.
;
_item.name '_valence_param.atom_2_valence'
_item.category_id valence_param
_item.mandatory_code yes
_item_type.code int
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_valence_param_atom_2_valence' cif_core.dic 2.3
save_
save__valence_param.B
_item_description.description
; The bond-valence parameter B used in the expression
s = exp[(Ro - R)/B]
where s is the valence of a bond of length R.
;
_item.name '_valence_param.B'
_item.category_id valence_param
_item.mandatory_code no
_item_type.code float
_item_units.code 'angstroms'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_valence_param_B' cif_core.dic 2.3
save_
save__valence_param.details
_item_description.description
; Details of or comments on the bond-valence parameters.
;
_item.name '_valence_param.details'
_item.category_id valence_param
_item.mandatory_code no
_item_type.code text
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_valence_param_details' cif_core.dic 2.3
save_
save__valence_param.id
_item_description.description
; An identifier for the valence parameters of a bond between
the given atoms.
;
_item.name '_valence_param.id'
_item.category_id valence_param
_item.mandatory_code no
_item_type.code code
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_valence_param_id' cif_core.dic 2.3
save_
save__valence_param.ref_id
_item_description.description
; An identifier which links to the reference to the source
from which the bond-valence parameters are taken. A child
of _valence_ref.id which it must match.
;
_item.name '_valence_param.ref_id'
_item.category_id valence_param
_item.mandatory_code no
_item_type.code code
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_valence_param_ref_id' cif_core.dic 2.3
save_
save__valence_param.Ro
_item_description.description
; The bond-valence parameter Ro used in the expression
s = exp[(Ro - R)/B]
where s is the valence of a bond of length R.
;
_item.name '_valence_param.Ro'
_item.category_id valence_param
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_valence_param_Ro' cif_core.dic 2.3
save_
#################
## VALENCE_REF ##
#################
save_valence_ref
_category.description
; Data items in the VALENCE_REF category list the references
from which the bond-valence parameters have been taken.
;
_category.id 'valence_ref'
_category.mandatory_code no
_category_key.name '_valence_ref.id'
save_
save__valence_ref.id
_item_description.description
; An identifier for items in this category. Parent of
_valence_param.ref_id, which must have the same value.
;
_item.name '_valence_ref.id'
_item.category_id valence_ref
_item.mandatory_code yes
_item_type.code code
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_valence_ref_id' cif_core.dic 2.3
save_
save__valence_ref.reference
_item_description.description
; Literature reference from which the valence parameters
identified by _valence_param.id were taken.
;
_item.name '_valence_ref.reference'
_item.category_id valence_ref
_item.mandatory_code no
_item_type.code text
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_valence_ref_reference' cif_core.dic 2.3
save_
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
###########################################################################
#
# File: mmcif_pdbx-def-2.dic
#
# PDB Exchange Data Dictionary
#
# This data dictionary contains definitions used by wwPDB for data exchange
# and data processing.
#
# Definition Section 2
#
#
###########################################################################
save_pdbx_audit
_category.description
; The PDBX_AUDIT holds current version information.
;
_category.id 'pdbx_audit'
_category.mandatory_code no
loop_
_category_key.name '_pdbx_audit.entry_id'
loop_
_category_group.id 'inclusive_group'
'audit_group'
save_
save__pdbx_audit.entry_id
_item_description.description
; The value of _pdbx_audit.entry_id identifies the data block.
;
_item.name '_pdbx_audit.entry_id'
_item.category_id pdbx_audit
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_audit.entry_id'
_item_linked.parent_name '_entry.id'
_item_examples.case 'BDL001'
save_
save__pdbx_audit.current_version
_item_description.description
; The value of _pdbx_audit.entry_id identifies the data block.
;
_item.name '_pdbx_audit.current_version'
_item.category_id pdbx_audit
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_audit.current_version'
_item_linked.parent_name '_audit.revision_id'
_item_examples.case '1'
save_
###
###
#######################
## PDBX_AUDIT_AUTHOR ##
#######################
save_pdbx_audit_author
_category.description
; Data items in the PDBX_AUDIT_AUTHOR category record details about
the author(s) of the data block.
;
_category.id pdbx_audit_author
_category.mandatory_code no
_category_key.name '_pdbx_audit_author.ordinal'
loop_
_category_group.id 'inclusive_group'
'audit_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
loop_
_pdbx_audit_author.name
_pdbx_audit_author.address
_pdbx_audit_author.ordinal
'Fitzgerald, Paula M.D.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
1
'McKeever, Brian M.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
2
'Van Middlesworth, J.F.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
3
'Springer, James P.'
; Department of Biophysical Chemistry
Merck Research Laboratories
P. O. Box 2000, Ry80M203
Rahway, New Jersey 07065
USA
;
4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_audit_author.address
_item_description.description
; The address of an author of this data block. If there are
multiple authors, _pdbx_audit_author.address is looped with
_pdbx_audit_author.name.
;
_item.name '_pdbx_audit_author.address'
_item.category_id pdbx_audit_author
_item.mandatory_code no
_item_type.code text
_item_examples.case
; Department
Institute
Street
City and postcode
COUNTRY
;
save_
save__pdbx_audit_author.name
_item_description.description
; The name of an author of this data block. If there are multiple
authors, _pdbx_audit_author.name is looped with _pdbx_audit_author.address.
The family name(s), followed by a comma and including any
dynastic compoents, precedes the first name(s) or initial(s).
;
_item.name '_pdbx_audit_author.name'
_item.category_id pdbx_audit_author
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A'
save_
save__pdbx_audit_author.ordinal
_item_description.description
; A unique sequential integer identifier for each author.
;
_item.name '_pdbx_audit_author.ordinal'
_item.category_id pdbx_audit_author
_item.mandatory_code yes
_item_type.code int
loop_
_item_examples.case 1 2 3
save_
###
###
save_pdbx_database_message
_category.description
; The PDBX_DATABASE_MESSAGE category provides information about
correspondance related to a structure deposition.
;
_category.id 'pdbx_database_message'
_category.mandatory_code no
loop_
_category_key.name '_pdbx_database_message.message_id'
'_pdbx_database_message.entry_id'
loop_
_category_group.id 'inclusive_group'
'database_group'
'pdbx_group'
save_
save__pdbx_database_message.entry_id
_item_description.description
; The value of _pdbx_database_message.entry_id identifies the data block.
;
_item.name '_pdbx_database_message.entry_id'
_item.category_id pdbx_database_message
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_database_message.entry_id'
_item_linked.parent_name '_entry.id'
_item_examples.case 'BDL001'
_item_aliases.alias_name '_ndb_database_message.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.message_id
_item_description.description
; This is an unique and sequential identifier for a message.
;
_item.name '_pdbx_database_message.message_id'
_item.category_id pdbx_database_message
_item.mandatory_code yes
_item_type.code text
_item_examples.case 'message 1'
_item_aliases.alias_name '_ndb_database_message.message_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.date
_item_description.description
; This is the date when a message was sent or received.
;
_item.name '_pdbx_database_message.date'
_item.category_id pdbx_database_message
_item.mandatory_code yes
_item_type.code yyyy-mm-dd:hh:mm
_item_aliases.alias_name '_ndb_database_message.date'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.content_type
_item_description.description
; This code defines the content of the message.
;
_item.name '_pdbx_database_message.content_type'
_item.category_id pdbx_database_message
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
DEPOSIT 'A component of a deposition or revision'
REMINDER 'A message reminding the depositor to send materials'
QUERY 'A query to a depositor for specific information'
OTHER 'A miscellaneous message'
_item_aliases.alias_name '_ndb_database_message.content_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.message_type
_item_description.description
; Defines how the message was sent or received.
;
_item.name '_pdbx_database_message.message_type'
_item.category_id pdbx_database_message
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
FAX 'A facsimile message'
EMAIL 'An electronic mail message'
MAIL 'A conventional mail message'
PHONE 'A phone message'
_item_aliases.alias_name '_ndb_database_message.message_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.sender
_item_description.description
; The name of the sender.
;
_item.name '_pdbx_database_message.sender'
_item.category_id pdbx_database_message
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_ndb_database_message.sender'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.sender_address_fax
_item_description.description
; The FAX phone number of the sender.
;
_item.name '_pdbx_database_message.sender_address_fax'
_item.category_id pdbx_database_message
_item.mandatory_code no
_item_type.code fax
_item_aliases.alias_name '_ndb_database_message.sender_address_fax'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.sender_address_phone
_item_description.description
; The phone number of the sender.
;
_item.name '_pdbx_database_message.sender_address_phone'
_item.category_id pdbx_database_message
_item.mandatory_code no
_item_type.code phone
_item_aliases.alias_name '_ndb_database_message.sender_address_phone'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.sender_address_email
_item_description.description
; The email address of the sender.
;
_item.name '_pdbx_database_message.sender_address_email'
_item.category_id pdbx_database_message
_item.mandatory_code no
_item_type.code email
_item_aliases.alias_name '_ndb_database_message.sender_address_email'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.sender_address_mail
_item_description.description
; The postal address of the sender.
;
_item.name '_pdbx_database_message.sender_address_mail'
_item.category_id pdbx_database_message
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_ndb_database_message.sender_address_mail'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.receiver
_item_description.description
; The name of the receiver.
;
_item.name '_pdbx_database_message.receiver'
_item.category_id pdbx_database_message
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_ndb_database_message.receiver'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.receiver_address_fax
_item_description.description
; The FAX phone number of the receiver.
;
_item.name '_pdbx_database_message.receiver_address_fax'
_item.category_id pdbx_database_message
_item.mandatory_code no
_item_type.code fax
_item_aliases.alias_name '_ndb_database_message.receiver_address_fax'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.receiver_address_phone
_item_description.description
; The phone number of the receiver.
;
_item.name '_pdbx_database_message.receiver_address_phone'
_item.category_id pdbx_database_message
_item.mandatory_code no
_item_type.code phone
_item_aliases.alias_name '_ndb_database_message.receiver_address_phone'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.receiver_address_email
_item_description.description
; The email address of the receiver.
;
_item.name '_pdbx_database_message.receiver_address_email'
_item.category_id pdbx_database_message
_item.mandatory_code no
_item_type.code email
_item_aliases.alias_name '_ndb_database_message.receiver_address_email'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.receiver_address_mail
_item_description.description
; The postal address of the receiver.
;
_item.name '_pdbx_database_message.receiver_address_mail'
_item.category_id pdbx_database_message
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_ndb_database_message.receiver_address_mail'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_message.message
_item_description.description
; The text of the message.
;
_item.name '_pdbx_database_message.message'
_item.category_id pdbx_database_message
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_ndb_database_message.message'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
###
save_pdbx_database_PDB_obs_spr
_category.description
; The PDBX_DATABASE_PDB_OBS_SPR category provides placeholders
for information on obsolete/superseded PDB entries
;
_category.id 'pdbx_database_PDB_obs_spr'
_category.mandatory_code no
loop_
_category_key.name '_pdbx_database_PDB_obs_spr.pdb_id'
'_pdbx_database_PDB_obs_spr.replace_pdb_id'
loop_
_category_group.id 'inclusive_group'
'database_group'
'pdbx_group'
save_
save__pdbx_database_PDB_obs_spr.id
_item_description.description
; Identifier for the type of obsolete entry to be added to this entry.
;
_item.name '_pdbx_database_PDB_obs_spr.id'
_item.category_id pdbx_database_PDB_obs_spr
_item.mandatory_code yes
_item_type.code code
_item_examples.case 'OBSLTE'
loop_
_item_enumeration.value 'OBSLTE' 'SPRSDE'
_item_aliases.alias_name '_ndb_database_PDB_obs_spr.id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_PDB_obs_spr.date
_item_description.description
; The date of replacement.
;
_item.name '_pdbx_database_PDB_obs_spr.date'
_item.category_id pdbx_database_PDB_obs_spr
_item.mandatory_code yes
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case '1997-03-30'
_item_aliases.alias_name '_ndb_database_PDB_obs_spr.date'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_PDB_obs_spr.pdb_id
_item_description.description
; The new PDB identifier for the replaced entry.
;
_item.name '_pdbx_database_PDB_obs_spr.pdb_id'
_item.category_id pdbx_database_PDB_obs_spr
_item.mandatory_code yes
_item_type.code code
_item_examples.case 2ABC
_item_aliases.alias_name '_ndb_database_PDB_obs_spr.pdb_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_PDB_obs_spr.replace_pdb_id
_item_description.description
; The PDB identifier for the replaced (OLD) entry.
;
_item.name '_pdbx_database_PDB_obs_spr.replace_pdb_id'
_item.category_id pdbx_database_PDB_obs_spr
_item.mandatory_code yes
_item_type.code code
_item_examples.case 3ABC
_item_aliases.alias_name '_ndb_database_PDB_obs_spr.replace_pdb_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
###
###
save_pdbx_database_proc
_category.description
; Internal records to track the data processing cycle.
;
_category.id 'pdbx_database_proc'
_category.mandatory_code no
loop_
_category_key.name '_pdbx_database_proc.cycle_id'
'_pdbx_database_proc.entry_id'
loop_
_category_group.id 'inclusive_group'
'database_group'
'pdbx_group'
_category_examples.case
;
_pdbx_database_proc.entry_id 'BDL001'
_pdbx_database_proc.cycle_id 1
_pdbx_database_proc.date_begin_cycle 1998-02-27
_pdbx_database_proc.date_end_cycle 1998-02-27
;
save_
save__pdbx_database_proc.entry_id
_item_description.description
; The value of _pdbx_database_proc.entry_id identifies the data block.
;
_item.name '_pdbx_database_proc.entry_id'
_item.category_id pdbx_database_proc
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_database_proc.entry_id'
_item_linked.parent_name '_entry.id'
_item_examples.case 'BDL001'
_item_aliases.alias_name '_ndb_database_proc.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_proc.cycle_id
_item_description.description
; This is a number of the processing cycle.
;
_item.name '_pdbx_database_proc.cycle_id'
_item.category_id pdbx_database_proc
_item.mandatory_code yes
_item_type.code code
_item_examples.case '1 for the initial cycle'
_item_aliases.alias_name '_ndb_database_proc.cycle_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_proc.date_begin_cycle
_item_description.description
; This is the date of the start of the processing cycle.
;
_item.name '_pdbx_database_proc.date_begin_cycle'
_item.category_id pdbx_database_proc
_item.mandatory_code yes
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-27
_item_aliases.alias_name '_ndb_database_proc.date_begin_cycle'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_proc.date_end_cycle
_item_description.description
; This is the date of the end of the processing cycle.
;
_item.name '_pdbx_database_proc.date_end_cycle'
_item.category_id pdbx_database_proc
_item.mandatory_code yes
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-27
_item_aliases.alias_name '_ndb_database_proc.date_end_cycle'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_proc.details
_item_description.description
; Special details about the current processing cycle.
;
_item.name '_pdbx_database_proc.details'
_item.category_id pdbx_database_proc
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_ndb_database_proc.details'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
###
###
save_pdbx_database_remark
_category.description
;
Data items in the PDBX_DATABASE_REMARK category record keep additional
information about the entry. They are mostly used to create
'non-standard' PDB REMARK annotations (6-99).
;
_category.id pdbx_database_remark
_category.mandatory_code no
_category_key.name '_pdbx_database_remark.id'
loop_
_category_group.id 'inclusive_group'
'database_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 1ABC
;
;
loop_
_pdbx_database_remark.id
_pdbx_database_remark.text
1
; THE NON-CRYSTALLOGRAPHIC RELATIONSHIP BETWEEN THE THREE
DOUBLE HELICES IN THE ASYMMETRIC UNIT IS DESCRIBED
IN THE MTRIX1-3 RECORDS.
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_database_remark.id
_item_description.description
; A unique identifier for the PDB remark record.
;
_item.name '_pdbx_database_remark.id'
_item.category_id pdbx_database_remark
_item.mandatory_code yes
_item_type.code int
_item_aliases.alias_name '_rcsb_database_PDB_remark.id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_remark.text
_item_description.description
; The full text of the PDB remark record.
;
_item.name '_pdbx_database_remark.text'
_item.category_id pdbx_database_remark
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_rcsb_database_PDB_remark.text'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
###
save_pdbx_database_status
_category.description
; These are internal RCSB records to keep track of data processing
and status of the entry.
;
_category.id 'pdbx_database_status'
_category.mandatory_code no
_category_key.name '_pdbx_database_status.entry_id'
loop_
_category_group.id 'inclusive_group'
'database_group'
'pdbx_group'
_category_examples.case
;
_pdbx_database_status.entry_id 1ABC
_pdbx_database_status.status_code REL
_pdbx_database_status.author_release_status_code REL
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.recvd_initial_deposition_date 1996-02-13
_pdbx_database_status.date_author_approval 1996-02-13
_pdbx_database_status.recvd_author_approval Y
_pdbx_database_status.author_approval_type EXPLICIT
_pdbx_database_status.hold_for_publication N
_pdbx_database_status.date_hold_coordinates 1996-02-13
_pdbx_database_status.date_hold_struct_fact 1996-02-13
_pdbx_database_status.date_of_PDB_release 1996-02-14
_pdbx_database_status.date_deposition_form 1996-02-13
_pdbx_database_status.date_coordinates 1996-02-13
_pdbx_database_status.date_struct_fact 1996-02-13
_pdbx_database_status.date_manuscript 1996-02-13
_pdbx_database_status.date_nmr_constraints ?
_pdbx_database_status.recvd_deposit_form Y
_pdbx_database_status.recvd_coordinates Y
_pdbx_database_status.recvd_struct_fact Y
_pdbx_database_status.recvd_manuscript Y
_pdbx_database_status.recvd_nmr_constraints N
;
save_
save__pdbx_database_status.status_code
_item_description.description
; Code for status of file.
;
_item.name '_pdbx_database_status.status_code'
_item.category_id pdbx_database_status
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
PROC 'Processing in progress'
WAIT 'Awaiting author approval'
REL 'Released'
HOLD 'On hold until yyyy-mm-dd'
HPUB 'On hold until publication'
OBS 'Entry has been obsoleted and replaced by another entry'
DEL 'Entry has been deleted'
WDRN 'Entry has been withdrawn'
BIB
'Only a bibliographic entry exists for this entry; there are no coordinates'
REV 'Entry currently under revision'
UPD 'Deprecated code'
loop_
_item_examples.case REL
HOLD
REV
BIB
_item_aliases.alias_name '_ndb_database_status.status_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.author_release_status_code
_item_description.description
; The release status authorized by the depositor.
;
_item.name '_pdbx_database_status.author_release_status_code'
_item.category_id pdbx_database_status
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
REL 'Release'
HOLD 'On hold until yyyy-mm-dd'
HPUB 'On hold until publication'
OBS 'Entry has been obsoleted and replaced by another entry'
WDRN 'Entry has been withdrawn'
_item_examples.case
;
REL = Release
HOLD = On hold until yyyy-mm-dd
HPUB = On hold until publication
OBS = Entry has been obsoleted and replaced by another entry
WDRN = Entry has been withdrawn by depositor
;
_item_aliases.alias_name '_ndb_database_status.author_release_status_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.status_code_sf
_item_description.description
; Code for status of structure factor file.
;
_item.name '_pdbx_database_status.status_code_sf'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
PROC 'Processing in progress'
REL 'Release'
HOLD 'On hold until yyyy-mm-dd'
HPUB 'On hold until publication'
OBS 'Entry has been obsoleted and replaced by another entry'
WDRN 'Entry has been withdrawn'
WAIT 'Awaiting author approval'
_item_examples.case
;
PROC = Processing in progress
REL = Release
HOLD = On hold until yyyy-mm-dd
HPUB = On hold until publication
OBS = Entry has been obsoleted and replaced by another entry
WDRN = Entry has been withdrawn by depositor
WAIT = Awaiting author approval
;
_item_aliases.alias_name '_ndb_database_status.status_code_sf'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.status_code_mr
_item_description.description
; Code for status of NMR constraints file.
;
_item.name '_pdbx_database_status.status_code_mr'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
PROC 'Processing in progress'
REL 'Release'
HOLD 'On hold until yyyy-mm-dd'
HPUB 'On hold until publication'
OBS 'Entry has been obsoleted and replaced by another entry'
WDRN 'Entry has been withdrawn'
WAIT 'Awaiting author approval'
_item_examples.case
;
PROC = Processing in progress
REL = Release
HOLD = On hold until yyyy-mm-dd
HPUB = On hold until publication
OBS = Entry has been obsoleted and replaced by another entry
WDRN = Entry has been withdrawn by depositor
WAIT = Awaiting author approval
;
_item_aliases.alias_name '_ndb_database_status.status_code_mr'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.dep_release_code_coordinates
_item_description.description
;
The deposited coordinates for this deposition will be released according
the value of this item.
;
_item.name '_pdbx_database_status.dep_release_code_coordinates'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code line
_item_default.value 'RELEASE NOW'
loop_
_item_enumeration.value
_item_enumeration.detail
'RELEASE NOW' 'Release immediately'
'HOLD FOR PUBLICATION' 'Hold until primary citation is published'
'HOLD FOR 6 WEEKS' 'Hold for 6 weeks'
'HOLD FOR 6 MONTHS' 'Hold for 6 months'
'HOLD FOR 1 YEAR' 'Hold for 1 year'
_item_examples.case
;
RELEASE NOW = Release immediately
HOLD FOR PUBLICATION = Hold until the primary citation is published
HOLD FOR 6 WEEKS = Hold for 6 weeks
HOLD FOR 6 MONTHS = Hold for 6 months
HOLD FOR 1 YEAR = Hold for 1 year
;
_item_aliases.alias_name '_ndb_database_status.dep_release_code_coordinates'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.dep_release_code_sequence
_item_description.description
;
The sequence information for this deposition will be released according
the value of this item. Setting this status code to "RELEASE NOW" indicates
that the macromolecular sequence(s) for this entry may be displayed in PDB
status reports prior to the release of the entry. Setting this status
code to "HOLD FOR RELEASE" conceals the sequence information in PDB status
reports until the coordinate data for this entry are released.
;
_item.name '_pdbx_database_status.dep_release_code_sequence'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code line
# _item_default.value 'RELEASE NOW'
loop_
_item_enumeration.value
_item_enumeration.detail
'RELEASE NOW' 'Release sequence information in status reports immediately'
'HOLD FOR RELEASE'
;Conceal sequence information in status reports until coordinate data
is released
;
_item_examples.case
;
RELEASE NOW = Release sequence information in status reports immediately
HOLD FOR RELEASE = Conceal sequence information in status reports until
coordinate data is release
;
_item_aliases.alias_name '_ndb_database_status.dep_release_code_sequence'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.dep_release_code_struct_fact
_item_description.description
;
The deposited structure factors for this deposition will be released according
the value of this item.
;
_item.name '_pdbx_database_status.dep_release_code_struct_fact'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code line
_item_default.value 'RELEASE NOW'
# loop_
# _item_enumeration.value
# _item_enumeration.detail
# 'RELEASE NOW' 'Release immediately'
# 'HOLD FOR PUBLICATION' 'Hold until primary citation is published'
# 'HOLD FOR 6 MONTHS' 'Hold for 6 months'
# 'HOLD FOR 1 YEAR' 'Hold for 1 year'
# 'HOLD FOR 4 YEARS' 'Hold for 4 years'
_item_examples.case
;
RELEASE NOW = Release immediately
HOLD FOR PUBLICATION = Hold until the primary citation is published
HOLD FOR 6 WEEKS = Hold for 6 weeks
HOLD FOR 6 MONTHS = Hold for 6 months
HOLD FOR 1 YEAR = Hold for 1 year
;
_item_aliases.alias_name '_ndb_database_status.dep_release_code_struct_fact'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.dep_release_code_nmr_constraints
_item_description.description
;
The deposited NMR constrait data for this deposition will be released according
the value of this item.
;
_item.name '_pdbx_database_status.dep_release_code_nmr_constraints'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code line
_item_default.value 'RELEASE NOW'
# loop_
# _item_enumeration.value
# _item_enumeration.detail
# 'RELEASE NOW' 'Release immediately'
# 'HOLD FOR PUBLICATION' 'Hold until primary citation is published'
# 'HOLD FOR 6 MONTHS' 'Hold for 6 months'
# 'HOLD FOR 1 YEAR' 'Hold for 1 year'
_item_examples.case
;
RELEASE NOW = Release immediately
HOLD FOR PUBLICATION = Hold until the primary citation is published
HOLD FOR 6 WEEKS = Hold for 6 weeks
HOLD FOR 6 MONTHS = Hold for 6 months
HOLD FOR 1 YEAR = Hold for 1 year
;
_item_aliases.alias_name
'_ndb_database_status.dep_release_code_nmr_constraints'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.entry_id
_item_description.description
; The value of _pdbx_database_status.entry_id identifies the data block.
;
_item.name '_pdbx_database_status.entry_id'
_item.category_id pdbx_database_status
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_database_status.entry_id'
_item_linked.parent_name '_entry.id'
_item_examples.case 'BDL001'
_item_aliases.alias_name '_ndb_database_status.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.recvd_deposit_form
_item_description.description
; This code indicates whether the deposition form for an entry
has been received.
;
_item.name '_pdbx_database_status.recvd_deposit_form'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code uchar1
loop_
_item_enumeration.value
_item_enumeration.detail
Y 'Yes'
N 'No'
_item_examples.case Y
_item_aliases.alias_name '_ndb_database_status.recvd_deposit_form'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_deposition_form
_item_description.description
; The date the deposition form is received.
;
_item.name '_pdbx_database_status.date_deposition_form'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1982-02-21
_item_aliases.alias_name '_ndb_database_status.date_deposition_form'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.recvd_coordinates
_item_description.description
; This code indicates whether the coordinates for an entry
have been received.
;
_item.name '_pdbx_database_status.recvd_coordinates'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code uchar1
loop_
_item_enumeration.value
_item_enumeration.detail
Y 'Yes'
N 'No'
_item_examples.case Y
_item_aliases.alias_name '_ndb_database_status.recvd_coordinates'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_coordinates
_item_description.description
; The date the coordinates are received.
;
_item.name '_pdbx_database_status.date_coordinates'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-21
_item_aliases.alias_name '_ndb_database_status.date_coordinates'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.recvd_struct_fact
_item_description.description
; This code indicates whether the structure factors for an entry
have been received.
;
_item.name '_pdbx_database_status.recvd_struct_fact'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code uchar1
loop_
_item_enumeration.value
_item_enumeration.detail
Y 'Yes'
N 'No'
_item_examples.case Y
_item_aliases.alias_name '_ndb_database_status.recvd_struct_fact'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_struct_fact
_item_description.description
; The date the structure factors are received.
;
_item.name '_pdbx_database_status.date_struct_fact'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-28
_item_aliases.alias_name '_ndb_database_status.date_struct_fact'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
#
save__pdbx_database_status.recvd_nmr_constraints
_item_description.description
; This code indicates whether the NMR contraint data for an entry
have been received.
;
_item.name '_pdbx_database_status.recvd_nmr_constraints'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code uchar1
loop_
_item_enumeration.value
_item_enumeration.detail
Y 'Yes'
N 'No'
_item_examples.case Y
_item_aliases.alias_name '_ndb_database_status.recvd_nmr_constraints'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_nmr_constraints
_item_description.description
; The date the structure factors are received.
;
_item.name '_pdbx_database_status.date_nmr_constraints'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-28
_item_aliases.alias_name '_ndb_database_status.date_nmr_constraints'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.recvd_internal_approval
_item_description.description
; This code indicates whether the internal approval for an entry
have been received.
;
_item.name '_pdbx_database_status.recvd_internal_approval'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code uchar1
loop_
_item_enumeration.value
_item_enumeration.detail
Y 'Yes'
N 'No'
_item_examples.case Y
_item_aliases.alias_name '_ndb_database_status.recvd_internal_approval'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.recvd_manuscript
_item_description.description
; This code indicates whether the manuscript for an entry
has been received.
;
_item.name '_pdbx_database_status.recvd_manuscript'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code uchar1
loop_
_item_enumeration.value
_item_enumeration.detail
Y 'Yes'
N 'No'
_item_examples.case Y
_item_aliases.alias_name '_ndb_database_status.recvd_manuscript'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_manuscript
_item_description.description
; The date the manuscript is received.
;
_item.name '_pdbx_database_status.date_manuscript'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-28
_item_aliases.alias_name '_ndb_database_status.date_manuscript'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.name_depositor
_item_description.description
; The last name of the depositor to be used in correspondance.
;
_item.name '_pdbx_database_status.name_depositor'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code text
_item_examples.case 'Smith'
_item_aliases.alias_name '_ndb_database_status.name_depositor'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.recvd_author_approval
_item_description.description
; This code indicates whether the author's approval for
an entry has been received.
;
_item.name '_pdbx_database_status.recvd_author_approval'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code uchar1
loop_
_item_enumeration.value
_item_enumeration.detail
Y 'Yes'
N 'No'
_item_examples.case Y
_item_aliases.alias_name '_ndb_database_status.recvd_author_approval'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.author_approval_type
_item_description.description
; This code indicates whether the author's approval for
an entry was received explicitly or implicitly. The
latter is automatically implied by failure to respond
to the validation summary within the prescribed period.
;
_item.name '_pdbx_database_status.author_approval_type'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
implicit
explicit
_item_examples.case
;
implicit = automatic approval by failure to acknowledge
explicit = approval via depositor acknowledgement
;
_item_aliases.alias_name '_ndb_database_status.author_approval_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_author_approval
_item_description.description
; The date the author's approval is received.
;
_item.name '_pdbx_database_status.date_author_approval'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-20
_item_aliases.alias_name '_ndb_database_status.date_author_approval'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.recvd_initial_deposition_date
_item_description.description
; The date of initial deposition. (The first message for
deposition has been received.)
;
_item.name '_pdbx_database_status.recvd_initial_deposition_date'
_item.category_id pdbx_database_status
_item.mandatory_code yes
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-21
_item_aliases.alias_name
'_ndb_database_status.recvd_initial_deposition_date'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_submitted
_item_description.description
; The date of complete deposition. This corresponds to the date
at which the PDB identifier is assigned.
;
_item.name '_pdbx_database_status.date_submitted'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-20
_item_aliases.alias_name '_ndb_database_status.date_submitted'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.rcsb_annotator
_item_description.description
; The initials of the annotator processing this entry.
;
_item.name '_pdbx_database_status.rcsb_annotator'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'BS' 'SJ' 'KB'
_item_aliases.alias_name '_ndb_database_status.rcsb_annotator'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_of_sf_release
_item_description.description
; The date of PDB/RCSB release. This corresponds to the date
at which the entry is placed into the public archive.
;
_item.name '_pdbx_database_status.date_of_sf_release'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd
_item_examples.case 1999-02-28
_item_aliases.alias_name '_ndb_database_status.date_of_sf_release'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_of_mr_release
_item_description.description
; The date of PDB/RCSB release. This corresponds to the date
at which the entry is placed into the public archive.
;
_item.name '_pdbx_database_status.date_of_mr_release'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd
_item_examples.case 1999-02-28
_item_aliases.alias_name '_ndb_database_status.date_of_mr_release'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_of_PDB_release
_item_description.description
; PDB release date. This is the date that appears in the PDB
REVDAT record.
;
_item.name '_pdbx_database_status.date_of_PDB_release'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-28
_item_aliases.alias_name '_ndb_database_status.date_of_PDB_release'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_hold_coordinates
_item_description.description
; At an author's request, a coordinate entry may be held after
processing for some period of time.
;
_item.name '_pdbx_database_status.date_hold_coordinates'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-28
_item_aliases.alias_name '_ndb_database_status.date_hold_coordinates'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_hold_struct_fact
_item_description.description
; At an author's request, the structure factors may be held after
processing for some period of time.
;
_item.name '_pdbx_database_status.date_hold_struct_fact'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-28
_item_aliases.alias_name '_ndb_database_status.date_hold_struct_fact'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.date_hold_nmr_constraints
_item_description.description
; At an author's request, the NMR constraint data may be held after
processing for some period of time.
;
_item.name '_pdbx_database_status.date_hold_nmr_constraints'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-28
_item_aliases.alias_name '_ndb_database_status.date_hold_nmr_constraints'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.hold_for_publication
_item_description.description
; At an author's request, an entry is to be held until
publication.
;
_item.name '_pdbx_database_status.hold_for_publication'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code uchar1
loop_
_item_enumeration.value
_item_enumeration.detail
Y 'Yes'
N 'No'
_item_examples.case Y
_item_aliases.alias_name '_ndb_database_status.hold_for_publication'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.SG_entry
_item_description.description
; This code indicates whether the entry belongs to
Structural Genomics Project.
;
_item.name '_pdbx_database_status.SG_entry'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code uchar1
loop_
_item_enumeration.value
_item_enumeration.detail
Y 'Yes'
N 'No'
_item_examples.case Y
_item_aliases.alias_name '_ndb_database_status.SG_entry'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.pdb_date_of_author_approval
_item_description.description
; This is the date when PDB received the author's approval for an
entry which has been processed by NDB. (This is a place holder
for entries processed before Jan. 1, 1996.)
;
_item.name '_pdbx_database_status.pdb_date_of_author_approval'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case 1983-02-27
_item_aliases.alias_name '_ndb_database_status.pdb_date_of_author_approval'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.deposit_site
_item_description.description
; The site where the file was deposited.
;
_item.name '_pdbx_database_status.deposit_site'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case NDB RCSB PDB EBI OSAKA BNL
loop_
_item_enumeration.value NDB RCSB PDB EBI OSAKA BNL
_item_aliases.alias_name '_ndb_database_status.deposit_site'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_status.process_site
_item_description.description
; The site where the file was deposited.
;
_item.name '_pdbx_database_status.process_site'
_item.category_id pdbx_database_status
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case NDB RCSB EBI OSAKA PDB PRAGUE
loop_
_item_enumeration.value
NDB RCSB EBI OSAKA PDB PRAGUE
_item_aliases.alias_name '_ndb_database_status.process_site'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
###
save_pdbx_entity_name
_category.description
; The PDBX_ENTITY_NAME records additional name information for
each entity.
;
_category.id pdbx_entity_name
_category.mandatory_code no
loop_
_category_key.name '_pdbx_entity_name.entity_id'
'_pdbx_entity_name.name'
'_pdbx_entity_name.name_type'
loop_
_category_group.id 'inclusive_group'
'entity_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_pdbx_entity_name.entity_id
_pdbx_entity_name.name
_pdbx_entity_name.name_type
1 "PLASTOCYANIN" 'SWS-NAME'
1 "Electron transport" 'SWS-KEYWORD'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_entity_name.entity_id
_item_description.description
; Pointer to _entity.id.
;
_item.name '_pdbx_entity_name.entity_id'
_item.category_id pdbx_entity_name
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_entity_name.entity_id'
_item_linked.parent_name '_entity.id'
_item_aliases.alias_name '_rcsb_entity_name.entity_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_entity_name.name
_item_description.description
; Entity name.
;
_item.name '_pdbx_entity_name.name'
_item.category_id pdbx_entity_name
_item.mandatory_code yes
_item_type.code line
_item_aliases.alias_name '_rcsb_entity_name.name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_entity_name.name_type
_item_description.description
; Entity name type.
;
_item.name '_pdbx_entity_name.name_type'
_item.category_id pdbx_entity_name
_item.mandatory_code yes
_item_type.code line
_item_aliases.alias_name '_rcsb_entity_name.name_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
loop_
_item_enumeration.value
'RCSB_NAME'
'RCSB_SYNONYM'
'SWS-NAME'
'SWS-SYNONYM'
'SWS-KEYWORD'
'GB-NAME'
'GB-SYNONYM'
'GB-KEYWORD'
save_
###
###
save_pdbx_prerelease_seq
_category.description
; This category provides a placeholder for pre-release
sequence information. After release this category
should be discarded.
;
_category.id pdbx_prerelease_seq
_category.mandatory_code no
_category_key.name '_pdbx_prerelease_seq.entity_id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
'pdbx_group'
loop_
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_pdbx_prerelease_seq.entity_id
_pdbx_prerelease_seq.seq_one_letter_code
1 'GKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD'
2 'HKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNN'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_prerelease_seq.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_pdbx_prerelease_seq.entity_id'
_item.category_id pdbx_prerelease_seq
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_prerelease_seq.entity_id'
_item_linked.parent_name '_entity.id'
_item_aliases.alias_name '_rcsb_prerelease_seq.entity_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_prerelease_seq.seq_one_letter_code
_item_description.description
; Chemical sequence expressed as string of one-letter
amino acid codes.
A for alanine or adenine
B for ambiguous asparagine/aspartic-acid
R for arginine
N for asparagine
D for aspartic-acid
C for cysteine or cystine or cytosine
Q for glutamine
E for glutamic-acid
Z for ambiguous glutamine/glutamic acid
G for glycine or guanine
H for histidine
I for isoleucine
L for leucine
K for lysine
M for methionine
F for phenylalanine
P for proline
S for serine
T for threonine or thymine
W for tryptophan
Y for tyrosine
V for valine
U for uracil
;
_item.name '_pdbx_prerelease_seq.seq_one_letter_code'
_item.category_id pdbx_prerelease_seq
_item.mandatory_code no
_item_type.code text
_item_examples.case
;
MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD
;
_item_aliases.alias_name '_rcsb_prerelease_seq.seq_one_letter_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
###
###
save_pdbx_poly_seq_scheme
_category.description
; The PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature
mapping for polymer entities.
;
_category.id pdbx_poly_seq_scheme
_category.mandatory_code no
loop_
_category_key.name '_pdbx_poly_seq_scheme.asym_id'
'_pdbx_poly_seq_scheme.entity_id'
'_pdbx_poly_seq_scheme.seq_id'
'_pdbx_poly_seq_scheme.mon_id'
loop_
_category_group.id 'inclusive_group'
'struct_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on NDB entry DDFB25
;
;
loop_
_pdbx_poly_seq_scheme.asym_id
_pdbx_poly_seq_scheme.entity_id
_pdbx_poly_seq_scheme.seq_id
_pdbx_poly_seq_scheme.mon_id
_pdbx_poly_seq_scheme.ndb_num
_pdbx_poly_seq_scheme.pdb_num
_pdbx_poly_seq_scheme.auth_num
_pdbx_poly_seq_scheme.pdb_mon_id
_pdbx_poly_seq_scheme.auth_mon_id
_pdbx_poly_seq_scheme.pdb_strand_id
_pdbx_poly_seq_scheme.pdb_ins_code
A 1 1 C 1 1 1 C C A .
A 1 2 G 2 2 2 G G A .
A 1 3 T 3 3 3 T T A .
A 1 4 +A 4 4 4 +A +A A .
A 1 5 C 5 5 5 C C A .
A 1 6 G 6 6 6 G G A .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_poly_seq_scheme.asym_id
_item_description.description
; Pointer to _atom_site.label_asym_id.
;
_item.name '_pdbx_poly_seq_scheme.asym_id'
_item.category_id pdbx_poly_seq_scheme
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_poly_seq_scheme.asym_id'
_item_linked.parent_name '_struct_asym.id'
loop_
_item_examples.case '1'
'A'
'2B3'
_item_aliases.alias_name '_ndb_poly_seq_scheme.id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_poly_seq_scheme.entity_id
_item_description.description
; Pointer to _entity.id.
;
_item.name '_pdbx_poly_seq_scheme.entity_id'
_item.category_id pdbx_poly_seq_scheme
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_poly_seq_scheme.entity_id'
_item_linked.parent_name '_entity.id'
_item_aliases.alias_name '_ndb_poly_seq_scheme.entity_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_poly_seq_scheme.seq_id
_item_description.description
; Pointer to _entity_poly_seq.num
;
_item.name '_pdbx_poly_seq_scheme.seq_id'
_item.category_id pdbx_poly_seq_scheme
_item.mandatory_code yes
_item_type.code code
_item_linked.parent_name '_pdbx_poly_seq_scheme.seq_id'
_item_linked.child_name '_entity_poly_seq.num'
_item_aliases.alias_name '_ndb_poly_seq_scheme.seq_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_poly_seq_scheme.mon_id
_item_description.description
; Pointer to _entity_poly_seq.mon_id.
;
_item.name '_pdbx_poly_seq_scheme.mon_id'
_item.category_id pdbx_poly_seq_scheme
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_poly_seq_scheme.mon_id'
_item_linked.parent_name '_entity_poly_seq.mon_id'
_item_aliases.alias_name '_ndb_poly_seq_scheme.mon_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_poly_seq_scheme.pdb_strand_id
_item_description.description
; PDB strand/chain id.
;
_item.name '_pdbx_poly_seq_scheme.pdb_strand_id'
_item.category_id pdbx_poly_seq_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_poly_seq_scheme.pdb_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_poly_seq_scheme.ndb_seq_num
_item_description.description
; NDB residue number.
;
_item.name '_pdbx_poly_seq_scheme.ndb_seq_num'
_item.category_id pdbx_poly_seq_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_poly_seq_scheme.ndb_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_poly_seq_scheme.pdb_seq_num
_item_description.description
; PDB residue number.
;
_item.name '_pdbx_poly_seq_scheme.pdb_seq_num'
_item.category_id pdbx_poly_seq_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_poly_seq_scheme.pdb_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_poly_seq_scheme.auth_seq_num
_item_description.description
; _atom_site.auth_seq_id
;
_item.name '_pdbx_poly_seq_scheme.auth_seq_num'
_item.category_id pdbx_poly_seq_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_poly_seq_scheme.auth_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_poly_seq_scheme.pdb_mon_id
_item_description.description
; PDB residue name.
;
_item.name '_pdbx_poly_seq_scheme.pdb_mon_id'
_item.category_id pdbx_poly_seq_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_poly_seq_scheme.pdb_mon_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_poly_seq_scheme.auth_mon_id
_item_description.description
; _atom_site.auth_comp_id
;
_item.name '_pdbx_poly_seq_scheme.auth_mon_id'
_item.category_id pdbx_poly_seq_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_poly_seq_scheme.auth_mon_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_poly_seq_scheme.pdb_ins_code
_item_description.description
; PDB insertion code.
;
_item.name '_pdbx_poly_seq_scheme.pdb_ins_code'
_item.category_id pdbx_poly_seq_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_poly_seq_scheme.pdb_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save_pdbx_nonpoly_scheme
_category.description
; The PDBX_NONPOLY_SCHEME category provides residue level nomenclature
mapping for non-polymer entities.
;
_category.id pdbx_nonpoly_scheme
_category.mandatory_code no
loop_
_category_key.name '_pdbx_nonpoly_scheme.asym_id'
'_pdbx_nonpoly_scheme.ndb_seq_num'
loop_
_category_group.id 'inclusive_group'
'struct_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.pdb_ins_code
C 3 HOH 100 100 100 HOH HOH C .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_nonpoly_scheme.asym_id
_item_description.description
; Pointer to _atom_site.label_asym_id.
;
_item.name '_pdbx_nonpoly_scheme.asym_id'
_item.category_id pdbx_nonpoly_scheme
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_nonpoly_scheme.asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
loop_
_item_examples.case '1'
'A'
'2B3'
_item_aliases.alias_name '_ndb_nonpoly_scheme.asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nonpoly_scheme.entity_id
_item_description.description
; Pointer to _atom_site.label_entity_id.
;
_item.name '_pdbx_nonpoly_scheme.entity_id'
_item.category_id pdbx_nonpoly_scheme
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_nonpoly_scheme.entity_id'
_item_linked.parent_name '_atom_site.label_entity_id'
_item_aliases.alias_name '_ndb_nonpoly_scheme.entity_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nonpoly_scheme.mon_id
_item_description.description
; Pointer to _atom_site.label_comp_id.
;
_item.name '_pdbx_nonpoly_scheme.mon_id'
_item.category_id pdbx_nonpoly_scheme
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_nonpoly_scheme.mon_id'
_item_linked.parent_name '_atom_site.label_comp_id'
_item_aliases.alias_name '_ndb_nonpoly_scheme.mon_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nonpoly_scheme.pdb_strand_id
_item_description.description
; PDB strand/chain id.
;
_item.name '_pdbx_nonpoly_scheme.pdb_strand_id'
_item.category_id pdbx_nonpoly_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_nonpoly_scheme.pdb_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nonpoly_scheme.ndb_seq_num
_item_description.description
; NDB/RCSB residue number.
;
_item.name '_pdbx_nonpoly_scheme.ndb_seq_num'
_item.category_id pdbx_nonpoly_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_nonpoly_scheme.ndb_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nonpoly_scheme.pdb_seq_num
_item_description.description
; PDB residue number.
;
_item.name '_pdbx_nonpoly_scheme.pdb_seq_num'
_item.category_id pdbx_nonpoly_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_nonpoly_scheme.pdb_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nonpoly_scheme.auth_seq_num
_item_description.description
; _atom_site.auth_seq_id
;
_item.name '_pdbx_nonpoly_scheme.auth_seq_num'
_item.category_id pdbx_nonpoly_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_nonpoly_scheme.auth_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nonpoly_scheme.pdb_mon_id
_item_description.description
; PDB residue name.
;
_item.name '_pdbx_nonpoly_scheme.pdb_mon_id'
_item.category_id pdbx_nonpoly_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_nonpoly_scheme.pdb_mon_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nonpoly_scheme.auth_mon_id
_item_description.description
; _atom_site.auth_comp_id
;
_item.name '_pdbx_nonpoly_scheme.auth_mon_id'
_item.category_id pdbx_nonpoly_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_nonpoly_scheme.auth_mon_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nonpoly_scheme.pdb_ins_code
_item_description.description
; PDB insertion code.
;
_item.name '_pdbx_nonpoly_scheme.pdb_ins_code'
_item.category_id pdbx_nonpoly_scheme
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_ndb_nonpoly_scheme.pdb_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
###
###
save_pdbx_refine
_category.description
; Data items in the PDBX_REFINE category record details about
additional structure refinement parameters which are needed
to complete legacy REMARK 3 refinement templates in PDB
format files.
;
_category.id pdbx_refine
_category.mandatory_code no
_category_key.name '_pdbx_refine.entry_id'
loop_
_category_group.id 'inclusive_group'
'refine_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - PDB placeholders for refinement program SHELX
;
;
_pdbx_refine.entry_id ABC001
_pdbx_refine.R_factor_all_4sig_cutoff 0.174
_pdbx_refine.R_factor_obs_4sig_cutoff 0.169
_pdbx_refine.number_reflns_obs_4sig_cutoff 1263
_pdbx_refine.free_R_factor_4sig_cutoff 0.216
_pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 164
_pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 1.29
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_refine.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_pdbx_refine.entry_id'
_item.category_id pdbx_refine
_item.mandatory_code yes
_item_linked.child_name '_pdbx_refine.entry_id'
_item_linked.parent_name '_entry.id'
_item_aliases.alias_name '_ndb_refine.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.R_factor_all_no_cutoff
_item_description.description
; R-value (all reflections, no cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.R_factor_all_no_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_ndb_refine.R_factor_all_no_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.R_factor_obs_no_cutoff
_item_description.description
; R-value (working set reflections, no cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.R_factor_obs_no_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_ndb_refine.R_factor_obs_no_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.free_R_factor_4sig_cutoff
_item_description.description
; R free value (4 sigma cutoff).
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.free_R_factor_4sig_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_examples.case 0.216
_item_aliases.alias_name '_ndb_refine.free_R_factor_4sig_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.free_R_factor_no_cutoff
_item_description.description
; Free R-value (no cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.free_R_factor_no_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_ndb_refine.free_R_factor_no_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.free_R_val_test_set_size_perc_no_cutoff
_item_description.description
; Free R-value test set size (in percent, no cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.free_R_val_test_set_size_perc_no_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name
'_ndb_refine.free_R_val_test_set_size_perc_no_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.free_R_val_test_set_ct_no_cutoff
_item_description.description
; Free R-value test set count (no cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.free_R_val_test_set_ct_no_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_ndb_refine.free_R_val_test_set_ct_no_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.number_reflns_obs_no_cutoff
_item_description.description
; Total number of reflections (no cutoff).
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.number_reflns_obs_no_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_ndb_refine.number_reflns_obs_no_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.R_factor_all_4sig_cutoff
_item_description.description
; R-value (all reflections, 4 sigma cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.R_factor_all_4sig_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_examples.case 0.174
_item_aliases.alias_name '_ndb_refine.R_factor_all_4sig_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.R_factor_obs_4sig_cutoff
_item_description.description
; R-value (working set, 4 sigma cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.R_factor_obs_4sig_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_examples.case 0.169
_item_aliases.alias_name '_ndb_refine.R_factor_obs_4sig_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.free_R_val_4sig_cutoff
_item_description.description
; Free R-value (4 sigma cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.free_R_val_4sig_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_ndb_refine.free_R_val_4sig_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff
_item_description.description
; Free R-value test set size (in percent, 4 sigma cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_examples.case 1.29
_item_aliases.alias_name
'_ndb_refine.free_R_val_test_set_size_perc_4sig_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.free_R_val_test_set_ct_4sig_cutoff
_item_description.description
; Free R-value test set count (4 sigma cutoff)
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.free_R_val_test_set_ct_4sig_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_examples.case 164
_item_aliases.alias_name
'_ndb_refine.free_R_val_test_set_ct_4sig_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine.number_reflns_obs_4sig_cutoff
_item_description.description
; Total number of reflections (4 sigma cutoff).
Placeholder for PDB mapping of SHELXL refinement data.
;
_item.name '_pdbx_refine.number_reflns_obs_4sig_cutoff'
_item.category_id pdbx_refine
_item.mandatory_code no
_item_type.code float
_item_examples.case 1263
_item_aliases.alias_name '_ndb_refine.number_reflns_obs_4sig_cutoff'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
#############################
## PDBX_STRUCT_SHEET_HBOND ##
#############################
save_pdbx_struct_sheet_hbond
_category.description
; Data items in the PDBX_STRUCT_SHEET_HBOND category record details
about the hydrogen bonding between residue ranges in a beta sheet.
This category is provided for cases where only a single hydrogen
bond is used to register the two residue ranges. Category
STRUCT_SHEET_HBOND should be used when the initial and terminal
hydrogen bonds for strand pair are known.
;
_category.id pdbx_struct_sheet_hbond
_category.mandatory_code no
loop_
_category_key.name '_pdbx_struct_sheet_hbond.sheet_id'
'_pdbx_struct_sheet_hbond.range_id_1'
'_pdbx_struct_sheet_hbond.range_id_2'
loop_
_category_group.id 'inclusive_group'
'struct_group'
'pdbx_group'
save_
save__pdbx_struct_sheet_hbond.range_id_1
_item_description.description
; This data item is a pointer to _struct_sheet_range.id in
the STRUCT_SHEET_RANGE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_id_1'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_id_1'
_item_linked.parent_name '_struct_sheet_range.id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_id_1'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_id_2
_item_description.description
; This data item is a pointer to _struct_sheet_range.id in
the STRUCT_SHEET_RANGE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_id_2'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_id_2'
_item_linked.parent_name '_struct_sheet_range.id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_id_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.sheet_id
_item_description.description
; This data item is a pointer to _struct_sheet.id in the
STRUCT_SHEET category.
;
_item.name '_pdbx_struct_sheet_hbond.sheet_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.sheet_id'
_item_linked.parent_name '_struct_sheet.id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.sheet_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__pdbx_struct_sheet_hbond.range_1_label_atom_id
_item_description.description
; A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_1_label_atom_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code yes
_item_type.code atcode
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_label_atom_id'
_item_linked.parent_name '_atom_site.label_atom_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_label_atom_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_1_label_seq_id
_item_description.description
; A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_1_label_seq_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_label_seq_id'
_item_linked.parent_name '_atom_site.label_seq_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_label_seq_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_1_label_comp_id
_item_description.description
; A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_1_label_comp_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code ucode
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_label_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_1_label_asym_id
_item_description.description
; A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_1_label_asym_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_label_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_1_auth_atom_id
_item_description.description
; A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_1_auth_atom_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code atcode
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_auth_atom_id'
_item_linked.parent_name '_atom_site.auth_atom_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_auth_atom_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_1_auth_seq_id
_item_description.description
; A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_1_auth_seq_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_auth_seq_id'
_item_linked.parent_name '_atom_site.auth_seq_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_auth_seq_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_1_auth_comp_id
_item_description.description
; A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_1_auth_comp_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code ucode
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_auth_comp_id'
_item_linked.parent_name '_atom_site.auth_comp_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_auth_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_1_auth_asym_id
_item_description.description
; A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_1_auth_asym_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_auth_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_1_PDB_ins_code
_item_description.description
; A component of the residue identifier for the first partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_1_PDB_ins_code'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_1_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_1_PDB_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__pdbx_struct_sheet_hbond.range_2_label_atom_id
_item_description.description
; A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.label_atom_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_2_label_atom_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code yes
_item_type.code atcode
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_label_atom_id'
_item_linked.parent_name '_atom_site.label_atom_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_label_atom_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_2_label_seq_id
_item_description.description
; A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_2_label_seq_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_label_seq_id'
_item_linked.parent_name '_atom_site.label_seq_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_label_seq_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_2_label_comp_id
_item_description.description
; A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_2_label_comp_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code ucode
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_label_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_2_label_asym_id
_item_description.description
; A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_2_label_asym_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_label_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_2_auth_atom_id
_item_description.description
; A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.auth_atom_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_2_auth_atom_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code atcode
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_auth_atom_id'
_item_linked.parent_name '_atom_site.auth_atom_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_auth_atom_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_2_auth_seq_id
_item_description.description
; A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_2_auth_seq_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_auth_seq_id'
_item_linked.parent_name '_atom_site.auth_seq_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_auth_seq_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_2_auth_comp_id
_item_description.description
; A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_2_auth_comp_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code ucode
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_auth_comp_id'
_item_linked.parent_name '_atom_site.auth_comp_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_auth_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_2_auth_asym_id
_item_description.description
; A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_2_auth_asym_id'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_auth_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_struct_sheet_hbond.range_2_PDB_ins_code
_item_description.description
; A component of the residue identifier for the second partner of the
registration hydrogen bond between two residue ranges in a sheet.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_struct_sheet_hbond.range_2_PDB_ins_code'
_item.category_id pdbx_struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_struct_sheet_hbond.range_2_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_rcsb_struct_sheet_hbond.range_2_PDB_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
###
save_pdbx_xplor_file
_category.description
;
Parameter and topology files used in X-PLOR/CNS refinement.
;
_category.id pdbx_xplor_file
_category.mandatory_code no
_category_key.name '_pdbx_xplor_file.serial_no'
loop_
_category_group.id 'inclusive_group'
'refine_group'
'pdbx_group'
loop_
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_pdbx_xplor_file.serial_no 1
_pdbx_xplor_file.param_file parm_hol.dat
_pdbx_xplor_file.topol_file topol_hol.dat
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_xplor_file.serial_no
_item_description.description
; Serial number.
;
_item.name '_pdbx_xplor_file.serial_no'
_item.category_id pdbx_xplor_file
_item.mandatory_code yes
_item_type.code code
_item_aliases.alias_name '_ndb_xplor_file.serial_no'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_xplor_file.param_file
_item_description.description
; Parameter file name in X-PLOR/CNS refinement.
;
_item.name '_pdbx_xplor_file.param_file'
_item.category_id pdbx_xplor_file
_item.mandatory_code no
_item_type.code line
_item_examples.case 'PARAM_NDBX_HIGH.DNA'
_item_aliases.alias_name '_ndb_xplor_file.param_file'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_xplor_file.topol_file
_item_description.description
; Topology file name in X-PLOR/CNS refinement.
;
_item.name '_pdbx_xplor_file.topol_file'
_item.category_id pdbx_xplor_file
_item.mandatory_code no
_item_type.code line
_item_examples.case 'TOP_NDBX.DNA'
_item_aliases.alias_name '_ndb_xplor_file.topol_file'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save_pdbx_refine_aux_file
_category.description
;
Auxilary parameter and topology files used in refinement.
;
_category.id pdbx_refine_aux_file
_category.mandatory_code no
_category_key.name '_pdbx_refine_aux_file.serial_no'
loop_
_category_group.id 'inclusive_group'
'refine_group'
'pdbx_group'
loop_
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_pdbx_refine_aux_file.serial_no 1
_pdbx_refine_aux_file.file_name parm_hol.dat
_pdbx_refine_aux_file.file_type PARAMETER
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_refine_aux_file.serial_no
_item_description.description
; Serial number.
;
_item.name '_pdbx_refine_aux_file.serial_no'
_item.category_id pdbx_refine_aux_file
_item.mandatory_code yes
_item_type.code code
_item_aliases.alias_name '_rcsb_refine_aux_file.serial_no'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine_aux_file.file_name
_item_description.description
; Auxilary file name.
;
_item.name '_pdbx_refine_aux_file.file_name'
_item.category_id pdbx_refine_aux_file
_item.mandatory_code no
_item_type.code line
_item_examples.case 'PARAM_NDBX_HIGH.DNA'
_item_aliases.alias_name '_rcsb_refine_aux_file.file_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_refine_aux_file.file_type
_item_description.description
; Auxilary file type.
;
_item.name '_pdbx_refine_aux_file.file_type'
_item.category_id pdbx_refine_aux_file
_item.mandatory_code no
_item_type.code line
_item_examples.case 'PARAMETER'
loop_
_item_enumeration.value 'PARAMETER' 'TOPOLOGY'
_item_aliases.alias_name '_rcsb_refine_aux_file.file_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
##
save_pdbx_database_related
_category.description
; Data items in PDBX_DATABASE_RELATED contain references to entries
that are related to the this entry.
;
_category.id pdbx_database_related
_category.mandatory_code no
loop_
_category_key.name '_pdbx_database_related.db_name'
'_pdbx_database_related.db_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
_category_examples.case
;
_pdbx_database_related.db_name PDB
_pdbx_database_related.db_id 1ABC
;
save_
save__pdbx_database_related.db_name
_item_description.description
; The name of the database containing the related entry.
;
_item.name '_pdbx_database_related.db_name'
_item.category_id pdbx_database_related
_item.mandatory_code yes
_item_type.code code
# loop_
# _item_enumeration.value 'PDB' 'NDB' 'BMRB' 'BMCD'
_item_examples.case
;
PDB - Protein Databank
NDB - Nucleic Acid Database
BMRB - BioMagResBank
BMCD - Biological Macromolecule Crystallization Database
;
_item_aliases.alias_name '_rcsb_database_related.db_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_database_related.details
_item_description.description
; A description of the related entry.
;
_item.name '_pdbx_database_related.details'
_item.category_id pdbx_database_related
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
;
1ABC contains the same protein complexed with Netropsin.
;
_item_aliases.alias_name '_rcsb_database_related.details'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
#
#
save__pdbx_database_related.db_id
_item_description.description
; The identifying code in the related database.
;
_item.name '_pdbx_database_related.db_id'
_item.category_id pdbx_database_related
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case '1ABC' 'BDL001'
_item_aliases.alias_name '_rcsb_database_related.db_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
#
save__pdbx_database_related.content_type
_item_description.description
; The identifying content type of the related entry.
;
_item.name '_pdbx_database_related.content_type'
_item.category_id pdbx_database_related
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'minimized average structure'
'representative structure'
'ensemble'
'derivative structure'
'native structure'
'other'
loop_
_item_enumeration.value
'minimized average structure'
'representative structure'
'ensemble'
'derivative structure'
'native structure'
'other'
_item_aliases.alias_name '_rcsb_database_related.content_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##########################
## PDBX_ENTITY_ASSEMBLY ##
##########################
save_pdbx_entity_assembly
_category.description
; The PDBX_ENTITY_ASSEMBLY category provides a chemical description
of the biological assembly studied in terms of its constituent
entities.
;
_category.id pdbx_entity_assembly
_category.mandatory_code no
loop_
_category_key.name '_pdbx_entity_assembly.id'
'_pdbx_entity_assembly.entity_id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; A complex composed of one copy of entities 1 and 2.
;
;
loop_
_pdbx_entity_assembly.id
_pdbx_entity_assembly.biol_id
_pdbx_entity_assembly.entity_id
_pdbx_entity_assembly.num_copies
1 1 1 1
1 1 2 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_entity_assembly.id
_item_description.description
; An identifier for the assembly.
;
_item.name '_pdbx_entity_assembly.id'
_item.category_id pdbx_entity_assembly
_item.mandatory_code yes
_item_type.code code
_item_aliases.alias_name '_rcsb_entity_assembly.id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_entity_assembly.entity_id
_item_description.description
; An enity identifier. A reference to _entity.id.
;
_item.name '_pdbx_entity_assembly.entity_id'
_item.category_id pdbx_entity_assembly
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_entity_assembly.entity_id'
_item_linked.parent_name '_entity.id'
_item_aliases.alias_name '_rcsb_entity_assembly.entity_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_entity_assembly.biol_id
_item_description.description
; An identifier for the assembly.
;
_item.name '_pdbx_entity_assembly.biol_id'
_item.category_id pdbx_entity_assembly
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_entity_assembly.biol_id'
_item_linked.parent_name '_struct_biol.id'
_item_aliases.alias_name '_rcsb_entity_assembly.biol_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_entity_assembly.num_copies
_item_description.description
; The number of copies of this entity in the assembly.
;
_item.name '_pdbx_entity_assembly.num_copies'
_item.category_id pdbx_entity_assembly
_item.mandatory_code yes
_item_type.code int
_item_aliases.alias_name '_rcsb_entity_assembly.num_copies'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
#########################
## PDBX_ENTITY_SRC_SYN ##
#########################
save_pdbx_entity_src_syn
_category.description
; PDBX_ENTITY_SRC_SYN records the details about each chemically
synthesized molecule (entity) in the asymmetric unit.
;
_category.id pdbx_entity_src_syn
_category.mandatory_code no
_category_key.name '_pdbx_entity_src_syn.entity_id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
'pdbx_group'
save_
save__pdbx_entity_src_syn.details
_item_description.description
; A description of special aspects of the source for the
synthetic entity.
;
_item.name '_pdbx_entity_src_syn.details'
_item.category_id pdbx_entity_src_syn
_item.mandatory_code no
_item_type.code text
_item_examples.case 'This sequence occurs naturally in humans.'
_item_aliases.alias_name '_rcsb_entity_src_syn.details'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_entity_src_syn.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_pdbx_entity_src_syn.entity_id'
_item.category_id pdbx_entity_src_syn
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_entity_src_syn.entity_id'
_item_linked.parent_name '_entity.id'
loop_
_item_examples.case
'1'
'2'
'3'
'4'
_item_aliases.alias_name '_rcsb_entity_src_syn.entity_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
### ---------------------------------------------------------------------------
### Supplemental items in existing mmCIF categories ...
###
###
save__atom_site.pdbx_auth_alt_id
_item_description.description
; Author's alternate location identifier.
;
_item.name '_atom_site.pdbx_auth_alt_id'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_atom_site.ndb_auth_alt_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site.pdbx_PDB_ins_code
_item_description.description
; PDB insertion code.
;
_item.name '_atom_site.pdbx_PDB_ins_code'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_atom_site.ndb_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site.pdbx_PDB_model_num
_item_description.description
; PDB model number.
;
_item.name '_atom_site.pdbx_PDB_model_num'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_atom_site.ndb_model'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site.pdbx_PDB_residue_no
_item_description.description
; PDB residue number.
;
_item.name '_atom_site.pdbx_PDB_residue_no'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_atom_site.ndb_PDB_residue_no'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site.pdbx_PDB_residue_name
_item_description.description
; PDB residue name.
;
_item.name '_atom_site.pdbx_PDB_residue_name'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_atom_site.ndb_PDB_residue_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site.pdbx_PDB_strand_id
_item_description.description
; PDB strand id.
;
_item.name '_atom_site.pdbx_PDB_strand_id'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_atom_site.ndb_PDB_strand_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site.pdbx_PDB_atom_name
_item_description.description
; PDB atom name.
;
_item.name '_atom_site.pdbx_PDB_atom_name'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_atom_site.ndb_PDB_atom_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site.pdbx_auth_atom_name
_item_description.description
; Author's atom name.
;
_item.name '_atom_site.pdbx_auth_atom_name'
_item.category_id atom_site
_item.mandatory_code no
_item_type.code atcode
_item_aliases.alias_name '_atom_site.ndb_auth_atom_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__atom_site_anisotrop.pdbx_auth_seq_id
_item_description.description
; Pointer to _atom_site.auth_seq_id
;
_item.name '_atom_site_anisotrop.pdbx_auth_seq_id'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_atom_site_anisotrop.pdbx_auth_seq_id'
_item_linked.parent_name '_atom_site.auth_seq_id'
_item_aliases.alias_name '_atom_site_anisotrop.ndb_PDB_residue_no'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site_anisotrop.pdbx_auth_alt_id
_item_description.description
; Pointer to _atom_site.pdbx_auth_alt_id.
;
_item.name '_atom_site_anisotrop.pdbx_auth_alt_id'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_atom_site_anisotrop.pdbx_auth_alt_id'
_item_linked.parent_name '_atom_site.pdbx_auth_alt_id'
# _item_aliases.alias_name '_atom_site_anisotrop.ndb_auth_alt_id'
# _item_aliases.dictionary 'cif_rcsb.dic'
# _item_aliases.version 1.1
save_
save__atom_site_anisotrop.pdbx_auth_asym_id
_item_description.description
; Pointer to _atom_site.auth_asym_id
;
_item.name '_atom_site_anisotrop.pdbx_auth_asym_id'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_atom_site_anisotrop.pdbx_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
_item_aliases.alias_name '_atom_site_anisotrop.ndb_PDB_strand_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site_anisotrop.pdbx_auth_atom_id
_item_description.description
; Pointer to _atom_site.auth_atom_id
;
_item.name '_atom_site_anisotrop.pdbx_auth_atom_id'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_type.code atcode
_item_linked.child_name '_atom_site_anisotrop.pdbx_auth_atom_id'
_item_linked.parent_name '_atom_site.auth_atom_id'
_item_aliases.alias_name '_atom_site_anisotrop.ndb_PDB_atom_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site_anisotrop.pdbx_auth_comp_id
_item_description.description
; Pointer to _atom_site.auth_comp_id
;
_item.name '_atom_site_anisotrop.pdbx_auth_comp_id'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_atom_site_anisotrop.pdbx_auth_comp_id'
_item_linked.parent_name '_atom_site.auth_comp_id'
_item_aliases.alias_name '_atom_site_anisotrop.ndb_PDB_residue_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site_anisotrop.pdbx_label_seq_id
_item_description.description
; Pointer to _atom_site.label_seq_id
;
_item.name '_atom_site_anisotrop.pdbx_label_seq_id'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_atom_site_anisotrop.pdbx_label_seq_id'
_item_linked.parent_name '_atom_site.label_seq_id'
_item_aliases.alias_name '_atom_site_anisotrop.ndb_label_seq_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site_anisotrop.pdbx_label_alt_id
_item_description.description
; Pointer to _atom_site.label_alt_id.
;
_item.name '_atom_site_anisotrop.pdbx_label_alt_id'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_atom_site_anisotrop.pdbx_label_alt_id'
_item_linked.parent_name '_atom_site.label_alt_id'
_item_aliases.alias_name '_atom_site_anisotrop.ndb_label_alt_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site_anisotrop.pdbx_label_asym_id
_item_description.description
; Pointer to _atom_site.label_asym_id
;
_item.name '_atom_site_anisotrop.pdbx_label_asym_id'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_atom_site_anisotrop.pdbx_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
_item_aliases.alias_name '_atom_site_anisotrop.ndb_label_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site_anisotrop.pdbx_label_atom_id
_item_description.description
; Pointer to _atom_site.label_atom_id
;
_item.name '_atom_site_anisotrop.pdbx_label_atom_id'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_type.code atcode
_item_linked.child_name '_atom_site_anisotrop.pdbx_label_atom_id'
_item_linked.parent_name '_atom_site.label_atom_id'
_item_aliases.alias_name '_atom_site_anisotrop.ndb_label_atom_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site_anisotrop.pdbx_label_comp_id
_item_description.description
; Pointer to _atom_site.label_comp_id
;
_item.name '_atom_site_anisotrop.pdbx_label_comp_id'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_atom_site_anisotrop.pdbx_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
_item_aliases.alias_name '_atom_site_anisotrop.ndb_label_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__atom_site_anisotrop.pdbx_PDB_ins_code
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code
;
_item.name '_atom_site_anisotrop.pdbx_PDB_ins_code'
_item.category_id atom_site_anisotrop
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_atom_site_anisotrop.pdbx_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_atom_site_anisotrop.ndb_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__cell.pdbx_unique_axis
_item_description.description
; To further identify unique axis if necessary. E.g., P 21 with
an unique C axis will have 'C' in this field.
;
_item.name '_cell.pdbx_unique_axis'
_item.category_id cell
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_cell.ndb_unique_axis'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__chem_comp.pdbx_synonyms
_item_description.description
; Synonym list for the component.
;
_item.name '_chem_comp.pdbx_synonyms'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code line
_item_examples.case ATP
_item_aliases.alias_name '_chem_comp.ndb_synonyms'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__chem_comp.pdbx_modification_details
_item_description.description
; For nonstandard components a text description
of modification of the parent component.
;
_item.name '_chem_comp.pdbx_modification_details'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code line
_item_examples.case ATP
_item_aliases.alias_name '_chem_comp.rcsb_modification_details'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__chem_comp.pdbx_component_no
_item_description.description
; A serial number used by PDB in the FORMUL record.
;
_item.name '_chem_comp.pdbx_component_no'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code int
_item_examples.case 3
_item_aliases.alias_name '_chem_comp.ndb_component_no'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__chem_comp.pdbx_type
_item_description.description
; A preliminary classification used by PDB.
;
_item.name '_chem_comp.pdbx_type'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code uline
save_
save__chem_comp.pdbx_formal_charge
_item_description.description
; The net integer charge assigned to this component. This is the
formal charge assignment normally found in chemical diagrams.
;
_item.name '_chem_comp.pdbx_formal_charge'
_item.category_id chem_comp
_item.mandatory_code no
_item_default.value 0
_item_type.code int
save_
save__chem_comp_atom.pdbx_align
_item_description.description
; Atom name alignment offset in PDB atom field.
;
_item.name '_chem_comp_atom.pdbx_align'
_item.category_id chem_comp
_item.mandatory_code no
_item_type.code int
save_
###
###
save__citation.pdbx_database_id_DOI
_item_description.description
; Document Object Identifier used by doi.org to uniquely
specify bibliographic entry.
;
_item.name '_citation.pdbx_database_id_DOI'
_item.category_id citation
_item.mandatory_code no
_item_type.code code
_item_examples.case 'DOI:10.2345/S1384107697000225'
_item_aliases.alias_name '_citation.rcsb_database_id_DOI'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__citation.pdbx_database_id_PubMed
_item_description.description
; Ascession number used by PubMed to categorize a specific
bibliographic entry.
;
_item.name '_citation.pdbx_database_id_PubMed'
_item.category_id citation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
_item_examples.case 12627512
_item_aliases.alias_name '_citation.rcsb_database_id_PubMed'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__computing.pdbx_structure_refinement_method
_item_description.description
; Program/package name for structure refinement method.
;
_item.name '_computing.pdbx_structure_refinement_method'
_item.category_id computing
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_computing.ndb_structure_refinement_method'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__computing.pdbx_data_reduction_ii
_item_description.description
; Program/package name for data reduction/intensity integration software
;
_item.name '_computing.pdbx_data_reduction_ii'
_item.category_id computing
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_computing.rcsb_data_reduction_ii'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__computing.pdbx_data_reduction_ds
_item_description.description
; Program/package name for data reduction/data scaling
;
_item.name '_computing.pdbx_data_reduction_ds'
_item.category_id computing
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_computing.rcsb_data_reduction_ds'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
##
##
save__diffrn_detector.pdbx_frames_total
_item_description.description
; The total number of data frames collected for this
data set.
;
_item.name '_diffrn_detector.pdbx_frames_total'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case 20 100
save_
save__diffrn_detector.pdbx_collection_time_total
_item_description.description
; The total number of seconds required to measure this
data set.
;
_item.name '_diffrn_detector.pdbx_collection_time_total'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_type.code float
_item_units.code seconds
loop_
_item_examples.case 120.0
save_
save__diffrn_detector.pdbx_collection_date
_item_description.description
; The date of data collection.
;
_item.name '_diffrn_detector.pdbx_collection_date'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case '1996-12-25'
_item_aliases.alias_name '_diffrn_detector.ndb_collection_date'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__diffrn_radiation.pdbx_monochromatic_or_laue_m_l
_item_description.description
; Monochromatic or Laue.
;
_item.name '_diffrn_radiation.pdbx_monochromatic_or_laue_m_l'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code code
_item_default.value 'M'
loop_
_item_enumeration.value
_item_enumeration.detail
'M' .
'L' .
loop_
_item_examples.case
'M'
'L'
_item_aliases.alias_name '_diffrn_radiation.ndb_monochromatic_or_laue_m_l'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__diffrn_radiation.pdbx_wavelength_list
_item_description.description
; Comma separated list of wavelengths or wavelength range.
;
_item.name '_diffrn_radiation.pdbx_wavelength_list'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code line
_item_aliases.alias_name '_diffrn_source.rcsb_wavelength_list'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__diffrn_radiation.pdbx_wavelength
_item_description.description
; Wavelength of radiation.
;
_item.name '_diffrn_radiation.pdbx_wavelength'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code line
_item_aliases.alias_name '_diffrn_source.rcsb_wavelength'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__diffrn_radiation.pdbx_diffrn_protocol
_item_description.description
; SINGLE WAVELENGTH, LAUE, or MAD.
;
_item.name '_diffrn_radiation.pdbx_diffrn_protocol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code line
_item_default.value 'SINGLE WAVELENGTH'
# loop_
# _item_enumeration.value
# 'SINGLE WAVELENGTH'
# 'MONOCHROMATIC'
# 'LAUE'
# 'MAD'
# 'OTHER'
loop_
_item_examples.case
'SINGLE WAVELENGTH'
'MONOCHROMATIC'
'LAUE'
'MAD'
'OTHER'
_item_aliases.alias_name '_diffrn_radiation.rcsb_diffrn_protocol'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__diffrn_source.pdbx_synchrotron_beamline
_item_description.description
; Synchrotron beamline.
;
_item.name '_diffrn_source.pdbx_synchrotron_beamline'
_item.category_id diffrn_source
_item.mandatory_code no
_item_type.code line
_item_aliases.alias_name '_diffrn_source.ndb_synchrotron_beamline'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__diffrn_source.pdbx_synchrotron_site
_item_description.description
; Synchrotron site.
;
_item.name '_diffrn_source.pdbx_synchrotron_site'
_item.category_id diffrn_source
_item.mandatory_code no
_item_type.code line
_item_aliases.alias_name '_diffrn_source.ndb_synchrotron_site'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__entity.pdbx_description
_item_description.description
; A description of the entity, with the name of the entity
in parenthesis.
Maps to PDB compound name.
;
_item.name '_entity.pdbx_description'
_item.category_id entity
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3')'
PROFLAVINE
'PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1))'
_item_aliases.alias_name '_entity.ndb_description'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity.pdbx_number_of_molecules
_item_description.description
; A place holder for the number of molecules of the entity in
the entry.
;
_item.name '_entity.pdbx_number_of_molecules'
_item.category_id entity
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case 1.0 2.0 3.0
_item_aliases.alias_name '_entity.ndb_number_of_molecules'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity.pdbx_parent_entity_id
_item_description.description
; An identifier for the parent entity if this entity
is part of a complex entity. For instance a chimeric
entity may be decomposed into several independent
chemical entities where each component entity was
obtained from a different source.
;
_item.name '_entity.pdbx_parent_entity_id'
_item.category_id entity
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_entity.pdbx_parent_entity_id'
_item_linked.parent_name '_entity.id'
loop_
_item_examples.case 1 2 3
_item_aliases.alias_name '_entity.rcsb_parent_entity_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity.pdbx_mutation
_item_description.description
; Details about any entity mutation(s).
;
_item.name '_entity.pdbx_mutation'
_item.category_id entity
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'Y31H'
'DEL(298-323)'
_item_aliases.alias_name '_entity_keywords.ndb_mutation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity.pdbx_fragment
_item_description.description
; Entity fragment description(s).
;
_item.name '_entity.pdbx_fragment'
_item.category_id entity
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'KLENOW FRAGMENT'
'REPLICASE OPERATOR HAIRPIN'
'C-TERMINAL DOMAIN'
_item_aliases.alias_name '_entity_keywords.ndb_fragment'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity.pdbx_ec
_item_description.description
; Enzyme Commission (EC) number(s)
;
_item.name '_entity.pdbx_ec'
_item.category_id entity
_item.mandatory_code no
_item_type.code line
_item_examples.case 2.7.7.7
_item_aliases.alias_name '_entity_keywords.ndb_ec'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity.pdbx_modification
_item_description.description
; Description(s) of any chemical or post-translational modifications
;
_item.name '_entity.pdbx_modification'
_item.category_id entity
_item.mandatory_code no
_item_type.code line
_item_aliases.alias_name '_entity_keywords.rcsb_modification'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity.pdbx_formula_weight_exptl
_item_description.description
; Experimentally determined formula mass in daltons of the entity
;
_item.name '_entity.pdbx_formula_weight_exptl'
_item.category_id entity
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1.0
1.0 1.0
_item_type.code float
_item_aliases.alias_name '_entity.rcsb_formula_weight_exptl'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity.pdbx_formula_weight_exptl_method
_item_description.description
; Method used to determine _entity.pdbx_formula_weight_exptl.
;
_item.name '_entity.pdbx_formula_weight_exptl_method'
_item.category_id entity
_item.mandatory_code no
_item_type.code line
_item_examples.case 'MASS SPEC'
loop_
_item_enumeration.value
'MASS SPEC'
save_
##
## ####
save__entity_keywords.pdbx_mutation
_item_description.description
; Entity mutation description(s).
;
_item.name '_entity_keywords.pdbx_mutation'
_item.category_id entity_keywords
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'Y31H'
'DEL(298-323)'
# _item_aliases.alias_name '_entity_keywords.ndb_mutation'
# _item_aliases.dictionary 'cif_rcsb.dic'
# _item_aliases.version 1.1
_item_related.related_name '_entity.pdbx_mutation'
_item_related.function_code replacedby
save_
save__entity_keywords.pdbx_fragment
_item_description.description
; Entity fragment description(s).
;
_item.name '_entity_keywords.pdbx_fragment'
_item.category_id entity_keywords
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'KLENOW FRAGMENT'
'REPLICASE OPERATOR HAIRPIN'
'C-TERMINAL DOMAIN'
# _item_aliases.alias_name '_entity_keywords.ndb_fragment'
# _item_aliases.dictionary 'cif_rcsb.dic'
# _item_aliases.version 1.1
_item_related.related_name '_entity.pdbx_fragment'
_item_related.function_code replacedby
save_
save__entity_keywords.pdbx_ec
_item_description.description
; Enzyme Commission (EC) number(s)
;
_item.name '_entity_keywords.pdbx_ec'
_item.category_id entity_keywords
_item.mandatory_code no
_item_type.code line
_item_examples.case 2.7.7.7
# _item_aliases.alias_name '_entity_keywords.ndb_ec'
# _item_aliases.dictionary 'cif_rcsb.dic'
# _item_aliases.version 1.1
_item_related.related_name '_entity.pdbx_mutation'
_item_related.function_code replacedby
save_
##
##
save__entity_poly.pdbx_strand_id
_item_description.description
; The PDB strand/chain id(s) corresponding to this polymer entity.
;
_item.name '_entity_poly.pdbx_strand_id'
_item.category_id entity_poly
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
A
B
'A,B,C'
_item_aliases.alias_name '_entity_poly.ndb_chain_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_poly.pdbx_seq_one_letter_code
_item_description.description
; Chemical sequence expressed as string of one-letter
amino acid codes. Modifications and non-standard
amino acids are coded as X.
;
_item.name '_entity_poly.pdbx_seq_one_letter_code'
_item.category_id entity_poly
_item.mandatory_code no
_item_type.code text
_item_examples.case
;
A for alanine or adenine
B for ambiguous asparagine/aspartic-acid
R for arginine
N for asparagine
D for aspartic-acid
C for cysteine or cystine or cytosine
Q for glutamine
E for glutamic-acid
Z for ambiguous glutamine/glutamic acid
G for glycine or guanine
H for histidine
I for isoleucine
L for leucine
K for lysine
M for methionine
F for phenylalanine
P for proline
S for serine
T for threonine or thymine
W for tryptophan
Y for tyrosine
V for valine
U for uracil
O for water
X for other
;
_item_aliases.alias_name '_entity_poly.ndb_seq_one_letter_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_poly.pdbx_seq_one_letter_code_can
_item_description.description
; Cannonical chemical sequence expressed as string of
one-letter amino acid codes. Modifications are coded
as the parent amino acid where possible.
A for alanine or adenine
B for ambiguous asparagine/aspartic-acid
R for arginine
N for asparagine
D for aspartic-acid
C for cysteine or cystine or cytosine
Q for glutamine
E for glutamic-acid
Z for ambiguous glutamine/glutamic acid
G for glycine or guanine
H for histidine
I for isoleucine
L for leucine
K for lysine
M for methionine
F for phenylalanine
P for proline
S for serine
T for threonine or thymine
W for tryptophan
Y for tyrosine
V for valine
U for uracil
;
_item.name '_entity_poly.pdbx_seq_one_letter_code_can'
_item.category_id entity_poly
_item.mandatory_code no
_item_type.code text
_item_examples.case
;
MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD
;
_item_aliases.alias_name '_entity_poly.ndb_seq_one_letter_code_can'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_poly.pdbx_target_identifier
_item_description.description
; The sequence's target identifier registered at target database.
;
_item.name '_entity_poly.pdbx_target_identifier'
_item.category_id entity_poly
_item.mandatory_code no
_item_type.code line
_item_examples.case 356560
save_
##
##
save__entity_src_gen.pdbx_gene_src_fragment
_item_description.description
; A domain or fragment of the molecule.
;
_item.name '_entity_src_gen.pdbx_gene_src_fragment'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'CYTOPLASM' 'NUCLEUS'
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_fragment'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_gene_src_gene
_item_description.description
; Identifies the gene.
;
_item.name '_entity_src_gen.pdbx_gene_src_gene'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_gene'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_gene_src_scientific_name
_item_description.description
; Scientific name of the organism.
;
_item.name '_entity_src_gen.pdbx_gene_src_scientific_name'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case
;
ESCHERICHIA COLI
HOMO SAPIENS
SACCHAROMYCES CEREVISIAE
;
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_scientific_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_gene_src_variant
_item_description.description
; Identifies the variant.
;
_item.name '_entity_src_gen.pdbx_gene_src_variant'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case 'DELTAH1DELTATRP'
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_variant'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_gene_src_cell_line
_item_description.description
; The specific line of cells.
;
_item.name '_entity_src_gen.pdbx_gene_src_cell_line'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case 'HELA CELLS'
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_cell_line'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_gene_src_atcc
_item_description.description
; American Type Culture Collection tissue culture number.
;
_item.name '_entity_src_gen.pdbx_gene_src_atcc'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case '6051'
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_atcc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_gene_src_organ
_item_description.description
; Organized group of tissues that carries on a specialized function.
;
_item.name '_entity_src_gen.pdbx_gene_src_organ'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'KIDNEY' 'LIVER' 'PANCREAS'
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_organ'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_gene_src_organelle
_item_description.description
; Organized structure within cell.
;
_item.name '_entity_src_gen.pdbx_gene_src_organelle'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case 'MITOCHONDRIA'
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_organelle'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_gene_src_plasmid
_item_description.description
; The source plasmid.
;
_item.name '_entity_src_gen.pdbx_gene_src_plasmid'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_plasmid'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_gene_src_plasmid_name
_item_description.description
; The source plasmid.
;
_item.name '_entity_src_gen.pdbx_gene_src_plasmid_name'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_plasmid_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_gene_src_cell
_item_description.description
; Cell type.
;
_item.name '_entity_src_gen.pdbx_gene_src_cell'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case 'ENDOTHELIAL'
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_cell'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_gene_src_cellular_location
_item_description.description
; Identifies the location inside (or outside) the cell.
;
_item.name '_entity_src_gen.pdbx_gene_src_cellular_location'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'CYTOPLASM' 'NUCLEUS'
_item_aliases.alias_name '_entity_src_gen.ndb_gene_src_cellular_location'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_gene
_item_description.description
; Specific gene which expressed the molecule.
;
_item.name '_entity_src_gen.pdbx_host_org_gene'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'HIV-1 POL' 'GLNS7' 'U1A (2-98, Y31H, Q36R)'
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_gene'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_organ
_item_description.description
; Specific organ which expressed the molecule.
;
_item.name '_entity_src_gen.pdbx_host_org_organ'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case KIDNEY
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_organ'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_variant
_item_description.description
; Variant of the organism used as the expression system.
;
_item.name '_entity_src_gen.pdbx_host_org_variant'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'TRP-LAC' 'LAMBDA DE3'
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_variant'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_cell_line
_item_description.description
; A specific line of cells used as the expression system.
;
_item.name '_entity_src_gen.pdbx_host_org_cell_line'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case 'HELA'
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_cell_line'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_atcc
_item_description.description
; Americal Tissue Culture Collection of the expression system.
;
_item.name '_entity_src_gen.pdbx_host_org_atcc'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_atcc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_culture_collection
_item_description.description
; Culture collection of the expression system.
;
_item.name '_entity_src_gen.pdbx_host_org_culture_collection'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_culture_collection'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_cell
_item_description.description
; Specific cell type which expressed the molecule.
;
_item.name '_entity_src_gen.pdbx_host_org_cell'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case ENDOTHELIAL
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_cell'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_organelle
_item_description.description
; Specific organelle which expressed the molecule.
;
_item.name '_entity_src_gen.pdbx_host_org_organelle'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case 'MITOCHONDRIA'
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_organelle'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_cellular_location
_item_description.description
; Identifies the location inside (or outside) the cell which
expressed the molecule.
;
_item.name '_entity_src_gen.pdbx_host_org_cellular_location'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'CYTOPLASM' 'NUCLEUS'
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_cellular_location'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_scientific_name
_item_description.description
;
The scientific name of the organism that served as host for the
production of the entity.
;
_item.name '_entity_src_gen.pdbx_host_org_scientific_name'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case
;
ESCHERICHIA COLI
HOMO SAPIENS
SACCHAROMYCES CEREVISIAE
;
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_scientific_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_strain
_item_description.description
;
The strain of the organism in which the entity was
expressed.
;
_item.name '_entity_src_gen.pdbx_host_org_strain'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case 'AR120'
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_strain'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_tissue
_item_description.description
;
The specific tissue which expressed the molecule.
;
_item.name '_entity_src_gen.pdbx_host_org_tissue'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'heart'
'liver'
'eye lens'
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_tissue'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_tissue_fraction
_item_description.description
;
The fraction of the tissue which expressed the
molecule.
;
_item.name '_entity_src_gen.pdbx_host_org_tissue_fraction'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'mitochondria'
'nucleus'
'membrane'
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_tissue_fraction'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_vector
_item_description.description
;
Identifies the vector used.
;
_item.name '_entity_src_gen.pdbx_host_org_vector'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'PBIT36' 'PET15B' 'PUC18'
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_vector'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_host_org_vector_type
_item_description.description
;
Identifies the type of vector used (plasmid, virus, or
cosmid).
;
_item.name '_entity_src_gen.pdbx_host_org_vector_type'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'COSMID' 'PLASMID'
_item_aliases.alias_name '_entity_src_gen.ndb_host_org_vector_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_gen.pdbx_description
_item_description.description
; Information on the source which is not given elsewhere.
;
_item.name '_entity_src_gen.pdbx_description'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_entity_src_gen.ndb_description'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__entity_src_nat.pdbx_organism_scientific
_item_description.description
; Scientific name of the organism of the natural source.
;
_item.name '_entity_src_nat.pdbx_organism_scientific'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'BOS TAURUS' 'SUS SCROFA' 'ASPERGILLUS ORYZAE'
_item_aliases.alias_name '_entity_src_nat.ndb_organism_scientific'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_nat.pdbx_secretion
_item_description.description
; Identifies the secretion from which the molecule was isolated.
;
_item.name '_entity_src_nat.pdbx_secretion'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'saliva' 'urine' 'venom'
_item_aliases.alias_name '_entity_src_nat.ndb_secretion'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_nat.pdbx_fragment
_item_description.description
; A domain or fragment of the molecule.
;
_item.name '_entity_src_nat.pdbx_fragment'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_entity_src_nat.ndb_fragment'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_nat.pdbx_variant
_item_description.description
; Identifies the variant.
;
_item.name '_entity_src_nat.pdbx_variant'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_entity_src_nat.ndb_variant'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_nat.pdbx_cell_line
_item_description.description
; The specific line of cells.
;
_item.name '_entity_src_nat.pdbx_cell_line'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
_item_examples.case 'HELA'
_item_aliases.alias_name '_entity_src_nat.ndb_cell_line'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_nat.pdbx_atcc
_item_description.description
; Americal Tissue Culture Collection number.
;
_item.name '_entity_src_nat.pdbx_atcc'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
_item_examples.case '6051'
_item_aliases.alias_name '_entity_src_nat.ndb_atcc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_nat.pdbx_cellular_location
_item_description.description
; Identifies the location inside (or outside) the cell.
;
_item.name '_entity_src_nat.pdbx_cellular_location'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_entity_src_nat.ndb_cellular_location'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_nat.pdbx_organ
_item_description.description
; Organized group of tissues that carries on a specialized function.
;
_item.name '_entity_src_nat.pdbx_organ'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
_item_examples.case KIDNEY
_item_aliases.alias_name '_entity_src_nat.ndb_organ'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_nat.pdbx_organelle
_item_description.description
; Organized structure within cell.
;
_item.name '_entity_src_nat.pdbx_organelle'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
_item_examples.case MITOCHONDRIA
_item_aliases.alias_name '_entity_src_nat.ndb_organelle'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_nat.pdbx_cell
_item_description.description
; A particular cell type.
;
_item.name '_entity_src_nat.pdbx_cell'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
_item_examples.case 'BHK-21'
_item_aliases.alias_name '_entity_src_nat.ndb_cell'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_nat.pdbx_plasmid_name
_item_description.description
; The plasmid containing the gene.
;
_item.name '_entity_src_nat.pdbx_plasmid_name'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
_item_examples.case 'pB322'
_item_aliases.alias_name '_entity_src_nat.ndb_plasmid_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__entity_src_nat.pdbx_plasmid_details
_item_description.description
; Details about the plasmid.
;
_item.name '_entity_src_nat.pdbx_plasmid_details'
_item.category_id entity_src_nat
_item.mandatory_code no
_item_type.code text
_item_examples.case 'PLC28 DERIVATIVE'
_item_aliases.alias_name '_entity_src_nat.ndb_plasmid_details'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__exptl_crystal_grow.pdbx_details
_item_description.description
; Text description of crystal grow procedure.
;
_item.name '_exptl_crystal_grow.pdbx_details'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'PEG 4000, potassium phosphate, magnesium chloride, cacodylate'
_item_aliases.alias_name '_exptl_crystal_grow.rcsb_details'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__exptl_crystal_grow.pdbx_pH_range
_item_description.description
; The range of pH values at which the crystal was grown. Used when
a point estimate of pH is not appropriate.
;
_item.name '_exptl_crystal_grow.pdbx_pH_range'
_item.category_id exptl_crystal_grow
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case '5.6 - 6.4'
_item_aliases.alias_name '_exptl_crystal_grow.rcsb_pH_range'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__exptl_crystal.pdbx_crystal_image_url
_item_description.description
; The URL for an a file containing the image of crystal.
;
_item.name '_exptl_crystal.pdbx_crystal_image_url'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code line
_item_aliases.alias_name '_exptl_crystal.rcsb_crystal_image_url'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__exptl_crystal.pdbx_crystal_image_format
_item_description.description
; The image format for the file containing the image of crystal specified
as an RFC2045/RFC2046 mime type.
;
_item.name '_exptl_crystal.pdbx_crystal_image_format'
_item.category_id exptl_crystal
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'jpeg'
'gif'
'tiff'
_item_aliases.alias_name '_exptl_crystal.rcsb_crystal_image_format'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
###
##################################
## PDBX_EXPTL_CRYSTAL_GROW_COMP ##
##################################
save_pdbx_exptl_crystal_grow_comp
_category.description
; Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record
details about the components of the solutions that were 'mixed'
to produce the crystal.
;
_category.id pdbx_exptl_crystal_grow_comp
_category.mandatory_code no
loop_
_category_key.name '_pdbx_exptl_crystal_grow_comp.comp_id'
'_pdbx_exptl_crystal_grow_comp.crystal_id'
loop_
_category_group.id 'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;loop_
_pdbx_exptl_crystal_grow_comp.crystal_id
_pdbx_exptl_crystal_grow_comp.sol_id
_pdbx_exptl_crystal_grow_comp.comp_id
_pdbx_exptl_crystal_grow_comp.comp_name
_pdbx_exptl_crystal_grow_comp.conc
_pdbx_exptl_crystal_grow_comp.conc_range
_pdbx_exptl_crystal_grow_comp.conc_units
4 'protein' 1 'protein' 25. . 'mg/ml'
4 'protein' 2 'Tris HCl' 20. . 'millimolar'
4 'protein' 3 'NaCl' 0.2 . 'molar'
4 'precipitant' 1 'PEG 4000' 12.5 . 'percent_weight_by_volume'
4 'precipitant' 2 'MES' 0.1 . 'molar'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_exptl_crystal_grow_comp.crystal_id
_item_description.description
; This data item is a pointer to _exptl_crystal.id in the
EXPTL_CRYSTAL category.
;
_item.name '_pdbx_exptl_crystal_grow_comp.crystal_id'
_item.category_id pdbx_exptl_crystal_grow_comp
_item.mandatory_code yes
_item_linked.child_name '_pdbx_exptl_crystal_grow_comp.crystal_id'
_item_linked.parent_name '_exptl_crystal.id'
save_
save__pdbx_exptl_crystal_grow_comp.comp_id
_item_description.description
; The value of _exptl_crystal_grow_comp.comp_id must uniquely identify
each item in the PDBX_EXPTL_CRYSTAL_GROW_COMP list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_pdbx_exptl_crystal_grow_comp.comp_id'
_item.category_id pdbx_exptl_crystal_grow_comp
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case '1'
'2'
save_
save__pdbx_exptl_crystal_grow_comp.comp_name
_item_description.description
; A common name for the component of the solution.
;
_item.name '_pdbx_exptl_crystal_grow_comp.comp_name'
_item.category_id pdbx_exptl_crystal_grow_comp
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'protein in buffer'
'acetic acid'
save_
save__pdbx_exptl_crystal_grow_comp.sol_id
_item_description.description
; An identifier for the solution to which the given solution
component belongs.
;
_item.name '_pdbx_exptl_crystal_grow_comp.sol_id'
_item.category_id pdbx_exptl_crystal_grow_comp
_item.mandatory_code no
_item_type.code line
_item_linked.child_name '_pdbx_exptl_crystal_grow_comp.sol_id'
_item_linked.parent_name '_pdbx_exptl_crystal_grow_sol.sol_id'
save_
save__pdbx_exptl_crystal_grow_comp.conc
_item_description.description
; The concentration value of the solution component.
;
_item.name '_pdbx_exptl_crystal_grow_comp.conc'
_item.category_id pdbx_exptl_crystal_grow_comp
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '200.'
'0.1'
save_
#
save__pdbx_exptl_crystal_grow_comp.conc_range
_item_description.description
; The concentration range of the solution component.
;
_item.name '_pdbx_exptl_crystal_grow_comp.conc_range'
_item.category_id pdbx_exptl_crystal_grow_comp
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case '200. - 230.'
'0.1 - 0.2'
save_
save__pdbx_exptl_crystal_grow_comp.conc_units
_item_description.description
; The concentration units for the solution component.
;
_item.name '_pdbx_exptl_crystal_grow_comp.conc_units'
_item.category_id pdbx_exptl_crystal_grow_comp
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'millimolar'
'percent_weight_by_volume'
'milligrams_per_milliliter'
save_
##
##
############################
## PDBX_EXPTL_CRYSTAL_SOL ##
############################
save_pdbx_exptl_crystal_grow_sol
_category.description
; Data items in the PDBX_EXPTL_CRYSTAL_GROW_SOL category record
details about the solutions that were 'mixed'
to produce the crystal.
;
_category.id pdbx_exptl_crystal_grow_sol
_category.mandatory_code no
loop_
_category_key.name '_pdbx_exptl_crystal_grow_sol.sol_id'
'_pdbx_exptl_crystal_grow_sol.crystal_id'
loop_
_category_group.id 'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_pdbx_exptl_crystal_grow_sol.crystal_id
_pdbx_exptl_crystal_grow_sol.sol_id
_pdbx_exptl_crystal_grow_sol.volume
_pdbx_exptl_crystal_grow_sol.volume_units
_pdbx_exptl_crystal_grow_sol.pH
1 'protein' 0.5 'microliter' 7.5
1 'precipitant' 0.5 'microliter' 7.3
1 'reservoir' 0.5 'milliliter' 7.3
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_exptl_crystal_grow_sol.crystal_id
_item_description.description
; This data item is a pointer to _exptl_crystal.id in the
EXPTL_CRYSTAL category.
;
_item.name '_pdbx_exptl_crystal_grow_sol.crystal_id'
_item.category_id pdbx_exptl_crystal_grow_sol
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_exptl_crystal_grow_sol.crystal_id'
_item_linked.parent_name '_exptl_crystal.id'
save_
save__pdbx_exptl_crystal_grow_sol.sol_id
_item_description.description
; An identifier for this solution (e.g. precipitant, reservoir, macromolecule)
;
_item.name '_pdbx_exptl_crystal_grow_sol.sol_id'
_item.category_id pdbx_exptl_crystal_grow_sol
_item.mandatory_code yes
_item_type.code line
loop_
_item_enumeration.value
"precipitant"
"reservoir"
"macromolecule"
save_
save__pdbx_exptl_crystal_grow_sol.volume
_item_description.description
; The volume of the solution.
;
_item.name '_pdbx_exptl_crystal_grow_sol.volume'
_item.category_id pdbx_exptl_crystal_grow_sol
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '200.'
'0.1'
save_
save__pdbx_exptl_crystal_grow_sol.volume_units
_item_description.description
; The volume units of the solution.
;
_item.name '_pdbx_exptl_crystal_grow_sol.volume_units'
_item.category_id pdbx_exptl_crystal_grow_sol
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'milliliter'
'micoliter'
save_
save__pdbx_exptl_crystal_grow_sol.pH
_item_description.description
; The pH of the solution.
;
_item.name '_pdbx_exptl_crystal_grow_sol.pH'
_item.category_id pdbx_exptl_crystal_grow_sol
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '7.2'
save_
##
##
#######################################
## PDBX_EXPTL_CRYSTAL_CRYO_TREATMENT ##
#######################################
save_pdbx_exptl_crystal_cryo_treatment
_category.description
; Data items in the PDBX_EXPTL_CRYSTAL_CRYO_TREATMENT category
record details cryogenic treatments applied to this crystal.
;
_category.id pdbx_exptl_crystal_cryo_treatment
_category.mandatory_code no
loop_
_category_key.name '_pdbx_exptl_crystal_cryo_treatment.crystal_id'
loop_
_category_group.id 'inclusive_group'
'exptl_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_pdbx_exptl_crystal_cryo_treatment.crystal_id 4
_pdbx_exptl_crystal_cryo_treatment.final_solution_details
; 25% (v/v) glycerol in precipitant solution
;
_pdbx_exptl_crystal_cryo_treatment.soaking_details
; A series of 1 min soaks beginning at 5% (v/v) glycerol in precipitant,
transiting to 20% (v/v) glycerol, and finally to 25% glycerol
;
_pdbx_exptl_crystal_cryo_treatment.cooling_details
; Direct immersion in liquid nitrogen
;
_pdbx_exptl_crystal_cryo_treatment.annealing_details ?
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_exptl_crystal_cryo_treatment.crystal_id
_item_description.description
; This data item is a pointer to _exptl_crystal.id in the
EXPTL_CRYSTAL category.
;
_item.name '_pdbx_exptl_crystal_cryo_treatment.crystal_id'
_item.category_id pdbx_exptl_crystal_cryo_treatment
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_exptl_crystal_cryo_treatment.crystal_id'
_item_linked.parent_name '_exptl_crystal.id'
save_
save__pdbx_exptl_crystal_cryo_treatment.final_solution_details
_item_description.description
; Details of the final solution used in the treatment of this crystal
;
_item.name '_pdbx_exptl_crystal_cryo_treatment.final_solution_details'
_item.category_id pdbx_exptl_crystal_cryo_treatment
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
; 25% (v/v) glycerol in precipitant solution
;
save_
save__pdbx_exptl_crystal_cryo_treatment.soaking_details
_item_description.description
; Details of the soaking treatment applied to this crystal.
;
_item.name '_pdbx_exptl_crystal_cryo_treatment.soaking_details'
_item.category_id pdbx_exptl_crystal_cryo_treatment
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
; A series of 1 min soaks beginning at 5% (v/v) glycerol in precipitant,
transiting to 20% (v/v) glycerol, and finally to 25% glycerol
;
save_
save__pdbx_exptl_crystal_cryo_treatment.cooling_details
_item_description.description
; Details of the cooling treatment applied to this crystal.
;
_item.name '_pdbx_exptl_crystal_cryo_treatment.cooling_details'
_item.category_id pdbx_exptl_crystal_cryo_treatment
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
; Direct immersion in liquid nitrogen
;
save_
save__pdbx_exptl_crystal_cryo_treatment.annealing_details
_item_description.description
; Details of the annealing treatment applied to this crystal.
;
_item.name '_pdbx_exptl_crystal_cryo_treatment.annealing_details'
_item.category_id pdbx_exptl_crystal_cryo_treatment
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
; 10 sec interruption of cold stream with plastic ruler.
Performed twice.
;
save_
##
save__geom_angle.pdbx_atom_site_PDB_ins_code_1
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_geom_angle.pdbx_atom_site_PDB_ins_code_1'
_item.category_id geom_angle
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_angle.pdbx_atom_site_PDB_ins_code_1'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name
'_geom_angle.ndb_atom_site_PDB_ins_code_1'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_angle.pdbx_atom_site_PDB_ins_code_2
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_geom_angle.pdbx_atom_site_PDB_ins_code_2'
_item.category_id geom_angle
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_angle.pdbx_atom_site_PDB_ins_code_2'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name
'_geom_angle.ndb_atom_site_PDB_ins_code_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_angle.pdbx_atom_site_PDB_ins_code_3
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_geom_angle.pdbx_atom_site_PDB_ins_code_3'
_item.category_id geom_angle
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_angle.pdbx_atom_site_PDB_ins_code_3'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_geom_angle.ndb_atom_site_PDB_ins_code_3'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_angle.pdbx_PDB_model_num
_item_description.description
; Pointer to _atom_site.pdbx_PDB_model_num
;
_item.name '_geom_angle.pdbx_PDB_model_num'
_item.category_id geom_angle
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_angle.pdbx_PDB_model_num'
_item_linked.parent_name '_atom_site.pdbx_PDB_model_num'
_item_aliases.alias_name '_geom_angle.ndb_model_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_bond.pdbx_atom_site_PDB_ins_code_1
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_geom_bond.pdbx_atom_site_PDB_ins_code_1'
_item.category_id geom_bond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_bond.pdbx_atom_site_PDB_ins_code_1'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_geom_bond.ndb_atom_site_PDB_ins_code_1'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_bond.pdbx_atom_site_PDB_ins_code_2
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_geom_bond.pdbx_atom_site_PDB_ins_code_2'
_item.category_id geom_bond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_bond.pdbx_atom_site_PDB_ins_code_2'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_geom_bond.ndb_atom_site_PDB_ins_code_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_bond.pdbx_PDB_model_num
_item_description.description
; Pointer to _atom_site.pdbx_PDB_model_num
;
_item.name '_geom_bond.pdbx_PDB_model_num'
_item.category_id geom_bond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_bond.pdbx_PDB_model_num'
_item_linked.parent_name '_atom_site.pdbx_PDB_model_num'
_item_aliases.alias_name '_geom_bond.ndb_model_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_contact.pdbx_atom_site_PDB_ins_code_1
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_geom_contact.pdbx_atom_site_PDB_ins_code_1'
_item.category_id geom_contact
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_contact.pdbx_atom_site_PDB_ins_code_1'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_geom_contact.ndb_atom_site_PDB_ins_code_1'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_contact.pdbx_atom_site_PDB_ins_code_2
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_geom_contact.pdbx_atom_site_PDB_ins_code_2'
_item.category_id geom_contact
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_contact.pdbx_atom_site_PDB_ins_code_2'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_geom_contact.ndb_atom_site_PDB_ins_code_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_contact.pdbx_PDB_model_num
_item_description.description
; Pointer to _atom_site.pdbx_PDB_model_num
;
_item.name '_geom_contact.pdbx_PDB_model_num'
_item.category_id geom_contact
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_contact.pdbx_PDB_model_num'
_item_linked.parent_name '_atom_site.pdbx_PDB_model_num'
_item_aliases.alias_name '_geom_contact.ndb_model_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_torsion.pdbx_atom_site_PDB_ins_code_1
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_geom_torsion.pdbx_atom_site_PDB_ins_code_1'
_item.category_id geom_torsion
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_torsion.pdbx_atom_site_PDB_ins_code_1'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_geom_torsion.ndb_atom_site_PDB_ins_code_1'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_torsion.pdbx_atom_site_PDB_ins_code_2
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_geom_torsion.pdbx_atom_site_PDB_ins_code_2'
_item.category_id geom_torsion
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_torsion.pdbx_atom_site_PDB_ins_code_2'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_geom_torsion.ndb_atom_site_PDB_ins_code_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_torsion.pdbx_atom_site_PDB_ins_code_3
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_geom_torsion.pdbx_atom_site_PDB_ins_code_3'
_item.category_id geom_torsion
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_torsion.pdbx_atom_site_PDB_ins_code_3'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_geom_torsion.ndb_atom_site_PDB_ins_code_3'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_torsion.pdbx_atom_site_PDB_ins_code_4
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_geom_torsion.pdbx_atom_site_PDB_ins_code_4'
_item.category_id geom_torsion
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_torsion.pdbx_atom_site_PDB_ins_code_4'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_geom_torsion.ndb_atom_site_PDB_ins_code_4'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__geom_torsion.pdbx_PDB_model_num
_item_description.description
; Pointer to _atom_site.pdbx_PDB_model_num
;
_item.name '_geom_torsion.pdbx_PDB_model_num'
_item.category_id geom_torsion
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_geom_torsion.pdbx_PDB_model_num'
_item_linked.parent_name '_atom_site.pdbx_PDB_model_num'
_item_aliases.alias_name '_geom_torsion.ndb_model_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__refine.pdbx_ls_sigma_I
_item_description.description
; Data cutoff (SIGMA(I))
;
_item.name '_refine.pdbx_ls_sigma_I'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_refine.ndb_ls_sigma_I'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine.pdbx_ls_sigma_F
_item_description.description
; Data cutoff (SIGMA(F))
;
_item.name '_refine.pdbx_ls_sigma_F'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_refine.ndb_ls_sigma_F'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine.pdbx_ls_sigma_Fsqd
_item_description.description
; Data cutoff (SIGMA(F^2))
;
_item.name '_refine.pdbx_ls_sigma_Fsqd'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
save_
save__refine.pdbx_data_cutoff_high_absF
_item_description.description
; Value of F at "high end" of data cutoff.
;
_item.name '_refine.pdbx_data_cutoff_high_absF'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_examples.case 17600
_item_aliases.alias_name '_refine.ndb_data_cutoff_high_absF'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine.pdbx_data_cutoff_high_rms_absF
_item_description.description
; Value of RMS |F| used as high data cutoff.
;
_item.name '_refine.pdbx_data_cutoff_high_rms_absF'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_examples.case 205.1
_item_aliases.alias_name '_refine.rcsb_data_cutoff_high_rms_absF'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine.pdbx_data_cutoff_low_absF
_item_description.description
; Value of F at "low end" of data cutoff.
;
_item.name '_refine.pdbx_data_cutoff_low_absF'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_examples.case 0.30
_item_aliases.alias_name '_refine.ndb_data_cutoff_low_absF'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine.pdbx_isotropic_thermal_model
_item_description.description
;
Whether the structure was refined with indvidual
isotropic, anisotropic or overall temperature factor.
;
_item.name '_refine.pdbx_isotropic_thermal_model'
_item.category_id refine
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case Isotropic Overall
_item_aliases.alias_name '_refine.ndb_isotropic_thermal_model'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine.pdbx_ls_cross_valid_method
_item_description.description
;
Whether the cross validataion method was used through
out or only at the end.
;
_item.name '_refine.pdbx_ls_cross_valid_method'
_item.category_id refine
_item.mandatory_code no
_item_type.code text
_item_examples.case 'FREE R-VALUE'
_item_aliases.alias_name '_refine.ndb_ls_cross_valid_method'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine.pdbx_method_to_determine_struct
_item_description.description
; Method(s) used to determine the structure.
;
_item.name '_refine.pdbx_method_to_determine_struct'
_item.category_id refine
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
'AB INITIO PHASING' ?
'DM' 'Direct Methods'
'ISAS ' 'Iterative Single wavelength Anomalous Scattering'
'ISIR' 'Iterative Single Isomorphous Replacement'
'ISIRAS' 'Iterative Single Isomorphous Replacement with Anomalous Scattering'
'MAD' 'Multi wavelength Anomalous Diffraction'
'MIR' 'Multiple Isomorphous Replacement'
'MIRAS' 'Multiple Isomorphous Replacement with Anomalous Scattering'
'MR' 'Molecular Replacement'
'SIR' 'Single Isomorphous Replacement'
'SIRAS' 'Single Isomorphous Replacement with Anomalous Scattering'
_item_aliases.alias_name '_refine.ndb_method_to_determine_struct'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine.pdbx_starting_model
_item_description.description
; Starting model for refinement. Starting model for
molecular replacement should refer to a previous
structure or experiment.
;
_item.name '_refine.pdbx_starting_model'
_item.category_id refine
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'BDL001'
_item_aliases.alias_name '_refine.ndb_starting_model'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine.pdbx_stereochemistry_target_values
_item_description.description
; Stereochemistry target values used in refinement.
;
_item.name '_refine.pdbx_stereochemistry_target_values'
_item.category_id refine
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_refine.ndb_stereochemistry_target_values'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine.pdbx_R_Free_selection_details
_item_description.description
; Details of the manner in which the cross validation
reflections were selected.
;
_item.name '_refine.pdbx_R_Free_selection_details'
_item.category_id refine
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'Random selection'
_item_aliases.alias_name '_refine.ndb_R_Free_selection_details'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine.pdbx_stereochem_target_val_spec_case
_item_description.description
;
Special case of stereochemistry target values used
in SHELXL refinement.
;
_item.name '_refine.pdbx_stereochem_target_val_spec_case'
_item.category_id refine
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_refine.ndb_stereochem_target_val_spec_case'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine_hist.pdbx_number_atoms_protein
_item_description.description
; Number of protein atoms included in refinement
;
_item.name '_refine_hist.pdbx_number_atoms_protein'
_item.category_id refine_hist
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_refine_hist.rcsb_number_atoms_protein'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine_hist.pdbx_number_atoms_nucleic_acid
_item_description.description
; Number of nucleic atoms included in refinement
;
_item.name '_refine_hist.pdbx_number_atoms_nucleic_acid'
_item.category_id refine_hist
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_refine_hist.rcsb_number_atoms_nucleic_acid'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine_hist.pdbx_number_atoms_ligand
_item_description.description
; Number of ligand atoms included in refinement
;
_item.name '_refine_hist.pdbx_number_atoms_ligand'
_item.category_id refine_hist
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_refine_hist.rcsb_number_atoms_ligand'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
#
save__refine_hist.pdbx_number_atoms_lipid
_item_description.description
; Number of lipid atoms included in refinement
;
_item.name '_refine_hist.pdbx_number_atoms_lipid'
_item.category_id refine_hist
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_refine_hist.rcsb_number_atoms_lipid'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine_hist.pdbx_number_atoms_carb
_item_description.description
; Number of carbohydrate atoms included in refinement
;
_item.name '_refine_hist.pdbx_number_atoms_carb'
_item.category_id refine_hist
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_refine_hist.rcsb_number_atoms_carb'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine_hist.pdbx_pseudo_atom_details
_item_description.description
; Details of pseduo atoms used to model unexplained density
;
_item.name '_refine_hist.pdbx_pseudo_atom_details'
_item.category_id refine_hist
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_refine_hist.rcsb_pseudo_atom_details'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
###
###
save__refine_ls_shell.pdbx_total_number_of_bins_used
_item_description.description
; Total number of bins used.
;
_item.name '_refine_ls_shell.pdbx_total_number_of_bins_used'
_item.category_id refine_ls_shell
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_refine_ls_shell.ndb_total_number_of_bins_used'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__refln.pdbx_F_calc_part_solvent
_item_description.description
; The calculated value of the structure factor in arbitrary
units reflecting only the contribution of the solvent model.
;
_item.name '_refln.pdbx_F_calc_part_solvent'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
_item_units.code arbitrary
_item_aliases.alias_name '_refln.rcsb_F_calc_part_solvent'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refln.pdbx_phase_calc_part_solvent
_item_description.description
; The calculated structure-factor phase in degrees reflecting
only the contribution of the solvent model.
;
_item.name '_refln.pdbx_phase_calc_part_solvent'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln.rcsb_phase_calc_part_solvent'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
_item_type.code float
_item_units.code degrees
save_
save__refln.pdbx_F_calc_with_solvent
_item_description.description
; The calculated value of the structure factor in arbitrary
units including the contribution of the solvent model.
;
_item.name '_refln.pdbx_F_calc_with_solvent'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
_item_units.code arbitrary
_item_aliases.alias_name '_refln.rcsb_F_calc_with_solvent'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refln.pdbx_phase_calc_with_solvent
_item_description.description
; The calculated structure-factor phase in degrees including
the contribution of the solvent model.
;
_item.name '_refln.pdbx_phase_calc_with_solvent'
_item.category_id refln
_item.mandatory_code no
_item_aliases.alias_name '_refln.rcsb_phase_calc_with_solvent'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
_item_type.code float
_item_units.code degrees
save_
##
##
save__reflns.pdbx_redundancy
_item_description.description
; Overall redundancy for this data set (%).
;
_item.name '_reflns.pdbx_redundancy'
_item.category_id reflns
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_reflns.ndb_redundancy'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__reflns.pdbx_Rmerge_I_obs
_item_description.description
; The R value for merging intensities satisfying the observed
criteria in this data set.
;
_item.name '_reflns.pdbx_Rmerge_I_obs'
_item.category_id reflns
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_reflns.ndb_Rmerge_I_obs'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__reflns.pdbx_Rmerge_I_all
_item_description.description
; The R value for merging all intensities in this data set.
;
_item.name '_reflns.pdbx_Rmerge_I_all'
_item.category_id reflns
_item.mandatory_code no
_item_type.code float
save_
save__reflns.pdbx_Rsym_value
_item_description.description
; R Sym value in percent.
;
_item.name '_reflns.pdbx_Rsym_value'
_item.category_id reflns
_item.mandatory_code no
_item_examples.case 2.0
_item_type.code float
_item_aliases.alias_name '_reflns.ndb_Rsym_value'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__reflns.pdbx_netI_over_av_sigmaI
_item_description.description
; Overall /
;
_item.name '_reflns.pdbx_netI_over_av_sigmaI'
_item.category_id reflns
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_reflns.ndb_netI_over_av_sigmaI'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__reflns.pdbx_netI_over_sigmaI
_item_description.description
; Overall
;
_item.name '_reflns.pdbx_netI_over_sigmaI'
_item.category_id reflns
_item.mandatory_code no
_item_type.code float
save_
save__reflns.pdbx_res_netI_over_av_sigmaI_2
_item_description.description
; Resolution (angstrom) for reflections with / = 2.
;
_item.name '_reflns.pdbx_res_netI_over_av_sigmaI_2'
_item.category_id reflns
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__reflns.pdbx_res_netI_over_sigmaI_2
_item_description.description
; Resolution (angstroms) for reflections with = 2.
;
_item.name '_reflns.pdbx_res_netI_over_sigmaI_2'
_item.category_id reflns
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__reflns.pdbx_chi_squared
_item_description.description
; Overall Chi-squared statistic.
;
_item.name '_reflns.pdbx_chi_squared'
_item.category_id reflns
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_reflns.rcsb_chi_squared'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__reflns.pdbx_scaling_rejects
_item_description.description
; Number of reflections rejected in scaling operations.
;
_item.name '_reflns.pdbx_scaling_rejects'
_item.category_id reflns
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_reflns.rcsb_scaling_rejects'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__reflns.pdbx_d_res_high_opt
_item_description.description
; The highest optical resolution for this reflection data set
as determined by computational method _reflns.pdbx_d_res_opt_method.
;
_item.name '_reflns.pdbx_d_res_high_opt'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns.rcsb_d_res_high_opt'
_item_aliases.dictionary cif_rcsb.dic
_item_aliases.version 1.1
_item_examples.case '1.2'
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__reflns.pdbx_d_res_low_opt
_item_description.description
; The lowest optical resolution for this reflection data set
as determined by computational method _reflns.pdbx_d_res_opt_method.
;
_item.name '_reflns.pdbx_d_res_low_opt'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns.rcsb_d_res_low_opt'
_item_aliases.dictionary cif_rcsb.dic
_item_aliases.version 1.1
_item_examples.case '20.5'
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__reflns.pdbx_d_res_opt_method
_item_description.description
; The computational method used to determine the optical
resolution limits _reflns.pdbx_d_res_high_opt and
_reflns.pdbx_d_res_low_opt.
;
_item.name '_reflns.pdbx_d_res_opt_method'
_item.category_id reflns
_item.mandatory_code no
_item_aliases.alias_name '_reflns.rcsb_d_res_opt_method'
_item_aliases.dictionary cif_rcsb.dic
_item_aliases.version 1.1
_item_examples.case 'SFCHECK'
_item_type.code text
save_
##
##
save__reflns_shell.pdbx_redundancy
_item_description.description
; Redundancy for the current shell.
;
_item.name '_reflns_shell.pdbx_redundancy'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_reflns_shell.ndb_redundancy'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__reflns_shell.pdbx_Rsym_value
_item_description.description
; R sym value in percent.
;
_item.name '_reflns_shell.pdbx_Rsym_value'
_item.category_id reflns_shell
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum
. 0.0
0.0 0.0
_item_type.code float
_item_aliases.alias_name '_reflns_shell.ndb_Rsym_value'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__reflns_shell.pdbx_chi_squared
_item_description.description
; Chi-squared statistic for this resolution shell.
;
_item.name '_reflns_shell.pdbx_chi_squared'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_reflns_shell.rcsb_chi_squared'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__reflns_shell.pdbx_netI_over_sigmaI_all
_item_description.description
; The mean of the ratio of the intensities to their
standard uncertainties of all reflections in the
resolution shell.
_reflns_shell.pdbx_meanI_over_sigmaI_all =
;
_item.name '_reflns_shell.pdbx_netI_over_sigmaI_all'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code float
save_
save__reflns_shell.pdbx_netI_over_sigmaI_obs
_item_description.description
; The mean of the ratio of the intensities to their
standard uncertainties of observed reflections
(see _reflns.observed_criterion) in the resolution shell.
_reflns_shell.pdbx_meanI_over_sigmaI_obs =
;
_item.name '_reflns_shell.pdbx_netI_over_sigmaI_obs'
_item.category_id reflns_shell
_item.mandatory_code no
_item_type.code float
save_
##
save__struct.pdbx_descriptor
_item_description.description
; An automatically generated descriptor for an NDB structure or
the unstructured content of the PDB COMPND record.
;
_item.name '_struct.pdbx_descriptor'
_item.category_id struct
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
;
5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3'
;
_item_aliases.alias_name '_struct.ndb_descriptor'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct.pdbx_model_details
_item_description.description
; Text description of the methodology which produced this
model structure.
;
_item.name '_struct.pdbx_model_details'
_item.category_id struct
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
;
This model was produced from a 10 nanosecond Amber/MD simulation
starting from PDB structure ID 1ABC.
;
_item_aliases.alias_name '_struct.rcsb_model_details'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct.pdbx_formula_weight
_item_description.description
; Estimated formula mass in daltons of the
deposited structure assembly.
;
_item.name '_struct.pdbx_formula_weight'
_item.category_id struct
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1.0
1.0 1.0
_item_type.code float
save_
save__struct.pdbx_formula_weight_method
_item_description.description
; Method used to determine _struct.pdbx_formula_weight.
;
_item.name '_struct.pdbx_formula_weight_method'
_item.category_id struct
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'MASS SPEC'
'CALCULATION'
save_
##
save__struct_asym.pdbx_modified
_item_description.description
; This data item indicates whether the structural elements are modified.
;
_item.name '_struct_asym.pdbx_modified'
_item.category_id struct_asym
_item.mandatory_code no
_item_type.code text
_item_examples.case 'y'
_item_aliases.alias_name '_struct_asym.ndb_modified'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_asym.pdbx_blank_PDB_chainid_flag
_item_description.description
; A flag indicating that this entity was originally labeled
with a blank PDB chain id.
;
_item.name '_struct_asym.pdbx_blank_PDB_chainid_flag'
_item.category_id struct_asym
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
Y 'Yes'
N 'No'
_item_aliases.alias_name '_struct_asym.rcsb_blank_PDB_chainid_flag'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__struct_biol.pdbx_parent_biol_id
_item_description.description
; An identifier for the parent biological assembly
if this biological unit is part of a complex assembly.
;
_item.name '_struct_biol.pdbx_parent_biol_id'
_item.category_id struct_biol
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_biol.pdbx_parent_biol_id'
_item_linked.parent_name '_struct_biol.id'
loop_
_item_examples.case 1 2 3
_item_aliases.alias_name '_struct_biol.rcsb_parent_biol_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_biol.pdbx_formula_weight
_item_description.description
; Estimated formula mass in daltons of the
biological assembly.
;
_item.name '_struct_biol.pdbx_formula_weight'
_item.category_id struct_biol
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1.0
1.0 1.0
_item_type.code float
save_
save__struct_biol.pdbx_formula_weight_method
_item_description.description
; Method used to determine _struct_biol.pdbx_formula_weight.
;
_item.name '_struct_biol.pdbx_formula_weight_method'
_item.category_id struct_biol
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'MASS SPEC'
'CALCULATION'
save_
##
##
save__struct_biol_gen.pdbx_full_symmetry_operation
_item_description.description
;
This item expresses category _struct_biol_gen.symmetry
on an X, Y and Z basis.
;
_item.name '_struct_biol_gen.pdbx_full_symmetry_operation'
_item.category_id struct_biol_gen
_item.mandatory_code no
_item_type.code code
_item_examples.case '-X, Y+1/2, -Z'
_item_aliases.alias_name '_struct_biol_gen.ndb_full_symmetry_operation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_biol_gen.pdbx_PDB_order
_item_description.description
; An ordering index used to reproduce the presentation of
chain order in the original PDB format data files.
;
_item.name '_struct_biol_gen.pdbx_PDB_order'
_item.category_id struct_biol_gen
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case 1 2 3
_item_aliases.alias_name '_struct_biol_gen.rcsb_pdb_order'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__struct_conf.pdbx_beg_PDB_ins_code
_item_description.description
; A component of the identifier for the residue at which the
conformation segment starts.
;
_item.name '_struct_conf.pdbx_beg_PDB_ins_code'
_item.category_id struct_conf
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_conf.pdbx_beg_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_struct_conf.ndb_beg_label_ins_code_pdb'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conf.pdbx_end_PDB_ins_code
_item_description.description
; A component of the identifier for the residue at which the
conformation segment ends.
;
_item.name '_struct_conf.pdbx_end_PDB_ins_code'
_item.category_id struct_conf
_item.mandatory_code no
_item_linked.child_name '_struct_conf.pdbx_end_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_struct_conf.ndb_end_label_ins_code_pdb'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conf.pdbx_PDB_helix_class
_item_description.description
; This item is a place holder for the helix class used in the PDB
HELIX record.
;
_item.name '_struct_conf.pdbx_PDB_helix_class'
_item.category_id struct_conf
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_struct_conf.ndb_helix_class_pdb'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conf.pdbx_PDB_helix_length
_item_description.description
;
A placeholder for the lengths of the helix of the PDB
HELIX record.
;
_item.name '_struct_conf.pdbx_PDB_helix_length'
_item.category_id struct_conf
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_struct_conf.ndb_length'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conf.pdbx_PDB_helix_id
_item_description.description
;
A placeholder for the helix identifier of the PDB
HELIX record.
;
_item.name '_struct_conf.pdbx_PDB_helix_id'
_item.category_id struct_conf
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_struct_conf.pdb_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__struct_conn.pdbx_ptnr1_PDB_ins_code
_item_description.description
; A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_site.ins_code in the
ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr1_PDB_ins_code'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_linked.child_name '_struct_conn.pdbx_ptnr1_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_struct_conn.ndb_ptnr1_label_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr1_auth_alt_id
_item_description.description
;
A component of the identifier for partner 1 of the
structure connection. This data item is a pointer to
_atom_site.pdbx_auth_alt_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr1_auth_alt_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'B'
_item_linked.child_name '_struct_conn.pdbx_ptnr1_auth_alt_id'
_item_linked.parent_name '_atom_site.pdbx_auth_alt_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr1_auth_alt_loc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr1_label_alt_id
_item_description.description
;
A component of the identifier for partner 1 of the
structure connection. This data item is a pointer to
_atom_site.label_alt_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr1_label_alt_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'B'
_item_linked.child_name '_struct_conn.pdbx_ptnr1_label_alt_id'
_item_linked.parent_name '_atom_site.label_alt_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr1_label_alt_loc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr1_standard_comp_id
_item_description.description
;
A placeholder for the standard residue name found in
the MODRES record of a PDB file.
;
_item.name '_struct_conn.pdbx_ptnr1_standard_comp_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'T' 'C' 'G' 'GLY' 'ALA' 'MET'
_item_aliases.alias_name '_struct_conn.ndb_ptnr1_standard_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr2_PDB_ins_code
_item_description.description
; A component of the identifier for partner 1 of the structure
connection.
This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr2_PDB_ins_code'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_linked.child_name '_struct_conn.pdbx_ptnr2_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_struct_conn.ndb_ptnr2_label_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr2_auth_alt_id
_item_description.description
;
A component of the identifier for partner 2 of the
structure connection. This data item is a pointer to
_atom_site.pdbx_auth_alt_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr2_auth_alt_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'B'
_item_linked.child_name '_struct_conn.pdbx_ptnr2_auth_alt_id'
_item_linked.parent_name '_atom_site.pdbx_auth_alt_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr2_auth_alt_loc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr2_label_alt_id
_item_description.description
;
A component of the identifier for partner 2 of the
structure connection. This data item is a pointer to
_atom_site.label_alt_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr2_label_alt_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'B'
_item_linked.child_name '_struct_conn.pdbx_ptnr2_label_alt_id'
_item_linked.parent_name '_atom_site.label_alt_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr2_label_alt_loc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr3_auth_alt_id
_item_description.description
;
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
_atom_site.auth_alt_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr3_auth_alt_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'B'
_item_linked.child_name '_struct_conn.pdbx_ptnr3_auth_alt_id'
_item_linked.parent_name '_atom_site.pdbx_auth_alt_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr3_auth_alt_loc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr3_auth_asym_id
_item_description.description
;
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
_atom_site.auth_asym_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr3_auth_asym_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'B' 'C'
_item_linked.child_name '_struct_conn.pdbx_ptnr3_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr3_auth_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr3_auth_atom_id
_item_description.description
;
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
_atom_site.auth_atom_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr3_auth_atom_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code atcode
_item_examples.case 'O5*'
_item_linked.child_name '_struct_conn.pdbx_ptnr3_auth_atom_id'
_item_linked.parent_name '_atom_site.auth_atom_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr3_auth_atom_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr3_auth_comp_id
_item_description.description
;
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
_atom_site.auth_comp_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr3_auth_comp_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'T' 'C' 'G' 'GLY' 'ALA' 'MET'
_item_linked.child_name '_struct_conn.pdbx_ptnr3_auth_comp_id'
_item_linked.parent_name '_atom_site.auth_comp_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr3_auth_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr3_PDB_ins_code
_item_description.description
;
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
_atom_site.pdbx_PDB_ins_code in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr3_PDB_ins_code'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_linked.child_name '_struct_conn.pdbx_ptnr3_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr3_auth_seq_id
_item_description.description
;
A component of the identifier for partner 1 of the
structure connection. This data item is a pointer to
_atom_site.auth_seq_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr3_auth_seq_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
_item_examples.case '12'
_item_linked.child_name '_struct_conn.pdbx_ptnr3_auth_seq_id'
_item_linked.parent_name '_atom_site.auth_seq_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr3_auth_seq_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__struct_conn.pdbx_ptnr3_label_alt_id
_item_description.description
;
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
_atom_site.label_alt_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr3_label_alt_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'B'
_item_linked.child_name '_struct_conn.pdbx_ptnr3_label_alt_id'
_item_linked.parent_name '_atom_site.label_alt_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_alt_loc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr3_label_asym_id
_item_description.description
;
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
_atom_site.label_asym_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr3_label_asym_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'B' 'C'
_item_linked.child_name '_struct_conn.pdbx_ptnr3_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr3_label_atom_id
_item_description.description
;
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
_atom_site.label_atom_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr3_label_atom_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code atcode
_item_examples.case 'O5*'
_item_linked.child_name '_struct_conn.pdbx_ptnr3_label_atom_id'
_item_linked.parent_name '_atom_site.label_atom_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_atom_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr3_label_comp_id
_item_description.description
;
A component of the identifier for partner 3 of the
structure connection. This data item is a pointer to
_atom_site.label_comp_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr3_label_comp_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'T' 'C' 'G' 'GLY' 'ALA' 'MET'
_item_linked.child_name '_struct_conn.pdbx_ptnr3_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_conn.pdbx_ptnr3_label_seq_id
_item_description.description
;
A component of the identifier for partner 1 of the
structure connection. This data item is a pointer to
_atom_site.label_seq_id in the ATOM_SITE category.
;
_item.name '_struct_conn.pdbx_ptnr3_label_seq_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
_item_examples.case '12'
_item_linked.child_name '_struct_conn.pdbx_ptnr3_label_seq_id'
_item_linked.parent_name '_atom_site.label_seq_id'
_item_aliases.alias_name '_struct_conn.ndb_ptnr3_label_seq_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__struct_conn.pdbx_PDB_id
_item_description.description
;
A placeholder for the PDB id in the case the category
is used to hold the information of the MODRES record of
a PDB file.
;
_item.name '_struct_conn.pdbx_PDB_id'
_item.category_id struct_conn
_item.mandatory_code no
_item_type.code code
_item_examples.case 1ABC
_item_aliases.alias_name '_struct_conn.ndb_PDB_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__struct_keywords.pdbx_keywords
_item_description.description
;
;
_item.name '_struct_keywords.pdbx_keywords'
_item.category_id struct_keywords
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'DNA'
'RNA'
'T-RNA'
'DNA/RNA'
'RIBOZYME'
'PROTEIN/DNA'
'PROTEIN/RNA'
'PEPTIDE NUCLEIC ACID'
'PEPTIDE NUCLEIC ACID/DNA'
'DNA-BINDING PROTEIN'
'RNA-BINDING PROTEIN'
_item_aliases.alias_name '_struct_keywords.ndb_keywords'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
##
save__struct_mon_prot_cis.pdbx_auth_asym_id_2
_item_description.description
; Pointer to _atom_site.auth_asym_id.
;
_item.name '_struct_mon_prot_cis.pdbx_auth_asym_id_2'
_item.category_id struct_mon_prot_cis
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_mon_prot_cis.pdbx_auth_asym_id_2'
_item_linked.parent_name '_atom_site.auth_asym_id'
_item_aliases.alias_name '_struct_mon_prot_cis.ndb_auth_asym_id_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_mon_prot_cis.pdbx_auth_comp_id_2
_item_description.description
; Pointer to _atom_site.auth_comp_id.
;
_item.name '_struct_mon_prot_cis.pdbx_auth_comp_id_2'
_item.category_id struct_mon_prot_cis
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_mon_prot_cis.pdbx_auth_comp_id_2'
_item_linked.parent_name '_atom_site.auth_comp_id'
_item_aliases.alias_name '_struct_mon_prot_cis.ndb_auth_comp_id_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_mon_prot_cis.pdbx_auth_seq_id_2
_item_description.description
; Pointer to _atom_site.auth_seq_id
;
_item.name '_struct_mon_prot_cis.pdbx_auth_seq_id_2'
_item.category_id struct_mon_prot_cis
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_mon_prot_cis.pdbx_auth_seq_id_2'
_item_linked.parent_name '_atom_site.auth_seq_id'
_item_aliases.alias_name '_struct_mon_prot_cis.ndb_auth_seq_id_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##jdw
save__struct_mon_prot_cis.pdbx_label_asym_id_2
_item_description.description
; Pointer to _atom_site.label_asym_id.
;
_item.name '_struct_mon_prot_cis.pdbx_label_asym_id_2'
_item.category_id struct_mon_prot_cis
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_mon_prot_cis.pdbx_label_asym_id_2'
_item_linked.parent_name '_atom_site.label_asym_id'
_item_aliases.alias_name '_struct_mon_prot_cis.ndb_label_asym_id_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_mon_prot_cis.pdbx_label_comp_id_2
_item_description.description
; Pointer to _atom_site.label_comp_id.
;
_item.name '_struct_mon_prot_cis.pdbx_label_comp_id_2'
_item.category_id struct_mon_prot_cis
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_mon_prot_cis.pdbx_label_comp_id_2'
_item_linked.parent_name '_atom_site.label_comp_id'
_item_aliases.alias_name '_struct_mon_prot_cis.ndb_label_comp_id_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_mon_prot_cis.pdbx_label_seq_id_2
_item_description.description
; Pointer to _atom_site.label_seq_id
;
_item.name '_struct_mon_prot_cis.pdbx_label_seq_id_2'
_item.category_id struct_mon_prot_cis
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_mon_prot_cis.pdbx_label_seq_id_2'
_item_linked.parent_name '_atom_site.label_seq_id'
_item_aliases.alias_name '_struct_mon_prot_cis.ndb_label_seq_id_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_mon_prot_cis.pdbx_PDB_ins_code
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code
;
_item.name '_struct_mon_prot_cis.pdbx_PDB_ins_code'
_item.category_id struct_mon_prot_cis
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_mon_prot_cis.pdbx_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_struct_mon_prot_cis.ndb_label_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_mon_prot_cis.pdbx_PDB_ins_code_2
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code
;
_item.name '_struct_mon_prot_cis.pdbx_PDB_ins_code_2'
_item.category_id struct_mon_prot_cis
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_mon_prot_cis.pdbx_PDB_ins_code_2'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_struct_mon_prot_cis.ndb_label_ins_code_2'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_mon_prot_cis.pdbx_PDB_model_num
_item_description.description
; Pointer to _atom_site.pdbx_PDB_model_num
;
_item.name '_struct_mon_prot_cis.pdbx_PDB_model_num'
_item.category_id struct_mon_prot_cis
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_mon_prot_cis.pdbx_PDB_model_num'
_item_linked.parent_name '_atom_site.pdbx_PDB_model_num'
_item_aliases.alias_name '_struct_mon_prot_cis.ndb_model_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_mon_prot_cis.pdbx_omega_angle
_item_description.description
; omega torsion angle
;
_item.name '_struct_mon_prot_cis.pdbx_omega_angle'
_item.category_id struct_mon_prot_cis
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_struct_mon_prot_cis.ndb_omega_angle'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_mon_prot_cis.pdbx_id
_item_description.description
; ordinal index
;
_item.name '_struct_mon_prot_cis.pdbx_id'
_item.category_id struct_mon_prot_cis
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_struct_mon_prot_cis.id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__struct_ref.pdbx_db_accession
_item_description.description
; Accession code of the reference database.
;
_item.name '_struct_ref.pdbx_db_accession'
_item.category_id struct_ref
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'P07617'
_item_aliases.alias_name '_struct_ref.rcsb_db_accession'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref.pdbx_seq_one_letter_code
_item_description.description
; Database chemical sequence expressed as string of one-letter
amino acid codes.
;
_item.name '_struct_ref.pdbx_seq_one_letter_code'
_item.category_id struct_ref
_item.mandatory_code no
_item_type.code text
_item_examples.case
;
A for alanine or adenine
B for ambiguous asparagine/aspartic-acid
R for arginine
N for asparagine
D for aspartic-acid
C for cysteine or cystine or cytosine
Q for glutamine
E for glutamic-acid
Z for ambiguous glutamine/glutamic acid
G for glycine or guanine
H for histidine
I for isoleucine
L for leucine
K for lysine
M for methionine
F for phenylalanine
P for proline
S for serine
T for threonine or thymine
W for tryptophan
Y for tyrosine
V for valine
U for uracil
O for water
X for other
;
_item_aliases.alias_name '_struct_ref.rcsb_seq_one_letter_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref.pdbx_align_begin
_item_description.description
;
Beginning index in the chemical sequence from the
reference database.
;
_item.name '_struct_ref.pdbx_align_begin'
_item.category_id struct_ref
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_aliases.alias_name '_struct_ref.rcsb_align_begin'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__struct_ref_seq.pdbx_strand_id
_item_description.description
; The PDB strand/chain ID .
;
_item.name '_struct_ref_seq.pdbx_strand_id'
_item.category_id struct_ref_seq
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'B'
_item_aliases.alias_name '_struct_ref_seq.ndb_chain_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq.pdbx_db_accession
_item_description.description
; Accession code of the reference database.
;
_item.name '_struct_ref_seq.pdbx_db_accession'
_item.category_id struct_ref_seq
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'P07617'
_item_aliases.alias_name '_struct_ref_seq.ndb_db_accession'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq.pdbx_db_align_beg_ins_code
_item_description.description
;
Initial insertion code of the sequence segment of the
reference database.
;
_item.name '_struct_ref_seq.pdbx_db_align_beg_ins_code'
_item.category_id struct_ref_seq
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_aliases.alias_name '_struct_ref_seq.ndb_db_align_beg_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq.pdbx_db_align_end_ins_code
_item_description.description
;
Ending insertion code of the sequence segment of the
reference database.
;
_item.name '_struct_ref_seq.pdbx_db_align_end_ins_code'
_item.category_id struct_ref_seq
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_aliases.alias_name '_struct_ref_seq.ndb_db_align_end_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq.pdbx_PDB_id_code
_item_description.description
; The PDB code of the structure.
;
_item.name '_struct_ref_seq.pdbx_PDB_id_code'
_item.category_id struct_ref_seq
_item.mandatory_code no
_item_type.code code
_item_examples.case '1BBP'
_item_aliases.alias_name '_struct_ref_seq.ndb_pdb_id_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq.pdbx_auth_seq_align_beg
_item_description.description
;
Initial position in the PDB sequence segment.
;
_item.name '_struct_ref_seq.pdbx_auth_seq_align_beg'
_item.category_id struct_ref_seq
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_aliases.alias_name '_struct_ref_seq.ndb_auth_seq_align_beg'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq.pdbx_auth_seq_align_end
_item_description.description
;
Ending position in the PDB sequence segment
;
_item.name '_struct_ref_seq.pdbx_auth_seq_align_end'
_item.category_id struct_ref_seq
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_aliases.alias_name '_struct_ref_seq.ndb_auth_seq_align_end'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__struct_ref_seq.pdbx_seq_align_beg_ins_code
_item_description.description
;
Initial insertion code of the PDB sequence segment.
;
_item.name '_struct_ref_seq.pdbx_seq_align_beg_ins_code'
_item.category_id struct_ref_seq
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_aliases.alias_name '_struct_ref_seq.ndb_seq_align_beg_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq.pdbx_seq_align_end_ins_code
_item_description.description
;
Ending insertion code of the sequence segment
;
_item.name '_struct_ref_seq.pdbx_seq_align_end_ins_code'
_item.category_id struct_ref_seq
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_aliases.alias_name '_struct_ref_seq.ndb_seq_align_end_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__struct_ref_seq_dif.pdbx_pdb_id_code
_item_description.description
;
The PDB ID code.
;
_item.name '_struct_ref_seq_dif.pdbx_pdb_id_code'
_item.category_id struct_ref_seq_dif
_item.mandatory_code no
_item_type.code code
_item_examples.case '1BBP'
_item_aliases.alias_name '_struct_ref_seq_dif.ndb_pdb_id_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq_dif.pdbx_pdb_strand_id
_item_description.description
; PDB strand/chain id.
;
_item.name '_struct_ref_seq_dif.pdbx_pdb_strand_id'
_item.category_id struct_ref_seq_dif
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'A' 'B'
_item_aliases.alias_name '_struct_ref_seq_dif.ndb_pdb_chain_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq_dif.pdbx_pdb_ins_code
_item_description.description
; Insertion code in PDB sequence
;
_item.name '_struct_ref_seq_dif.pdbx_pdb_ins_code'
_item.category_id struct_ref_seq_dif
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_aliases.alias_name '_struct_ref_seq_dif.ndb_pdb_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq_dif.pdbx_auth_seq_num
_item_description.description
; Insertion code in PDB sequence
;
_item.name '_struct_ref_seq_dif.pdbx_auth_seq_num'
_item.category_id struct_ref_seq_dif
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case '1' '2'
_item_aliases.alias_name '_struct_ref_seq_dif.ndb_auth_seq_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq_dif.pdbx_seq_db_name
_item_description.description
; Sequence database name.
;
_item.name '_struct_ref_seq_dif.pdbx_seq_db_name'
_item.category_id struct_ref_seq_dif
_item.mandatory_code no
_item_type.code code
_item_examples.case 'SWS'
_item_aliases.alias_name '_struct_ref_seq_dif.ndb_seq_db_name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq_dif.pdbx_seq_db_accession_code
_item_description.description
; Sequence database accession number.
;
_item.name '_struct_ref_seq_dif.pdbx_seq_db_accession_code'
_item.category_id struct_ref_seq_dif
_item.mandatory_code no
_item_type.code code
_item_examples.case 'P07617'
_item_aliases.alias_name '_struct_ref_seq_dif.ndb_seq_db_accession_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ref_seq_dif.pdbx_seq_db_seq_num
_item_description.description
; Sequence database sequence number.
;
_item.name '_struct_ref_seq_dif.pdbx_seq_db_seq_num'
_item.category_id struct_ref_seq_dif
_item.mandatory_code no
_item_type.code code
_item_examples.case '142'
_item_aliases.alias_name '_struct_ref_seq_dif.ndb_seq_db_seq_num'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__struct_sheet_range.pdbx_beg_PDB_ins_code
_item_description.description
; A component of the identifier for the residue at which the
beta sheet range begins. Insertion code.
;
_item.name '_struct_sheet_range.pdbx_beg_PDB_ins_code'
_item.category_id struct_sheet_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_range.pdbx_beg_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_struct_sheet_range.ndb_beg_label_ins_code_pdb'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_range.pdbx_end_PDB_ins_code
_item_description.description
; A component of the identifier for the residue at which the
beta sheet range ends. Insertion code.
;
_item.name '_struct_sheet_range.pdbx_end_PDB_ins_code'
_item.category_id struct_sheet_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_range.pdbx_end_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name '_struct_sheet_range.ndb_end_label_ins_code_pdb'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__struct_sheet_hbond.pdbx_range_1_beg_auth_comp_id
_item_description.description
; Pointer to _atom_site.auth_comp_id
;
_item.name '_struct_sheet_hbond.pdbx_range_1_beg_auth_comp_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_beg_auth_comp_id'
_item_linked.parent_name '_atom_site.auth_comp_id'
_item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_beg_auth_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_1_beg_auth_asym_id
_item_description.description
; Pointer to _atom_site.auth_asym_id.
;
_item.name '_struct_sheet_hbond.pdbx_range_1_beg_auth_asym_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_beg_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
_item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_beg_auth_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_1_end_auth_comp_id
_item_description.description
; Pointer to _atom_site.auth_comp_id.
;
_item.name '_struct_sheet_hbond.pdbx_range_1_end_auth_comp_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_end_auth_comp_id'
_item_linked.parent_name '_atom_site.auth_comp_id'
_item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_end_auth_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_1_end_auth_asym_id
_item_description.description
; Pointer to _atom_site.auth_comp_id.
;
_item.name '_struct_sheet_hbond.pdbx_range_1_end_auth_asym_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_end_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
_item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_end_auth_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_1_beg_label_comp_id
_item_description.description
; Pointer to _atom_site.label_comp_id
;
_item.name '_struct_sheet_hbond.pdbx_range_1_beg_label_comp_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_beg_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
_item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_beg_label_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_1_beg_label_asym_id
_item_description.description
; Pointer to _atom_site.label_asym_id.
;
_item.name '_struct_sheet_hbond.pdbx_range_1_beg_label_asym_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_beg_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
_item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_beg_label_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_1_beg_PDB_ins_code
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_struct_sheet_hbond.pdbx_range_1_beg_PDB_ins_code'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_beg_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name
'_struct_sheet_hbond.ndb_range_1_beg_label_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_1_end_label_comp_id
_item_description.description
; Pointer to _atom_site.label_comp_id.
;
_item.name '_struct_sheet_hbond.pdbx_range_1_end_label_comp_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_end_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
_item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_end_label_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_1_end_label_asym_id
_item_description.description
; Pointer to _atom_site.label_asym_id.
;
_item.name '_struct_sheet_hbond.pdbx_range_1_end_label_asym_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_end_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
_item_aliases.alias_name '_struct_sheet_hbond.ndb_range_1_end_label_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_1_end_PDB_ins_code
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_struct_sheet_hbond.pdbx_range_1_end_PDB_ins_code'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_1_end_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name
'_struct_sheet_hbond.ndb_range_1_end_label_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_2_beg_label_comp_id
_item_description.description
; Pointer to _atom_site.label_comp_id.
;
_item.name '_struct_sheet_hbond.pdbx_range_2_beg_label_comp_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_2_beg_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
_item_aliases.alias_name '_struct_sheet_hbond.ndb_range_2_beg_label_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_2_beg_label_asym_id
_item_description.description
; Pointer to _atom_site.label_asym_id.
;
_item.name '_struct_sheet_hbond.pdbx_range_2_beg_label_asym_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_2_beg_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
_item_aliases.alias_name
'_struct_sheet_hbond.ndb_range_2_beg_label_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_2_beg_PDB_ins_code
_item_description.description
; Pointer to _atom_site.pdbx_PDB_ins_code.
;
_item.name '_struct_sheet_hbond.pdbx_range_2_beg_PDB_ins_code'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_2_beg_PDB_ins_code'
_item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
_item_aliases.alias_name
'_struct_sheet_hbond.ndb_range_2_beg_label_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_2_end_label_comp_id
_item_description.description
; Pointer to _atom_site.label_comp_id.
;
_item.name '_struct_sheet_hbond.pdbx_range_2_end_label_comp_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_2_end_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
_item_aliases.alias_name
'_struct_sheet_hbond.ndb_range_2_end_label_comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_2_end_label_asym_id
_item_description.description
; Pointer to _atom_site.label_asym_id.
;
_item.name '_struct_sheet_hbond.pdbx_range_2_end_label_asym_id'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_struct_sheet_hbond.pdbx_range_2_end_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
_item_aliases.alias_name
'_struct_sheet_hbond.ndb_range_2_end_label_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_sheet_hbond.pdbx_range_2_end_label_ins_code
_item_description.description
; Place holder for PDB insertion code.
;
_item.name '_struct_sheet_hbond.pdbx_range_2_end_label_ins_code'
_item.category_id struct_sheet_hbond
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name
'_struct_sheet_hbond.ndb_range_2_end_label_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
##
save__struct_site.pdbx_num_residues
_item_description.description
; Number of residues in the site.
;
_item.name '_struct_site.pdbx_num_residues'
_item.category_id struct_site
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_struct_site.rcsb_num_residues'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_site_gen.pdbx_auth_ins_code
_item_description.description
; PDB insertion code.
;
_item.name '_struct_site_gen.pdbx_auth_ins_code'
_item.category_id struct_site_gen
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_struct_site_gen.ndb_ins_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_site_gen.pdbx_num_res
_item_description.description
; Number of residues in the site.
;
_item.name '_struct_site_gen.pdbx_num_res'
_item.category_id struct_site_gen
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_struct_site_gen.ndb_num_res'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__symmetry.pdbx_full_space_group_name_H-M
_item_description.description
; Used for PDB space group:
Example: 'C 1 2 1' (instead of C 2)
'P 1 2 1' (instead of P 2)
'P 1 21 1' (instead of P 21)
'P 1 1 21' (instead of P 21 -unique C axis)
'H 3' (instead of R 3 -hexagonal)
'H 3 2' (instead of R 3 2 -hexagonal)
;
_item.name '_symmetry.pdbx_full_space_group_name_H-M'
_item.category_id symmetry
_item.mandatory_code no
_item_type.code line
_item_examples.case
;
Example: 'C 1 2 1' (instead of C 2)
'P 1 2 1' (instead of P 2)
'P 1 21 1' (instead of P 21)
'P 1 1 21' (instead of P 21 -unique C axis)
'H 3' (instead of R 3 -hexagonal)
'H 3 2' (instead of R 3 2 -hexagonal)
;
_item_aliases.alias_name '_symmetry.ndb_full_space_group_name_H-M'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save__refine.pdbx_overall_ESU_R
_item_description.description
; Overall estimated standard uncertainties of positional
parameters based on R value.
;
_item.name '_refine.pdbx_overall_ESU_R'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_overall_ESU_R'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
_item_type.code float
save_
save__refine.pdbx_overall_ESU_R_Free
_item_description.description
; Overall estimated standard uncertainties of positional
parameters based on R value.
;
_item.name '_refine.pdbx_overall_ESU_R_Free'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_refine.rcsb_overall_ESU_R_Free'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
###
save_pdbx_refine_tls
_category.description
; Data items in the REFINE_TLS category record details about
TLS parameters used in structure refinement. Note that the
intention is primarily to describe directly refined TLS
parameters, although other methods of obtaining TLS parameters
may be covered, see item _pdbx_refine_tls.method
;
_category.id pdbx_refine_tls
_category.mandatory_code no
loop_
_category_key.name '_pdbx_refine_tls.id'
loop_
_category_group.id 'inclusive_group'
'refine_group'
'ccp4_group'
save_
save__pdbx_refine_tls.id
_item_description.description
; The value of _pdbx_refine_tls.id must uniquely identify a record in
the PDBX_REFINE_TLS list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_pdbx_refine_tls.id'
_item.category_id pdbx_refine_tls
_item.mandatory_code yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_pdbx_refine_tls_group.refine_tls_id' '_pdbx_refine_tls.id'
_item_type.code code
loop_
_item_examples.case 1
A
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.id' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.id' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.details
_item_description.description
; A description of the TLS group, such as a domain name or a
chemical group name.
;
_item.name '_pdbx_refine_tls.details'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'Chain A catalytic domain'
'Chain A Tyr 56 side chain'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.details' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.details' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.method
_item_description.description
; The method by which the TLS parameters were obtained.
;
_item.name '_pdbx_refine_tls.method'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail refined
; TLS parameters refined directly
against crystallographic residual
;
fitted
; TLS parameters fitted to previously
refined anisotropic displacement
parameters
;
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.method' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.method' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.origin_x
_item_description.description
; The x coordinate in angstroms of the origin to which the
TLS parameters are referred, specified according to
a set of orthogonal Cartesian axes related to the cell axes as
given in _atom_sites.Cartn_transform_axes.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
;
_item.name '_pdbx_refine_tls.origin_x'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_dependent.dependent_name
'_pdbx_refine_tls.origin_y'
'_pdbx_refine_tls.origin_z'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.origin_x' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.origin_x' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.origin_y
_item_description.description
; The y coordinate in angstroms of the origin to which the
TLS parameters are referred, specified according to
a set of orthogonal Cartesian axes related to the cell axes as
given in _atom_sites.Cartn_transform_axes.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
;
_item.name '_pdbx_refine_tls.origin_y'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_dependent.dependent_name
'_pdbx_refine_tls.origin_x'
'_pdbx_refine_tls.origin_z'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.origin_y' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.origin_y' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.origin_z
_item_description.description
; The z coordinate in angstroms of the origin to which the
TLS parameters are referred, specified according to
a set of orthogonal Cartesian axes related to the cell axes as
given in _atom_sites.Cartn_transform_axes.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
;
_item.name '_pdbx_refine_tls.origin_z'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_dependent.dependent_name
'_pdbx_refine_tls.origin_x'
'_pdbx_refine_tls.origin_y'
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.origin_z' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.origin_z' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[1][1]
_item_description.description
; The [1][1] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.T[1][1]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[1][1]_esd'
associated_esd
_item_units.code angstroms_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[1][1]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[1][1]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[1][1]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.T[1][1].
;
_item.name '_pdbx_refine_tls.T[1][1]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[1][1]'
associated_value
_item_units.code angstroms_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[1][1]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[1][1]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[1][2]
_item_description.description
; The [1][2] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.T[1][2]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[1][2]_esd'
associated_esd
_item_units.code angstroms_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[1][2]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[1][2]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[1][2]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.T[1][2].
;
_item.name '_pdbx_refine_tls.T[1][2]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[1][2]'
associated_value
_item_units.code angstroms_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[1][2]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[1][2]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[1][3]
_item_description.description
; The [1][3] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.T[1][3]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[1][3]_esd'
associated_esd
_item_units.code angstroms_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[1][3]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[1][3]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[1][3]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.T[1][3].
;
_item.name '_pdbx_refine_tls.T[1][3]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[1][3]'
associated_value
_item_units.code angstroms_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[1][3]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[1][3]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[2][2]
_item_description.description
; The [2][2] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.T[2][2]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[2][2]_esd'
associated_esd
_item_units.code angstroms_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[2][2]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[2][2]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[2][2]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.T[2][2].
;
_item.name '_pdbx_refine_tls.T[2][2]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[2][2]'
associated_value
_item_units.code angstroms_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[2][2]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[2][2]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[2][3]
_item_description.description
; The [2][3] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.T[2][3]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[2][3]_esd'
associated_esd
_item_units.code angstroms_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[2][3]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[2][3]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[2][3]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.T[2][3].
;
_item.name '_pdbx_refine_tls.T[2][3]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[2][3]'
associated_value
_item_units.code angstroms_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[2][3]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[2][3]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[3][3]
_item_description.description
; The [3][3] element of the translation tensor T. This should
be given in the same coordinate frame and units as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.T[3][3]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[3][3]_esd'
associated_esd
_item_units.code angstroms_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[3][3]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[3][3]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.T[3][3]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.T[3][3].
;
_item.name '_pdbx_refine_tls.T[3][3]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.T[3][3]'
associated_value
_item_units.code angstroms_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.T[3][3]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.T[3][3]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[1][1]
_item_description.description
; The [1][1] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.L[1][1]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[1][1]_esd'
associated_esd
_item_units.code degrees_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[1][1]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[1][1]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[1][1]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.L[1][1].
;
_item.name '_pdbx_refine_tls.L[1][1]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[1][1]'
associated_value
_item_units.code degrees_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[1][1]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[1][1]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[1][2]
_item_description.description
; The [1][2] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.L[1][2]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[1][2]_esd'
associated_esd
_item_units.code degrees_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[1][2]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[1][2]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[1][2]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.L[1][2].
;
_item.name '_pdbx_refine_tls.L[1][2]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[1][2]'
associated_value
_item_units.code degrees_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[1][2]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[1][2]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[1][3]
_item_description.description
; The [1][3] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.L[1][3]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[1][3]_esd'
associated_esd
_item_units.code degrees_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[1][3]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[1][3]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[1][3]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.L[1][3].
;
_item.name '_pdbx_refine_tls.L[1][3]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[1][3]'
associated_value
_item_units.code degrees_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[1][3]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[1][3]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[2][2]
_item_description.description
; The [2][2] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.L[2][2]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[2][2]_esd'
associated_esd
_item_units.code degrees_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[2][2]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[2][2]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[2][2]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.L[2][2].
;
_item.name '_pdbx_refine_tls.L[2][2]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[2][2]'
associated_value
_item_units.code degrees_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[2][2]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[2][2]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[2][3]
_item_description.description
; The [2][3] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.L[2][3]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[2][3]_esd'
associated_esd
_item_units.code degrees_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[2][3]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[2][3]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[2][3]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.L[2][3].
;
_item.name '_pdbx_refine_tls.L[2][3]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[2][3]'
associated_value
_item_units.code degrees_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[2][3]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[2][3]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[3][3]
_item_description.description
; The [3][3] element of the libration tensor L. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
;
_item.name '_pdbx_refine_tls.L[3][3]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[3][3]_esd'
associated_esd
_item_units.code degrees_squared
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[3][3]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[3][3]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.L[3][3]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.L[3][3].
;
_item.name '_pdbx_refine_tls.L[3][3]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.L[3][3]'
associated_value
_item_units.code degrees_squared
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.L[3][3]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.L[3][3]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[1][1]
_item_description.description
; The [1][1] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
The trace of S is indeterminate by crystallography, and should
be set to zero.
;
_item.name '_pdbx_refine_tls.S[1][1]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[1][1]_esd'
associated_esd
_item_units.code angstroms_degrees
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[1][1]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[1][1]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[1][1]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.S[1][1].
;
_item.name '_pdbx_refine_tls.S[1][1]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[1][1]'
associated_value
_item_units.code angstroms_degrees
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[1][1]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[1][1]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[1][2]
_item_description.description
; The [1][2] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
;
_item.name '_pdbx_refine_tls.S[1][2]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[1][2]_esd'
associated_esd
_item_units.code angstroms_degrees
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[1][2]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[1][2]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[1][2]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.S[1][2].
;
_item.name '_pdbx_refine_tls.S[1][2]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[1][2]'
associated_value
_item_units.code angstroms_degrees
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[1][2]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[1][2]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[1][3]
_item_description.description
; The [1][3] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
;
_item.name '_pdbx_refine_tls.S[1][3]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[1][3]_esd'
associated_esd
_item_units.code angstroms_degrees
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[1][3]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[1][3]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[1][3]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.S[1][3].
;
_item.name '_pdbx_refine_tls.S[1][3]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[1][3]'
associated_value
_item_units.code angstroms_degrees
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[1][3]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[1][3]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[2][1]
_item_description.description
; The [2][1] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
;
_item.name '_pdbx_refine_tls.S[2][1]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[2][1]_esd'
associated_esd
_item_units.code angstroms_degrees
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[2][1]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[2][1]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[2][1]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.S[2][1].
;
_item.name '_pdbx_refine_tls.S[2][1]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[2][1]'
associated_value
_item_units.code angstroms_degrees
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[2][1]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[2][1]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[2][2]
_item_description.description
; The [2][2] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
The trace of S is indeterminate by crystallography, and should
be set to zero.
;
_item.name '_pdbx_refine_tls.S[2][2]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[2][2]_esd'
associated_esd
_item_units.code angstroms_degrees
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[2][2]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[2][2]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[2][2]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.S[2][2].
;
_item.name '_pdbx_refine_tls.S[2][2]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[2][2]'
associated_value
_item_units.code angstroms_degrees
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[2][2]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[2][2]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[2][3]
_item_description.description
; The [2][3] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
;
_item.name '_pdbx_refine_tls.S[2][3]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[2][3]_esd'
associated_esd
_item_units.code angstroms_degrees
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[2][3]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[2][3]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[2][3]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.S[2][3].
;
_item.name '_pdbx_refine_tls.S[2][3]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[2][3]'
associated_value
_item_units.code angstroms_degrees
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[2][3]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[2][3]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[3][1]
_item_description.description
; The [3][1] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
;
_item.name '_pdbx_refine_tls.S[3][1]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[3][1]_esd'
associated_esd
_item_units.code angstroms_degrees
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[3][1]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[3][1]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[3][1]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.S[3][1].
;
_item.name '_pdbx_refine_tls.S[3][1]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[3][1]'
associated_value
_item_units.code angstroms_degrees
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[3][1]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[3][1]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[3][2]
_item_description.description
; The [3][2] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
If the origin is omitted, it is assumed to be the centre of
reaction of the group, in which case S must be symmetric
;
_item.name '_pdbx_refine_tls.S[3][2]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[3][2]_esd'
associated_esd
_item_units.code angstroms_degrees
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[3][2]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[3][2]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[3][2]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.S[3][2].
;
_item.name '_pdbx_refine_tls.S[3][2]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[3][2]'
associated_value
_item_units.code angstroms_degrees
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[3][2]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[3][2]_esd' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[3][3]
_item_description.description
; The [3][3] element of the screw-rotation tensor S. This should
be given in the same coordinate frame as the
corresponding anisotropic displacement parameters.
The trace of S is indeterminate by crystallography, and should
be set to zero.
;
_item.name '_pdbx_refine_tls.S[3][3]'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[3][3]_esd'
associated_esd
_item_units.code angstroms_degrees
_item_type_conditions.code esd
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[3][3]' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[3][3]' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls.S[3][3]_esd
_item_description.description
; The estimated standard deviation of _pdbx_refine_tls.S[3][3].
;
_item.name '_pdbx_refine_tls.S[3][3]_esd'
_item.category_id pdbx_refine_tls
_item.mandatory_code no
_item_type.code float
_item_default.value 0.0
loop_
_item_related.related_name
_item_related.function_code '_pdbx_refine_tls.S[3][3]'
associated_value
_item_units.code angstroms_degrees
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls.S[3][3]_esd' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls.S[3][3]_esd' 'cif_ccp4.dic' 1.0
save_
save_pdbx_refine_tls_group
_category.description
; Data items in the PDBX_REFINE_TLS_GROUP category record details about
a fragment of a TLS group.
Properties of the TLS group are recorded in PDBX_REFINE_TLS
;
_category.id pdbx_refine_tls_group
_category.mandatory_code no
loop_
_category_key.name '_pdbx_refine_tls_group.id'
loop_
_category_group.id 'inclusive_group'
'refine_group'
'ccp4_group'
save_
save__pdbx_refine_tls_group.id
_item_description.description
; The value of _pdbx_refine_tls_group.id must uniquely identify
a record in the REFINE_TLS_GROUP list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_pdbx_refine_tls_group.id'
_item.category_id pdbx_refine_tls_group
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case 1
A
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls_group.id' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls_group.id' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls_group.refine_tls_id
_item_description.description
; This data item is a pointer to _pdbx_refine_tls.id in the
REFINE_TLS category.
;
_item.name '_pdbx_refine_tls_group.refine_tls_id'
_item.category_id pdbx_refine_tls_group
_item.mandatory_code yes
_item_type.code code
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls_group.refine_tls_id' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls_group.refine_tls_id' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls_group.beg_label_asym_id
_item_description.description
; A component of the identifier for the residue at which the
TLS fragment range begins.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_refine_tls_group.beg_label_asym_id'
_item.category_id pdbx_refine_tls_group
_item.mandatory_code no
loop_
_item_linked.child_name
_item_linked.parent_name
'_pdbx_refine_tls_group.beg_label_asym_id' '_atom_site.label_asym_id'
loop_
_item_examples.case O
2B3
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls_group.beg_label_asym_id' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls_group.beg_label_asym_id' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls_group.beg_label_seq_id
_item_description.description
; A component of the identifier for the residue at which the
TLS fragment range begins.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_refine_tls_group.beg_label_seq_id'
_item.category_id pdbx_refine_tls_group
_item.mandatory_code no
loop_
_item_linked.child_name
_item_linked.parent_name
'_pdbx_refine_tls_group.beg_label_seq_id' '_atom_site.label_seq_id'
loop_
_item_examples.case 1
303
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls_group.beg_label_seq_id' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls_group.beg_label_seq_id' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls_group.beg_auth_asym_id
_item_description.description
; A component of the identifier for the residue at which the
TLS fragment range begins.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_refine_tls_group.beg_auth_asym_id'
_item.category_id pdbx_refine_tls_group
_item.mandatory_code no
loop_
_item_linked.child_name
_item_linked.parent_name
'_pdbx_refine_tls_group.beg_auth_asym_id' '_atom_site.auth_asym_id'
loop_
_item_examples.case O
2B3
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls_group.beg_auth_asym_id' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls_group.beg_auth_asym_id' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls_group.beg_auth_seq_id
_item_description.description
; A component of the identifier for the residue at which the
TLS fragment range begins.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_refine_tls_group.beg_auth_seq_id'
_item.category_id pdbx_refine_tls_group
_item.mandatory_code no
loop_
_item_linked.child_name
_item_linked.parent_name
'_pdbx_refine_tls_group.beg_auth_seq_id' '_atom_site.auth_seq_id'
loop_
_item_examples.case 1
5A
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls_group.beg_auth_asym_id' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls_group.beg_auth_asym_id' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls_group.end_label_asym_id
_item_description.description
; A component of the identifier for the residue at which the
TLS fragment range ends.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_refine_tls_group.end_label_asym_id'
_item.category_id pdbx_refine_tls_group
_item.mandatory_code no
loop_
_item_linked.child_name
_item_linked.parent_name
'_pdbx_refine_tls_group.end_label_asym_id' '_atom_site.label_asym_id'
loop_
_item_examples.case O
2B3
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls_group.end_label_asym_id' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls_group.end_label_asym_id' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls_group.end_label_seq_id
_item_description.description
; A component of the identifier for the residue at which the
TLS fragment range ends.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_refine_tls_group.end_label_seq_id'
_item.category_id pdbx_refine_tls_group
_item.mandatory_code no
loop_
_item_linked.child_name
_item_linked.parent_name
'_pdbx_refine_tls_group.end_label_seq_id' '_atom_site.label_seq_id'
loop_
_item_examples.case 1
303
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls_group.end_label_seq_id' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls_group.end_label_seq_id' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls_group.end_auth_asym_id
_item_description.description
; A component of the identifier for the residue at which the
TLS fragment range ends.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_refine_tls_group.end_auth_asym_id'
_item.category_id pdbx_refine_tls_group
_item.mandatory_code no
loop_
_item_linked.child_name
_item_linked.parent_name
'_pdbx_refine_tls_group.end_auth_asym_id' '_atom_site.auth_asym_id'
loop_
_item_examples.case O
2B3
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls_group.end_auth_asym_id' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls_group.end_auth_asym_id' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls_group.end_auth_seq_id
_item_description.description
; A component of the identifier for the residue at which the
TLS fragment range ends.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_refine_tls_group.end_auth_seq_id'
_item.category_id pdbx_refine_tls_group
_item.mandatory_code no
loop_
_item_linked.child_name
_item_linked.parent_name
'_pdbx_refine_tls_group.end_auth_seq_id' '_atom_site.auth_seq_id'
loop_
_item_examples.case 1
5A
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls_group.end_auth_seq_id' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls_group.end_auth_seq_id' 'cif_ccp4.dic' 1.0
save_
save__pdbx_refine_tls_group.selection
_item_description.description
; A description of the subset of atoms in the specified
range included in the TLS fragment.
;
_item.name '_pdbx_refine_tls_group.selection'
_item.category_id pdbx_refine_tls_group
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail all
; all atoms in specified range
;
mnc
; main chain atoms only
;
sdc
; side chain atoms only
;
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_ccp4_refine_tls_group.selection' 'cif_rcsb.dic' 1.1
'_ccp4_refine_tls_group.selection' 'cif_ccp4.dic' 1.0
save_
#
save__refine.pdbx_solvent_vdw_probe_radii
_item_description.description
; CCP4 solvent proble van der Waals radii
;
_item.name '_refine.pdbx_solvent_vdw_probe_radii'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine.ccp4_solvent_vdw_probe_radii' 'cif_rcsb.dic' 1.1
'_refine.ccp4_solvent_vdw_probe_radii' 'cif_ccp4.dic' 1.0
save_
save__refine.pdbx_solvent_ion_probe_radii
_item_description.description
; CCP4 solvent ion proble radii
;
_item.name '_refine.pdbx_solvent_ion_probe_radii'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine.ccp4_solvent_ion_probe_radii' 'cif_rcsb.dic' 1.1
'_refine.ccp4_solvent_ion_probe_radii' 'cif_ccp4.dic' 1.0
save_
save__refine.pdbx_solvent_shrinkage_radii
_item_description.description
; CCP4 solvent shrinkage radii
;
_item.name '_refine.pdbx_solvent_shrinkage_radii'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version
'_refine.ccp4_solvent_shrinkage_radii' 'cif_rcsb.dic' 1.1
'_refine.ccp4_solvent_shrinkage_radii' 'cif_ccp4.dic' 1.0
save_
#########################
## PDBX_CONTACT_AUTHOR ##
#########################
save_pdbx_contact_author
_category.description
; Data items in the PDBX_CONTACT_AUTHOR category record details
about the name and address of the author to be contacted
concerning the contents of this data block. This category atomizes
information to a greater degree than the standard AUDIT_CONTACT_AUTHOR
category.
;
_category.id pdbx_contact_author
_category.mandatory_code no
_category_key.name '_pdbx_contact_author.id'
loop_
_category_group.id 'inclusive_group'
'audit_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
_pdbx_contact_author.id 1
_pdbx_contact_author.name_salutation 'Dr.'
_pdbx_contact_author.name_first 'Paula'
_pdbx_contact_author.name_last 'Fitzgerald'
_pdbx_contact_author.name_mi 'M.D.'
_pdbx_contact_author.address_1 'Department of Biophysical Chemistry'
_pdbx_contact_author.address_2 'Merck Research Laboratories'
_pdbx_contact_author.address_3 'P. O. Box 2000, Ry80M203'
_pdbx_contact_author.city 'Rahway'
_pdbx_contact_author.state_province 'New Jersey'
_pdbx_contact_author.postal_code 07065
_pdbx_contact_author.country 'UNITED STATES'
_pdbx_contact_author.phone '908 594 5510'
_pdbx_contact_author.fax '908 594 6645'
_pdbx_contact_author.email 'paula_fitzgerald@merck.com'
_pdbx_contact_author.role 'principal investigator'
_pdbx_contact_author.organization_type 'commercial'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_contact_author.id
_item_description.description
; A unique integer identifier for this author
;
_item.name '_pdbx_contact_author.id'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code int
_item_examples.case
; 1 2 3
;
loop_
_item_enumeration.value 1 2 3 4 5 6 7 8 9 10
save_
save__pdbx_contact_author.address_1
_item_description.description
; The mailing address of the author of the data block to whom
correspondence should be addressed, line 1 of 3.
;
_item.name '_pdbx_contact_author.address_1'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code text
_item_examples.case
; 610 Taylor Road
;
save_
save__pdbx_contact_author.address_2
_item_description.description
; The mailing address of the author of the data block to whom
correspondence should be addressed, line 2 of 3.
;
_item.name '_pdbx_contact_author.address_2'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code text
_item_examples.case
; Department of Chemistry and Chemical Biology
;
save_
save__pdbx_contact_author.address_3
_item_description.description
; The mailing address of the author of the data block to whom
correspondence should be addressed, line 3 of 3.
;
_item.name '_pdbx_contact_author.address_3'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code text
_item_examples.case
; Busch Campus
;
save_
save__pdbx_contact_author.city
_item_description.description
; The mailing address of the author of the data block to whom
correspondence should be addressed, city.
;
_item.name '_pdbx_contact_author.city'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code line
_item_examples.case
; Piscataway
;
save_
save__pdbx_contact_author.state_province
_item_description.description
; The mailing address of the author of the data block to whom
correspondence should be addressed, state or province.
;
_item.name '_pdbx_contact_author.state_province'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code line
_item_examples.case
; New Jersey
;
save_
save__pdbx_contact_author.postal_code
_item_description.description
; The mailing address of the author of the data block to whom
correspondence should be addressed, zip code.
;
_item.name '_pdbx_contact_author.postal_code'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code line
_item_examples.case
; 08854
;
save_
save__pdbx_contact_author.email
_item_description.description
; The electronic mail address of the author of the data block to
whom correspondence should be addressed, in a form recognisable
to international networks.
;
_item.name '_pdbx_contact_author.email'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'name@host.domain.country'
'bm@iucr.ac.uk'
save_
save__pdbx_contact_author.fax
_item_description.description
; The facsimile telephone number of the author of the data
block to whom correspondence should be addressed.
The recommended style includes the international dialing
prefix, the area code in parentheses, followed by the
local number with no spaces.
;
_item.name '_pdbx_contact_author.fax'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case '12(34) 947 7334'
'732 445 0103'
save_
save__pdbx_contact_author.name_first
_item_description.description
; The first name of the author of the data block to whom correspondence
should be addressed.
;
_item.name '_pdbx_contact_author.name_first'
_item.category_id pdbx_contact_author
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case 'Percival'
'Loyd'
'Susan'
save_
save__pdbx_contact_author.name_last
_item_description.description
; The last name of the author of the data block to whom correspondence
should be addressed.
;
_item.name '_pdbx_contact_author.name_last'
_item.category_id pdbx_contact_author
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case 'Samuels'
'Rodgers'
save_
save__pdbx_contact_author.name_mi
_item_description.description
; The middle initial(s) of the author of the data block to whom correspondence
should be addressed.
;
_item.name '_pdbx_contact_author.name_mi'
_item.category_id pdbx_contact_author
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case 'T.'
'M.F.'
save_
save__pdbx_contact_author.name_salutation
_item_description.description
; The salutation of the author of the data block to whom correspondence
should be addressed.
;
_item.name '_pdbx_contact_author.name_salutation'
_item.category_id pdbx_contact_author
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case 'Dr.'
'Prof.'
'Mr.'
'Ms.'
'Mrs.'
loop_
_item_enumeration.value 'Dr.'
'Prof.'
'Mr.'
'Ms.'
'Mrs.'
save_
save__pdbx_contact_author.country
_item_description.description
; The country of the author of the data block to whom
correspondence should be addressed.
;
_item.name '_pdbx_contact_author.country'
_item.category_id pdbx_contact_author
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case
'UNITED STATES'
'UNITED KINGDOM'
'AUSTRALIA'
loop_
_item_enumeration.value
'UNITED STATES'
'AFGHANISTAN'
'ALBANIA'
'ALGERIA'
'AMERICAN SAMOA'
'ANDORRA'
'ANGOLA'
'ANGUILLA'
'ANTARCTICA'
'ANTIGUA AND BARBUDA'
'ARGENTINA'
'ARMENIA'
'ARUBA'
'AUSTRALIA'
'AUSTRIA'
'AZERBAIJAN'
'BAHAMAS'
'BAHRAIN'
'BANGLADESH'
'BARBADOS'
'BELARUS'
'BELGIUM'
'BELIZE'
'BENIN'
'BERMUDA'
'BHUTAN'
'BOLIVIA'
'BOSNIA AND HERZEGOVINA'
'BOTSWANA'
'BOUVET ISLAND'
'BRAZIL'
'BRITISH INDIAN OCEAN TERRITORY'
'BRUNEI DARUSSALAM'
'BULGARIA'
'BURKINA FASO'
'BURUNDI'
'CAMBODIA'
'CAMEROON'
'CANADA'
'CAPE VERDE'
'CAYMAN ISLANDS'
'CENTRAL AFRICAN REPUBLIC'
'CHAD'
'CHILE'
'CHINA'
'CHRISTMAS ISLAND'
'COCOS (KEELING) ISLANDS'
'COLOMBIA'
'COMOROS'
'CONGO'
'CONGO, THE DEMOCRATIC REPUBLIC OF THE'
'COOK ISLANDS'
'COSTA RICA'
'COTE D'IVOIRE'
'CROATIA'
'CUBA'
'CYPRUS'
'CZECH REPUBLIC'
'DENMARK'
'DJIBOUTI'
'DOMINICA'
'DOMINICAN REPUBLIC'
v'ECUADOR'
'EGYPT'
'EL SALVADOR'
'EQUATORIAL GUINEA'
'ERITREA'
'ESTONIA'
'ETHIOPIA'
'FALKLAND ISLANDS (MALVINAS)'
'FAROE ISLANDS'
'FIJI'
'FINLAND'
'FRANCE'
'FRENCH GUIANA'
'FRENCH POLYNESIA'
'FRENCH SOUTHERN TERRITORIES'
'GABON'
'GAMBIA'
'GEORGIA'
'GERMANY'
'GHANA'
'GIBRALTAR'
'GREECE'
'GREENLAND'
'GRENADA'
'GUADELOUPE'
'GUAM'
'GUATEMALA'
'GUINEA'
'GUINEA-BISSAU'
'GUYANA'
'HAITI'
'HEARD ISLAND AND MCDONALD ISLANDS'
'HOLY SEE (VATICAN CITY STATE)'
'HONDURAS'
'HONG KONG'
'HUNGARY'
'ICELAND'
'INDIA'
'INDONESIA'
'IRAN, ISLAMIC REPUBLIC OF'
'IRAQ'
'IRELAND'
'ISRAEL'
'ITALY'
'JAMAICA'
'JAPAN'
'JORDAN'
'KAZAKHSTAN'
'KENYA'
'KIRIBATI'
'KOREA, DEMOCRATIC PEOPLE'S REPUBLIC OF'
'KOREA, REPUBLIC OF'
'KUWAIT'
'KYRGYZSTAN'
'LAO PEOPLE'S DEMOCRATIC REPUBLIC'
'LATVIA'
'LEBANON'
'LESOTHO'
'LIBERIA'
'LIBYAN ARAB JAMAHIRIYA'
'LIECHTENSTEIN'
'LITHUANIA'
'LUXEMBOURG'
'MACAO'
'MACEDONIA, THE FORMER YUGOSLAV REPUBLIC OF'
'MADAGASCAR'
'MALAWI'
'MALAYSIA'
'MALDIVES'
'MALI'
'MALTA'
'MARSHALL ISLANDS'
'MARTINIQUE'
'MAURITANIA'
'MAURITIUS'
'MAYOTTE'
'MEXICO'
'MICRONESIA, FEDERATED STATES OF'
'MOLDOVA, REPUBLIC OF'
'MONACO'
'MONGOLIA'
'MONTSERRAT'
'MOROCCO'
'MOZAMBIQUE'
'MYANMAR'
'NAMIBIA'
'NAURU'
'NEPAL'
'NETHERLANDS'
'NETHERLANDS ANTILLES'
'NEW CALEDONIA'
'NEW ZEALAND'
'NICARAGUA'
'NIGER'
'NIGERIA'
'NIUE'
'NORFOLK ISLAND'
'NORTHERN MARIANA ISLANDS'
'NORWAY'
'OMAN'
'PAKISTAN'
'PALAU'
'PALESTINIAN TERRITORY, OCCUPIED'
'PANAMA'
'PAPUA NEW GUINEA'
'PARAGUAY'
'PERU'
'PHILIPPINES'
'PITCAIRN'
'POLAND'
'PORTUGAL'
'PUERTO RICO'
'QATAR'
'REUNION'
'ROMANIA'
'RUSSIAN FEDERATION'
'RWANDA'
'SAINT HELENA'
'SAINT KITTS AND NEVIS'
'SAINT LUCIA'
'SAINT PIERRE AND MIQUELON'
'SAINT VINCENT AND THE GRENADINES'
'SAMOA'
'SAN MARINO'
'SAO TOME AND PRINCIPE'
'SAUDI ARABIA'
'SENEGAL'
'SERBIA AND MONTENEGRO'
'SEYCHELLES'
'SIERRA LEONE'
'SINGAPORE'
'SLOVAKIA'
'SLOVENIA'
'SOLOMON ISLANDS'
'SOMALIA'
'SOUTH AFRICA'
'SOUTH GEORGIA AND THE SOUTH SANDWICH ISLANDS'
'SPAIN'
'SRI LANKA'
'SUDAN'
'SURINAME'
'SVALBARD AND JAN MAYEN'
'SWAZILAND'
'SWEDEN'
'SWITZERLAND'
'SYRIAN ARAB REPUBLIC'
'TAIWAN, PROVINCE OF CHINA'
'TAJIKISTAN'
'TANZANIA, UNITED REPUBLIC OF'
'THAILAND'
'TIMOR-LESTE'
'TOGO'
'TOKELAU'
'TONGA'
'TRINIDAD AND TOBAGO'
'TUNISIA'
'TURKEY'
'TURKMENISTAN'
'TURKS AND CAICOS ISLANDS'
'TUVALU'
'UGANDA'
'UKRAINE'
'UNITED ARAB EMIRATES'
'UNITED KINGDOM'
'UNITED STATES MINOR OUTLYING ISLANDS'
'URUGUAY'
'UZBEKISTAN'
'VANUATU'
'VENEZUELA'
'VIET NAM'
'VIRGIN ISLANDS, BRITISH'
'VIRGIN ISLANDS, U.S.'
'WALLIS AND FUTUNA'
'WESTERN SAHARA'
'YEMEN'
'ZAMBIA'
'ZIMBABWE'
save_
save__pdbx_contact_author.phone
_item_description.description
; The telephone number of the author of the data block to whom
correspondence should be addressed.
The recommended style includes the international dialing
prefix, the area code in parentheses, followed by the
local number and any extension number prefixed by 'x',
with no spaces. The earlier convention of including
the international dialing prefixes in parentheses is no longer
recommended.
;
_item.name '_pdbx_contact_author.phone'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case '12 (34) 947 7330'
'947 732 0103 x8320'
save_
save__pdbx_contact_author.role
_item_description.description
; The role of this author in the project depositing this data.
;
_item.name '_pdbx_contact_author.role'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'principal investigator'
'responsible scientist'
'investigator'
loop_
_item_enumeration.value 'principal investigator'
'responsible scientist'
'investigator'
save_
save__pdbx_contact_author.organization_type
_item_description.description
; The organization type to which this author is affiliated.
;
_item.name '_pdbx_contact_author.organization_type'
_item.category_id pdbx_contact_author
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case 'academic'
'commercial'
'government'
'other'
loop_
_item_enumeration.value 'academic'
'commercial'
'government'
'other'
save_
save__struct_ref_seq_dif.pdbx_ordinal
_item_description.description
; A synthetic integer primary key for this category.
;
_item.name '_struct_ref_seq_dif.pdbx_ordinal'
_item.category_id struct_ref_seq_dif
_item.mandatory_code yes
_item_type.code int
_item_aliases.alias_name '_struct_ref_seq_dif.rcsb_ordinal'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
#####################
## PDBX_SG_PROJECT ##
#####################
save_pdbx_SG_project
_category.description
; Data items in the PDBX_CONTACT_AUTHOR category record details
about the Structural Genomics Project and name and initials
for each Center.
;
_category.id pdbx_SG_project
_category.mandatory_code no
_category_key.name '_pdbx_SG_project.id'
loop_
_category_group.id 'inclusive_group'
'audit_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
_pdbx_SG_project.id 1
_pdbx_SG_project.project_name 'PSI, Protein Structure Initiative'
_pdbx_SG_project.full_name_of_center 'Berkeley Structural Genomics Center'
_pdbx_SG_project.initial_of_center BSGC
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_SG_project.id
_item_description.description
; A unique integer identifier for this center
;
_item.name '_pdbx_SG_project.id'
_item.category_id pdbx_SG_project
_item.mandatory_code yes
_item_type.code int
_item_examples.case
; 1 2 3
;
loop_
_item_enumeration.value 1 2 3 4 5 6 7 8 9 10
save_
save__pdbx_SG_project.project_name
_item_description.description
; The value identifies the Structural Genomics project.
;
_item.name '_pdbx_SG_project.project_name'
_item.category_id pdbx_SG_project
_item.mandatory_code no
_item_type.code text
_item_examples.case 'PSI, Protein Structure Initiative'
loop_
_item_enumeration.value
'PSI, Protein Structure Initiative'
'NPPSFA, National Project on Protein Structural and Functional Analyses'
save_
save__pdbx_SG_project.full_name_of_center
_item_description.description
; The value identifies the full name of center.
;
_item.name '_pdbx_SG_project.full_name_of_center'
_item.category_id pdbx_SG_project
_item.mandatory_code no
_item_type.code text
_item_examples.case 'Berkeley Structural Genomics Center'
loop_
_item_enumeration.value
'Bacterial targets at IGS-CNRS France'
'Berkeley Structural Genomics Center'
'Center for Eukaryotic Structural Genomics'
'Israel Structural Proteomics Center'
'Joint Center for Structural Genomics'
'Marseilles Structural Genomics Program @ AFMB'
'Midwest Center for Structural Genomics'
'Montreal-Kingston Bacterial Structural Genomics Initiative'
'Mycobacterium Tuberculosis Structural Proteomics Project'
'New York Structural Genomics Research Consortium'
'Northeast Structural Genomics Consortium'
'Oxford Protein Production Facility'
'Paris-Sud Yeast Structural Genomics'
'Protein Structure Factory'
'RIKEN Structural Genomics/Proteomics Initiative'
'Southeast Collaboratory for Structural Genomics'
'Structural Genomics Consortium'
'Structural Genomics of Pathogenic Protozoa Consortium'
'Structural Proteomics in Europe'
'Structure 2 Function Project'
'TB Structural Genomics Consortium'
save_
save__pdbx_SG_project.initial_of_center
_item_description.description
; The value identifies the full name of center.
;
_item.name '_pdbx_SG_project.initial_of_center'
_item.category_id pdbx_SG_project
_item.mandatory_code no
_item_type.code text
_item_examples.case 'BSGC'
loop_
_item_enumeration.value
'BIGS'
'BSGC'
'CESG'
'ISPC'
'JCSG'
'MSGP'
'MCSG'
'BSGI'
'XMTB'
'NYSGRC'
'NESG'
'OPPF'
'YSG'
'PSF'
'RSGI'
'SECSG'
'SGC'
'SGPP'
'SPINE'
'S2F'
'TBSGC'
save_
### EOF mmcif_pdbx-def-1.dic
###########################################################################
#
# File: mmcif_pdbx-def-3.dic
#
# PDB Exchange Data Dictionary
#
# This data dictionary contains definitions used by wwPDB for data exchange
# and data processing.
#
# Definition Section 3
#
#
###########################################################################
##
##
save_pdbx_nmr_details
_category.description
;
Experimental details of the NMR study that have not been
described elsewhere in this deposition.
;
_category.id pdbx_nmr_details
_category.mandatory_code no
loop_
_category_key.name
'_pdbx_nmr_details.entry_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
save_
save__pdbx_nmr_details.entry_id
_item_description.description
; The entry ID for the structure determination.
;
_item.name '_pdbx_nmr_details.entry_id'
_item.category_id pdbx_nmr_details
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_nmr_details.entry_id'
_item_linked.parent_name '_entry.id'
_item_aliases.alias_name '_rcsb_nmr_details.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_details.text
_item_description.description
; Additional details describing the NMR experiment.
;
_item.name '_pdbx_nmr_details.text'
_item.category_id pdbx_nmr_details
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
;
This structure was determined using standard 2D homonuclear techniques.
;
;
The structure was determined using triple-resonance NMR spectroscopy.
;
_item_aliases.alias_name '_rcsb_nmr_details.text'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
## provided to hold a simple solution description.
save_pdbx_nmr_sample_details
_category.description
;
Complete description of each NMR sample, including the solvent
system used.
;
_category.id pdbx_nmr_sample_details
_category.mandatory_code no
loop_
_category_key.name
'_pdbx_nmr_sample_details.solution_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
This example was taken from the study of MCP-1 which is a dimer under the
conditions studied. Three solutions with different isotope compositions were
studied.
;
;
loop_
_pdbx_nmr_sample_details.solution_id
_pdbx_nmr_sample_details.solvent_system
_pdbx_nmr_sample_details.contents
1 MCP-1 '2 mM U-15N,13C, H2O 90 %, D2O 10 %'
2 MCP-1 '1 mM U-50% 15N, MCP-1 1 mM U-50% 13C, H2O 90 %, D2O 10 %'
3 MCP-1 '2 mM U-15N, H2O 90 %, D2O 10 %'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_nmr_sample_details.solution_id
_item_description.description
;
The name (number) of the sample.
;
_item.name '_pdbx_nmr_sample_details.solution_id'
_item.category_id pdbx_nmr_sample_details
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case
'1'
'2'
'3'
_item_aliases.alias_name '_rcsb_nmr_sample_details.solution_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_sample_details.contents
_item_description.description
;
A complete description of each NMR sample. Include the concentration
and concentration units for each component (include buffers, etc.). For each
component describe the isotopic composition, including the % labeling level,
if known.
For example:
1. Uniform (random) labeling with 15N: U-15N
2. Uniform (random) labeling with 13C, 15N at known labeling
levels: U-95% 13C;U-98% 15N
3. Residue selective labeling: U-95% 15N-Thymine
4. Site specific labeling: 95% 13C-Ala18,
5. Natural abundance labeling in an otherwise uniformly labeled
biomolecule is designated by NA: U-13C; NA-K,H
;
_item.name '_pdbx_nmr_sample_details.contents'
_item.category_id pdbx_nmr_sample_details
_item.mandatory_code no
_item_type.code text
_item_examples.case
;
2mM Ribonuclease U-15N,13C; 50mM phosphate buffer NA; 90% H2O, 10% D2O
;
_item_aliases.alias_name '_rcsb_nmr_sample_details.contents'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_sample_details.solvent_system
_item_description.description
;
The solvent system used for this sample.
;
_item.name '_pdbx_nmr_sample_details.solvent_system'
_item.category_id pdbx_nmr_sample_details
_item.mandatory_code no
_item_type.code text
_item_examples.case
;
90% H2O, 10% D2O
;
_item_aliases.alias_name '_rcsb_nmr_sample_details.solvent_system'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save_pdbx_nmr_exptl_sample
_category.description
; The chemical constituents of
each NMR sample. Each sample is identified by a number and
each component in the sample is identified by name.
;
_category.id pdbx_nmr_exptl_sample
_category.mandatory_code no
loop_
_category_key.name
'_pdbx_nmr_exptl_sample.solution_id'
'_pdbx_nmr_exptl_sample.component'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
This example was taken from the study of MCP-1 which is a dimer under the
conditions studied. Three solutions with different isotope compositions were
studied.
;
#
;
loop_
_pdbx_nmr_exptl_sample.solution_id
_pdbx_nmr_exptl_sample.component
_pdbx_nmr_exptl_sample.concentration
_pdbx_nmr_exptl_sample.concentration_units
_pdbx_nmr_exptl_sample.isotopic_labeling
1 MCP-1 2 'mM' 'U-15N,13C'
1 H2O 90 '%' .
1 D2O 10 '%' .
;
;
Example 2
This example was taken from the study of MCP-1 which is a dimer under the
conditions studied. Three solutions with different isotope compositions were
studied.
;
#
;
loop_
_pdbx_nmr_exptl_sample.solution_id
_pdbx_nmr_exptl_sample.component
_pdbx_nmr_exptl_sample.concentration
_pdbx_nmr_exptl_sample.concentration_units
_pdbx_nmr_exptl_sample.isotopic_labeling
2 MCP-1 1 'mM' 'U-50% 15N'
2 H2O 90 '%' .
2 D2O 10 '%' .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_nmr_exptl_sample.solution_id
_item_description.description
; The name (number) of the sample.
;
_item.name '_pdbx_nmr_exptl_sample.solution_id'
_item.category_id pdbx_nmr_exptl_sample
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case
'1'
'2'
'3'
_item_aliases.alias_name '_rcsb_nmr_exptl_sample.solution_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl_sample.component
_item_description.description
; The name of each component in the sample
;
_item.name '_pdbx_nmr_exptl_sample.component'
_item.category_id pdbx_nmr_exptl_sample
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case
'ribonuclease'
'DNA strand 1'
'TRIS buffer'
'sodium chloride'
'H2O'
'D2O'
_item_aliases.alias_name '_rcsb_nmr_exptl_sample.component'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl_sample.concentration
_item_description.description
; The concentration value of the component.
;
_item.name '_pdbx_nmr_exptl_sample.concentration'
_item.category_id pdbx_nmr_exptl_sample
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case
'2.0'
'2.7'
'0.01'
_item_aliases.alias_name '_rcsb_nmr_exptl_sample.concentration'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl_sample.concentration_units
_item_description.description
; The concentration units of the component.
;
_item.name '_pdbx_nmr_exptl_sample.concentration_units'
_item.category_id pdbx_nmr_exptl_sample
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case
'mg/mL for mg per milliliter'
'mM for millimolar'
'% for percent by volume'
loop_
_item_enumeration.value
_item_enumeration.detail
'%' 'percent by volume'
'mM' 'millimolar'
'mg/mL' 'mg per milliliter'
'M' 'molar'
'g/L' 'grams per liter'
_item_aliases.alias_name '_rcsb_nmr_exptl_sample.concentration_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl_sample.isotopic_labeling
_item_description.description
; The isotopic composition of each component, including
the % labeling level, if known. For example:
1. Uniform (random) labeling with 15N: U-15N
2. Uniform (random) labeling with 13C, 15N at known labeling
levels: U-95% 13C;U-98% 15N
3. Residue selective labeling: U-95% 15N-Thymine
4. Site specific labeling: 95% 13C-Ala18,
5. Natural abundance labeling in an otherwise uniformly labled
biomolecule is designated by NA: U-13C; NA-K,H
;
_item.name '_pdbx_nmr_exptl_sample.isotopic_labeling'
_item.category_id pdbx_nmr_exptl_sample
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'U-13C,15N'
'U-2H'
loop_
_item_enumeration.value
'U-15N'
'U-13C'
'U-15N,13C'
'U-2H'
'other'
_item_aliases.alias_name '_rcsb_nmr_exptl_sample.isotopic_labeling'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
### ##########################################################################
###
save_pdbx_nmr_exptl_sample_conditions
_category.description
;
The experimental conditions used to for each sample. Each set of conditions
is identified by a numerical code.
;
_category.id pdbx_nmr_exptl_sample_conditions
_category.mandatory_code no
loop_
_category_key.name
'_pdbx_nmr_exptl_sample_conditions.conditions_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; This example was taken from a pH stability study.
;
#
;
loop_
_pdbx_nmr_exptl_sample_conditions.conditions_id
_pdbx_nmr_exptl_sample_conditions.temperature
_pdbx_nmr_exptl_sample_conditions.pressure
_pdbx_nmr_exptl_sample_conditions.pH
_pdbx_nmr_exptl_sample_conditions.ionic_strength
1 298 ambient 7 '25mM NaCl'
2 298 ambient 3 '25mM NaCl'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_nmr_exptl_sample_conditions.conditions_id
_item_description.description
; The condition number as defined above.
;
_item.name '_pdbx_nmr_exptl_sample_conditions.conditions_id'
_item.category_id pdbx_nmr_exptl_sample_conditions
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case
'1'
'2'
'3'
_item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.conditions_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl_sample_conditions.temperature
_item_description.description
; The temperature (in Kelvin) at which NMR data were
collected.
;
_item.name '_pdbx_nmr_exptl_sample_conditions.temperature'
_item.category_id pdbx_nmr_exptl_sample_conditions
_item.mandatory_code no
_item_type.code float-range
loop_
_item_examples.case
'298'
_item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.temperature'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl_sample_conditions.pressure_units
_item_description.description
; The units of pressure at which NMR data were collected.
;
_item.name '_pdbx_nmr_exptl_sample_conditions.pressure_units'
_item.category_id pdbx_nmr_exptl_sample_conditions
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case
'Pa'
'atm'
'Torr'
_item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.pressure_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl_sample_conditions.pressure
_item_description.description
; The pressure at which NMR data were collected.
;
_item.name '_pdbx_nmr_exptl_sample_conditions.pressure'
_item.category_id pdbx_nmr_exptl_sample_conditions
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'ambient'
'1atm'
_item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.pressure'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl_sample_conditions.pH
_item_description.description
; The pH at which the NMR data were collected.
;
_item.name '_pdbx_nmr_exptl_sample_conditions.pH'
_item.category_id pdbx_nmr_exptl_sample_conditions
_item.mandatory_code no
_item_type.code float-range
loop_
_item_examples.case
'3.1'
'7.0'
_item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.pH'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl_sample_conditions.ionic_strength
_item_description.description
; The ionic strength at which the NMR data were collected -in lieu of
this enter the concentration and identity of the salt in the sample.
;
_item.name '_pdbx_nmr_exptl_sample_conditions.ionic_strength'
_item.category_id pdbx_nmr_exptl_sample_conditions
_item.mandatory_code no
_item_type.code line
# loop_
# _item_examples.case
# '3.1'
# '7.0'
_item_aliases.alias_name '_rcsb_nmr_exptl_sample_conditions.ionic_strength'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
### ##########################################################################
###
save_pdbx_nmr_spectrometer
_category.description
;
The details about each spectrometer used to collect data for this
deposition.
;
_category.id pdbx_nmr_spectrometer
_category.mandatory_code no
_category_key.name '_pdbx_nmr_spectrometer.spectrometer_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; The instruments described here are the ones used for the MCP-1 studies.
;
#
;
loop_
_pdbx_nmr_spectrometer.spectrometer_id
_pdbx_nmr_spectrometer.type
_pdbx_nmr_spectrometer.field_strength
1 'Bruker AMX' 600
2 'Bruker AMX' 500
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_nmr_spectrometer.spectrometer_id
_item_description.description
;
Assign a numerical ID to each instrument.
;
_item.name '_pdbx_nmr_spectrometer.spectrometer_id'
_item.category_id pdbx_nmr_spectrometer
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case
'1'
'2'
'3'
_item_aliases.alias_name '_rcsb_nmr_spectrometer.spectrometer_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_spectrometer.model
_item_description.description
;
The model of the NMR spectrometer.
;
_item.name '_pdbx_nmr_spectrometer.model'
_item.category_id pdbx_nmr_spectrometer
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'AVANCE'
'WH'
'WM'
'AM'
'AMX'
'DMX'
'DRX'
'MSL'
'OMEGA'
'OMEGA PSG'
'GX'
'GSX'
'A'
'AL'
'EC'
'EX'
'LA'
'ECP'
'VXRS'
'UNITY'
'UNITYPLUS'
'INOVA'
_item_aliases.alias_name '_rcsb_nmr_spectrometer.model'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_spectrometer.type
_item_description.description
;
Select the instrument manufacturer(s) and the model(s) of the NMR(s)
used for this work.
;
_item.name '_pdbx_nmr_spectrometer.type'
_item.category_id pdbx_nmr_spectrometer
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'Bruker WH'
'Bruker WM'
'Bruker AM'
'Bruker AMX'
'Bruker DMX'
'Bruker DRX'
'Bruker MSL'
'Bruker AVANCE'
'GE Omega'
'GE Omega PSG'
'JEOL GX'
'JEOL GSX'
'JEOL A'
'JEOL AL'
'JEOL EC'
'JEOL EX'
'JEOL LA'
'JEOL ECP'
'Varian VXRS'
'Varian UNITY'
'Varian UNITYplus'
'Varian INOVA'
'other'
_item_aliases.alias_name '_rcsb_nmr_spectrometer.type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_spectrometer.manufacturer
_item_description.description
;
The name of the manufacturer of the spectrometer.
;
_item.name '_pdbx_nmr_spectrometer.manufacturer'
_item.category_id pdbx_nmr_spectrometer
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'Varian'
'Bruker'
'JEOL'
'GE'
_item_aliases.alias_name '_rcsb_nmr_spectrometer.manufacturer'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_spectrometer.field_strength
_item_description.description
;
Select the field strength for protons in MHz.
;
_item.name '_pdbx_nmr_spectrometer.field_strength'
_item.category_id pdbx_nmr_spectrometer
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case
'360'
'400'
'500'
'600'
'750'
'800'
'850'
'900'
'950'
'1000'
_item_aliases.alias_name '_rcsb_nmr_spectrometer.field_strength'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
### ##########################################################################
###
save_pdbx_nmr_exptl
_category.description
;
In this section, enter information on those experiments that were
used to generate constraint data. For each NMR experiment indicate
which sample and which sample conditions were used for the experiment.
;
_category.id pdbx_nmr_exptl
_category.mandatory_code no
loop_
_category_key.name
'_pdbx_nmr_exptl.experiment_id'
'_pdbx_nmr_exptl.conditions_id'
'_pdbx_nmr_exptl.solution_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; This example was taken from the MCP-1 study.
;
#
;
loop_
_pdbx_nmr_exptl.experiment_id
_pdbx_nmr_exptl.solution_id
_pdbx_nmr_exptl.conditions_id
_pdbx_nmr_exptl.type
1 3 1 '3D_15N-separated_NOESY'
2 1 1 '3D_13C-separated_NOESY'
3 1 2 '4D_13C/15N-separated_NOESY'
4 1 1 '4D_13C-separated_NOESY'
5 1 1 '3D_15N-separated_ROESY'
6 3 1 '3D_13C-separated_ROESY'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_nmr_exptl.experiment_id
_item_description.description
; A numerical ID for each experiment.
;
_item.name '_pdbx_nmr_exptl.experiment_id'
_item.category_id pdbx_nmr_exptl
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case
'1'
'2'
'3'
_item_aliases.alias_name '_rcsb_nmr_exptl.experiment_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl.conditions_id
_item_description.description
; The number to identify the set of sample conditions.
;
_item.name '_pdbx_nmr_exptl.conditions_id'
_item.category_id pdbx_nmr_exptl
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case
'1'
'2'
'3'
_item_aliases.alias_name '_rcsb_nmr_exptl.conditions_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl.solution_id
_item_description.description
; The solution_id from the Experimental Sample to identify the sample
that these conditions refer to.
[Remember to save the entries here before returning to the
Experimental Sample form]
;
_item.name '_pdbx_nmr_exptl.solution_id'
_item.category_id pdbx_nmr_exptl
_item.mandatory_code yes
_item_type.code code
loop_
_item_examples.case
'1'
'2'
'3'
_item_aliases.alias_name '_rcsb_nmr_exptl.solution_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_exptl.type
_item_description.description
; The type of NMR experiment.
;
_item.name '_pdbx_nmr_exptl.type'
_item.category_id pdbx_nmr_exptl
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'2D NOESY'
'3D_15N-separated_NOESY'
'3D_13C-separated_NOESY'
'4D_13C-separated_NOESY'
'4D_13C/15N-separated_NOESY'
'3D_15N-separated_ROESY'
'3D_13C-separated_ROESY'
'HNCA-J'
'HNHA'
'DQF-COSY'
'P-COSY'
'PE-COSY'
'E-COSY'
_item_aliases.alias_name '_rcsb_nmr_exptl.type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
### ##########################################################################
###
save_pdbx_nmr_software
_category.description
;
Description of the software that was used for data collection, data processing,
data analysis, structure calculations and refinement. The description should
include the name of the software, the author of the software and the version used.
;
_category.id pdbx_nmr_software
_category.mandatory_code no
loop_
_category_key.name '_pdbx_nmr_software.name'
'_pdbx_nmr_software.version'
'_pdbx_nmr_software.classification'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; This example describes the software used in the MCP-1 study.
;
#
;
loop_
_pdbx_nmr_software.name
_pdbx_nmr_software.authors
_pdbx_nmr_software.version
_pdbx_nmr_software.classification
UXNMR Bruker 940501.3 'collection'
FELIX Hare 1.1 'processing'
ANSIG Kraulis 3.0 'data analysis'
X-PLOR Brunger 3.8 'structure calculation'
X-PLOR Brunger 3.8 'refinement'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_nmr_software.classification
_item_description.description
; The purpose of the software.
;
_item.name '_pdbx_nmr_software.classification'
_item.category_id pdbx_nmr_software
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case
'collection'
'processing'
'data analysis'
'structure solution'
'refinement'
'iterative matrix relaxation'
# loop_
# _item_enumeration.value
# 'collection'
# 'processing'
# 'data analysis'
# 'structure solution'
# 'refinement'
# 'iterative matrix relaxation'
_item_aliases.alias_name '_rcsb_nmr_software.classification'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_software.name
_item_description.description
; The name of the software used for the task.
;
_item.name '_pdbx_nmr_software.name'
_item.category_id pdbx_nmr_software
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case
'ANSIG'
'AURELIA'
'AZARA'
'CHARMM'
'CORMA'
'DIANA'
'DYANA'
'DSPACE'
'DISGEO'
'DGII'
'DISMAN'
'DINOSAUR'
'DISCOVER'
'FELIX'
'FT_NMR'
'GROMOS'
'IRMA'
'MARDIGRAS'
'NMRPipe'
'SA'
'UXNMR'
'VNMR'
'X-PLOR'
'XWINNMR'
_item_aliases.alias_name '_rcsb_nmr_software.name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_software.version
_item_description.description
; The version of the software.
;
_item.name '_pdbx_nmr_software.version'
_item.category_id pdbx_nmr_software
_item.mandatory_code yes
_item_type.code line
loop_
_item_examples.case
'940501.3'
'2.1'
_item_aliases.alias_name '_rcsb_nmr_software.version'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_software.authors
_item_description.description
; The name of the authors of the software used in this
procedure.
;
_item.name '_pdbx_nmr_software.authors'
_item.category_id pdbx_nmr_software
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'Brunger'
'Guentert'
_item_aliases.alias_name '_rcsb_nmr_software.authors'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
### ##########################################################################
###
save_pdbx_nmr_constraints
_category.description
; This section provides a tabulation of constraint data.
;
_category.id pdbx_nmr_constraints
_category.mandatory_code no
_category_key.name '_pdbx_nmr_constraints.entry_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; This example uses the data from the MCP-1 structure determination. Remember
this is a dimer so there are intersubunit constraints as well as intrasubunit
constraints.
;
#
;
loop_
_pdbx_nmr_constraints.entry_id
_pdbx_nmr_constraints.NOE_constraints_total
_pdbx_nmr_constraints.NOE_intraresidue_total_count
_pdbx_nmr_constraints.NOE_sequential_total_count
_pdbx_nmr_constraints.NOE_medium_range_total_count
_pdbx_nmr_constraints.NOE_long_range_total_count
_pdbx_nmr_constraints.protein_phi_angle_constraints_total_count
1ABC 4458 1144 272 1004 1356 96
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_nmr_constraints.entry_id
_item_description.description
; You can leave this blank as an ID will be assigned by the MSD
to the constraint file.
;
_item.name '_pdbx_nmr_constraints.entry_id'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_nmr_constraints.entry_id'
_item_linked.parent_name '_entry.id'
_item_aliases.alias_name '_rcsb_nmr_constraints.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NOE_constraints_total
_item_description.description
; The total number of all NOE constraints used in the final
structure calculation.
;
_item.name '_pdbx_nmr_constraints.NOE_constraints_total'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'4458'
_item_aliases.alias_name '_rcsb_nmr_constraints.NOE_constraints_total'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NOE_intraresidue_total_count
_item_description.description
; The total number of all intraresidue, [i-j]=0, NOE constraints
used in the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NOE_intraresidue_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'1144'
_item_aliases.alias_name '_rcsb_nmr_constraints.NOE_intraresidue_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NOE_interentity_total_count
_item_description.description
; The total number of interentity, NOE constraints
used in the final structure calculation. This field should only be
if system is complex -i.e more than one entity e.g. a dimer or ligand-protein
complex
;
_item.name '_pdbx_nmr_constraints.NOE_interentity_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'272'
_item_aliases.alias_name '_rcsb_nmr_constraints.NOE_interentity_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NOE_sequential_total_count
_item_description.description
; The total number of sequential, [i-j]=1, NOE constraints used
in the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NOE_sequential_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'1004'
_item_aliases.alias_name '_rcsb_nmr_constraints.NOE_sequential_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NOE_medium_range_total_count
_item_description.description
; The total number of medium range 1<[i-j]<=5 NOE constraints used
in the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NOE_medium_range_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'682'
_item_aliases.alias_name '_rcsb_nmr_constraints.NOE_medium_range_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NOE_long_range_total_count
_item_description.description
; The total number of long range [i-j]>5 NOE constraints used
in the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NOE_long_range_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'1356'
_item_aliases.alias_name '_rcsb_nmr_constraints.NOE_long_range_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.protein_phi_angle_constraints_total_count
_item_description.description
; The total number of phi angle constraints used in the final structure
calculation
;
_item.name '_pdbx_nmr_constraints.protein_phi_angle_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'96'
_item_aliases.alias_name '_rcsb_nmr_constraints.protein_phi_angle_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.protein_psi_angle_constraints_total_count
_item_description.description
; The total number of psi angle constraints used in the final structure
calculation.
;
_item.name '_pdbx_nmr_constraints.protein_psi_angle_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'0'
_item_aliases.alias_name '_rcsb_nmr_constraints.protein_psi_angle_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.protein_chi_angle_constraints_total_count
_item_description.description
; The total number of chi angle constraints used in the final structure
calculation.
;
_item.name '_pdbx_nmr_constraints.protein_chi_angle_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'66'
_item_aliases.alias_name '_rcsb_nmr_constraints.protein_chi_angle_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.protein_other_angle_constraints_total_count
_item_description.description
; The total number of other angle constraints used in the final structure
calculation.
;
_item.name '_pdbx_nmr_constraints.protein_other_angle_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'0'
_item_aliases.alias_name '_rcsb_nmr_constraints.protein_other_angle_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NOE_interproton_distance_evaluation
_item_description.description
; Describe the method used to quantify the NOE and ROE values.
;
_item.name '_pdbx_nmr_constraints.NOE_interproton_distance_evaluation'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
;
NOE buildup curves with 50, 75, 150 ms mixing times were
analyzed.
;
;
Noesy cross peak intensities were classified into three different
catagories with distances of 1.8-2.7 A, 1.8-3.5 A, 1.8- 5.0 A for strong,
medium and weak NOEs.
;
_item_aliases.alias_name '_rcsb_nmr_constraints.NOE_interproton_distance_evaluation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NOE_pseudoatom_corrections
_item_description.description
; Describe any corrections made for pseudoatoms
;
_item.name '_pdbx_nmr_constraints.NOE_pseudoatom_corrections'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
;
Pseudo-atoms nomenclature and corrections according to Wuethrich, Billeter,
and Braun, J. Mol.Biol.(1983) 169, 949-961.
;
;
Pseudoatoms were not used.
;
_item_aliases.alias_name '_rcsb_nmr_constraints.NOE_pseudoatom_corrections'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NOE_motional_averaging_correction
_item_description.description
;Describe any corrections that were made to the NOE data for motional averaging.
;
_item.name '_pdbx_nmr_constraints.NOE_motional_averaging_correction'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'Replace with item example text'
_item_aliases.alias_name '_rcsb_nmr_constraints.NOE_motional_averaging_correction'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__pdbx_nmr_constraints.hydrogen_bond_constraints_total_count
_item_description.description
; The total number of hydrogen bond constraints used in the final
structure calculation.
;
_item.name '_pdbx_nmr_constraints.hydrogen_bond_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'6'
_item_aliases.alias_name '_rcsb_nmr_constraints.hydrogen_bond_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.disulfide_bond_constraints_total_count
_item_description.description
; The total number of disulfide bond constraints used in the final
structure calculation.
;
_item.name '_pdbx_nmr_constraints.disulfide_bond_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'3'
_item_aliases.alias_name '_rcsb_nmr_constraints.disulfide_bond_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count
_item_description.description
; The total number of nucleic acid alpha-angle constraints used in
the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'18'
_item_aliases.alias_name '_rcsb_nmr_constraints.NA_alpha-angle_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NA_beta-angle_constraints_total_count
_item_description.description
; The total number of nucleic acid beta-angle constraints used in
the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NA_beta-angle_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'24'
_item_aliases.alias_name '_rcsb_nmr_constraints.NA_beta-angle_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count
_item_description.description
; The total number of nucleic acid gamma-angle constraints used in
the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'12'
_item_aliases.alias_name '_rcsb_nmr_constraints.NA_gamma-angle_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NA_delta-angle_constraints_total_count
_item_description.description
; The total number of nucleic acid delta-angle constraints used in
the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NA_delta-angle_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'15'
_item_aliases.alias_name '_rcsb_nmr_constraints.NA_delta-angle_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count
_item_description.description
; The total number of nucleic acid epsilon-angle constraints used
in the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'31'
_item_aliases.alias_name '_rcsb_nmr_constraints.NA_epsilon-angle_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NA_chi-angle_constraints_total_count
_item_description.description
; The total number of nucleic acid chi-angle constraints used
in the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NA_chi-angle_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'15'
_item_aliases.alias_name '_rcsb_nmr_constraints.NA_chi-angle_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NA_other-angle_constraints_total_count
_item_description.description
; The total number of nucleic acid other-angle constraints used
in the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NA_other-angle_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'5'
_item_aliases.alias_name '_rcsb_nmr_constraints.NA_other-angle_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count
_item_description.description
; The total number of nucleic acid sugar pucker constraints used
in the final structure calculation.
;
_item.name '_pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count'
_item.category_id pdbx_nmr_constraints
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'10'
_item_aliases.alias_name '_rcsb_nmr_constraints.NA_sugar_pucker_constraints_total_count'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
###
### ##########################################################################
###
save_pdbx_nmr_ensemble
_category.description
; This category contains the information that describes the
ensemble of deposited structures. If only an average structure
has been deposited skip this section.
;
_category.id pdbx_nmr_ensemble
_category.mandatory_code no
_category_key.name '_pdbx_nmr_ensemble.entry_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;This example uses the data from the MCP-1 study.
;
#
;
loop_
_pdbx_nmr_ensemble.entry_id
_pdbx_nmr_ensemble.conformers_calculated_total_number
_pdbx_nmr_ensemble.conformers_submitted_total_number
_pdbx_nmr_ensemble.conformer_selection_criteria
_pdbx_nmr_ensemble.representative_conformer
1ABC 40 20 'structures with the least restraint violations' 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_nmr_ensemble.entry_id
_item_description.description
; Leave this blank as the ID is provided by the MSD
;
_item.name '_pdbx_nmr_ensemble.entry_id'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_nmr_ensemble.entry_id'
_item_linked.parent_name '_entry.id'
_item_aliases.alias_name '_rcsb_nmr_ensemble.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.conformers_calculated_total_number
_item_description.description
; The total number of conformer (models) that were calculated in the final round.
;
_item.name '_pdbx_nmr_ensemble.conformers_calculated_total_number'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'40'
_item_aliases.alias_name '_rcsb_nmr_ensemble.conformers_calculated_total_number'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.conformers_submitted_total_number
_item_description.description
; The number of conformer (models) that are submitted for the ensemble.
;
_item.name '_pdbx_nmr_ensemble.conformers_submitted_total_number'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'20'
_item_aliases.alias_name '_rcsb_nmr_ensemble.conformers_submitted_total_number'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.conformer_selection_criteria
_item_description.description
;
By highlighting the appropriate choice(s), describe how the submitted
conformer (models) were selected.
;
_item.name '_pdbx_nmr_ensemble.conformer_selection_criteria'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'structures with the lowest energy'
'structures with the least restraint violations'
'structures with acceptable covalent geometry'
'structures with favorable non-bond energy'
'target function'
'back calculated data agree with experimental NOESY spectrum'
'all calculated structures submitted'
; The submitted conformer models are the 25 structures with the lowest
energy.
;
; The submitted conformer models are those with the fewest number of
constraint violations.
;
_item_aliases.alias_name '_rcsb_nmr_ensemble.conformer_selection_criteria'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.representative_conformer
_item_description.description
; The number of the conformer identified as most representative.
;
_item.name '_pdbx_nmr_ensemble.representative_conformer'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'20'
_item_aliases.alias_name '_rcsb_nmr_ensemble.representative_conformer'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.average_constraints_per_residue
_item_description.description
; The average number of constraints per residue for the ensemble
;
_item.name '_pdbx_nmr_ensemble.average_constraints_per_residue'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'30.2'
_item_aliases.alias_name '_rcsb_nmr_ensemble.average_constraints_per_residue'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.average_constraint_violations_per_residue
_item_description.description
; The average number of constraint violations on a per residue basis for
the ensemble.
;
_item.name '_pdbx_nmr_ensemble.average_constraint_violations_per_residue'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
'0.25'
_item_aliases.alias_name '_rcsb_nmr_ensemble.average_constraint_violations_per_residue'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.maximum_distance_constraint_violation
_item_description.description
; The maximum distance constraint violation for the ensemble.
;
_item.name '_pdbx_nmr_ensemble.maximum_distance_constraint_violation'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_examples.case
'0.4'
_item_aliases.alias_name '_rcsb_nmr_ensemble.maximum_distance_constraint_violation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.average_distance_constraint_violation
_item_description.description
; The average distance restraint violation for the ensemble.
;
_item.name '_pdbx_nmr_ensemble.average_distance_constraint_violation'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_examples.case
'0.11'
_item_aliases.alias_name '_rcsb_nmr_ensemble.average_distance_constraint_violation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation
_item_description.description
; The maximum upper distance constraint violation for the ensemble.
;
_item.name '_pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_examples.case
'0.4'
_item_aliases.alias_name '_rcsb_nmr_ensemble.maximum_upper_distance_constraint_violation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation
_item_description.description
; The maximum lower distance constraint violation for the ensemble.
;
_item.name '_pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_examples.case
'0.3'
_item_aliases.alias_name '_rcsb_nmr_ensemble.maximum_lower_distance_constraint_violation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.distance_constraint_violation_method
_item_description.description
; Describe the method used to calculate the distance constraint violation statistics,
i.e. are they calculated over all the distance constraints or calculated for
violations only?
;
_item.name '_pdbx_nmr_ensemble.distance_constraint_violation_method'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'Statistics were calculated over all of the distance constraints.'
'Statistics were calculated for violations only'
_item_aliases.alias_name '_rcsb_nmr_ensemble.distance_constraint_violation_method'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation
_item_description.description
; The maximum torsion angle constraint violation for the ensemble.
;
_item.name '_pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
loop_
_item_examples.case
'4'
_item_aliases.alias_name '_rcsb_nmr_ensemble.maximum_torsion_angle_constraint_violation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.average_torsion_angle_constraint_violation
_item_description.description
; The average torsion angle constraint violation for the ensemble.
;
_item.name '_pdbx_nmr_ensemble.average_torsion_angle_constraint_violation'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
loop_
_item_examples.case
'2.4'
_item_aliases.alias_name '_rcsb_nmr_ensemble.average_torsion_angle_constraint_violation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble.torsion_angle_constraint_violation_method
_item_description.description
; This item describes the method used to calculate the torsion angle constraint violation statistics.
i.e. are the entered values based on all torsion angle or calculated for violations only?
;
_item.name '_pdbx_nmr_ensemble.torsion_angle_constraint_violation_method'
_item.category_id pdbx_nmr_ensemble
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'Statistics were calculated over all the torsion angle constraints.'
'Statistics were calculated for torsion angle constraints violations only.'
_item_aliases.alias_name '_rcsb_nmr_ensemble.torsion_angle_constraint_violation_method'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
### ##########################################################################
###
save_pdbx_nmr_ensemble_rms
_category.description
; Structural statistics are derived from molecular dynamics and simulated annealing
programs.
;
_category.id pdbx_nmr_ensemble_rms
_category.mandatory_code no
_category_key.name '_pdbx_nmr_ensemble_rms.entry_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; This example is derived from the MCP-1 structure calculation statistics.
For this structure the statistics were calculated over residues 5-69 for
both the monomer and dimer .
;
#
;
loop_
_pdbx_nmr_ensemble_rms.entry_id
_pdbx_nmr_ensemble_rms.residue_range_begin
_pdbx_nmr_ensemble_rms.chain_range_begin
_pdbx_nmr_ensemble_rms.residue_range_end
_pdbx_nmr_ensemble_rms.chain_range_end
_pdbx_nmr_ensemble_rms.atom_type
_pdbx_nmr_ensemble_rms.distance_rms_dev
_pdbx_nmr_ensemble_rms.distance_rms_dev_error
1ABC 5 A 69 A 'all heavy atoms' 0.22 0.06
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_nmr_ensemble_rms.entry_id
_item_description.description
; '?'
;
_item.name '_pdbx_nmr_ensemble_rms.entry_id'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_nmr_ensemble_rms.entry_id'
_item_linked.parent_name '_entry.id'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.residue_range_begin
_item_description.description
; Structure statistics are often calculated only over the well-ordered region(s)
of the biopolymer. Portions of the macromolecule are often mobile and
disordered, hence they are excluded in calculating the statistics. To define
the range(s) over which the statistics are calculated, enter the beginning
residue number(s): e.g. if the regions used were 5-32 and 41-69, enter 5,41
;
_item.name '_pdbx_nmr_ensemble_rms.residue_range_begin'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
5 41
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.residue_range_begin'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.chain_range_begin
_item_description.description
; The beginning chain id.
;
_item.name '_pdbx_nmr_ensemble_rms.chain_range_begin'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code code
_item_examples.case A
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.chain_range_begin'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.residue_range_end
_item_description.description
; The ending residue number: e.g. 32,69.
;
_item.name '_pdbx_nmr_ensemble_rms.residue_range_end'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code int
loop_
_item_examples.case
32 69
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.residue_range_end'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.chain_range_end
_item_description.description
; The ending chain id:
;
_item.name '_pdbx_nmr_ensemble_rms.chain_range_end'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code code
_item_examples.case A
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.chain_range_end'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.atom_type
_item_description.description
; Statistics are often calculated over only some of the atoms,
e.g. backbone, or heavy atoms. Describe which type of atoms are used for
the statistical analysis.
;
_item.name '_pdbx_nmr_ensemble_rms.atom_type'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'backbone atoms'
'heavy atoms'
loop_
_item_enumeration.value
'backbone heavy atoms'
'side chain heavy atoms'
'all heavy atoms'
'all atoms'
'all backbone atoms'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.atom_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.distance_rms_dev
_item_description.description
; The distance rmsd to the mean structure for the ensemble of structures.
;
_item.name '_pdbx_nmr_ensemble_rms.distance_rms_dev'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_examples.case
'0.22'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.distance_rms_dev'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.distance_rms_dev_error
_item_description.description
; The error in the distance rmsd.
;
_item.name '_pdbx_nmr_ensemble_rms.distance_rms_dev_error'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_examples.case
'0.07'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.distance_rms_dev_error'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.covalent_bond_rms_dev
_item_description.description
; The covalent bond rmsd to the target value for the ensemble.
;
_item.name '_pdbx_nmr_ensemble_rms.covalent_bond_rms_dev'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_examples.case
'0.0066'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.covalent_bond_rms_dev'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.covalent_bond_rms_dev_error
_item_description.description
; The error in the covalent bond rmsd.
;
_item.name '_pdbx_nmr_ensemble_rms.covalent_bond_rms_dev_error'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_examples.case
'0.0001'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.covalent_bond_rms_dev_error'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.bond_angle_rms_dev
_item_description.description
; The bond angle rmsd to the target values for the ensemble.
;
_item.name '_pdbx_nmr_ensemble_rms.bond_angle_rms_dev'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
loop_
_item_examples.case
'0.60'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.bond_angle_rms_dev'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.bond_angle_rms_dev_error
_item_description.description
; The error in the bond angle rmsd.
;
_item.name '_pdbx_nmr_ensemble_rms.bond_angle_rms_dev_error'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
loop_
_item_examples.case
'0.01'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.bond_angle_rms_dev_error'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev
_item_description.description
; The improper torsion angle rmsd to the target values for the ensemble.
;
_item.name '_pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
loop_
_item_examples.case
'0.64'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.improper_torsion_angle_rms_dev'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev_error
_item_description.description
; The error in the improper torsion angle rmsd.
;
_item.name '_pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev_error'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
loop_
_item_examples.case
'0.04'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.improper_torsion_angle_rms_dev_error'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev
_item_description.description
; The peptide planarity rmsd.
;
_item.name '_pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_examples.case
'0.11'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.peptide_planarity_rms_dev'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev_error
_item_description.description
; The error in the peptide planarity rmsd.
;
_item.name '_pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev_error'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
loop_
_item_examples.case
'0.05'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.peptide_planarity_rms_dev_error'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev
_item_description.description
; The dihedral angle rmsd to the target values for the ensemble.
;
_item.name '_pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
loop_
_item_examples.case
'0.66'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.dihedral_angles_rms_dev'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev_error
_item_description.description
; The error of the rmsd dihedral angles.
;
_item.name '_pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev_error'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
loop_
_item_examples.case
'0.07'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.dihedral_angles_rms_dev_error'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_ensemble_rms.coord_average_rmsd_method
_item_description.description
; Describe the method for calculating the coordinate average rmsd.
;
_item.name '_pdbx_nmr_ensemble_rms.coord_average_rmsd_method'
_item.category_id pdbx_nmr_ensemble_rms
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'Replace with item example text'
_item_aliases.alias_name '_rcsb_nmr_ensemble_rms.coord_average_rmsd_method'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
### ##########################################################################
###
save_pdbx_nmr_representative
_category.description
; An average structure is often calculated in addition to the ensemble, or one
of the ensemble is selected as a representative structure. This section
describes selection of the representative structure.
;
_category.id pdbx_nmr_representative
_category.mandatory_code no
_category_key.name '_pdbx_nmr_representative.entry_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; This example is drawn from the MCP-1 structure.
;
#
;
_pdbx_nmr_representative.entry_id 1ABC
_pdbx_nmr_representative.conformer_id 15
_pdbx_nmr_representative.selection_criteria 'lowest energy'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_nmr_representative.entry_id
_item_description.description
; msd will assign the ID.
;
_item.name '_pdbx_nmr_representative.entry_id'
_item.category_id pdbx_nmr_representative
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_nmr_representative.entry_id'
_item_linked.parent_name '_entry.id'
_item_aliases.alias_name '_rcsb_nmr_representative.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_representative.conformer_id
_item_description.description
; If a member of the ensemble has been selected as a representative
structure, identify it by its model number.
;
_item.name '_pdbx_nmr_representative.conformer_id'
_item.category_id pdbx_nmr_representative
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'15'
_item_aliases.alias_name '_rcsb_nmr_representative.conformer_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_representative.selection_criteria
_item_description.description
;
By highlighting the appropriate choice(s), describe the criteria used to
select this structure as a representative structure, or if an average
structure has been calculated describe how this was done.
;
_item.name '_pdbx_nmr_representative.selection_criteria'
_item.category_id pdbx_nmr_representative
_item.mandatory_code no
_item_type.code line
# loop_
# _item_enumeration.value
# 'closest to the average'
# 'lowest energy'
# 'fewest violations'
# 'minimized average structure'
_item_examples.case
;
The structure closest to the average.
The structure with the lowest energy was selected.
The structure with the fewest number of violations was selected.
A minimized average structure was calculated.
;
_item_aliases.alias_name '_rcsb_nmr_representative.selection_criteria'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save_pdbx_nmr_refine
_category.description
;
Describe the method and details of the refinement of the deposited structure.
;
_category.id pdbx_nmr_refine
_category.mandatory_code no
_category_key.name '_pdbx_nmr_refine.entry_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; This example is drawn from the MCP-1 structure.
;
;
loop_
_pdbx_nmr_refine.entry_id
_pdbx_nmr_refine.method
1ABC 'torsion angle dynamics'
;
save_
save__pdbx_nmr_refine.entry_id
_item_description.description
; You can leave this blank as an ID will be assigned by the RCSB
to the constraint file.
;
_item.name '_pdbx_nmr_refine.entry_id'
_item.category_id pdbx_nmr_refine
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_nmr_refine.entry_id'
_item_linked.parent_name '_entry.id'
_item_aliases.alias_name '_rcsb_nmr_refine.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_refine.method
_item_description.description
; The method used to determine the structure.
;
_item.name '_pdbx_nmr_refine.method'
_item.category_id pdbx_nmr_refine
_item.mandatory_code yes
_item_type.code text
_item_examples.case
;
distance geometry
simulated annealing
molecular dynamics
matrix relaxation
torsion angle dynamics
;
_item_aliases.alias_name '_rcsb_nmr_refine.method'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_refine.details
_item_description.description
; Additional details about the NMR refinement.
;
_item.name '_pdbx_nmr_refine.details'
_item.category_id pdbx_nmr_refine
_item.mandatory_code no
_item_type.code text
_item_examples.case
;
Additional comments about the NMR refinement can be placed here, e.g.
the structures are based on a total of 3344 restraints, 3167 are NOE-derived
distance constraints, 68 dihedral angle restraints,109 distance restraints
from hydrogen bonds.
;
_item_aliases.alias_name '_rcsb_nmr_refine.details'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
##
save_pdbx_nmr_force_constants
_category.description
;
The final force constants, including units, employed for the various
experimental constraints, covalent geometry constraints, and the non-bonded
interaction terms in the target function used for simulated annealing.
;
_category.id pdbx_nmr_force_constants
_category.mandatory_code no
loop_
_category_key.name
'_pdbx_nmr_force_constants.entry_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - -
;
This example is taken from a study of BAF, a dimeric DNA binding protein.
The final force constants in the target function used for simulated
annealing are: Experimental Constraint terms: Distance (NOE,H-bonds),
Torsion angles, J coupling, 13C shifts, 1H shifts, Dipolar coupling,
D isotope shifts Covalent Geometry Constraint terms: Bond lengths,
Angles, Impropers Non-bonded Interaction terms: van der Waals,
Type of van der Waals term, Conformational database potential,
Radius of gyration.
;
#
;
_pdbx_nmr_force_constants.entry_id 1ABC
_pdbx_nmr_force_constants.exptl_distance_term 30.
_pdbx_nmr_force_constants.exptl_distance_term_units 'kcal/mol/A**2'
_pdbx_nmr_force_constants.exptl_torsion_angles_term 200.
_pdbx_nmr_force_constants.exptl_torsion_angles_term_units 'kcal/mol/rad**2'
_pdbx_nmr_force_constants.exptl_J_coupling_term 1.
_pdbx_nmr_force_constants.exptl_J_coupling_term_units 'kcal/mol/Hz**2'
_pdbx_nmr_force_constants.exptl_13C_shift_term 0.5
_pdbx_nmr_force_constants.exptl_13C_shift_term_units 'kcal/mol/ppm**2'
_pdbx_nmr_force_constants.exptl_1H_shift_term 7.5
_pdbx_nmr_force_constants.exptl_1H_shift_term_units 'kcal/mol/ppm**2'
_pdbx_nmr_force_constants.covalent_geom_bond_term 1000.
_pdbx_nmr_force_constants.covalent_geom_bond_term_units 'kcal/mol/A**2'
_pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_type 4.
_pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_type_units 'kcal/mol/A**4'
;
save_
save__pdbx_nmr_force_constants.entry_id
_item_description.description
; You can leave this blank as an ID will be assigned by the RCSB.
;
_item.name '_pdbx_nmr_force_constants.entry_id'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_nmr_force_constants.entry_id'
_item_linked.parent_name '_entry.id'
_item_aliases.alias_name '_rcsb_nmr_force_constants.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.exptl_distance_term
_item_description.description
; The final force constant for distance (NOEs) constraints
term employed in the target function used for simulated annealing.
;
_item.name '_pdbx_nmr_force_constants.exptl_distance_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '30'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_distance_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__pdbx_nmr_force_constants.exptl_distance_term_units
_item_description.description
; The units for the force constant for the distance
constraints term.
;
_item.name '_pdbx_nmr_force_constants.exptl_distance_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/ A**2'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/A**2' 'kilocalories per mole per square angstrom'
'kJ/mol/nm**2' 'kilojoules per mole per square nanometer'
'other' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_distance_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.exptl_torsion_angles_term
_item_description.description
; The final force constant for the torsion angle term employed in
the target function used for simulated annealing.
;
_item.name '_pdbx_nmr_force_constants.exptl_torsion_angles_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '200'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_torsion_angles_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.exptl_torsion_angles_term_units
_item_description.description
; The units for the force constant for the torsion angle
constraints term.
;
_item.name '_pdbx_nmr_force_constants.exptl_torsion_angles_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/rad**2'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/rad**2' 'kilocalories per mole per square radian'
'kJ/mol/rad**2' 'kilojoules per mole per square radian'
'author' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_torsion_angles_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__pdbx_nmr_force_constants.exptl_J_coupling_term
_item_description.description
; The final force constant for J coupling term employed in the
target function used for simulated annealing.
;
_item.name '_pdbx_nmr_force_constants.exptl_J_coupling_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '1'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_J_coupling_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.exptl_J_coupling_term_units
_item_description.description
; The units for the force constant for the J coupling term.
;
_item.name '_pdbx_nmr_force_constants.exptl_J_coupling_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/Hz**2'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/Hz**2' 'kilocalories per mole per square angstrom'
'kJ/mol/Hz**2' 'kilojoules per mole per square nanometer'
'other' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_J_coupling_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.exptl_13C_shift_term
_item_description.description
; The final force constant for 13C shift constraints term employed
in the target function used for simulated annealing.
;
_item.name '_pdbx_nmr_force_constants.exptl_13C_shift_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '0.5'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_13C_shift_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.exptl_13C_shift_term_units
_item_description.description
; The units for the force constant for the 13C shift constraints
term.
;
_item.name '_pdbx_nmr_force_constants.exptl_13C_shift_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/ppm**2'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/ppm**2' 'kilocalories per mole per part per million squared'
'kJ/mol/ppm**2' 'kilojoules per mole per part per million squared'
'other' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_13C_shift_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save__pdbx_nmr_force_constants.exptl_1H_shift_term
_item_description.description
; The final force constant for 1H shift constraints term employed
in the target function used for simulated annealing.
;
_item.name '_pdbx_nmr_force_constants.exptl_1H_shift_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '7.5'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_1H_shift_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.exptl_1H_shift_term_units
_item_description.description
; The units for the force constant for the 1H shift constraints term.
;
_item.name '_pdbx_nmr_force_constants.exptl_1H_shift_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/ppm**2'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/ppm**2' 'kilocalories per mole per part per million squared'
'kJ/mol/ppm**2' 'kilojoules per mole per part per million squared'
'other' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_1H_shift_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.exptl_dipolar_coupling_term
_item_description.description
; The final force constant for dipolar coupling constraint term
employed in the target function used for simulated annealing.
;
_item.name '_pdbx_nmr_force_constants.exptl_dipolar_coupling_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '1'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_dipolar_coupling_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.exptl_dipolar_coupling_term_units
_item_description.description
; The units for the force constant for the dipolar coupling
constraints term.
;
_item.name '_pdbx_nmr_force_constants.exptl_dipolar_coupling_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/Hz**2'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/Hz**2' 'kilocalories per mole per Hertz squared'
'kJ/mol/Hz**2' 'kilojoules per mole per Hertz squared'
'other' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_dipolar_coupling_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.exptl_D_isotope_shift_term
_item_description.description
; The final force constant for Deuterium isotope shift constraints
term employed in the target function used for simulated annealing.
;
_item.name '_pdbx_nmr_force_constants.exptl_D_isotope_shift_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '0.5'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_D_isotope_shift_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
###
### NEXT
save__pdbx_nmr_force_constants.exptl_D_isotope_shift_term_units
_item_description.description
; The units for the force constant for the Deuterium isotope
shift constraints term.
;
_item.name '_pdbx_nmr_force_constants.exptl_D_isotope_shift_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/ppb**2'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/ppb**2' 'kilocalories per mole per part per billion squared'
'kJ/mol/ppb**2' 'kilojoules per mole per part per billion squared'
'other' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.exptl_D_isotope_shift_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.covalent_geom_bond_term
_item_description.description
; The final force constant for the covalent geometry bond length
constraints term employed in the target function used for simulated
annealing.
;
_item.name '_pdbx_nmr_force_constants.covalent_geom_bond_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '1000'
_item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_bond_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.covalent_geom_bond_term_units
_item_description.description
; The units for the force constant for the covalent geometry bond
length constraints term.
;
_item.name '_pdbx_nmr_force_constants.covalent_geom_bond_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/A**2'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/A**2' 'kilocalories per mole per square angstrom'
'kJ/mol/nm**2' 'kilojoules per mole per square nanometer'
'other' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_bond_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.covalent_geom_angles_term
_item_description.description
; The final force constant for covalent geometry angle constraints
term employed in the target function used for simulated annealing.
;
_item.name '_pdbx_nmr_force_constants.covalent_geom_angles_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '500'
_item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_angles_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.covalent_geom_angles_term_units
_item_description.description
; The units for the force constant for the covalent geometry angle
constraints term.
;
_item.name '_pdbx_nmr_force_constants.covalent_geom_angles_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/rad**2'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/rad**2' 'kilocalories per mole per radian squared'
'kJ/mol/rad**2' 'kilojoules per mole per radian squared'
'other' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_angles_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.covalent_geom_impropers_term
_item_description.description
; The final force constant for covalent geometry impropers
contstraints term employed in the target function used for simulated
annealing.
;
_item.name '_pdbx_nmr_force_constants.covalent_geom_impropers_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '500'
_item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_impropers_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.covalent_geom_impropers_term_units
_item_description.description
; The units for the force constant for the covalent geometry
impropers constraints term.
;
_item.name '_pdbx_nmr_force_constants.covalent_geom_impropers_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/rad**2'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/rad**2' 'kilocalories per mole per radian squared'
'kJ/mol/rad**2' 'kilojoules per mole per radian squared'
'other' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.covalent_geom_impropers_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_type
_item_description.description
; The type of van der Waals term employed in the target function
used for simulated annealing.
;
_item.name '_pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_type'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'quartic'
loop_
_item_enumeration.value 'quartic' 'other'
_item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_van_der_Waals_term_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term
_item_description.description
; The force constant used for the non-bonded interaction van der Waals
term employed in the target function used for simulated annealing.
;
_item.name '_pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '4'
_item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_van_der_Waals_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_units
_item_description.description
; The units for the force constant for the van der Waals term.
;
_item.name '_pdbx_nmr_force_constants.non-bonded_inter_van_der_Waals_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/ A**4'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/A**4' 'kilocalories per mole per Angstrom to the 4th power'
'kJ/mol/nm**4' 'kilojoules per mole per nanometer to the 4th power'
'other' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_van_der_Waals_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.non-bonded_inter_conf_db_potential_term
_item_description.description
; The force constant used for the non-bonded interaction conformational
database potential term employed in the target function used for simulated
annealing.
;
_item.name '_pdbx_nmr_force_constants.non-bonded_inter_conf_db_potential_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '1.0'
_item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_conf_db_potential_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term
_item_description.description
; The force constant used for the non-bonded interaction radius of
gyration term employed in the target function used for simulated annealing.
;
_item.name '_pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code float
loop_
_item_examples.case '100'
_item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_radius_of_gyration_term'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term_units
_item_description.description
; The units for the force constant for the radius of gyration term.
;
_item.name '_pdbx_nmr_force_constants.non-bonded_inter_radius_of_gyration_term_units'
_item.category_id pdbx_nmr_force_constants
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case 'kcal/mol/ A**2'
loop_
_item_enumeration.value
_item_enumeration.detail
'kcal/mol/ A**2' 'kilocalories per mole per square Angstrom'
'kJ/mol/ nm**4' 'kilojoules per mole per square nanometer'
'other' 'author added units'
_item_aliases.alias_name '_rcsb_nmr_force_constants.non-bonded_inter_radius_of_gyration_term_units'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
### EOF mmcif_pdbx-def-2.dic###########################################################################
#
# File: mmcif_pdbx-def-4.dic
#
# PDB Exchange Data Dictionary
#
# This data dictionary contains definitions used by wwPDB for data exchange
# and data processing.
#
# Definition Section 4
#
#
###########################################################################
##
## Additional aliases required only for NDB/RCSB use:
##
save__refine.overall_SU_B
# _item.name '_refine.overall_SU_B'
# _item.category_id refine
# _item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_overall_ESU_B'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
# _item_type.code float
save_
save__refine.overall_SU_ML
# _item.name '_refine.overall_SU_ML'
# _item.category_id refine
# _item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_overall_ESU_ML'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
# _item_type.code float
save_
save__refine_hist.number_atoms_solvent
# _item.name '_refine_hist.number_atoms_solvent'
# _item.category_id refine_hist
# _item.mandatory_code no
_item_aliases.alias_name '_refine_hist.rcsb_number_atoms_solvent'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
# _item_type.code int
save_
save__refine_hist.number_atoms_total
# _item.name '_refine_hist.number_atoms_total'
# _item.category_id refine_hist
# _item.mandatory_code no
_item_aliases.alias_name '_refine_hist.rcsb_number_atoms_total'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
# _item_type.code int
save_
##
## NDB Specific definitions
##
##########################
## NDB_STRUCT_CONF_NA ##
##########################
save_ndb_struct_conf_na
_category.description
; Data items in the NDB_STRUCT_CONF_NA category
describes secondary structure features in this entry.
;
_category.id ndb_struct_conf_na
_category.mandatory_code no
loop_
_category_key.name '_ndb_struct_conf_na.entry_id'
'_ndb_struct_conf_na.feature'
loop_
_category_group.id 'inclusive_group'
'struct_group'
'ndb_group'
_ndb_category_examples.case
;
loop_
_ndb_struct_conf_na.entry_id
_ndb_struct_conf_na.feature
_ndb_struct_conf_na.feature_count
rcsb000001 'double helix' 1
rcsb000001 'b-form double helix' 1
rcsb000001 'quadruple helix' 1
;
save_
save__ndb_struct_conf_na.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the
ENTRY category.
;
_item.name '_ndb_struct_conf_na.entry_id'
_item.category_id ndb_struct_conf_na
_item.mandatory_code yes
_item_linked.child_name '_ndb_struct_conf_na.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__ndb_struct_conf_na.feature
_item_description.description
; This data item identifies a secondary structure
feature of this entry.
;
_item.name '_ndb_struct_conf_na.feature'
_item.category_id ndb_struct_conf_na
_item.mandatory_code yes
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'double helix' .
'a-form double helix' .
'b-form double helix' .
'z-form double helix' .
'other right-handed double helix' .
'triple helix' .
'quadruple helix' .
'parallel strands' .
'internal loop' .
'bulge loop' .
'tetraloop' .
'hairpin loop' .
'two-way junction' .
'three-way junction' .
'four-way junction' .
'mismatched base pair' .
save_
save__ndb_struct_conf_na.feature_count
_item_description.description
; This data item counts the number of occurences of
this feature in this entry.
;
_item.name '_ndb_struct_conf_na.feature_count'
_item.category_id ndb_struct_conf_na
_item.mandatory_code no
_item_type.code int
save_
#############################
## NDB_STRUCT_FEATURE_NA ##
#############################
save_ndb_struct_feature_na
_category.description
; Data items in the NDB_STRUCT_FEATURE_NA category
describes tertiary and other special structural
features in this entry.
;
_category.id ndb_struct_feature_na
_category.mandatory_code no
loop_
_category_key.name '_ndb_struct_feature_na.entry_id'
'_ndb_struct_feature_na.feature'
loop_
_category_group.id 'inclusive_group'
'struct_group'
'ndb_group'
_ndb_category_examples.case
;
loop_
_ndb_struct_feature_na.entry_id
_ndb_struct_feature_na.feature
_ndb_struct_feature_na.feature_count
rcsb000001 'intercalated base' 1
rcsb000001 'bent/kinked double helix' 1
;
save_
save__ndb_struct_feature_na.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the
ENTRY category.
;
_item.name '_ndb_struct_feature_na.entry_id'
_item.category_id ndb_struct_feature_na
_item.mandatory_code yes
_item_linked.child_name '_ndb_struct_feature_na.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__ndb_struct_feature_na.feature
_item_description.description
; This data item identifies a structural
feature of this entry.
;
_item.name '_ndb_struct_feature_na.feature'
_item.category_id ndb_struct_feature_na
_item.mandatory_code yes
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'pseudoknot' .
'intercalated base' .
'backbone turn' .
'intramolecular base triplet' .
'ribose zipper' .
'purine platform' .
'bent/kinked double helix' .
save_
save__ndb_struct_feature_na.feature_count
_item_description.description
; This data item counts the number of occurences of
this feature in this entry.
;
_item.name '_ndb_struct_feature_na.feature_count'
_item.category_id ndb_struct_feature_na
_item.mandatory_code no
_item_type.code int
save_
#############################
## NDB_STRUCT_NA_BASE_PAIR ##
#############################
save_ndb_struct_na_base_pair
_category.description
; Data items in the NDB_STRUCT_NA_BASE_PAIR category record details
of base pairing interactions.
;
_category.id ndb_struct_na_base_pair
_category.mandatory_code no
loop_
_category_key.name '_ndb_struct_na_base_pair.model_number'
'_ndb_struct_na_base_pair.i_label_comp_id'
'_ndb_struct_na_base_pair.i_label_asym_id'
'_ndb_struct_na_base_pair.i_label_seq_id'
'_ndb_struct_na_base_pair.i_symmetry'
'_ndb_struct_na_base_pair.j_label_comp_id'
'_ndb_struct_na_base_pair.j_label_asym_id'
'_ndb_struct_na_base_pair.j_label_seq_id'
'_ndb_struct_na_base_pair.j_symmetry'
loop_
_category_group.id 'inclusive_group'
'struct_group'
'ndb_group'
loop_
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_ndb_struct_na_base_pair.model_number
_ndb_struct_na_base_pair.i_label_comp_id
_ndb_struct_na_base_pair.i_label_asym_id
_ndb_struct_na_base_pair.i_label_seq_id
_ndb_struct_na_base_pair.i_symmetry
_ndb_struct_na_base_pair.j_label_comp_id
_ndb_struct_na_base_pair.j_label_asym_id
_ndb_struct_na_base_pair.j_label_seq_id
_ndb_struct_na_base_pair.j_symmetry
_ndb_struct_na_base_pair.shear
_ndb_struct_na_base_pair.stretch
_ndb_struct_na_base_pair.stagger
_ndb_struct_na_base_pair.buckle
_ndb_struct_na_base_pair.propeller
_ndb_struct_na_base_pair.opening
1 G A 1 1_555 C A 8 7_555 -0.396 -0.156 -0.018 -5.523 -6.752 -3.291
1 G A 2 1_555 C A 7 7_555 -0.094 -0.220 -0.334 -4.727 -9.765 2.311
1 G A 3 1_555 C A 6 7_555 -0.285 -0.239 0.008 -6.454 -12.575 -1.181
# ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__ndb_struct_na_base_pair.model_number
_item_description.description
;
Describes the model number of the the base pair.
This data item is a pointer to _atom_site.ndb_model in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.model_number'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair.model_number'
_item_linked.parent_name '_atom_site.pdbx_PDB_model_num'
save_
save__ndb_struct_na_base_pair.pair_number
_item_description.description
;
Sequential number of pair in the pair sequence.
;
_item.name '_ndb_struct_na_base_pair.pair_number'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code int
save_
save__ndb_struct_na_base_pair.pair_name
_item_description.description
;
Text label for this base pair.
;
_item.name '_ndb_struct_na_base_pair.pair_name'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code line
save_
save__ndb_struct_na_base_pair.i_label_asym_id
_item_description.description
;
Describes the asym id of the i-th base in the base pair.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.i_label_asym_id'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair.i_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
save_
save__ndb_struct_na_base_pair.i_label_comp_id
_item_description.description
;
Describes the component id of the i-th base in the base pair.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.i_label_comp_id'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair.i_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
save_
save__ndb_struct_na_base_pair.i_label_seq_id
_item_description.description
;
Describes the sequence number of the i-th base in the base pair.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.i_label_seq_id'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair.i_label_seq_id'
_item_linked.parent_name '_atom_site.label_seq_id'
save_
save__ndb_struct_na_base_pair.i_symmetry
_item_description.description
; Describes the symmetry operation that should be applied to the
coordinates of the i-th base to generate the first partner
in the base pair.
;
_item.name '_ndb_struct_na_base_pair.i_symmetry'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__ndb_struct_na_base_pair.j_label_asym_id
_item_description.description
;
Describes the asym id of the j-th base in the base pair.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.j_label_asym_id'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair.j_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
save_
save__ndb_struct_na_base_pair.j_label_comp_id
_item_description.description
;
Describes the component id of the j-th base in the base pair.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.j_label_comp_id'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair.j_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
save_
save__ndb_struct_na_base_pair.j_label_seq_id
_item_description.description
;
Describes the sequence number of the j-th base in the base pair.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.j_label_seq_id'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair.j_label_seq_id'
_item_linked.parent_name '_atom_site.label_seq_id'
save_
save__ndb_struct_na_base_pair.j_symmetry
_item_description.description
; Describes the symmetry operation that should be applied to the
coordinates of the j-th base to generate the second partner
in the base pair.
;
_item.name '_ndb_struct_na_base_pair.j_symmetry'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__ndb_struct_na_base_pair.i_auth_asym_id
_item_description.description
;
Describes the asym id of the i-th base in the base pair.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.i_auth_asym_id'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair.i_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
save_
save__ndb_struct_na_base_pair.i_auth_seq_id
_item_description.description
;
Describes the sequence number of the i-th base in the base pair.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.i_auth_seq_id'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair.i_auth_seq_id'
_item_linked.parent_name '_atom_site.auth_seq_id'
save_
save__ndb_struct_na_base_pair.i_PDB_ins_code
_item_description.description
;
Describes the PDB insertion code of the i-th base in the base pair.
This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.i_PDB_ins_code'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
# _item_linked.child_name '_ndb_struct_na_base_pair.i_PDB_ins_code'
# _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
save_
save__ndb_struct_na_base_pair.j_auth_asym_id
_item_description.description
;
Describes the asym id of the j-th base in the base pair.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.j_auth_asym_id'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair.j_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
save_
save__ndb_struct_na_base_pair.j_auth_seq_id
_item_description.description
;
Describes the sequence number of the j-th base in the base pair.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.j_auth_seq_id'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair.j_auth_seq_id'
_item_linked.parent_name '_atom_site.auth_seq_id'
save_
save__ndb_struct_na_base_pair.j_PDB_ins_code
_item_description.description
;
Describes the PDB insertion code of the j-th base in the base pair.
This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair.j_PDB_ins_code'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code yes
_item_type.code code
# _item_linked.child_name '_ndb_struct_na_base_pair.j_PDB_ins_code'
# _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
save_
save__ndb_struct_na_base_pair.shear
_item_description.description
;
The value of the base pair shear parameter.
;
_item.name '_ndb_struct_na_base_pair.shear'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair.stretch
_item_description.description
;
The value of the base pair stretch parameter.
;
_item.name '_ndb_struct_na_base_pair.stretch'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair.stagger
_item_description.description
;
The value of the base pair stagger parameter.
;
_item.name '_ndb_struct_na_base_pair.stagger'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair.buckle
_item_description.description
;
The value of the base pair buckle parameter.
;
_item.name '_ndb_struct_na_base_pair.buckle'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair.propeller
_item_description.description
;
The value of the base pair propeller parameter.
;
_item.name '_ndb_struct_na_base_pair.propeller'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair.opening
_item_description.description
;
The value of the base pair opening parameter.
;
_item.name '_ndb_struct_na_base_pair.opening'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair.hbond_type_12
_item_description.description
;
Base pair classification of Westhoff and Leontis.
;
_item.name '_ndb_struct_na_base_pair.hbond_type_12'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code no
_item_type.code int
save_
save__ndb_struct_na_base_pair.hbond_type_28
_item_description.description
;
Base pair classification of Saenger
;
_item.name '_ndb_struct_na_base_pair.hbond_type_28'
_item.category_id ndb_struct_na_base_pair
_item.mandatory_code no
_item_type.code int
save_
##################################
## NDB_STRUCT_NA_BASE_PAIR_STEP ##
##################################
save_ndb_struct_na_base_pair_step
_category.description
; Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details
of base pair step interactions.
;
_category.id ndb_struct_na_base_pair_step
_category.mandatory_code no
loop_
_category_key.name '_ndb_struct_na_base_pair_step.model_number'
'_ndb_struct_na_base_pair_step.i_label_comp_id_1'
'_ndb_struct_na_base_pair_step.i_label_asym_id_1'
'_ndb_struct_na_base_pair_step.i_label_seq_id_1'
'_ndb_struct_na_base_pair_step.i_symmetry_1'
'_ndb_struct_na_base_pair_step.j_label_comp_id_1'
'_ndb_struct_na_base_pair_step.j_label_asym_id_1'
'_ndb_struct_na_base_pair_step.j_label_seq_id_1'
'_ndb_struct_na_base_pair_step.j_symmetry_1'
'_ndb_struct_na_base_pair_step.i_label_comp_id_2'
'_ndb_struct_na_base_pair_step.i_label_asym_id_2'
'_ndb_struct_na_base_pair_step.i_label_seq_id_2'
'_ndb_struct_na_base_pair_step.i_symmetry_2'
'_ndb_struct_na_base_pair_step.j_label_comp_id_2'
'_ndb_struct_na_base_pair_step.j_label_asym_id_2'
'_ndb_struct_na_base_pair_step.j_label_seq_id_2'
'_ndb_struct_na_base_pair_step.j_symmetry_2'
loop_
_category_group.id 'inclusive_group'
'struct_group'
'ndb_group'
loop_
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_ndb_struct_na_base_pair_step.model_number
_ndb_struct_na_base_pair_step.i_label_comp_id_1
_ndb_struct_na_base_pair_step.i_label_asym_id_1
_ndb_struct_na_base_pair_step.i_label_seq_id_1
_ndb_struct_na_base_pair_step.i_symmetry_1
_ndb_struct_na_base_pair_step.j_label_comp_id_1
_ndb_struct_na_base_pair_step.j_label_asym_id_1
_ndb_struct_na_base_pair_step.j_label_seq_id_1
_ndb_struct_na_base_pair_step.j_symmetry_1
_ndb_struct_na_base_pair_step.i_label_comp_id_2
_ndb_struct_na_base_pair_step.i_label_asym_id_2
_ndb_struct_na_base_pair_step.i_label_seq_id_2
_ndb_struct_na_base_pair_step.i_symmetry_2
_ndb_struct_na_base_pair_step.j_label_comp_id_2
_ndb_struct_na_base_pair_step.j_label_asym_id_2
_ndb_struct_na_base_pair_step.j_label_seq_id_2
_ndb_struct_na_base_pair_step.j_symmetry_2
_ndb_struct_na_base_pair_step.shift
_ndb_struct_na_base_pair_step.slide
_ndb_struct_na_base_pair_step.rise
_ndb_struct_na_base_pair_step.tilt
_ndb_struct_na_base_pair_step.roll
_ndb_struct_na_base_pair_step.twist
1 G A 1 1_555 C A 8 7_555 G A 2 1_555 C A 7 7_555 0.369 -1.414 3.339 3.056 9.755 33.530
1 G A 2 1_555 C A 7 7_555 G A 3 1_555 C A 6 7_555 0.176 -1.672 3.371 -1.176 6.725 30.004
# ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__ndb_struct_na_base_pair_step.model_number
_item_description.description
;
Describes the model number of the the base pair step.
This data item is a pointer to _atom_site.ndb_model in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.model_number'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.model_number'
_item_linked.parent_name '_atom_site.pdbx_PDB_model_num'
save_
save__ndb_struct_na_base_pair_step.step_number
_item_description.description
;
The sequence number of this step in the step sequence.
;
_item.name '_ndb_struct_na_base_pair_step.step_number'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code int
save_
save__ndb_struct_na_base_pair_step.step_name
_item_description.description
;
The text name of this step.
;
_item.name '_ndb_struct_na_base_pair_step.step_name'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code line
save_
save__ndb_struct_na_base_pair_step.i_label_asym_id_1
_item_description.description
;
Describes the asym id of the i-th base in the first base pair
of the step.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_label_asym_id_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_asym_id_1'
_item_linked.parent_name '_atom_site.label_asym_id'
save_
save__ndb_struct_na_base_pair_step.i_label_comp_id_1
_item_description.description
;
Describes the component id of the i-th base in the first base pair
of the step.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_label_comp_id_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_comp_id_1'
_item_linked.parent_name '_atom_site.label_comp_id'
save_
save__ndb_struct_na_base_pair_step.i_label_seq_id_1
_item_description.description
;
Describes the sequence number of the i-th base in the first base pair
of the step.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_label_seq_id_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_seq_id_1'
_item_linked.parent_name '_atom_site.label_seq_id'
save_
save__ndb_struct_na_base_pair_step.i_symmetry_1
_item_description.description
; Describes the symmetry operation that should be applied to the
coordinates of the i-th base to generate the first partner
in the first base pair of the step.
;
_item.name '_ndb_struct_na_base_pair_step.i_symmetry_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__ndb_struct_na_base_pair_step.j_label_asym_id_1
_item_description.description
;
Describes the asym id of the j-th base in the first base pair
of the step.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_label_asym_id_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_asym_id_1'
_item_linked.parent_name '_atom_site.label_asym_id'
save_
save__ndb_struct_na_base_pair_step.j_label_comp_id_1
_item_description.description
;
Describes the component id of the j-th base in the first base pair
of the step.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_label_comp_id_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_comp_id_1'
_item_linked.parent_name '_atom_site.label_comp_id'
save_
save__ndb_struct_na_base_pair_step.j_label_seq_id_1
_item_description.description
;
Describes the sequence number of the j-th base in the first base pair
of the step.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_label_seq_id_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_seq_id_1'
_item_linked.parent_name '_atom_site.label_seq_id'
save_
save__ndb_struct_na_base_pair_step.j_symmetry_1
_item_description.description
; Describes the symmetry operation that should be applied to the
coordinates of the j-th base to generate the second partner
in the first base pair of the step.
;
_item.name '_ndb_struct_na_base_pair_step.j_symmetry_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__ndb_struct_na_base_pair_step.i_label_asym_id_2
_item_description.description
;
Describes the asym id of the i-th base in the second base pair
of the step.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_label_asym_id_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_asym_id_2'
_item_linked.parent_name '_atom_site.label_asym_id'
save_
save__ndb_struct_na_base_pair_step.i_label_comp_id_2
_item_description.description
;
Describes the component id of the i-th base in the second base pair
of the step.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_label_comp_id_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_comp_id_2'
_item_linked.parent_name '_atom_site.label_comp_id'
save_
save__ndb_struct_na_base_pair_step.i_label_seq_id_2
_item_description.description
;
Describes the sequence number of the i-th base in the second base pair
of the step.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_label_seq_id_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.i_label_seq_id_2'
_item_linked.parent_name '_atom_site.label_seq_id'
save_
save__ndb_struct_na_base_pair_step.i_symmetry_2
_item_description.description
; Describes the symmetry operation that should be applied to the
coordinates of the i-th base to generate the first partner
in the second base pair of the step.
;
_item.name '_ndb_struct_na_base_pair_step.i_symmetry_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__ndb_struct_na_base_pair_step.j_label_asym_id_2
_item_description.description
;
Describes the asym id of the j-th base in the second base pair
of the step.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_label_asym_id_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_asym_id_2'
_item_linked.parent_name '_atom_site.label_asym_id'
save_
save__ndb_struct_na_base_pair_step.j_label_comp_id_2
_item_description.description
;
Describes the component id of the j-th base in the second base pair
of the step.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_label_comp_id_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_comp_id_2'
_item_linked.parent_name '_atom_site.label_comp_id'
save_
save__ndb_struct_na_base_pair_step.j_label_seq_id_2
_item_description.description
;
Describes the sequence number of the j-th base in the second base pair
of the step.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_label_seq_id_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.j_label_seq_id_2'
_item_linked.parent_name '_atom_site.label_seq_id'
save_
save__ndb_struct_na_base_pair_step.j_symmetry_2
_item_description.description
; Describes the symmetry operation that should be applied to the
coordinates of the j-th base to generate the second partner
in the second base pair of the step.
;
_item.name '_ndb_struct_na_base_pair_step.j_symmetry_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_default.value 1_555
_item_type.code symop
loop_
_item_examples.case
_item_examples.detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
save_
save__ndb_struct_na_base_pair_step.i_auth_asym_id_1
_item_description.description
;
Describes the author's asym id of the i-th base in the first
base pair of the step.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_auth_asym_id_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.i_auth_asym_id_1'
_item_linked.parent_name '_atom_site.auth_asym_id'
save_
save__ndb_struct_na_base_pair_step.i_auth_seq_id_1
_item_description.description
;
Describes the author's sequence number of the i-th base in the
first base pair of the step.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_auth_seq_id_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.i_auth_seq_id_1'
_item_linked.parent_name '_atom_site.auth_seq_id'
save_
save__ndb_struct_na_base_pair_step.i_PDB_ins_code_1
_item_description.description
;
Describes the PDB insertion code of the i-th base in the
first base pair of the step.
This data item is a pointer to _atom_site.pdbx_PDB_ins_code in
the ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_PDB_ins_code_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
# _item_linked.child_name '_ndb_struct_na_base_pair_step.i_PDB_ins_code_1'
# _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
save_
save__ndb_struct_na_base_pair_step.j_auth_asym_id_1
_item_description.description
;
Describes the author's asym id of the j-th base in the first
base pair of the step.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_auth_asym_id_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.j_auth_asym_id_1'
_item_linked.parent_name '_atom_site.auth_asym_id'
save_
save__ndb_struct_na_base_pair_step.j_auth_seq_id_1
_item_description.description
;
Describes the author's sequence number of the j-th base in the
first base pair of the step.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_auth_seq_id_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.j_auth_seq_id_1'
_item_linked.parent_name '_atom_site.auth_seq_id'
save_
save__ndb_struct_na_base_pair_step.j_PDB_ins_code_1
_item_description.description
;
Describes the PDB insertion code of the j-th base in the
first base pair of the step.
This data item is a pointer to _atom_site.pdbx_PDB_ins_code in
the ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_PDB_ins_code_1'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
# _item_linked.child_name '_ndb_struct_na_base_pair_step.j_PDB_ins_code_1'
# _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
save_
save__ndb_struct_na_base_pair_step.i_auth_asym_id_2
_item_description.description
;
Describes the author's asym id of the i-th base in the second
base pair of the step.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_auth_asym_id_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.i_auth_asym_id_2'
_item_linked.parent_name '_atom_site.auth_asym_id'
save_
save__ndb_struct_na_base_pair_step.i_auth_seq_id_2
_item_description.description
;
Describes the author's sequence number of the i-th base in the
second base pair of the step.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_auth_seq_id_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.i_auth_seq_id_2'
_item_linked.parent_name '_atom_site.auth_seq_id'
save_
save__ndb_struct_na_base_pair_step.i_PDB_ins_code_2
_item_description.description
;
Describes the PDB insertion code of the i-th base in the
second base pair of the step.
This data item is a pointer to _atom_site.pdbx_PDB_ins_code in
the ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.i_PDB_ins_code_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
# _item_linked.child_name '_ndb_struct_na_base_pair_step.i_PDB_ins_code_2'
# _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
save_
save__ndb_struct_na_base_pair_step.j_auth_asym_id_2
_item_description.description
;
Describes the author's asym id of the j-th base in the second
base pair of the step.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_auth_asym_id_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.j_auth_asym_id_2'
_item_linked.parent_name '_atom_site.auth_asym_id'
save_
save__ndb_struct_na_base_pair_step.j_auth_seq_id_2
_item_description.description
;
Describes the author's sequence number of the j-th base in the
second base pair of the step.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_auth_seq_id_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ndb_struct_na_base_pair_step.j_auth_seq_id_2'
_item_linked.parent_name '_atom_site.auth_seq_id'
save_
save__ndb_struct_na_base_pair_step.j_PDB_ins_code_2
_item_description.description
;
Describes the PDB insertion code of the j-th base in the
second base pair of the step.
This data item is a pointer to _atom_site.pdbx_PDB_ins_code in
the ATOM_SITE category.
;
_item.name '_ndb_struct_na_base_pair_step.j_PDB_ins_code_2'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code yes
_item_type.code code
# _item_linked.child_name '_ndb_struct_na_base_pair_step.j_PDB_ins_code_2'
# _item_linked.parent_name '_atom_site.pdbx_PDB_ins_code'
save_
save__ndb_struct_na_base_pair_step.shift
_item_description.description
;
The value of the base pair step shift parameter.
;
_item.name '_ndb_struct_na_base_pair_step.shift'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair_step.slide
_item_description.description
;
The value of the base pair step slide parameter.
;
_item.name '_ndb_struct_na_base_pair_step.slide'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair_step.rise
_item_description.description
;
The value of the base pair step rise parameter.
;
_item.name '_ndb_struct_na_base_pair_step.rise'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair_step.tilt
_item_description.description
;
The value of the base pair step tilt parameter.
;
_item.name '_ndb_struct_na_base_pair_step.tilt'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair_step.roll
_item_description.description
;
The value of the base pair step roll parameter.
;
_item.name '_ndb_struct_na_base_pair_step.roll'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair_step.twist
_item_description.description
;
The value of the base pair step twist parameter.
;
_item.name '_ndb_struct_na_base_pair_step.twist'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair_step.x_displacement
_item_description.description
;
The value of the base pair step X displacement parameter.
;
_item.name '_ndb_struct_na_base_pair_step.x_displacement'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair_step.y_displacement
_item_description.description
;
The value of the base pair step Y displacement parameter.
;
_item.name '_ndb_struct_na_base_pair_step.y_displacement'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair_step.helical_rise
_item_description.description
;
The value of the base pair step helical rise parameter.
;
_item.name '_ndb_struct_na_base_pair_step.helical_rise'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair_step.inclination
_item_description.description
;
The value of the base pair step inclination parameter.
;
_item.name '_ndb_struct_na_base_pair_step.inclination'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair_step.tip
_item_description.description
;
The value of the base pair step twist parameter.
;
_item.name '_ndb_struct_na_base_pair_step.tip'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
save__ndb_struct_na_base_pair_step.helical_twist
_item_description.description
;
The value of the base pair step helical twist parameter.
;
_item.name '_ndb_struct_na_base_pair_step.helical_twist'
_item.category_id ndb_struct_na_base_pair_step
_item.mandatory_code no
_item_type.code float
save_
##
##
save_ndb_original_ndb_coordinates
_category.description
; Placeholder category for PDB coordinate data.
;
_category.id ndb_original_ndb_coordinates
_category.mandatory_code no
loop_
_category_key.name '_ndb_original_ndb_coordinates.coord_section'
loop_
_category_group.id 'inclusive_group'
'ndb_group'
save_
save__ndb_original_ndb_coordinates.coord_section
_item_description.description
;
;
_item.name '_ndb_original_ndb_coordinates.coord_section'
_item.category_id ndb_original_ndb_coordinates
_item.mandatory_code yes
_item_type.code text
save_
##
##
save_pdbx_entity_nonpoly
_category.description
;
;
_category.id pdbx_entity_nonpoly
_category.mandatory_code no
_category_key.name '_pdbx_entity_nonpoly.entity_id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
'rcsb_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_entity_nonpoly.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_pdbx_entity_nonpoly.entity_id'
_item.category_id pdbx_entity_nonpoly
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_entity_nonpoly.entity_id'
_item_linked.parent_name '_entity.id'
_item_aliases.alias_name '_rcsb_entity_nonpoly.entity_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_entity_nonpoly.comp_id
_item_description.description
; This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
;
_item.name '_pdbx_entity_nonpoly.comp_id'
_item.category_id pdbx_entity_nonpoly
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_entity_nonpoly.comp_id'
_item_linked.parent_name '_chem_comp.id'
_item_aliases.alias_name '_rcsb_entity_nonpoly.comp_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_entity_nonpoly.name
_item_description.description
; A name for the non-polymer entity
;
_item.name '_pdbx_entity_nonpoly.name'
_item.category_id pdbx_entity_nonpoly
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_rcsb_entity_nonpoly.name'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
#
### EOF mmcif_pdbx-def-4.dic
###########################################################################
#
# File: mmcif_pdbx-def-5.dic
#
# PDB Exchange Data Dictionary
#
# This data dictionary contains definitions used by wwPDB for data exchange
# and data processing.
#
# Definition Section 5
# This section primarily contains extensions for
# data extraction by PDB_EXTRACT.
#
###########################################################################
save_pdbx_phasing_dm
_category.description
; Data items in the PDBX_PHASING_DM category record details about
density modification
;
_category.id pdbx_phasing_dm
_category.mandatory_code no
_category_key.name '_pdbx_phasing_dm.entry_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - density modification from resolve
;
;
_pdbx_phasing_dm.entry_id ABC001
_pdbx_phasing_dm.fom_acentric 0.85
_pdbx_phasing_dm.fom_centric 0.79
_pdbx_phasing_dm.fom 0.85
_pdbx_phasing_dm.reflns_acentric 11351
_pdbx_phasing_dm.reflns_centric 1135
_pdbx_phasing_dm.reflns 12486
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_phasing_dm.entry_id
_item_description.description
; The value of _pdbx_phasing_dm.entry_id identifies the data block.
;
_item.name '_pdbx_phasing_dm.entry_id'
_item.category_id pdbx_phasing_dm
_item.mandatory_code yes
_item_type.code code
_item_aliases.alias_name '_pdbx_phasing_dm.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm.method
_item_description.description
; The value of _pdbx_phasing_dm.method identifies the method used for
density modification
;
_item.name '_pdbx_phasing_dm.method'
_item.category_id pdbx_phasing_dm
_item.mandatory_code no
_item_type.code line
_item_aliases.alias_name '_pdbx_phasing_dm.method'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm.mask_type
_item_description.description
; The value of _pdbx_phasing_dm.mask_type identifies the type of mask used for
density modification
;
_item.name '_pdbx_phasing_dm.mask_type'
_item.category_id pdbx_phasing_dm
_item.mandatory_code no
_item_type.code line
_item_aliases.alias_name '_pdbx_phasing_dm.mask_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm.fom_acentric
_item_description.description
; The value of _pdbx_phasing_dm.fom_acentric identifies the figure of merit
for acentric data
;
_item.name '_pdbx_phasing_dm.fom_acentric'
_item.category_id pdbx_phasing_dm
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm.fom_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm.fom_centric
_item_description.description
; The value of _pdbx_phasing_dm.fom_centric identifies the figure of merit
for acentric data
;
_item.name '_pdbx_phasing_dm.fom_centric'
_item.category_id pdbx_phasing_dm
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm.fom_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm.fom
_item_description.description
; The value of _pdbx_phasing_dm.fom identifies the figure of merit
for all the data
;
_item.name '_pdbx_phasing_dm.fom'
_item.category_id pdbx_phasing_dm
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm.fom'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm.reflns_acentric
_item_description.description
; The value of _pdbx_phasing_dm.reflns_acentric identifies the number
of acentric reflections.
;
_item.name '_pdbx_phasing_dm.reflns_acentric'
_item.category_id pdbx_phasing_dm
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_dm.reflns_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm.reflns_centric
_item_description.description
; The value of _pdbx_phasing_dm.reflns_centric identifies the number
of centric reflections.
;
_item.name '_pdbx_phasing_dm.reflns_centric'
_item.category_id pdbx_phasing_dm
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_dm.reflns_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm.reflns
_item_description.description
; The value of _pdbx_phasing_dm.reflns identifies the number
of centric and acentric reflections.
;
_item.name '_pdbx_phasing_dm.reflns'
_item.category_id pdbx_phasing_dm
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_dm.reflns'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm.delta_phi_initial
_item_description.description
; The value of _pdbx_phasing_dm.delta_phi_initial identifies phase difference
before density modification
;
_item.name '_pdbx_phasing_dm.delta_phi_initial'
_item.category_id pdbx_phasing_dm
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm.delta_phi_initial'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm.delta_phi_final
_item_description.description
; The value of _pdbx_phasing_dm.delta_phi_final identifies phase difference
after density modification
;
_item.name '_pdbx_phasing_dm.delta_phi_final'
_item.category_id pdbx_phasing_dm
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm.delta_phi_final'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
### next category, _pdbx_phasing_dm_shell ###
save_pdbx_phasing_dm_shell
_category.description
; Data items in the PDBX_PHASING_DM_SHELL category record details about
density modification in resolution shell.
;
_category.id pdbx_phasing_dm_shell
_category.mandatory_code no
loop_
_category_key.name '_pdbx_phasing_dm_shell.d_res_low'
'_pdbx_phasing_dm_shell.d_res_high'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - density modification with shells
;
;
loop_
_pdbx_phasing_dm_shell.d_res_low
_pdbx_phasing_dm_shell.d_res_high
_pdbx_phasing_dm_shell.reflns
_pdbx_phasing_dm_shell.fom
_pdbx_phasing_dm_shell.delta_phi_final
100.00 7.73 502 0.879 24.7
7.73 6.24 506 0.857 29.2
6.24 5.50 504 0.838 29.2
5.50 5.02 502 0.851 25.3
5.02 4.67 503 0.831 22.7
# .......
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_phasing_dm_shell.d_res_high
_item_description.description
; The value of _pdbx_phasing_dm_shell.d_res_high identifies high resolution
;
_item.name '_pdbx_phasing_dm_shell.d_res_high'
_item.category_id pdbx_phasing_dm_shell
_item.mandatory_code yes
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm_shell.d_res_high'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm_shell.d_res_low
_item_description.description
; The value of _pdbx_phasing_dm_shell.d_res_low identifies low resolution
;
_item.name '_pdbx_phasing_dm_shell.d_res_low'
_item.category_id pdbx_phasing_dm_shell
_item.mandatory_code yes
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm_shell.d_res_low'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm_shell.fom_acentric
_item_description.description
; The value of _pdbx_phasing_dm_shell.fom_acentric identifies the figure of merit
for acentric data with resolution shells
;
_item.name '_pdbx_phasing_dm_shell.fom_acentric'
_item.category_id pdbx_phasing_dm_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm_shell.fom_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm_shell.fom_centric
_item_description.description
; The value of _pdbx_phasing_dm_shell.fom_centric identifies the figure of merit
for centric data with resolution shells.
;
_item.name '_pdbx_phasing_dm_shell.fom_centric'
_item.category_id pdbx_phasing_dm_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm_shell.fom_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm_shell.fom
_item_description.description
; The value of _pdbx_phasing_dm_shell.fom identifies the figure of merit
for all the data with resolution shells.
;
_item.name '_pdbx_phasing_dm_shell.fom'
_item.category_id pdbx_phasing_dm_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm_shell.fom'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm_shell.reflns_acentric
_item_description.description
; The value of _pdbx_phasing_dm_shell.reflns_acentric identifies the number
of acentric reflections with resolution shells.
;
_item.name '_pdbx_phasing_dm_shell.reflns_acentric'
_item.category_id pdbx_phasing_dm_shell
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_dm_shell.reflns_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm_shell.reflns_centric
_item_description.description
; The value of _pdbx_phasing_dm_shell.reflns_centric identifies the number
of centric reflections with resolution shells.
;
_item.name '_pdbx_phasing_dm_shell.reflns_centric'
_item.category_id pdbx_phasing_dm_shell
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_dm_shell.reflns_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm_shell.reflns
_item_description.description
; The value of _pdbx_phasing_dm_shell.reflns identifies the number
of centric and acentric reflections with resolution shells.
;
_item.name '_pdbx_phasing_dm_shell.reflns'
_item.category_id pdbx_phasing_dm_shell
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_dm_shell.reflns'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm_shell.delta_phi_initial
_item_description.description
; The value of _pdbx_phasing_dm_shell.delta_phi_initial identifies phase difference
before density modification with resolution shells.
;
_item.name '_pdbx_phasing_dm_shell.delta_phi_initial'
_item.category_id pdbx_phasing_dm_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm_shell.delta_phi_initial'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_dm_shell.delta_phi_final
_item_description.description
; The value of _pdbx_phasing_dm_shell.delta_phi_final identifies phase difference
after density modification with resolution shells.
;
_item.name '_pdbx_phasing_dm_shell.delta_phi_final'
_item.category_id pdbx_phasing_dm_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_dm_shell.delta_phi_final'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_d_res_low
_item_description.description
; _phasing_MAD.pdbx_d_res_low records the lowest resolution
for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_d_res_low'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_d_res_low'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_d_res_high
_item_description.description
; _phasing_MAD.pdbx_d_res_high records the highest resolution
for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_d_res_high'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_d_res_high'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_reflns_acentric
_item_description.description
; _phasing_MAD.pdbx_reflns_acentric records the number of
acentric reflections for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_reflns_acentric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_phasing_MAD.pdbx_reflns_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_reflns_centric
_item_description.description
; _phasing_MAD.pdbx_reflns_centric records the number of
centric reflections for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_reflns_centric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_phasing_MAD.pdbx_reflns_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_reflns
_item_description.description
; _phasing_MAD.pdbx_reflns records the number of
reflections used for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_reflns'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_phasing_MAD.pdbx_reflns'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_fom_acentric
_item_description.description
; _phasing_MAD.pdbx_fom_acentric records the figure of merit
using acentric data for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_fom_acentric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_fom_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_fom_centric
_item_description.description
; _phasing_MAD.pdbx_fom_centric records the figure of merit
using centric data for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_fom_centric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_fom_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_fom
_item_description.description
; _phasing_MAD.pdbx_fom records the figure of merit
for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_fom'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_fom'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_R_cullis_centric
_item_description.description
; _phasing_MAD.pdbx_R_cullis_centric records R_cullis
using centric data for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_R_cullis_centric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_R_cullis_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_R_cullis_acentric
_item_description.description
; _phasing_MAD.pdbx_R_cullis_acentric records R_cullis
using acentric data for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_R_cullis_acentric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_R_cullis_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_R_cullis
_item_description.description
; _phasing_MAD.pdbx_R_cullis records R_cullis
for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_R_cullis'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_R_cullis'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_R_kraut_centric
_item_description.description
; _phasing_MAD.pdbx_R_kraut_centric records R_kraut
using centric data for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_R_kraut_centric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_R_kraut_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_R_kraut_acentric
_item_description.description
; _phasing_MAD.pdbx_R_kraut_acentric records R_kraut
using acentric data for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_R_kraut_acentric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_R_kraut_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_R_kraut
_item_description.description
; _phasing_MAD.pdbx_R_kraut records R_kraut
for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_R_kraut'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_R_kraut'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_loc_centric
_item_description.description
; _phasing_MAD.pdbx_loc_centric records lack of closure
using centric data for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_loc_centric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_loc_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_loc_acentric
_item_description.description
; _phasing_MAD.pdbx_loc_acentric records lack of closure
using acentric data for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_loc_acentric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_loc_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_loc
_item_description.description
; _phasing_MAD.pdbx_loc records lack of closure
for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_loc'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_loc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_power_centric
_item_description.description
; _phasing_MAD.pdbx_power_centric records phasing power
using centric data for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_power_centric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_power_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_power_acentric
_item_description.description
; _phasing_MAD.pdbx_power_acentric records phasing power
using acentric data for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_power_acentric'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_power_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_power
_item_description.description
; _phasing_MAD.pdbx_power records phasing power
for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_power'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD.pdbx_power'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_number_data_sets
_item_description.description
; _phasing_MAD.pdbx_loc records the number
of data sets used for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_number_data_sets'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_phasing_MAD.pdbx_number_data_sets'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD.pdbx_anom_scat_method
_item_description.description
; _phasing_MAD.pdbx_anom_scat_method records the method
used to locate anomalous scatterers for MAD phasing.
;
_item.name '_phasing_MAD.pdbx_anom_scat_method'
_item.category_id phasing_MAD
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_phasing_MAD.pdbx_anom_scat_method'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
save_pdbx_phasing_MAD_shell
_category.description
; Data items in the PDBX_PHASING_MAD_SHELL category record details about
the phasing of the structure, when methods involving multiple
anomalous dispersion techniques are involved (note: the
values are overall, but broken down into shells of resolution)
;
_category.id pdbx_phasing_MAD_shell
_category.mandatory_code no
loop_
_category_key.name '_pdbx_phasing_MAD_shell.d_res_low'
'_pdbx_phasing_MAD_shell.d_res_high'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_pdbx_phasing_MAD_shell.d_res_low
_pdbx_phasing_MAD_shell.d_res_high
_pdbx_phasing_MAD_shell.reflns_acentric
_pdbx_phasing_MAD_shell.fom_acentric
_pdbx_phasing_MAD_shell.reflns_centric
_pdbx_phasing_MAD_shell.fom_centric
22.60 7.77 64 0.886 23 0.641
7.77 5.67 132 0.863 32 0.642
5.67 4.68 182 0.842 27 0.737
4.68 4.07 209 0.789 24 0.682
4.07 3.65 246 0.772 27 0.633
3.65 3.34 260 0.752 31 0.700
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_phasing_MAD_shell.d_res_low
_item_description.description
; _pdbx_phasing_MAD_shell.d_res_low records the lower resolution
for the shell.
;
_item.name '_pdbx_phasing_MAD_shell.d_res_low'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code yes
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.d_res_low'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.d_res_high
_item_description.description
; _pdbx_phasing_MAD_shell.d_res_high records the higher resolution
for the shell.
;
_item.name '_pdbx_phasing_MAD_shell.d_res_high'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code yes
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.d_res_high'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.reflns_acentric
_item_description.description
; _pdbx_phasing_MAD_shell.reflns_acentric records the number of
acentric reflections for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.reflns_acentric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.reflns_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.reflns_centric
_item_description.description
; _pdbx_phasing_MAD_shell.reflns_centric records the number of
centric reflections for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.reflns_centric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.reflns_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.reflns
_item_description.description
; _pdbx_phasing_MAD_shell.reflns records the number of
reflections used for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.reflns'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.reflns'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.fom_acentric
_item_description.description
; _pdbx_phasing_MAD_shell.fom_acentric records the figure of merit
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.fom_acentric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.fom_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.fom_centric
_item_description.description
; _pdbx_phasing_MAD_shell.fom_centric records the figure of merit
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.fom_centric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.fom_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.fom
_item_description.description
; _pdbx_phasing_MAD_shell.fom records the figure of merit
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.fom'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.fom'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.R_cullis_centric
_item_description.description
; _pdbx_phasing_MAD_shell.R_cullis_centric records R_cullis
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.R_cullis_centric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_cullis_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.R_cullis_acentric
_item_description.description
; _pdbx_phasing_MAD_shell.R_cullis_acentric records R_cullis
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.R_cullis_acentric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_cullis_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.R_cullis
_item_description.description
; _pdbx_phasing_MAD_shell.R_cullis records R_cullis
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.R_cullis'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_cullis'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.R_kraut_centric
_item_description.description
; _pdbx_phasing_MAD_shell.R_kraut_centric records R_kraut
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.R_kraut_centric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_kraut_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.R_kraut_acentric
_item_description.description
; _pdbx_phasing_MAD_shell.r_kraut_acentric records R_kraut
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.R_kraut_acentric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_kraut_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.R_kraut
_item_description.description
; _pdbx_phasing_MAD_shell.R_kraut records R_kraut
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.R_kraut'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.R_kraut'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.loc_centric
_item_description.description
; _pdbx_phasing_MAD_shell.loc_centric records lack of closure
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.loc_centric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.loc_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.loc_acentric
_item_description.description
; _pdbx_phasing_MAD_shell.loc_acentric records lack of closure
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.loc_acentric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.loc_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.loc
_item_description.description
; _pdbx_phasing_MAD_shell.loc records lack of closure
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.loc'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.loc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.power_centric
_item_description.description
; _pdbx_phasing_MAD_shell.power_centric records phasing powe
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.power_centric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.power_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.power_acentric
_item_description.description
; _pdbx_phasing_MAD_shell.power_acentric records phasing powe
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.power_acentric'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.power_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_shell.power
_item_description.description
; _pdbx_phasing_MAD_shell.loc records phasing power
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_shell.power'
_item.category_id pdbx_phasing_MAD_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_shell.power'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
### next category, _pdbx_phasing_MAD_set ###
save_pdbx_phasing_MAD_set
_category.description
; Record details about each phasing set: (Note: the phasing
set is different from data set. for example: if there are
three data sets, the inflection point (IP), the peak (PK)
and the high remote (HR), the combination of the phasing
set will be IP_iso, PK_iso (the isomorphous repleacement
with HR as 'native'), IP_ano, PK_ano and HR_ano (the
anomalous difference with itself). Therefore, there are
five set used for phasing.
;
_category.id pdbx_phasing_MAD_set
_category.mandatory_code no
_category_key.name '_pdbx_phasing_MAD_set.id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - three wavelengths
;
;
loop_
_pdbx_phasing_MAD_set.id
_pdbx_phasing_MAD_set.d_res_low
_pdbx_phasing_MAD_set.d_res_high
_pdbx_phasing_MAD_set.reflns_acentric
_pdbx_phasing_MAD_set.reflns_centric
_pdbx_phasing_MAD_set.R_cullis_acentric
_pdbx_phasing_MAD_set.R_cullis_centric
ISO_1 22.60 2.00 5387 471 0.000 0.000
ISO_2 22.60 2.00 5365 469 0.803 0.718
ISO_3 22.60 2.00 5317 460 0.658 0.500
ANO_1 22.60 2.00 5278 0 0.841 0.000
ANO_2 22.60 2.00 5083 0 0.649 0.000
ANO_3 22.60 2.00 5329 0 0.829 0.000
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_phasing_MAD_set.id
_item_description.description
; _pdbx_phasing_MAD_set.id records phase set name
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.id'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code yes
_item_type.code code
_item_aliases.alias_name '_pdbx_phasing_MAD_set.id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.d_res_low
_item_description.description
; _pdbx_phasing_MAD_set.d_res_low records the lowerest
resolution for phasing set.
;
_item.name '_pdbx_phasing_MAD_set.d_res_low'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.d_res_low'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.d_res_high
_item_description.description
; _pdbx_phasing_MAD_set.d_res_high records the highest resolution
for the phasing set.
;
_item.name '_pdbx_phasing_MAD_set.d_res_high'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.d_res_high'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.number_of_sites
_item_description.description
; _pdbx_phasing_MAD_set.number_of_sites records the number of site
refined for the phasing set.
;
_item.name '_pdbx_phasing_MAD_set.number_of_sites'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_MAD_set.number_of_sites'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.reflns_acentric
_item_description.description
; _pdbx_phasing_MAD_set.reflns_acentric records the number of
acentric reflections for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.reflns_acentric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_MAD_set.reflns_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.reflns_centric
_item_description.description
; _pdbx_phasing_MAD_set.reflns_centric records the number of
centric reflections for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.reflns_centric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_MAD_set.reflns_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.reflns
_item_description.description
; _pdbx_phasing_MAD_set.reflns records the number of
reflections used for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.reflns'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_MAD_set.reflns'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.fom_acentric
_item_description.description
; _pdbx_phasing_MAD_set.fom_acentric records the figure of merit
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.fom_acentric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.fom_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.fom_centric
_item_description.description
; _pdbx_phasing_MAD_set.fom_centric records the figure of merit
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.fom_centric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.fom_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.fom
_item_description.description
; _pdbx_phasing_MAD_set.fom records the figure of merit
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.fom'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.fom'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.R_cullis_centric
_item_description.description
; _pdbx_phasing_MAD_set.R_cullis_centric records R_cullis
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.R_cullis_centric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.R_cullis_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.R_cullis_acentric
_item_description.description
; _pdbx_phasing_MAD_set.R_cullis_acentric records R_cullis
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.R_cullis_acentric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.R_cullis_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.R_cullis
_item_description.description
; _pdbx_phasing_MAD_set.R_cullis records R_cullis
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.R_cullis'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.R_cullis'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.R_kraut_centric
_item_description.description
; _pdbx_phasing_MAD_set.R_kraut_centric records r_kraut
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.R_kraut_centric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.R_kraut_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.R_kraut_acentric
_item_description.description
; _pdbx_phasing_MAD_set.r_kraut_acentric records r_kraut
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.R_kraut_acentric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.R_kraut_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.R_kraut
_item_description.description
; _pdbx_phasing_MAD_set.R_kraut records R_kraut
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.R_kraut'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.R_kraut'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.loc_centric
_item_description.description
; _pdbx_phasing_MAD_set.loc_centric records lack of closure
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.loc_centric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.loc_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.loc_acentric
_item_description.description
; _pdbx_phasing_MAD_set.loc_acentric records lack of closure
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.loc_acentric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.loc_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.loc
_item_description.description
; _pdbx_phasing_MAD_set.loc records lack of closure
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.loc'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.loc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.power_centric
_item_description.description
; _pdbx_phasing_MAD_set.power_centric records phasing powe
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.power_centric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.power_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.power_acentric
_item_description.description
; _pdbx_phasing_MAD_set.power_acentric records phasing powe
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.power_acentric'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.power_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set.power
_item_description.description
; _pdbx_phasing_MAD_set.power records phasing power
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set.power'
_item.category_id pdbx_phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set.power'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
### next category, _pdbx_phasing_MAD_set_shell ###
save_pdbx_phasing_MAD_set_shell
_category.description
; The same as category pdbx_phasing_MAD_set, but
broken into shells.
;
_category.id pdbx_phasing_MAD_set_shell
_category.mandatory_code no
loop_
_category_key.name '_pdbx_phasing_MAD_set_shell.id'
'_pdbx_phasing_MAD_set_shell.d_res_low'
'_pdbx_phasing_MAD_set_shell.d_res_high'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - three wavelengths (SHARP example)
;
;
loop_
_pdbx_phasing_MAD_set_shell.id
_pdbx_phasing_MAD_set_shell.d_res_low
_pdbx_phasing_MAD_set_shell.d_res_high
_pdbx_phasing_MAD_set_shell.reflns_acentric
_pdbx_phasing_MAD_set_shell.reflns_centric
_pdbx_phasing_MAD_set_shell.R_cullis_acentric
_pdbx_phasing_MAD_set_shell.R_cullis_centric
_pdbx_phasing_MAD_set_shell.power_acentric
_pdbx_phasing_MAD_set_shell.power_centric
ISO_1 22.60 7.77 64 23 0.000 0.000 0.000 0.000
ISO_1 7.77 5.67 130 32 0.000 0.000 0.000 0.000
ISO_1 5.67 4.68 182 27 0.000 0.000 0.000 0.000
ISO_1 4.68 4.07 207 24 0.000 0.000 0.000 0.000
ANO_1 22.60 7.77 62 0 0.610 0.000 1.804 0.000
ANO_1 7.77 5.67 129 0 0.532 0.000 2.382 0.000
ANO_1 5.67 4.68 178 0 0.673 0.000 1.858 0.000
ANO_1 4.68 4.07 204 0 0.755 0.000 1.605 0.000
# .........
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_phasing_MAD_set_shell.id
_item_description.description
; _pdbx_phasing_MAD_set_shell.id records phase set name
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.id'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code yes
_item_type.code code
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.d_res_low
_item_description.description
; _pdbx_phasing_MAD_set_shell.d_res_low records the lowerest
resolution for phasing set.
;
_item.name '_pdbx_phasing_MAD_set_shell.d_res_low'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code yes
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.d_res_low'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.d_res_high
_item_description.description
; _pdbx_phasing_MAD_set_shell.d_res_high records the highest resolution
for the phasing set.
;
_item.name '_pdbx_phasing_MAD_set_shell.d_res_high'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code yes
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.d_res_high'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.reflns_acentric
_item_description.description
; _pdbx_phasing_MAD_set_shell.reflns_acentric records the number of
acentric reflections for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.reflns_acentric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.reflns_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.reflns_centric
_item_description.description
; _pdbx_phasing_MAD_set_shell.reflns_centric records the number of
centric reflections for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.reflns_centric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.reflns_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.reflns
_item_description.description
; _pdbx_phasing_MAD_set_shell.reflns records the number of
reflections used for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.reflns'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.reflns'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.fom_acentric
_item_description.description
; _pdbx_phasing_MAD_set_shell.fom_acentric records the figure of merit
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.fom_acentric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.fom_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.fom_centric
_item_description.description
; _pdbx_phasing_MAD_set_shell.fom_centric records the figure of merit
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.fom_centric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.fom_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.fom
_item_description.description
; _pdbx_phasing_MAD_set_shell.fom records the figure of merit
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.fom'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.fom'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.R_cullis_centric
_item_description.description
; _pdbx_phasing_MAD_set_shell.R_cullis_centric records R_cullis
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.R_cullis_centric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_cullis_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.R_cullis_acentric
_item_description.description
; _pdbx_phasing_MAD_set_shell.R_cullis_acentric records R_cullis
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.R_cullis_acentric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_cullis_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.R_cullis
_item_description.description
; _pdbx_phasing_MAD_set_shell.R_cullis records R_cullis
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.R_cullis'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_cullis'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.R_kraut_centric
_item_description.description
; _pdbx_phasing_MAD_set_shell.R_kraut_centric records R_kraut
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.R_kraut_centric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_kraut_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.R_kraut_acentric
_item_description.description
; _pdbx_phasing_MAD_set_shell.R_kraut_acentric records R_kraut
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.R_kraut_acentric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_kraut_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.R_kraut
_item_description.description
; _pdbx_phasing_MAD_set_shell.R_kraut records R_kraut
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.R_kraut'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.R_kraut'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.loc_centric
_item_description.description
; _pdbx_phasing_MAD_set_shell.loc_centric records lack of closure
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.loc_centric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.loc_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.loc_acentric
_item_description.description
; _pdbx_phasing_MAD_set_shell.loc_acentric records lack of closure
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.loc_acentric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.loc_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.loc
_item_description.description
; _pdbx_phasing_MAD_set_shell.loc records lack of closure
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.loc'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.loc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.power_centric
_item_description.description
; _pdbx_phasing_MAD_set_shell.power_centric records phasing power
using centric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.power_centric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.power_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.power_acentric
_item_description.description
; _pdbx_phasing_MAD_set_shell.power_acentric records phasing power
using acentric data for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.power_acentric'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.power_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_shell.power
_item_description.description
; _pdbx_phasing_MAD_set_shell.power records phasing power
for MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_shell.power'
_item.category_id pdbx_phasing_MAD_set_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_shell.power'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
### next category, _pdbx_phasing_MAD_set_site ###
save_pdbx_phasing_MAD_set_site
_category.description
; record the details (coordinates etc.) of anomalous scatters.
;
_category.id pdbx_phasing_MAD_set_site
_category.mandatory_code no
_category_key.name '_pdbx_phasing_MAD_set_site.id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - anomalous scatters is Se
;
;
loop_
_pdbx_phasing_MAD_set_site.id
_pdbx_phasing_MAD_set_site.atom_type_symbol
_pdbx_phasing_MAD_set_site.Cartn_x
_pdbx_phasing_MAD_set_site.Cartn_y
_pdbx_phasing_MAD_set_site.Cartn_z
_pdbx_phasing_MAD_set_site.B_iso
_pdbx_phasing_MAD_set_site.Occupancy
1 SE 25.9407 -0.103471 17.4094 15.2561 1
2 SE 30.6534 6.62359 9.93063 12.9102 1
3 SE -3.26506 15.5546 53.9529 30.5239 1
# .......
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_phasing_MAD_set_site.id
_item_description.description
; _pdbx_phasing_MAD_set_site.id records the number of site
obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.id'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.atom_type_symbol
_item_description.description
; _pdbx_phasing_MAD_set_site.atom_type_symbol records the name of site
obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.atom_type_symbol'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.atom_type_symbol'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.Cartn_x
_item_description.description
; _pdbx_phasing_MAD_set_site.Cartn_x records the X Cartesian
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.Cartn_x'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_x'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.Cartn_y
_item_description.description
; _pdbx_phasing_MAD_set_site.Cartn_y records the Y Cartesian
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.Cartn_y'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_y'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.Cartn_z
_item_description.description
; _pdbx_phasing_MAD_set_site.Cartn_z records the Z Cartesian
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.Cartn_z'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_z'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.Cartn_x_esd
_item_description.description
; _pdbx_phasing_MAD_set_site.Cartn_x_esd records the estimated
standard deviation X Cartesian
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.Cartn_x_esd'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_x_esd'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.Cartn_y_esd
_item_description.description
; _pdbx_phasing_MAD_set_site.Cartn_y_esd records the estimated
standard deviation Y Cartesian
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.Cartn_y_esd'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_y_esd'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.Cartn_z_esd
_item_description.description
; _pdbx_phasing_MAD_set_site.Cartn_z_esd records the estimated
standard deviation Z Cartesian
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.Cartn_z_esd'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.Cartn_z_esd'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.fract_x
_item_description.description
; _pdbx_phasing_MAD_set_site.fract_x records the X fractional
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.fract_x'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_x'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.fract_y
_item_description.description
; _pdbx_phasing_MAD_set_site.fract_y records the Y fractional
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.fract_y'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_y'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.fract_z
_item_description.description
; _pdbx_phasing_MAD_set_site.fract_z records the Z fractional
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.fract_z'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_z'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.fract_x_esd
_item_description.description
; _pdbx_phasing_MAD_set_site.fract_x_esd records the estimated
standard deviation X fractional
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.fract_x_esd'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_x_esd'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.fract_y_esd
_item_description.description
; _pdbx_phasing_MAD_set_site.fract_y_esd records the estimated
standard deviation Y fractional
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.fract_y_esd'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_y_esd'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.fract_z_esd
_item_description.description
; _pdbx_phasing_MAD_set_site.fract_z_esd records the estimated
standard deviation Z fractional
coordinate of site obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.fract_z_esd'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.fract_z_esd'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.b_iso
_item_description.description
; _pdbx_phasing_MAD_set_site.b_iso records isotropic
temperature factor parameterthe for the site
obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.b_iso'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.b_iso'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.b_iso_esd
_item_description.description
; _pdbx_phasing_MAD_set_site.b_iso_esd records estimated
standard deviation of isotropic
temperature factor parameterthe for the site
obtained from MAD phasing.
;
_item.name '_pdbx_phasing_MAD_set_site.b_iso_esd'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.b_iso_esd'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.occupancy
_item_description.description
; _pdbx_phasing_MAD_set_site.occupancy records the fraction
of the atom type presented at this site.
;
_item.name '_pdbx_phasing_MAD_set_site.occupancy'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.occupancy'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.occupancy_esd
_item_description.description
; _pdbx_phasing_MAD_set_site.occupancy_esd records estimated
standard deviation of the fraction
of the atom type presented at this site.
;
_item.name '_pdbx_phasing_MAD_set_site.occupancy_esd'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.occupancy_esd'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
### new items for _phasing_MAD_set ###
save__phasing_MAD_set.pdbx_atom_type
_item_description.description
; record the type of heavy atoms which produce anomolous singal.
;
_item.name '_phasing_MAD_set.pdbx_atom_type'
_item.category_id phasing_MAD_set
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_phasing_MAD_set.pdbx_atom_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD_set.pdbx_f_prime_refined
_item_description.description
; record the refined f_prime (not from experiment).
;
_item.name '_phasing_MAD_set.pdbx_f_prime_refined'
_item.category_id phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD_set.pdbx_f_prime_refined'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MAD_set.pdbx_f_double_prime_refined
_item_description.description
; record the refined f_double_prime (not from experiment).
;
_item.name '_phasing_MAD_set.pdbx_f_double_prime_refined'
_item.category_id phasing_MAD_set
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MAD_set.pdbx_f_double_prime_refined'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
### new items for _pdbx_phasing_MAD_set_site ###
save__pdbx_phasing_MAD_set_site.set_id
_item_description.description
; record the phasing set.
;
_item.name '_pdbx_phasing_MAD_set_site.set_id'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.set_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MAD_set_site.occupancy_iso
_item_description.description
; The relative real isotropic occupancy of the atom type
present at this heavy-atom site in a given atom site.
;
_item.name '_pdbx_phasing_MAD_set_site.occupancy_iso'
_item.category_id pdbx_phasing_MAD_set_site
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MAD_set_site.occupancy_iso'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
### new items for _refine_ls_restr_ncs ###
save__refine_ls_restr_ncs.pdbx_type
_item_description.description
; record the type of NCS restraint. (for example: tight positional)
;
_item.name '_refine_ls_restr_ncs.pdbx_type'
_item.category_id refine_ls_restr_ncs
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_refine_ls_restr_ncs.pdbx_type'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine_ls_restr_ncs.pdbx_asym_id
_item_description.description
; record the chain ID.
;
_item.name '_refine_ls_restr_ncs.pdbx_asym_id'
_item.category_id refine_ls_restr_ncs
_item.mandatory_code no
_item_type.code code
_item_aliases.alias_name '_refine_ls_restr_ncs.pdbx_asym_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine_ls_restr_ncs.pdbx_number
_item_description.description
; record the residue number .
;
_item.name '_refine_ls_restr_ncs.pdbx_number'
_item.category_id refine_ls_restr_ncs
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_refine_ls_restr_ncs.pdbx_number'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine_ls_restr_ncs.pdbx_rms
_item_description.description
; record the standard divation between one segment to another
;
_item.name '_refine_ls_restr_ncs.pdbx_rms'
_item.category_id refine_ls_restr_ncs
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_refine_ls_restr_ncs.pdbx_rms'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__refine_ls_restr_ncs.pdbx_weight
_item_description.description
; record the weight used for NCS restraint.
;
_item.name '_refine_ls_restr_ncs.pdbx_weight'
_item.category_id refine_ls_restr_ncs
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_refine_ls_restr_ncs.pdbx_weight'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
### new items for _struct_ncs_dom_lim ###
save__struct_ncs_dom_lim.pdbx_component_id
_item_description.description
; record the number of component used for NCS.
;
_item.name '_struct_ncs_dom_lim.pdbx_component_id'
_item.category_id struct_ncs_dom_lim
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_struct_ncs_dom_lim.pdbx_component_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__struct_ncs_dom_lim.pdbx_refine_code
_item_description.description
; record the refinement code number (from CCP4.)
;
_item.name '_struct_ncs_dom_lim.pdbx_refine_code'
_item.category_id struct_ncs_dom_lim
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_struct_ncs_dom_lim.pdbx_refine_code'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
### new items for _refine_analyze ###
save__refine_analyze.pdbx_Luzzati_d_res_high_obs
_item_description.description
; record the high resolution for calculating Luzzati statistics.
;
_item.name '_refine_analyze.pdbx_Luzzati_d_res_high_obs'
_item.category_id refine_analyze
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_refine_analyze.pdbx_Luzzati_d_res_high_obs'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
#-------------------------------
### new items for _phasing_MIR_shell ###
save__phasing_MIR.pdbx_number_derivatives
_item_description.description
; The number of derivatives used in this phasing experiment.
;
_item.name '_phasing_MIR.pdbx_number_derivatives'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_type.code int
save_
save__phasing_MIR_shell.pdbx_loc_centric
_item_description.description
; record lack of closure from centric reflection for each shell.
;
_item.name '_phasing_MIR_shell.pdbx_loc_centric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_shell.pdbx_loc_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_shell.pdbx_loc_acentric
_item_description.description
; record lack of closure from acentric reflection for each shell.
;
_item.name '_phasing_MIR_shell.pdbx_loc_acentric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_shell.pdbx_loc_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_shell.pdbx_power_centric
_item_description.description
; record phasing power from centric reflection for each shell.
;
_item.name '_phasing_MIR_shell.pdbx_power_centric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_shell.pdbx_power_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_shell.pdbx_power_acentric
_item_description.description
; record phasing power from acentric reflection for each shell.
;
_item.name '_phasing_MIR_shell.pdbx_power_acentric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_shell.pdbx_power_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_shell.pdbx_R_kraut_centric
_item_description.description
; record R_Kraut from from centric reflection for each shell.
;
_item.name '_phasing_MIR_shell.pdbx_R_kraut_centric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_shell.pdbx_R_kraut_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_shell.pdbx_R_kraut_acentric
_item_description.description
; record R_kraut from from acentric reflection for each shell.
;
_item.name '_phasing_MIR_shell.pdbx_R_kraut_acentric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_shell.pdbx_R_kraut_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_shell.pdbx_R_cullis_centric
_item_description.description
; record R_Cullis from from centric reflection for each shell.
;
_item.name '_phasing_MIR_shell.pdbx_R_cullis_centric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_shell.pdbx_R_cullis_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_shell.pdbx_R_cullis_acentric
_item_description.description
; record R_Cullis from from acentric reflection for each shell.
;
_item.name '_phasing_MIR_shell.pdbx_R_cullis_acentric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_shell.pdbx_R_cullis_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
### new items for _phasing_MIR_der ###
save__phasing_MIR_der.pdbx_R_kraut_centric
_item_description.description
; record R_kraut obtained from centric data for each derivative.
;
_item.name '_phasing_MIR_der.pdbx_R_kraut_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der.pdbx_R_kraut_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der.pdbx_R_kraut_acentric
_item_description.description
; record R_kraut obtained from acentric data for each derivative.
;
_item.name '_phasing_MIR_der.pdbx_R_kraut_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der.pdbx_R_kraut_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der.pdbx_R_kraut
_item_description.description
; record R_kraut obtained from all data data for each derivative.
;
_item.name '_phasing_MIR_der.pdbx_R_kraut'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der.pdbx_R_kraut'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der.pdbx_loc_centric
_item_description.description
; record lack of closure obtained from centric data for
each derivative.
;
_item.name '_phasing_MIR_der.pdbx_loc_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der.pdbx_loc_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der.pdbx_loc_acentric
_item_description.description
; record lack of closure obtained from acentric data for
each derivative.
;
_item.name '_phasing_MIR_der.pdbx_loc_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der.pdbx_loc_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der.pdbx_loc
_item_description.description
; record lack of closure obtained from all data for
each derivative.
;
_item.name '_phasing_MIR_der.pdbx_loc'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der.pdbx_loc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der.pdbx_fom_centric
_item_description.description
; record figure of merit obtained from centric data for
each derivative.
;
_item.name '_phasing_MIR_der.pdbx_fom_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der.pdbx_fom_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der.pdbx_fom_acentric
_item_description.description
; record figure of merit obtained from acentric data for
each derivative.
;
_item.name '_phasing_MIR_der.pdbx_fom_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der.pdbx_fom_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der.pdbx_fom
_item_description.description
; record figure of merit obtained from all data for
each derivative.
;
_item.name '_phasing_MIR_der.pdbx_fom'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der.pdbx_fom'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der.pdbx_power
_item_description.description
; record phasing power for each derivative.
;
_item.name '_phasing_MIR_der.pdbx_power'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der.pdbx_power'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der.pdbx_R_cullis
_item_description.description
; record R_cullis for each derivative.
;
_item.name '_phasing_MIR_der.pdbx_R_cullis'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der.pdbx_R_cullis'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der.pdbx_reflns
_item_description.description
; record number of reflections used for each derivative.
;
_item.name '_phasing_MIR_der.pdbx_reflns'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_phasing_MIR_der.pdbx_reflns'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
### new items for _phasing_MIR_der_shell ###
save__phasing_MIR_der_shell.pdbx_R_cullis_centric
_item_description.description
; record R Cullis obtained from centric data for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_R_cullis_centric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_R_cullis_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der_shell.pdbx_R_cullis_acentric
_item_description.description
; record R Cullis obtained from acentric data for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_R_cullis_acentric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_R_cullis_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der_shell.pdbx_R_kraut_centric
_item_description.description
; record R Kraut obtained from centric data for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_R_kraut_centric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_R_kraut_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der_shell.pdbx_R_kraut_acentric
_item_description.description
; record R Kraut obtained from acentric data for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_R_kraut_acentric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_R_kraut_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der_shell.pdbx_loc_centric
_item_description.description
; record lack of closure obtained from centric data for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_loc_centric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_loc_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der_shell.pdbx_loc_acentric
_item_description.description
; record lack of closure obtained from acentric data for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_loc_acentric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_loc_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der_shell.pdbx_power_centric
_item_description.description
; record phasing power obtained from centric data for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_power_centric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_power_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der_shell.pdbx_power_acentric
_item_description.description
; record phasing power obtained from acentric data for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_power_acentric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_power_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der_shell.pdbx_fom_centric
_item_description.description
; record figure of merit obtained from centric data for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_fom_centric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_fom_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der_shell.pdbx_fom_acentric
_item_description.description
; record figure of merit obtained from acentric data for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_fom_acentric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_fom_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der_shell.pdbx_reflns_centric
_item_description.description
; record number of centric reflections used for phasing for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_reflns_centric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_reflns_centric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__phasing_MIR_der_shell.pdbx_reflns_acentric
_item_description.description
; record number of acentric reflections used for phasing for each
derivative, but broken into resolution shells
;
_item.name '_phasing_MIR_der_shell.pdbx_reflns_acentric'
_item.category_id phasing_MIR_der_shell
_item.mandatory_code no
_item_type.code int
_item_aliases.alias_name '_phasing_MIR_der_shell.pdbx_reflns_acentric'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
##
### category, _pdbx_phasing_MR
save_pdbx_phasing_MR
_category.description
; Data items in the PDBX_PHASING_MR category record details about
molecular replacement.
;
_category.id pdbx_phasing_MR
_category.mandatory_code no
_category_key.name '_pdbx_phasing_MR.entry_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'phasing_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - molecular replacement example from program CNS.
;
;
_pdbx_phasing_MR.entry_id ABC001
_pdbx_phasing_MR.method_rotation 'real-space rotation search'
_pdbx_phasing_MR.d_res_high_rotation 3.8
_pdbx_phasing_MR.d_res_low_rotation 13.0
_pdbx_phasing_MR.sigma_F_rotation 1.0
_pdbx_phasing_MR.reflns_percent_rotation 97.8
_pdbx_phasing_MR.method_translation 'gerneral using PC-refinement= e2e2'
_pdbx_phasing_MR.d_res_high_translation 4.0
_pdbx_phasing_MR.d_res_low_translation 15.0
_pdbx_phasing_MR.sigma_F_translation 0
_pdbx_phasing_MR.reflns_percent_translation 97.7
_pdbx_phasing_MR.correlation_coeff_Fo_to_Fc 0.586
_pdbx_phasing_MR.packing 0.3086
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_phasing_MR.entry_id
_item_description.description
; The value of _pdbx_phasing_MR.entry_id identifies the data block.
;
_item.name '_pdbx_phasing_MR.entry_id'
_item.category_id pdbx_phasing_MR
_item.mandatory_code yes
_item_type.code code
_item_aliases.alias_name '_pdbx_phasing_MR.entry_id'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.method_rotation
_item_description.description
; The value of _pdbx_phasing_MR.method_rotation identifies the method
used for rotation search. For example, the rotation method may be
realspace, fastdirect, or direct.
.
;
_item.name '_pdbx_phasing_MR.method_rotation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code line
_item_aliases.alias_name '_pdbx_phasing_MR.method_rotation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.d_res_high_rotation
_item_description.description
; The value of _pdbx_phasing_MR.d_res_high_rotation identifies
the highest resolution used for rotation search.
;
_item.name '_pdbx_phasing_MR.d_res_high_rotation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.d_res_high_rotation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.d_res_low_rotation
_item_description.description
; The value of _pdbx_phasing_MR.d_res_low_rotation identifies
the lowest resolution used for rotation search.
;
_item.name '_pdbx_phasing_MR.d_res_low_rotation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.d_res_low_rotation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.sigma_F_rotation
_item_description.description
; The value of _pdbx_phasing_MR.sigma_F_rotation identifies the
sigma cut off of structure factor used for rotation search.
;
_item.name '_pdbx_phasing_MR.sigma_F_rotation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.sigma_F_rotation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.sigma_I_rotation
_item_description.description
; The value of _pdbx_phasing_MR.sigma_I_rotation identifies the
sigma cut off of intensity used for rotation search.
;
_item.name '_pdbx_phasing_MR.sigma_I_rotation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.sigma_I_rotation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.reflns_percent_rotation
_item_description.description
; The value of _pdbx_phasing_MR.reflns_percent_rotation identifies the
completness of data used for rotation search.
;
_item.name '_pdbx_phasing_MR.reflns_percent_rotation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.reflns_percent_rotation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.method_translation
_item_description.description
; The value of _pdbx_phasing_MR.method_translation identifies the method
used for translation search. For example in CNS, the translation method
may be "general" or "phased" with PC refinement target using
"fastf2f2" "e2e2" "e1e1" "f2f2" "f1f1" "residual" "vector".
.
;
_item.name '_pdbx_phasing_MR.method_translation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code line
_item_aliases.alias_name '_pdbx_phasing_MR.method_translation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.d_res_high_translation
_item_description.description
; The value of _pdbx_phasing_MR.d_res_high_translation identifies
the highest resolution used for translation search.
;
_item.name '_pdbx_phasing_MR.d_res_high_translation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.d_res_high_translation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.d_res_low_translation
_item_description.description
; The value of _pdbx_phasing_MR.d_res_low_translation identifies
the lowest resolution used for translation search.
;
_item.name '_pdbx_phasing_MR.d_res_low_translation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.d_res_low_translation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.sigma_F_translation
_item_description.description
; The value of _pdbx_phasing_MR.sigma_F_translation identifies the
sigma cut off of structure factor used for translation search.
;
_item.name '_pdbx_phasing_MR.sigma_F_translation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.sigma_F_translation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.sigma_I_translation
_item_description.description
; The value of _pdbx_phasing_MR.sigma_I_translation identifies the
sigma cut off of intensity used for translation search.
;
_item.name '_pdbx_phasing_MR.sigma_I_translation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.sigma_I_translation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.reflns_percent_translation
_item_description.description
; The value of _pdbx_phasing_MR.reflns_percent_translation identifies the
completness of data used for translation search.
;
_item.name '_pdbx_phasing_MR.reflns_percent_translation'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.reflns_percent_translation'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.correlation_coeff_Io_to_Ic
_item_description.description
; The value of _pdbx_phasing_MR.correlation_coeff_Io_to_Ic identifies
the correlation between the observed and the calculated intensity
(~|F|^2) after rotation and translation.
;
_item.name '_pdbx_phasing_MR.correlation_coeff_Io_to_Ic'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.correlation_coeff_Io_to_Ic'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.correlation_coeff_Fo_to_Fc
_item_description.description
; The value of _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc identifies
the correlation between the observed and the calculated structure
factor after rotation and translation.
;
_item.name '_pdbx_phasing_MR.correlation_coeff_Fo_to_Fc'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.correlation_coeff_Fo_to_Fc'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.R_factor
_item_description.description
; The value of _pdbx_phasing_MR.R_factor identifies the R factor
(defined as uasual) after rotation and translation.
;
_item.name '_pdbx_phasing_MR.R_factor'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.R_factor'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.R_rigid_body
_item_description.description
; The value of _pdbx_phasing_MR.R_rigid_body identifies the R factor
for rigid body refinement after rotation and translation.(In general,
rigid body refinement has to be carried out after molecular
replacement.
;
_item.name '_pdbx_phasing_MR.R_rigid_body'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.R_rigid_body'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.packing
_item_description.description
; The value of _pdbx_phasing_MR.packing identifies the packing of
search model in the unit cell. Too many crystallographic contacts
may indicate a bad search.
;
_item.name '_pdbx_phasing_MR.packing'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code float
_item_aliases.alias_name '_pdbx_phasing_MR.packing'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.model_details
_item_description.description
; The value of _pdbx_phasing_MR.model_details records the details of
model used. For example, the original model can be truncated by
deleting side chains, doubtful parts, using the monomer if the
original model was an oligomer. The search model may be one
domain of a large molecule. What is the pdb IDs.
;
_item.name '_pdbx_phasing_MR.model_details'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code text
_item_aliases.alias_name '_pdbx_phasing_MR.model_details'
_item_aliases.dictionary 'cif_rcsb.dic'
_item_aliases.version 1.1
save_
save__pdbx_phasing_MR.native_set_id
_item_description.description
; The data set that was treated as the native in this
experiment.
This data item is a pointer to _phasing_set.id in the
PHASING_SET category.
;
_item.name '_pdbx_phasing_MR.native_set_id'
_item.category_id pdbx_phasing_MR
_item.mandatory_code no
_item_type.code line
_item_linked.child_name '_pdbx_phasing_MR.native_set_id'
_item_linked.parent_name '_phasing_set.id'
save_
save__phasing_set.pdbx_temp_details
_item_description.description
; The value of _phasing_set.pdbx_temp_details describes any
special details about the data collection temperature
for this phasing data set.
;
_item.name '_phasing_set.pdbx_temp_details'
_item.category_id phasing_set
_item.mandatory_code no
_item_type.code text
save_
save__phasing_set.pdbx_d_res_high
_item_description.description
; The smallest value in angstroms for the interplanar spacings
for the reflections in this shell. This is called the highest
resolution.
;
_item.name '_phasing_set.pdbx_d_res_high'
_item.category_id phasing_set
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_set.pdbx_d_res_low
_item_description.description
; The highest value in angstroms for the interplanar spacings
for the reflections in this shell. This is called the lowest
resolution.
;
_item.name '_phasing_set.pdbx_d_res_low'
_item.category_id phasing_set
_item.mandatory_code yes
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refln.pdbx_I_plus
_item_description.description
; The intensity of the I(h,k,l) partner of
the Friedel pair.
;
_item.name '_refln.pdbx_I_plus'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
save__refln.pdbx_I_minus
_item_description.description
; The intensity of the I(-h,-k,-l) partner
of the Friedel pair.
;
_item.name '_refln.pdbx_I_minus'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
save__refln.pdbx_F_plus
_item_description.description
; The structure factor F(h,k,l) of the Friedel pair.
;
_item.name '_refln.pdbx_F_plus'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
save__refln.pdbx_F_minus
_item_description.description
; The structure factor F(-h,-k,-l) of the Friedel pair.
;
_item.name '_refln.pdbx_F_minus'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
save__refln.pdbx_I_plus_sigma
_item_description.description
; The standard uncertainty (derived from measurement) of the
intensity I(h,k,l) partner of the Friedel pair.
;
_item.name '_refln.pdbx_I_plus_sigma'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
save__refln.pdbx_I_minus_sigma
_item_description.description
; The standard uncertainty (derived from measurement) of the
intensity I(-h,-k,-l) partner of the Friedel pair.
;
_item.name '_refln.pdbx_I_minus_sigma'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
save__refln.pdbx_F_minus_sigma
_item_description.description
; The standard uncertainty (derived from measurement) of the
structure factor F(-h,-k,-l) of the Friedel pair.
;
_item.name '_refln.pdbx_F_minus_sigma'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
save__refln.pdbx_F_plus_sigma
_item_description.description
; The standard uncertainty (derived from measurement) of the
structure factor F(h,k,l) of the Friedel pair.
;
_item.name '_refln.pdbx_F_plus_sigma'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
save__refln.pdbx_HL_A_iso
_item_description.description
; The isomorphous Hendrickson-Lattman coefficient A~iso~ for this
reflection.
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
;
_item.name '_refln.pdbx_HL_A_iso'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
save__refln.pdbx_HL_B_iso
_item_description.description
; The isomorphous Hendrickson-Lattman coefficient B~iso~ for this
reflection.
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
;
_item.name '_refln.pdbx_HL_B_iso'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
save__refln.pdbx_HL_C_iso
_item_description.description
; The isomorphous Hendrickson-Lattman coefficient C~iso~ for this
reflection.
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
;
_item.name '_refln.pdbx_HL_C_iso'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
save__refln.pdbx_HL_D_iso
_item_description.description
; The isomorphous Hendrickson-Lattman coefficient D~iso~ for this
reflection.
Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta
Cryst. B26, 136-143.
;
_item.name '_refln.pdbx_HL_D_iso'
_item.category_id refln
_item.mandatory_code no
_item_type.code float
save_
### EOF mmcif_pdbx-def-5.dic
###########################################################################
#
# File: mmcif_pdbx-def-6.dic
#
# PDB Exchange Data Dictionary
#
# This data dictionary contains definitions used by wwPDB for data exchange
# and data processing.
#
# Definition Section 6
#
#
###########################################################################
save__entity.pdbx_target_id
_item_description.description
; The value of _entity.target_id points to a TARGETDB target idenitifier
from which this entity was generated.
;
_item.name '_entity.pdbx_target_id'
_item.category_id entity
_item.mandatory_code no
_item_type.code code
save_
save_pdbx_entity_prod_protocol
_category.description
; This category contains descriptive protocols for the production
of this entity.
;
_category.id pdbx_entity_prod_protocol
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_prod_protocol.entry_id'
'_pdbx_entity_prod_protocol.entity_id'
'_pdbx_entity_prod_protocol.protocol_type'
save_
save__pdbx_entity_prod_protocol.entry_id
_item_description.description
; The value of _pdbx_entity_prod_protocol.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id.
;
_item.name '_pdbx_entity_prod_protocol.entry_id'
_item.category_id pdbx_entity_prod_protocol
_item.mandatory_code yes
_item_type.code code
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_prod_protocol.entry_id'
save_
save__pdbx_entity_prod_protocol.entity_id
_item_description.description
; The value of _pdbx_entity_prod_protocol.entity_id uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category.
;
_item.name '_pdbx_entity_prod_protocol.entity_id'
_item.category_id pdbx_entity_prod_protocol
_item.mandatory_code yes
_item_type.code code
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_prod_protocol.entity_id'
save_
save__pdbx_entity_prod_protocol.protocol
_item_description.description
; The protocol description associated with the protocol_type employed
in the production of this entity.
;
_item.name '_pdbx_entity_prod_protocol.protocol'
_item.category_id pdbx_entity_prod_protocol
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_entity_prod_protocol.protocol_type
_item_description.description
; The one of a set of protocol types associated with the production
of this entity.
;
_item.name '_pdbx_entity_prod_protocol.protocol_type'
_item.category_id pdbx_entity_prod_protocol
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
"selection"
"PCR"
"cloning"
"expression"
"growth"
"purification"
"NMR"
"other"
save_
####################
## ENTITY_SRC_GEN ##
####################
save__entity_src_gen.entity_id
_item_description.description
; This data item is a pointer to _entity.id in the ENTITY category.
;
_item.name '_entity_src_gen.entity_id'
_item.mandatory_code yes
save_
save__entity_src_gen.host_org_common_name
_item_description.description
; The common name of the organism that served as host for the
production of the entity. Where full details of the protein
production are available it would be expected that this item
be derived from _entity_src_gen_express.host_org_common_name
or via _entity_src_gen_express.host_org_tax_id
;
_item.name '_entity_src_gen.host_org_common_name'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'yeast'
'bacteria'
save_
save__entity_src_gen.host_org_details
_item_description.description
; A description of special aspects of the organism that served as
host for the production of the entity. Where full details of
the protein production are available it would be expected that
this item would derived from _entity_src_gen_express.host_org_details
;
_item.name '_entity_src_gen.host_org_details'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
save_
save__entity_src_gen.host_org_strain
_item_description.description
; The strain of the organism in which the entity was expressed.
Where full details of the protein production are available
it would be expected that this item be derived from
_entity_src_gen_express.host_org_strain or via
_entity_src_gen_express.host_org_tax_id
;
_item.name '_entity_src_gen.host_org_strain'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'DH5a'
'BMH 71-18'
save_
save__entity_src_gen.plasmid_details
_item_description.description
; A description of special aspects of the plasmid that produced the
entity in the host organism. Where full details of the protein
production are available it would be expected that this item
would be derived from _pdbx_construct.details of the construct
pointed to from _entity_src_gen_express.plasmid_id.
;
_item.name '_entity_src_gen.plasmid_details'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
save_
save__entity_src_gen.plasmid_name
_item_description.description
; The name of the plasmid that produced the entity in the host
organism. Where full details of the protein production are available
it would be expected that this item would be derived from
_pdbx_construct.name of the construct pointed to from
_entity_src_gen_express.plasmid_id.
;
_item.name '_entity_src_gen.plasmid_name'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'pET3C'
'pT123sab'
save_
save__entity_src_gen.pdbx_host_org_variant
_item_description.description
; Variant of the organism used as the expression system. Where
full details of the protein production are available it would
be expected that this item be derived from
entity_src_gen_express.host_org_variant or via
_entity_src_gen_express.host_org_tax_id
;
_item.name '_entity_src_gen.pdbx_host_org_variant'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'TRP-LAC' 'LAMBDA DE3'
save_
save__entity_src_gen.pdbx_host_org_cell_line
_item_description.description
; A specific line of cells used as the expression system. Where
full details of the protein production are available it would
be expected that this item would be derived from
entity_src_gen_express.host_org_cell_line
;
_item.name '_entity_src_gen.pdbx_host_org_cell_line'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case 'HELA'
save_
save__entity_src_gen.pdbx_host_org_atcc
_item_description.description
; Americal Tissue Culture Collection of the expression system. Where
full details of the protein production are available it would
be expected that this item would be derived from
_entity_src_gen_express.host_org_culture_collection
;
_item.name '_entity_src_gen.pdbx_host_org_atcc'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
save_
save__entity_src_gen.pdbx_host_org_culture_collection
_item_description.description
; Culture collection of the expression system. Where
full details of the protein production are available it would
be expected that this item would be derived somehwere, but
exactly where is not clear.
;
_item.name '_entity_src_gen.pdbx_host_org_culture_collection'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
save_
save__entity_src_gen.pdbx_host_org_cell
_item_description.description
; Cell type from which the gene is derived. Where
entity.target_id is provided this should be derived from
details of the target.
;
_item.name '_entity_src_gen.pdbx_host_org_cell'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
_item_examples.case ENDOTHELIAL
save_
save__entity_src_gen.pdbx_host_org_scientific_name
_item_description.description
; The scientific name of the organism that served as host for the
production of the entity. Where full details of the protein
production are available it would be expected that this item
would be derived from _entity_src_gen_express.host_org_scientific_name
or via _entity_src_gen_express.host_org_tax_id
;
_item.name '_entity_src_gen.pdbx_host_org_scientific_name'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'ESCHERICHIA COLI'
'SACCHAROMYCES CEREVISIAE'
save_
save__entity_src_gen.pdbx_host_org_tissue
_item_description.description
; The specific tissue which expressed the molecule. Where full details
of the protein production are available it would be expected that this
item would be derived from _entity_src_gen_express.host_org_tissue
;
_item.name '_entity_src_gen.pdbx_host_org_tissue'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'heart'
'liver'
'eye lens'
save_
save__entity_src_gen.pdbx_host_org_vector
_item_description.description
; Identifies the vector used. Where full details of the protein
production are available it would be expected that this item
would be derived from _entity_src_gen_clone.vector_name.
;
_item.name '_entity_src_gen.pdbx_host_org_vector'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'PBIT36' 'PET15B' 'PUC18'
save_
save__entity_src_gen.pdbx_host_org_vector_type
_item_description.description
; Identifies the type of vector used (plasmid, virus, or cosmid).
Where full details of the protein production are available it
would be expected that this item would be derived from
_entity_src_gen_express.vector_type.
;
_item.name '_entity_src_gen.pdbx_host_org_vector_type'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'COSMID' 'PLASMID'
save_
save__entity_src_gen.expression_system_id
_item_description.description
; A unique identifier for the expression system. This
should be extracted from a local list of expression
systems.
;
_item.name '_entity_src_gen.expression_system_id'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code uline
save_
save__entity_src_gen.gene_src_dev_stage
_item_description.description
; A string to indicate the life-cycle or cell development
cycle in which the gene is expressed and the mature
protein is active.
;
_item.name '_entity_src_gen.gene_src_dev_stage'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_type.code text
save_
save__entity_src_gen.start_construct_id
_item_description.description
; A pointer to _pdbx_construct.id in the PDBX_CONSTRUCT category.
The indentified sequence is the initial construct.
;
_item.name '_entity_src_gen.start_construct_id'
_item.category_id entity_src_gen
_item.mandatory_code no
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_entity_src_gen.start_construct_id'
save_
#############################
# ENTITY_SRC_GEN_PROD_OTHER #
#############################
#
# _pdbx_entity_src_gen_prod_other.entry_id
# _pdbx_entity_src_gen_prod_other.entity_id
# _pdbx_entity_src_gen_prod_other.step_id
# _pdbx_entity_src_gen_prod_other.next_step_id
# _pdbx_entity_src_gen_prod_other.end_construct_id
# _pdbx_entity_src_gen_prod_other.process_name
# _pdbx_entity_src_gen_prod_other.date
# _pdbx_entity_src_gen_prod_other.robot_id
# _pdbx_entity_src_gen_prod_other.details
#
save_pdbx_entity_src_gen_prod_other
_category.description
; This category contains details for process steps that are
not explicitly catered for elsewhere. It provides some basic
details as well as placeholders for a list of parameters and
values (the category PDBX_ENTITY_SRC_GEN_PROD_OTHER_PARAMETER).
Note that processes that have been modelled explicitly should
not be represented using this category.
;
_category.id pdbx_entity_src_gen_prod_other
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_prod_other.entry_id'
'_pdbx_entity_src_gen_prod_other.entity_id'
'_pdbx_entity_src_gen_prod_other.step_id'
save_
save__pdbx_entity_src_gen_prod_other.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_prod_other.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_prod_other.entry_id'
_item.category_id pdbx_entity_src_gen_prod_other
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_other.entry_id'
save_
save__pdbx_entity_src_gen_prod_other.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_prod_other.entity_id uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category. This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_prod_other.entity_id'
_item.category_id pdbx_entity_src_gen_prod_other
_item.mandatory_code yes
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_other.entity_id'
save_
save__pdbx_entity_src_gen_prod_other.step_id
_item_description.description
; This item is the unique identifier for this process step.
;
_item.name '_pdbx_entity_src_gen_prod_other.step_id'
_item.category_id pdbx_entity_src_gen_prod_other
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_prod_other.next_step_id
_item_description.description
; This item unique identifier for the next production step.
This allows a workflow to have multiple entry points leading
to a single product.
;
_item.name '_pdbx_entity_src_gen_prod_other.next_step_id'
_item.category_id pdbx_entity_src_gen_prod_other
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_prod_other.end_construct_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced nucleic acid sequence is that of the
product of the process step.
;
_item.name '_pdbx_entity_src_gen_prod_other.end_construct_id'
_item.category_id pdbx_entity_src_gen_prod_other
_item.mandatory_code no
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_other.end_construct_id'
save_
save__pdbx_entity_src_gen_prod_other.robot_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id in the
PDBX_ROBOT_SYSTEM category. The referenced robot is the
robot responsible for the process step
;
_item.name '_pdbx_entity_src_gen_prod_other.robot_id'
_item.category_id pdbx_entity_src_gen_prod_other
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_other.robot_id'
save_
save__pdbx_entity_src_gen_prod_other.date
_item_description.description
; The date of this process step.
;
_item.name '_pdbx_entity_src_gen_prod_other.date'
_item.category_id pdbx_entity_src_gen_prod_other
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_entity_src_gen_prod_other.process_name
_item_description.description
; Name of this process step.
;
_item.name '_pdbx_entity_src_gen_prod_other.process_name'
_item.category_id pdbx_entity_src_gen_prod_other
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_prod_other.details
_item_description.description
; Additional details of this process step.
;
_item.name '_pdbx_entity_src_gen_prod_other.details'
_item.category_id pdbx_entity_src_gen_prod_other
_item.mandatory_code no
_item_type.code text
save_
############################################
# PDBX_ENTITY_SRC_GEN_PROD_OTHER_PARAMETER #
############################################
#
# _pdbx_entity_src_gen_prod_other_parameter.entry_id
# _pdbx_entity_src_gen_prod_other_parameter.entity_id
# _pdbx_entity_src_gen_prod_other_parameter.step_id
# _pdbx_entity_src_gen_prod_other_parameter.name
# _pdbx_entity_src_gen_prod_other_parameter.value
#
save_pdbx_entity_src_gen_prod_other_parameter
_category.description
; This category contains parameters and values required to capture
information about a particular process step
;
_category.id pdbx_entity_src_gen_prod_other_parameter
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_prod_other_parameter.entry_id'
'_pdbx_entity_src_gen_prod_other_parameter.entity_id'
'_pdbx_entity_src_gen_prod_other_parameter.step_id'
'_pdbx_entity_src_gen_prod_other_parameter.parameter'
save_
save__pdbx_entity_src_gen_prod_other_parameter.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_prod_other_parameter.entry_id is a pointer
to _pdbx_entity_src_gen_prod_other.entry.id
;
_item.name '_pdbx_entity_src_gen_prod_other_parameter.entry_id'
_item.category_id pdbx_entity_src_gen_prod_other_parameter
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_prod_other.entry_id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_other_parameter.entry_id'
save_
save__pdbx_entity_src_gen_prod_other_parameter.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_prod_other_parameter.entity_id is a pointer
to _pdbx_entity_src_gen_prod_other.entity_id
;
_item.name '_pdbx_entity_src_gen_prod_other_parameter.entity_id'
_item.category_id pdbx_entity_src_gen_prod_other_parameter
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_prod_other.entity_id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_other_parameter.entity_id'
save_
save__pdbx_entity_src_gen_prod_other_parameter.step_id
_item_description.description
; This item is a pointer to _pdbx_entity_src_gen_prod_other.step_id
;
_item.name '_pdbx_entity_src_gen_prod_other_parameter.step_id'
_item.category_id pdbx_entity_src_gen_prod_other_parameter
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_prod_other.step_id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_other_parameter.step_id'
save_
save__pdbx_entity_src_gen_prod_other_parameter.parameter
_item_description.description
; The name of the parameter associated with the process step
;
_item.name '_pdbx_entity_src_gen_prod_other_parameter.parameter'
_item.category_id pdbx_entity_src_gen_prod_other_parameter
_item.mandatory_code yes
_item_type.code line
save_
save__pdbx_entity_src_gen_prod_other_parameter.value
_item_description.description
; The value of the parameter
;
_item.name '_pdbx_entity_src_gen_prod_other_parameter.value'
_item.category_id pdbx_entity_src_gen_prod_other_parameter
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_entity_src_gen_prod_other_parameter.details
_item_description.description
; Additional details about the parameter
;
_item.name '_pdbx_entity_src_gen_prod_other_parameter.details'
_item.category_id pdbx_entity_src_gen_prod_other_parameter
_item.mandatory_code yes
_item_type.code text
save_
################################
# PDBX_ENTITY_SRC_GEN_PROD_PCR #
################################
#
# _pdbx_entity_src_gen_prod_pcr.entry_id
# _pdbx_entity_src_gen_prod_pcr.entity_id
# _pdbx_entity_src_gen_prod_pcr.step_id
# _pdbx_entity_src_gen_prod_pcr.next_step_id
# _pdbx_entity_src_gen_prod_pcr.end_construct_id
# _pdbx_entity_src_gen_prod_pcr.forward_primer_id
# _pdbx_entity_src_gen_prod_pcr.reverse_primer_id
# _pdbx_entity_src_gen_prod_pcr.reaction_details
# _pdbx_entity_src_gen_prod_pcr.purification_details
# _pdbx_entity_src_gen_prod_pcr.date
# _pdbx_entity_src_gen_prod_pcr.robot_id
#
# _pdbx_entity_src_gen_prod_pcr.summary
#
save_pdbx_entity_src_gen_prod_pcr
_category.description
; This category contains details for the PCR steps used in
the overall protein production process. The PCR is assumed
to be applied to the result of the previous production step, or the
gene source if this is the first production step.
;
_category.id pdbx_entity_src_gen_prod_pcr
_category.mandatory_code no
loop_
_category_key.name
'_pdbx_entity_src_gen_prod_pcr.entry_id'
'_pdbx_entity_src_gen_prod_pcr.entity_id'
'_pdbx_entity_src_gen_prod_pcr.step_id'
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - hypothetical example
;
;
_pdbx_entity_src_gen_prod_pcr.entry_id 111000111
_pdbx_entity_src_gen_prod_pcr.entity_id 222000111
_pdbx_entity_src_gen_prod_pcr.step_id 1
_pdbx_entity_src_gen_prod_pcr.next_step_id 2
_pdbx_entity_src_gen_prod_pcr.end_construct_id 440050000111
_pdbx_entity_src_gen_prod_pcr.robot_id 5
_pdbx_entity_src_gen_prod_pcr.date '2002-07-12:15:13'
_pdbx_entity_src_gen_prod_pcr.forward_primer_id 2
_pdbx_entity_src_gen_prod_pcr.reverse_primer_id 3
_pdbx_entity_src_gen_prod_pcr.reaction_details
; Annealing temperature = 70 C
Annealing time = 60 s
Extending temperature = 74 C
Extending time = 120 s
Melting temperature = 95 C
Melting time = 120 s
Number of cycles = 40
Polymerase = KOD
Template = 10 pmol
Primer = 25 pmol
Total volume = 25 ul
;
_pdbx_entity_src_gen_prod_pcr.purification_details
; No purification
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_entity_src_gen_prod_pcr.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_prod_pcr.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_prod_pcr.entry_id'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.entry_id'
save_
save__pdbx_entity_src_gen_prod_pcr.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_prod_pcr.entity_id uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category. This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_prod_pcr.entity_id'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code yes
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.entity_id'
save_
save__pdbx_entity_src_gen_prod_pcr.step_id
_item_description.description
; This item is the unique identifier for this PCR step.
;
_item.name '_pdbx_entity_src_gen_prod_pcr.step_id'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_prod_pcr.next_step_id
_item_description.description
; This item unique identifier for the next production step.
This allows a workflow to have multiple entry points leading
to a single product.
;
_item.name '_pdbx_entity_src_gen_prod_pcr.next_step_id'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_prod_pcr.end_construct_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced nucleic acid sequence is that of the
PCR product.
;
_item.name '_pdbx_entity_src_gen_prod_pcr.end_construct_id'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code no
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.end_construct_id'
save_
save__pdbx_entity_src_gen_prod_pcr.robot_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id in the
PDBX_ROBOT_SYSTEM category. The referenced robot is the
robot responsible for the PCR reaction (normally the heat
cycler).
;
_item.name '_pdbx_entity_src_gen_prod_pcr.robot_id'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.robot_id'
save_
save__pdbx_entity_src_gen_prod_pcr.date
_item_description.description
; The date of this production step.
;
_item.name '_pdbx_entity_src_gen_prod_pcr.date'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_entity_src_gen_prod_pcr.forward_primer_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category.
The referenced nucleic acid sequence is that of the forward primer.
;
_item.name '_pdbx_entity_src_gen_prod_pcr.forward_primer_id'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.forward_primer_id'
save_
save__pdbx_entity_src_gen_prod_pcr.reverse_primer_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category.
The referenced nucleic acid sequence is that of the reverse primer.
;
_item.name '_pdbx_entity_src_gen_prod_pcr.reverse_primer_id'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_pcr.reverse_primer_id'
save_
save__pdbx_entity_src_gen_prod_pcr.reaction_details
_item_description.description
; String value containing details of the PCR reaction.
;
_item.name '_pdbx_entity_src_gen_prod_pcr.reaction_details'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_prod_pcr.purification_details
_item_description.description
; String value containing details of any purification of the
product of the PCR reaction.
;
_item.name '_pdbx_entity_src_gen_prod_pcr.purification_details'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_prod_pcr.summary
_item_description.description
; Summary of the details of the PCR reaction any purification of the
product of the PCR reaction.
;
_item.name '_pdbx_entity_src_gen_prod_pcr.summary'
_item.category_id pdbx_entity_src_gen_prod_pcr
_item.mandatory_code no
_item_type.code text
save_
###################################
# PDBX_ENTITY_SRC_GEN_PROD_DIGEST #
###################################
#
# _pdbx_entity_src_gen_prod_digest.entry_id
# _pdbx_entity_src_gen_prod_digest.entity_id
# _pdbx_entity_src_gen_prod_digest.step_id
# _pdbx_entity_src_gen_prod_digest.next_step_id
# _pdbx_entity_src_gen_prod_digest.restriction_enzyme_1
# _pdbx_entity_src_gen_prod_digest.restriction_enzyme_2
# _pdbx_entity_src_gen_prod_digest.purification_details
# _pdbx_entity_src_gen_prod_digest.date
# _pdbx_entity_src_gen_prod_digest.robot_id
#
# _pdbx_entity_src_gen_prod_digest.summary
#
save_pdbx_entity_src_gen_prod_digest
_category.description
; This category contains details for the DIGEST steps used in
the overall protein production process. The digestion is assumed
to be applied to the result of the previous production step, or the
gene source if this is the first production step.
;
_category.id pdbx_entity_src_gen_prod_digest
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_prod_digest.entry_id'
'_pdbx_entity_src_gen_prod_digest.entity_id'
'_pdbx_entity_src_gen_prod_digest.step_id'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - hypothetical example
;
;
_pdbx_entity_src_gen_prod_digest.entry_id 111000111
_pdbx_entity_src_gen_prod_digest.entity_id 222000111
_pdbx_entity_src_gen_prod_digest.step_id 2
_pdbx_entity_src_gen_prod_digest.next_step_id 3
_pdbx_entity_src_gen_prod_digest.end_construct_id 440050000123
_pdbx_entity_src_gen_prod_digest.robot_id 5
_pdbx_entity_src_gen_prod_digest.date '2002-07-12:15:13'
_pdbx_entity_src_gen_prod_digest.restriction_enzyme_1 'NcoI'
_pdbx_entity_src_gen_prod_digest.restriction_enzyme_2 'BamII'
_pdbx_entity_src_gen_prod_digest.purification_details
; No purification
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_entity_src_gen_prod_digest.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_prod_digest.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_prod_digest.entry_id'
_item.category_id pdbx_entity_src_gen_prod_digest
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_digest.entry_id'
save_
save__pdbx_entity_src_gen_prod_digest.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_prod_digest.entity_id uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category. This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_prod_digest.entity_id'
_item.category_id pdbx_entity_src_gen_prod_digest
_item.mandatory_code yes
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_digest.entity_id'
save_
save__pdbx_entity_src_gen_prod_digest.step_id
_item_description.description
; This item is the unique identifier for this digestion step.
;
_item.name '_pdbx_entity_src_gen_prod_digest.step_id'
_item.category_id pdbx_entity_src_gen_prod_digest
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_prod_digest.next_step_id
_item_description.description
; This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
;
_item.name '_pdbx_entity_src_gen_prod_digest.next_step_id'
_item.category_id pdbx_entity_src_gen_prod_digest
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_prod_digest.end_construct_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the
PDBX_CONSTRUCT category. The referenced nucleic acid sequence
is that of the digest product
;
_item.name '_pdbx_entity_src_gen_prod_digest.end_construct_id'
_item.category_id pdbx_entity_src_gen_prod_digest
_item.mandatory_code no
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_digest.end_construct_id'
save_
save__pdbx_entity_src_gen_prod_digest.robot_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
;
_item.name '_pdbx_entity_src_gen_prod_digest.robot_id'
_item.category_id pdbx_entity_src_gen_prod_digest
_item.mandatory_code no
_item_type.code code
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_prod_digest.robot_id'
save_
save__pdbx_entity_src_gen_prod_digest.date
_item_description.description
; The date of this production step.
;
_item.name '_pdbx_entity_src_gen_prod_digest.date'
_item.category_id pdbx_entity_src_gen_prod_digest
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
_item_examples.case '2003-12-25'
save_
save__pdbx_entity_src_gen_prod_digest.restriction_enzyme_1
_item_description.description
; The first enzyme used in the restriction digestion. The sites at
which this cuts can be derived from the sequence.
;
_item.name '_pdbx_entity_src_gen_prod_digest.restriction_enzyme_1'
_item.category_id pdbx_entity_src_gen_prod_digest
_item.mandatory_code yes
_item_type.code text
_item_examples.case 'BamIII'
save_
save__pdbx_entity_src_gen_prod_digest.restriction_enzyme_2
_item_description.description
; The second enzyme used in the restriction digestion. The sites at
which this cuts can be derived from the sequence.
;
_item.name '_pdbx_entity_src_gen_prod_digest.restriction_enzyme_2'
_item.category_id pdbx_entity_src_gen_prod_digest
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_prod_digest.purification_details
_item_description.description
; String value containing details of any purification of the
product of the digestion.
;
_item.name '_pdbx_entity_src_gen_prod_digest.purification_details'
_item.category_id pdbx_entity_src_gen_prod_digest
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_prod_digest.summary
_item_description.description
; Summary of the details of restriction digestion any purification of the
product of the digestion.
;
_item.name '_pdbx_entity_src_gen_prod_digest.summary'
_item.category_id pdbx_entity_src_gen_prod_digest
_item.mandatory_code no
_item_type.code text
save_
########################
# ENTITY_SRC_GEN_CLONE #
########################
#
# _pdbx_entity_src_gen_clone.entry_id
# _pdbx_entity_src_gen_clone.entity_id
# _pdbx_entity_src_gen_clone.step_id
# _pdbx_entity_src_gen_clone.next_step_id
# _pdbx_entity_src_gen_clone.end_construct_id
# _pdbx_entity_src_gen_clone.robot_id
# _pdbx_entity_src_gen_clone.date
# _pdbx_entity_src_gen_clone.gene_insert_method
# _pdbx_entity_src_gen_clone.vector_name
# _pdbx_entity_src_gen_clone.vector_details
# _pdbx_entity_src_gen_clone.transformation_method
# _pdbx_entity_src_gen_clone.marker
# _pdbx_entity_src_gen_clone.verification_method
# _pdbx_entity_src_gen_clone.purification_details
#
#
# _pdbx_entity_src_gen_clone.summary
#
save_pdbx_entity_src_gen_clone
_category.description
; This category contains details for the cloning steps used in
the overall protein production process. Each row in PDBX_ENTITY_SRC_GEN_CLONE
should have an equivalent row in either PDBX_ENTITY_SRC_GEN_CLONE_LIGATION or
PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION. If only summary information is
provided data in the later two categories may be omitted.
;
_category.id pdbx_entity_src_gen_clone
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_clone.entry_id'
'_pdbx_entity_src_gen_clone.entity_id'
'_pdbx_entity_src_gen_clone.step_id'
save_
save__pdbx_entity_src_gen_clone.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_clone.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_clone.entry_id'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_clone.entry_id'
save_
save__pdbx_entity_src_gen_clone.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_clone.entity_id uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category. This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_clone.entity_id'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code yes
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_clone.entity_id'
save_
save__pdbx_entity_src_gen_clone.step_id
_item_description.description
; This item is the unique identifier for this cloning step.
;
_item.name '_pdbx_entity_src_gen_clone.step_id'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_clone.next_step_id
_item_description.description
; This item unique identifier for the next production step.
This allows a workflow to have multiple entry points leading
to a single product.
;
_item.name '_pdbx_entity_src_gen_clone.next_step_id'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_clone.end_construct_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced nucleic acid sequence is that of the
cloned product.
;
_item.name '_pdbx_entity_src_gen_clone.end_construct_id'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code no
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_clone.end_construct_id'
save_
save__pdbx_entity_src_gen_clone.robot_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id in the
PDBX_ROBOT_SYSTEM category.
;
_item.name '_pdbx_entity_src_gen_clone.robot_id'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_clone.robot_id'
save_
save__pdbx_entity_src_gen_clone.date
_item_description.description
; The date of this production step.
;
_item.name '_pdbx_entity_src_gen_clone.date'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_entity_src_gen_clone.gene_insert_method
_item_description.description
; The method used to insert the gene into the vector. For 'Ligation', an
PDBX_ENTITY_SRC_GEN_CLONE_LIGATION entry with matching .step_id is expected. For
'Recombination', an PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION entry with matching
.step_id is expected.
;
_item.name '_pdbx_entity_src_gen_clone.gene_insert_method'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
L 'Ligation'
R 'Recombination'
save_
save__pdbx_entity_src_gen_clone.vector_name
_item_description.description
; The name of the vector used in this cloning step.
;
_item.name '_pdbx_entity_src_gen_clone.vector_name'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_clone.vector_details
_item_description.description
; Details of any modifications made to the named vector.
;
_item.name '_pdbx_entity_src_gen_clone.vector_details'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_clone.transformation_method
_item_description.description
; The method used to transform the expression cell line with the vector
;
_item.name '_pdbx_entity_src_gen_clone.transformation_method'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
H 'Heat shock'
E 'Electroporation'
C 'Calcium shock'
save_
save__pdbx_entity_src_gen_clone.marker
_item_description.description
; The type of marker included to allow selection of transformed cells
;
_item.name '_pdbx_entity_src_gen_clone.marker'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
A 'Antibiotic resistance'
F 'Fluorescence'
save_
save__pdbx_entity_src_gen_clone.verification_method
_item_description.description
; The method used to verify that the incorporated gene is correct
;
_item.name '_pdbx_entity_src_gen_clone.verification_method'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
P 'PCR on plasmid'
R 'Restriction enzyme digestion'
D 'DNA sequencing'
save_
save__pdbx_entity_src_gen_clone.purification_details
_item_description.description
; Details of any purification of the product.
;
_item.name '_pdbx_entity_src_gen_clone.purification_details'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_clone.summary
_item_description.description
; Summary of ligation or recombionation cloning used, the associated
verification method and any purification of the product.
;
_item.name '_pdbx_entity_src_gen_clone.summary'
_item.category_id pdbx_entity_src_gen_clone
_item.mandatory_code no
_item_type.code text
save_
######################################
# PDBX_ENTITY_SRC_GEN_CLONE_LIGATION #
######################################
#
# _pdbx_entity_src_gen_clone_ligation.entry_id
# _pdbx_entity_src_gen_clone_ligation.entity_id
# _pdbx_entity_src_gen_clone_ligation.step_id
# _pdbx_entity_src_gen_clone_ligation.cleavage_enzymes
# _pdbx_entity_src_gen_clone_ligation.ligation_enzymes
# _pdbx_entity_src_gen_clone_ligation.temperature
# _pdbx_entity_src_gen_clone_ligation.time
# _pdbx_entity_src_gen_clone_ligation.details
#
save_pdbx_entity_src_gen_clone_ligation
_category.description
; This category contains details for the ligation-based cloning steps used in
the overall protein production process.
_pdbx_entity_src_gen_clone_ligation.clone_step_id in this category
must point at a defined _pdbx_entity_src_gen_clone.step_id. The details in
PDBX_ENTITY_SRC_GEN_CLONE_LIGATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE
to cover ligation dependent cloning steps.
;
_category.id pdbx_entity_src_gen_clone_ligation
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_clone_ligation.entry_id'
'_pdbx_entity_src_gen_clone_ligation.entity_id'
'_pdbx_entity_src_gen_clone_ligation.step_id'
save_
save__pdbx_entity_src_gen_clone_ligation.entry_id
_item_description.description
; This item is a pointer to _pdbx_entity_src_gen_clone.entry_id in the
PDBX_ENTITY_SRC_GEN_CLONE category.
;
_item.name '_pdbx_entity_src_gen_clone_ligation.entry_id'
_item.category_id pdbx_entity_src_gen_clone_ligation
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_clone.entry_id'
_item_linked.child_name '_pdbx_entity_src_gen_clone_ligation.entry_id'
save_
save__pdbx_entity_src_gen_clone_ligation.entity_id
_item_description.description
; This item is a pointer to _pdbx_entity_src_gen_clone.entity_id in the
PDBX_ENTITY_SRC_GEN_CLONE category.
;
_item.name '_pdbx_entity_src_gen_clone_ligation.entity_id'
_item.category_id pdbx_entity_src_gen_clone_ligation
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_clone.entity_id'
_item_linked.child_name '_pdbx_entity_src_gen_clone_ligation.entity_id'
save_
save__pdbx_entity_src_gen_clone_ligation.step_id
_item_description.description
; This item is a pointer to _pdbx_entity_src_gen_clone.step_id in the
PDBX_ENTITY_SRC_GEN_CLONE category.
;
_item.name '_pdbx_entity_src_gen_clone_ligation.step_id'
_item.category_id pdbx_entity_src_gen_clone_ligation
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_clone.step_id'
_item_linked.child_name '_pdbx_entity_src_gen_clone_ligation.step_id'
save_
save__pdbx_entity_src_gen_clone_ligation.cleavage_enzymes
_item_description.description
; The names of the enzymes used to cleave the vector. In addition an enzyme
used to blunt the cut ends, etc., should be named here.
;
_item.name '_pdbx_entity_src_gen_clone_ligation.cleavage_enzymes'
_item.category_id pdbx_entity_src_gen_clone_ligation
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_entity_src_gen_clone_ligation.ligation_enzymes
_item_description.description
; The names of the enzymes used to ligate the gene into the cleaved vector.
;
_item.name '_pdbx_entity_src_gen_clone_ligation.ligation_enzymes'
_item.category_id pdbx_entity_src_gen_clone_ligation
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_entity_src_gen_clone_ligation.temperature
_item_description.description
; The temperature at which the ligation experiment was performed, in degrees
celsius.
;
_item.name '_pdbx_entity_src_gen_clone_ligation.temperature'
_item.category_id pdbx_entity_src_gen_clone_ligation
_item.mandatory_code yes
_item_type.code float
_item_units.code celsius
save_
save__pdbx_entity_src_gen_clone_ligation.time
_item_description.description
; The duration of the ligation reaction in minutes.
;
_item.name '_pdbx_entity_src_gen_clone_ligation.time'
_item.category_id pdbx_entity_src_gen_clone_ligation
_item.mandatory_code yes
_item_type.code int
_item_units.code minutes
save_
save__pdbx_entity_src_gen_clone_ligation.details
_item_description.description
; Any details to be associated with this ligation step, e.g. the protocol.
;
_item.name '_pdbx_entity_src_gen_clone_ligation.details'
_item.category_id pdbx_entity_src_gen_clone_ligation
_item.mandatory_code no
_item_type.code text
save_
###########################################
# PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION #
###########################################
#
# _pdbx_entity_src_gen_clone_recombination.entry__id
# _pdbx_entity_src_gen_clone_recombination.entity_id
# _pdbx_entity_src_gen_clone_recombination.step_id
# _pdbx_entity_src_gen_clone_recombination.system
# _pdbx_entity_src_gen_clone_recombination.recombination_enzymes
# _pdbx_entity_src_gen_clone_recombination.details
#
save_pdbx_entity_src_gen_clone_recombination
_category.description
; This category contains details for the recombination-based cloning steps
used in the overall protein production process. It is assumed that these
reactions will use commercially available kits.
_pdbx_entity_src_gen_clone_recombination.clone_step_id in this category
must point at a defined _pdbx_entity_src_gen_clone.step_id. The details in
PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE
to cover recombination dependent cloning steps.
;
_category.id pdbx_entity_src_gen_clone_recombination
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_clone_recombination.entry_id'
'_pdbx_entity_src_gen_clone_recombination.entity_id'
'_pdbx_entity_src_gen_clone_recombination.step_id'
save_
save__pdbx_entity_src_gen_clone_recombination.entry_id
_item_description.description
; This item is a pointer to _pdbx_entity_src_gen_clone.entry_id in the
PDBX_ENTITY_SRC_GEN_CLONE category.
;
_item.name '_pdbx_entity_src_gen_clone_recombination.entry_id'
_item.category_id pdbx_entity_src_gen_clone_recombination
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_clone.entry_id'
_item_linked.child_name '_pdbx_entity_src_gen_clone_recombination.entry_id'
save_
save__pdbx_entity_src_gen_clone_recombination.entity_id
_item_description.description
; This item is a pointer to _pdbx_entity_src_gen_clone.entity_id in the
PDBX_ENTITY_SRC_GEN_CLONE category.
;
_item.name '_pdbx_entity_src_gen_clone_recombination.entity_id'
_item.category_id pdbx_entity_src_gen_clone_recombination
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_clone.entity_id'
_item_linked.child_name '_pdbx_entity_src_gen_clone_recombination.entity_id'
save_
save__pdbx_entity_src_gen_clone_recombination.step_id
_item_description.description
; This item is a pointer to _pdbx_entity_src_gen_clone.step_id in the
PDBX_ENTITY_SRC_GEN_CLONE category.
;
_item.name '_pdbx_entity_src_gen_clone_recombination.step_id'
_item.category_id pdbx_entity_src_gen_clone_recombination
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_clone.step_id'
_item_linked.child_name '_pdbx_entity_src_gen_clone_recombination.step_id'
save_
save__pdbx_entity_src_gen_clone_recombination.system
_item_description.description
; The name of the recombination system.
;
_item.name '_pdbx_entity_src_gen_clone_recombination.system'
_item.category_id pdbx_entity_src_gen_clone_recombination
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
G 'Gateway Tm'
I 'Infusion/Creator Tm'
N 'Novagen's system - name?'
save_
save__pdbx_entity_src_gen_clone_recombination.recombination_enzymes
_item_description.description
; The names of the enzymes used for this recombination step.
;
_item.name '_pdbx_entity_src_gen_clone_recombination.recombination_enzymes'
_item.category_id pdbx_entity_src_gen_clone_recombination
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
B 'Gateway BP clonase'
L 'Gateway LR clonase'
T 'Topoisomerase'
C 'Cre recombinase'
I 'Infusion enzyme - name?'
save_
save__pdbx_entity_src_gen_clone_recombination.details
_item_description.description
; Any details to be associated with this recombination step, e.g. the protocol
or differences from the manufacturer's specified protocol.
;
_item.name '_pdbx_entity_src_gen_clone_recombination.details'
_item.category_id pdbx_entity_src_gen_clone_recombination
_item.mandatory_code no
_item_type.code text
save_
###############################
# PDBX_ENTITY_SRC_GEN_EXPRESS #
###############################
#
# _pdbx_entity_src_gen_express.entry_id
# _pdbx_entity_src_gen_express.entity_id
# _pdbx_entity_src_gen_express.step_id
# _pdbx_entity_src_gen_express.next_step_id
# _pdbx_entity_src_gen_express.end_construct_id
# _pdbx_entity_src_gen_express.robot_id
# _pdbx_entity_src_gen_express.date
# _pdbx_entity_src_gen_express.promoter_type
# _pdbx_entity_src_gen_express.plasmid_id
# _pdbx_entity_src_gen_express.vector_type
# _pdbx_entity_src_gen_express.N_terminal_seq_tag
# _pdbx_entity_src_gen_express.C_terminal_seq_tag
# _pdbx_entity_src_gen_express.host_org_scientific_name
# _pdbx_entity_src_gen_express.host_org_common_name
# _pdbx_entity_src_gen_express.host_org_variant
# _pdbx_entity_src_gen_express.host_org_strain
# _pdbx_entity_src_gen_express.host_org_tissue
# _pdbx_entity_src_gen_express.host_org_tax_id
# _pdbx_entity_src_gen_express.host_org_culture_collection
# _pdbx_entity_src_gen_express.host_org_cell_line
# _pdbx_entity_src_gen_express.host_org_details
# _pdbx_entity_src_gen_express.culture_base_media
# _pdbx_entity_src_gen_express.culture_additives
# _pdbx_entity_src_gen_express.culture_volume
# _pdbx_entity_src_gen_express.culture_time
# _pdbx_entity_src_gen_express.culture_temperature
# _pdbx_entity_src_gen_express.inducer
# _pdbx_entity_src_gen_express.inducer_concentration
# _pdbx_entity_src_gen_express.induction_details
# _pdbx_entity_src_gen_express.multiplicity_of_infection
# _pdbx_entity_src_gen_express.induction_growth_time
# _pdbx_entity_src_gen_express.induction_temperature
# _pdbx_entity_src_gen_express.harvesting_details
# _pdbx_entity_src_gen_express.storage_details
#
# _pdbx_entity_src_gen_express.summary
#
save_pdbx_entity_src_gen_express
_category.description
; This category contains details for the EXPRESSION steps used in
the overall protein production process. It is hoped that this category
will cover all forms of cell-based expression by reading induction as
induction/transformation/transfection.
;
_category.id pdbx_entity_src_gen_express
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_express.entry_id'
'_pdbx_entity_src_gen_express.entity_id'
'_pdbx_entity_src_gen_express.step_id'
save_
save__pdbx_entity_src_gen_express.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_express.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_express.entry_id'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code code
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_express.entry_id'
save_
save__pdbx_entity_src_gen_express.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_express.entity_id uniquely identifies
each protein contained in the project target complex proteins whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category.
This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_express.entity_id'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code code
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_express.entity_id'
save_
save__pdbx_entity_src_gen_express.step_id
_item_description.description
; This item is the unique identifier for this expression step.
;
_item.name '_pdbx_entity_src_gen_express.step_id'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_express.next_step_id
_item_description.description
; This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
;
_item.name '_pdbx_entity_src_gen_express.next_step_id'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_express.end_construct_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product.
;
_item.name '_pdbx_entity_src_gen_express.end_construct_id'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code int
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_express.end_construct_id'
save_
save__pdbx_entity_src_gen_express.robot_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
;
_item.name '_pdbx_entity_src_gen_express.robot_id'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_express.robot_id'
save_
save__pdbx_entity_src_gen_express.date
_item_description.description
; The date of production step.
;
_item.name '_pdbx_entity_src_gen_express.date'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_entity_src_gen_express.promoter_type
_item_description.description
; The nature of the promoter controlling expression of the gene.
;
_item.name '_pdbx_entity_src_gen_express.promoter_type'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code text
_item_examples.case 'T7 LacZ'
save_
save__pdbx_entity_src_gen_express.plasmid_id
_item_description.description
; This item is a pointer to _pdbx_construct.id in the
PDBX_CONSTRUCT category. The referenced entry will contain
the nucleotide sequence that is to be expressed, including tags.
;
_item.name '_pdbx_entity_src_gen_express.plasmid_id'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code code
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_express.plasmid_id'
save_
save__pdbx_entity_src_gen_express.vector_type
_item_description.description
; Identifies the type of vector used (plasmid, virus, or cosmid)
in the expression system.
;
_item.name '_pdbx_entity_src_gen_express.vector_type'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_entity_src_gen_express.N_terminal_seq_tag
_item_description.description
; Any N-terminal sequence tag as a string of one letter amino acid codes.
;
_item.name '_pdbx_entity_src_gen_express.N_terminal_seq_tag'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_entity_src_gen_express.C_terminal_seq_tag
_item_description.description
; Any C-terminal sequence tag as a string of one letter amino acid codes
;
_item.name '_pdbx_entity_src_gen_express.C_terminal_seq_tag'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_entity_src_gen_express.host_org_scientific_name
_item_description.description
; The scientific name of the organism that served as host for the
expression system. It is expected that either this item or
_pdbx_entity_src_gen_express.host_org_tax_id should be populated.
;
_item.name '_pdbx_entity_src_gen_express.host_org_scientific_name'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_entity_src_gen_express.host_org_common_name
_item_description.description
; The common name of the organism that served as host for the
expression system. Where _pdbx_entity_src_gen_express.host_org_tax_id
is populated it is expected that this item may be derived by
look up against the taxonomy database.
;
_item.name '_pdbx_entity_src_gen_express.host_org_common_name'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_entity_src_gen_express.host_org_variant
_item_description.description
; The vairant of the organism that served as host for the expression
system. Where _pdbx_entity_src_gen_express.host_org_tax_id is
populated it is expected that this item may be derived by a
look up against the taxonomy database.
;
_item.name '_pdbx_entity_src_gen_express.host_org_variant'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_entity_src_gen_express.host_org_strain
_item_description.description
; The strain of the organism that served as host for the expression
system. Where _pdbx_entity_src_gen_express.host_org_tax_id is
populated it is expected that this item may be derived by a
look up against the taxonomy database.
;
_item.name '_pdbx_entity_src_gen_express.host_org_strain'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_entity_src_gen_express.host_org_tissue
_item_description.description
; The specific tissue which expressed the molecule.
;
_item.name '_pdbx_entity_src_gen_express.host_org_tissue'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_entity_src_gen_express.host_org_culture_collection
_item_description.description
; Culture collection of the expression system
;
_item.name '_pdbx_entity_src_gen_express.host_org_culture_collection'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_entity_src_gen_express.host_org_cell_line
_item_description.description
; A specific line of cells used as the expression system
;
_item.name '_pdbx_entity_src_gen_express.host_org_cell_line'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_entity_src_gen_express.host_org_tax_id
_item_description.description
; The id for the NCBI taxonomy node corresponding to the organism that
served as host for the expression system.
;
_item.name '_pdbx_entity_src_gen_express.host_org_tax_id'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_entity_src_gen_express.host_org_details
_item_description.description
; A description of special aspects of the organism that served as
host for the expression system.
;
_item.name '_pdbx_entity_src_gen_express.host_org_details'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_express.culture_base_media
_item_description.description
; The name of the base media in which the expression host was grown.
;
_item.name '_pdbx_entity_src_gen_express.culture_base_media'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_express.culture_additives
_item_description.description
; Any additives to the base media in which the expression host was grown.
;
_item.name '_pdbx_entity_src_gen_express.culture_additives'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_express.culture_volume
_item_description.description
; The volume of media in milliliters in which the expression host was grown.
;
_item.name '_pdbx_entity_src_gen_express.culture_volume'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code float
_item_units.code milliliters
save_
save__pdbx_entity_src_gen_express.culture_time
_item_description.description
; The time in hours for which the expression host was allowed to grow
prior to induction/transformation/transfection.
;
_item.name '_pdbx_entity_src_gen_express.culture_time'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code float
_item_units.code hours
save_
save__pdbx_entity_src_gen_express.culture_temperature
_item_description.description
; The temperature in degrees celsius at which the expression host was allowed
to grow prior to induction/transformation/transfection.
;
_item.name '_pdbx_entity_src_gen_express.culture_temperature'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code float
_item_units.code celsius
save_
save__pdbx_entity_src_gen_express.inducer
_item_description.description
; The chemical name of the inducing agent.
;
_item.name '_pdbx_entity_src_gen_express.inducer'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_entity_src_gen_express.inducer_concentration
_item_description.description
; Concentration of the inducing agent.
;
_item.name '_pdbx_entity_src_gen_express.inducer_concentration'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code float
_item_units.code mg_per_ml
save_
save__pdbx_entity_src_gen_express.induction_details
_item_description.description
; Details of induction/transformation/transfection.
;
_item.name '_pdbx_entity_src_gen_express.induction_details'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_express.multiplicity_of_infection
_item_description.description
; The multiplicity of infection for genes introduced by transfection, eg.
for baculovirus-based expression.
;
_item.name '_pdbx_entity_src_gen_express.multiplicity_of_infection'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code float
_item_units.code arbitrary
save_
save__pdbx_entity_src_gen_express.induction_timepoint
_item_description.description
; The time in hours after induction/transformation/transfection at which
the optical density of the culture was measured.
;
_item.name '_pdbx_entity_src_gen_express.induction_timepoint'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code float
_item_units.code hours
save_
save__pdbx_entity_src_gen_express.induction_temperature
_item_description.description
; The temperature in celsius at which the induced/transformed/transfected
cells were grown.
;
_item.name '_pdbx_entity_src_gen_express.induction_temperature'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code yes
_item_type.code float
_item_units.code celsius
save_
save__pdbx_entity_src_gen_express.harvesting_details
_item_description.description
; Details of the harvesting protocol.
;
_item.name '_pdbx_entity_src_gen_express.harvesting_details'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_express.storage_details
_item_description.description
; Details of how the harvested culture was stored.
;
_item.name '_pdbx_entity_src_gen_express.storage_details'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_express.summary
_item_description.description
; Summary of the details of the expression steps used in protein production.
;
_item.name '_pdbx_entity_src_gen_express.summary'
_item.category_id pdbx_entity_src_gen_express
_item.mandatory_code no
_item_type.code text
save_
#########################################
# PDBX_ENTITY_SRC_GEN_EXPRESS_TIMEPOINT #
#########################################
#
# _pdbx_entity_src_gen_express_timepoint.entry_id
# _pdbx_entity_src_gen_express_timepoint.entity_id
# _pdbx_entity_src_gen_express_timepoint.step_id
# _pdbx_entity_src_gen_express_timepoint.serial
# _pdbx_entity_src_gen_express_timepoint.time
# _pdbx_entity_src_gen_express_timepoint.OD
#
save_pdbx_entity_src_gen_express_timepoint
_category.description
; This category contains details for OD time series used to monitor a
given EXPRESSION step used in the overall protein production process.
;
_category.id pdbx_entity_src_gen_express_timepoint
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_express_timepoint.entry_id'
'_pdbx_entity_src_gen_express_timepoint.entity_id'
'_pdbx_entity_src_gen_express_timepoint.step_id'
'_pdbx_entity_src_gen_express_timepoint.serial'
save_
save__pdbx_entity_src_gen_express_timepoint.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_express_timepoint.entry_id is a pointer
to _pdbx_entity_src_gen_express.entry_id
;
_item.name '_pdbx_entity_src_gen_express_timepoint.entry_id'
_item.category_id pdbx_entity_src_gen_express_timepoint
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_express.entry_id'
_item_linked.child_name '_pdbx_entity_src_gen_express_timepoint.entry_id'
save_
save__pdbx_entity_src_gen_express_timepoint.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_express_timepoint.entity_id is a pointer
to _pdbx_entity_src_gen_express.entity_id
;
_item.name '_pdbx_entity_src_gen_express_timepoint.entity_id'
_item.category_id pdbx_entity_src_gen_express_timepoint
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_express.entity_id'
_item_linked.child_name '_pdbx_entity_src_gen_express_timepoint.entity_id'
save_
save__pdbx_entity_src_gen_express_timepoint.step_id
_item_description.description
; This item is a pointer to _pdbx_entity_src_gen_express.step_id
;
_item.name '_pdbx_entity_src_gen_express_timepoint.step_id'
_item.category_id pdbx_entity_src_gen_express_timepoint
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_entity_src_gen_express.step_id'
_item_linked.child_name '_pdbx_entity_src_gen_express_timepoint.step_id'
save_
save__pdbx_entity_src_gen_express_timepoint.serial
_item_description.description
; This items uniquely defines a timepoint within a series.
;
_item.name '_pdbx_entity_src_gen_express_timepoint.serial'
_item.category_id pdbx_entity_src_gen_express_timepoint
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_express_timepoint.OD
_item_description.description
; The optical density of the expression culture in arbitrary units at the
timepoint specified.
;
_item.name '_pdbx_entity_src_gen_express_timepoint.OD'
_item.category_id pdbx_entity_src_gen_express_timepoint
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_express_timepoint.time
_item_description.description
; The time in hours after induction/transformation/transfection at which
the optical density of the culture was measured.
;
_item.name '_pdbx_entity_src_gen_express_timepoint.time'
_item.category_id pdbx_entity_src_gen_express_timepoint
_item.mandatory_code yes
_item_type.code int
save_
#############################
# PDBX_ENTITY_SRC_GEN_LYSIS #
#############################
#
# _pdbx_entity_src_gen_lysis.entry_id
# _pdbx_entity_src_gen_lysis.entity_id
# _pdbx_entity_src_gen_lysis.step_id
# _pdbx_entity_src_gen_lysis.next_step_id
# _pdbx_entity_src_gen_lysis.end_construct_id
# _pdbx_entity_src_gen_lysis.date
# _pdbx_entity_src_gen_lysis.robot_id
# _pdbx_entity_src_gen_lysis.method
# _pdbx_entity_src_gen_lysis.buffer_id
# _pdbx_entity_src_gen_lysis.buffer_volume
# _pdbx_entity_src_gen_lysis.temperature
# _pdbx_entity_src_gen_lysis.time
# _pdbx_entity_src_gen_lysis.details
#
save_pdbx_entity_src_gen_lysis
_category.description
; This category contains details for the cell lysis steps used in
the overall protein production process.
;
_category.id pdbx_entity_src_gen_lysis
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_lysis.entry_id'
'_pdbx_entity_src_gen_lysis.entity_id'
'_pdbx_entity_src_gen_lysis.step_id'
save_
save__pdbx_entity_src_gen_lysis.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_lysis.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_lysis.entry_id'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_lysis.entry_id'
save_
save__pdbx_entity_src_gen_lysis.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_lysis.entity_id uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category. This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_lysis.entity_id'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code yes
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_lysis.entity_id'
save_
save__pdbx_entity_src_gen_lysis.step_id
_item_description.description
; This item is the unique identifier for this lysis step.
;
_item.name '_pdbx_entity_src_gen_lysis.step_id'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_lysis.next_step_id
_item_description.description
; This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
;
_item.name '_pdbx_entity_src_gen_lysis.next_step_id'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_lysis.end_construct_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product after lysis.
;
_item.name '_pdbx_entity_src_gen_lysis.end_construct_id'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code no
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_lysis.end_construct_id'
save_
save__pdbx_entity_src_gen_lysis.robot_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
;
_item.name '_pdbx_entity_src_gen_lysis.robot_id'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_lysis.robot_id'
save_
save__pdbx_entity_src_gen_lysis.date
_item_description.description
; The date of this production step.
;
_item.name '_pdbx_entity_src_gen_lysis.date'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_entity_src_gen_lysis.method
_item_description.description
; The lysis method.
;
_item.name '_pdbx_entity_src_gen_lysis.method'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
S 'Sonication'
D 'Detergent'
B 'Sonication and detergent'
save_
save__pdbx_entity_src_gen_lysis.buffer_id
_item_description.description
; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the lysis was performed.
;
_item.name '_pdbx_entity_src_gen_lysis.buffer_id'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code yes
_item_type.code code
_item_linked.parent_name '_pdbx_buffer.id'
_item_linked.child_name '_pdbx_entity_src_gen_lysis.buffer_id'
save_
save__pdbx_entity_src_gen_lysis.buffer_volume
_item_description.description
; The volume in milliliters of buffer in which the lysis was performed.
;
_item.name '_pdbx_entity_src_gen_lysis.buffer_volume'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code yes
_item_type.code float
_item_units.code milliliters
save_
save__pdbx_entity_src_gen_lysis.temperature
_item_description.description
; The temperature in degrees celsius at which the lysis was performed.
;
_item.name '_pdbx_entity_src_gen_lysis.temperature'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code yes
_item_type.code float
_item_units.code celsius
save_
save__pdbx_entity_src_gen_lysis.time
_item_description.description
; The time in seconds of the lysis experiment.
;
_item.name '_pdbx_entity_src_gen_lysis.time'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code yes
_item_type.code float
_item_units.code minutes
save_
save__pdbx_entity_src_gen_lysis.details
_item_description.description
; String value containing details of the lysis protocol.
;
_item.name '_pdbx_entity_src_gen_lysis.details'
_item.category_id pdbx_entity_src_gen_lysis
_item.mandatory_code no
_item_type.code text
save_
##############################
# PDBX_ENTITY_SRC_GEN_REFOLD #
##############################
#
# _pdbx_entity_src_gen_refold.entry_id
# _pdbx_entity_src_gen_refold.entity_id
# _pdbx_entity_src_gen_refold.step_id
# _pdbx_entity_src_gen_refold.next_step_id
# _pdbx_entity_src_gen_refold.end_construct_id
# _pdbx_entity_src_gen_refold.robot_id
# _pdbx_entity_src_gen_refold.date
# _pdbx_entity_src_gen_refold.denature_buffer_id
# _pdbx_entity_src_gen_refold.refold_buffer_id
# _pdbx_entity_src_gen_refold.temperature
# _pdbx_entity_src_gen_refold.time
# _pdbx_entity_src_gen_refold.storage_buffer_id
# _pdbx_entity_src_gen_refold.details
#
save_pdbx_entity_src_gen_refold
_category.description
; This category contains details for the refolding steps used in
the overall protein production process.
;
_category.id pdbx_entity_src_gen_refold
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_refold.entry_id'
'_pdbx_entity_src_gen_refold.entity_id'
'_pdbx_entity_src_gen_refold.step_id'
save_
save__pdbx_entity_src_gen_refold.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_refold.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_refold.entry_id'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_refold.entry_id'
save_
save__pdbx_entity_src_gen_refold.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_refold.entity_id uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category. This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_refold.entity_id'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code yes
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_refold.entity_id'
save_
save__pdbx_entity_src_gen_refold.step_id
_item_description.description
; This item is the unique identifier for this refolding step.
;
_item.name '_pdbx_entity_src_gen_refold.step_id'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_refold.next_step_id
_item_description.description
; This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
;
_item.name '_pdbx_entity_src_gen_refold.next_step_id'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_refold.end_construct_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product after the refolding
step.
;
_item.name '_pdbx_entity_src_gen_refold.end_construct_id'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code no
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_refold.end_construct_id'
save_
save__pdbx_entity_src_gen_refold.robot_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
;
_item.name '_pdbx_entity_src_gen_refold.robot_id'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_refold.robot_id'
save_
save__pdbx_entity_src_gen_refold.date
_item_description.description
; The date of this production step.
;
_item.name '_pdbx_entity_src_gen_refold.date'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_entity_src_gen_refold.denature_buffer_id
_item_description.description
; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the protein was denatured.
;
_item.name '_pdbx_entity_src_gen_refold.denature_buffer_id'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_buffer.id'
_item_linked.child_name '_pdbx_entity_src_gen_refold.denature_buffer_id'
save_
save__pdbx_entity_src_gen_refold.refold_buffer_id
_item_description.description
; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the protein was refolded.
;
_item.name '_pdbx_entity_src_gen_refold.refold_buffer_id'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_buffer.id'
_item_linked.child_name '_pdbx_entity_src_gen_refold.refold_buffer_id'
save_
save__pdbx_entity_src_gen_refold.temperature
_item_description.description
; The temperature in degrees celsius at which the protein was refolded.
;
_item.name '_pdbx_entity_src_gen_refold.temperature'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code yes
_item_type.code float
_item_units.code celsius
save_
save__pdbx_entity_src_gen_refold.time
_item_description.description
; The time in hours over which the protein was refolded.
;
_item.name '_pdbx_entity_src_gen_refold.time'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code yes
_item_type.code float
_item_units.code hours
save_
save__pdbx_entity_src_gen_refold.storage_buffer_id
_item_description.description
; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the refolded protein was stored.
;
_item.name '_pdbx_entity_src_gen_refold.storage_buffer_id'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_buffer.id'
_item_linked.child_name '_pdbx_entity_src_gen_refold.storage_buffer_id'
save_
save__pdbx_entity_src_gen_refold.details
_item_description.description
; String value containing details of the refolding.
;
_item.name '_pdbx_entity_src_gen_refold.details'
_item.category_id pdbx_entity_src_gen_refold
_item.mandatory_code no
_item_type.code text
save_
###################################
# PDBX_ENTITY_SRC_GEN_PROTEOLYSIS #
###################################
#
# _pdbx_entity_src_gen_proteolysis.entry_id
# _pdbx_entity_src_gen_proteolysis.entity_id
# _pdbx_entity_src_gen_proteolysis.step_id
# _pdbx_entity_src_gen_proteolysis.next_step_id
# _pdbx_entity_src_gen_proteolysis.end_construct_id
# _pdbx_entity_src_gen_proteolysis.date
# _pdbx_entity_src_gen_proteolysis.robot_id
# _pdbx_entity_src_gen_proteolysis.details
# _pdbx_entity_src_gen_proteolysis.protease
# _pdbx_entity_src_gen_proteolysis.protein_protease_ratio
# _pdbx_entity_src_gen_proteolysis.cleavage_buffer
# _pdbx_entity_src_gen_proteolysis.cleavage_temperature
# _pdbx_entity_src_gen_proteolysis.cleavage_time
#
save_pdbx_entity_src_gen_proteolysis
_category.description
; This category contains details for the protein purification
tag removal steps used in the overall protein production process
;
_category.id pdbx_entity_src_gen_proteolysis
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_proteolysis.entry_id'
'_pdbx_entity_src_gen_proteolysis.entity_id'
'_pdbx_entity_src_gen_proteolysis.step_id'
save_
save__pdbx_entity_src_gen_proteolysis.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_proteolysis.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_proteolysis.entry_id'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_proteolysis.entry_id'
save_
save__pdbx_entity_src_gen_proteolysis.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_proteolysis.entity_id uniquely identifies
each protein contained in the project target complex proteins whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category. This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_proteolysis.entity_id'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code yes
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_proteolysis.entity_id'
save_
save__pdbx_entity_src_gen_proteolysis.step_id
_item_description.description
; This item is the unique identifier for this tag removal step.
;
_item.name '_pdbx_entity_src_gen_proteolysis.step_id'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_proteolysis.next_step_id
_item_description.description
; This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
;
_item.name '_pdbx_entity_src_gen_proteolysis.next_step_id'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_proteolysis.end_construct_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product after the proteolysis
step.
;
_item.name '_pdbx_entity_src_gen_proteolysis.end_construct_id'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code no
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_proteolysis.end_construct_id'
save_
save__pdbx_entity_src_gen_proteolysis.robot_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
;
_item.name '_pdbx_entity_src_gen_proteolysis.robot_id'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_proteolysis.robot_id'
save_
save__pdbx_entity_src_gen_proteolysis.date
_item_description.description
; The date of production step.
;
_item.name '_pdbx_entity_src_gen_proteolysis.date'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_entity_src_gen_proteolysis.details
_item_description.description
; Details of this tag removal step.
;
_item.name '_pdbx_entity_src_gen_proteolysis.details'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_proteolysis.protease
_item_description.description
; The name of the protease used for cleavage.
;
_item.name '_pdbx_entity_src_gen_proteolysis.protease'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_entity_src_gen_proteolysis.protein_protease_ratio
_item_description.description
; The ratio of protein to protease used for the cleavage.
= mol protein / mol protease
;
_item.name '_pdbx_entity_src_gen_proteolysis.protein_protease_ratio'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code no
_item_type.code float
save_
save__pdbx_entity_src_gen_proteolysis.cleavage_buffer_id
_item_description.description
; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the cleavage was performed.
;
_item.name '_pdbx_entity_src_gen_proteolysis.cleavage_buffer_id'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code no
_item_linked.parent_name '_pdbx_buffer.id'
_item_linked.child_name '_pdbx_entity_src_gen_proteolysis.cleavage_buffer_id'
save_
save__pdbx_entity_src_gen_proteolysis.cleavage_temperature
_item_description.description
; The temperature in degrees celsius at which the cleavage was performed.
;
_item.name '_pdbx_entity_src_gen_proteolysis.cleavage_temperature'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code no
_item_type.code float
_item_units.code celsius
save_
save__pdbx_entity_src_gen_proteolysis.cleavage_time
_item_description.description
; The time in minutes for the cleavage reaction
;
_item.name '_pdbx_entity_src_gen_proteolysis.cleavage_time'
_item.category_id pdbx_entity_src_gen_proteolysis
_item.mandatory_code no
_item_type.code float
_item_units.code minutes
save_
#############################
# PDBX_ENTITY_SRC_GEN_CHROM #
#############################
#
# _pdbx_entity_src_gen_chrom.entry_id
# _pdbx_entity_src_gen_chrom.entity_id
# _pdbx_entity_src_gen_chrom.step_id
# _pdbx_entity_src_gen_chrom.next_step_id
# _pdbx_entity_src_gen_chrom.end_construct_id
# _pdbx_entity_src_gen_chrom.robot_id
# _pdbx_entity_src_gen_chrom.date
# _pdbx_entity_src_gen_chrom.column_type
# _pdbx_entity_src_gen_chrom.column_volume
# _pdbx_entity_src_gen_chrom.column_temperature
# _pdbx_entity_src_gen_chrom.equilibration_buffer
# _pdbx_entity_src_gen_chrom.flow_rate
# _pdbx_entity_src_gen_chrom.elution_protocol
# _pdbx_entity_src_gen_chrom.sample_prep_details
# _pdbx_entity_src_gen_chrom.sample_volume
# _pdbx_entity_src_gen_chrom.protein_concentration
# _pdbx_entity_src_gen_chrom.volume_fraction
# _pdbx_entity_src_gen_chrom.volume_pooled_fractions
# _pdbx_entity_src_gen_chrom.yield_pooled_fractions
# _pdbx_entity_src_gen_chrom.yield_method
# _pdbx_entity_src_gen_chrom.post_treatment
save_pdbx_entity_src_gen_chrom
_category.description
; This category contains details for the chromatographic steps used in the
purification of the protein.
;
_category.id pdbx_entity_src_gen_chrom
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_chrom.entry_id'
'_pdbx_entity_src_gen_chrom.entity_id'
'_pdbx_entity_src_gen_chrom.step_id'
save_
save__pdbx_entity_src_gen_chrom.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_chrom.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_chrom.entry_id'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_chrom.entry_id'
save_
save__pdbx_entity_src_gen_chrom.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_chrom.entity_id uniquely identifies
each protein contained in the project target complex proteins whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category. This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_chrom.entity_id'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_chrom.entity_id'
save_
save__pdbx_entity_src_gen_chrom.step_id
_item_description.description
; This item is the unique identifier for this chromatography step.
;
_item.name '_pdbx_entity_src_gen_chrom.step_id'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_chrom.next_step_id
_item_description.description
; This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
;
_item.name '_pdbx_entity_src_gen_chrom.next_step_id'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_chrom.end_construct_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product after the
chromatography step.
;
_item.name '_pdbx_entity_src_gen_chrom.end_construct_id'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code no
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_chrom.end_construct_id'
save_
save__pdbx_entity_src_gen_chrom.robot_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
;
_item.name '_pdbx_entity_src_gen_chrom.robot_id'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_chrom.robot_id'
save_
save__pdbx_entity_src_gen_chrom.date
_item_description.description
; The date of production step.
;
_item.name '_pdbx_entity_src_gen_chrom.date'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_entity_src_gen_chrom.column_type
_item_description.description
; The type of column used in this step.
;
_item.name '_pdbx_entity_src_gen_chrom.column_type'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_entity_src_gen_chrom.column_volume
_item_description.description
; The volume of the column used in this step.
;
_item.name '_pdbx_entity_src_gen_chrom.column_volume'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_type.code float
_item_units.code milliliters
save_
save__pdbx_entity_src_gen_chrom.column_temperature
_item_description.description
; The temperature in degrees celsius at which this column was run.
;
_item.name '_pdbx_entity_src_gen_chrom.column_temperature'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_type.code float
_item_units.code celsius
save_
save__pdbx_entity_src_gen_chrom.equilibration_buffer_id
_item_description.description
; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the column was equilibrated.
;
_item.name '_pdbx_entity_src_gen_chrom.equilibration_buffer_id'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_buffer.id'
_item_linked.child_name '_pdbx_entity_src_gen_chrom.equilibration_buffer_id'
save_
save__pdbx_entity_src_gen_chrom.flow_rate
_item_description.description
; The rate at which the equilibration buffer flowed through the column.
;
_item.name '_pdbx_entity_src_gen_chrom.flow_rate'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code no
_item_type.code float
_item_units.code ml_per_min
save_
save__pdbx_entity_src_gen_chrom.elution_buffer_id
_item_description.description
; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that with which the protein was eluted.
;
_item.name '_pdbx_entity_src_gen_chrom.elution_buffer_id'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_buffer.id'
_item_linked.child_name '_pdbx_entity_src_gen_chrom.elution_buffer_id'
save_
save__pdbx_entity_src_gen_chrom.elution_protocol
_item_description.description
; Details of the elution protocol.
;
_item.name '_pdbx_entity_src_gen_chrom.elution_protocol'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_chrom.sample_prep_details
_item_description.description
; Details of the sample preparation prior to running the column.
;
_item.name '_pdbx_entity_src_gen_chrom.sample_prep_details'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_chrom.sample_volume
_item_description.description
; The volume of protein solution run on the column.
;
_item.name '_pdbx_entity_src_gen_chrom.sample_volume'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_type.code float
_item_units.code milliliters
save_
save__pdbx_entity_src_gen_chrom.sample_concentration
_item_description.description
; The concentration of the protein solution put onto the column.
;
_item.name '_pdbx_entity_src_gen_chrom.sample_concentration'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code no
_item_type.code float
_item_units.code mg_per_ml
save_
save__pdbx_entity_src_gen_chrom.sample_conc_method
_item_description.description
; The method used to determine the concentration of the protein solution put
onto the column.
;
_item.name '_pdbx_entity_src_gen_chrom.sample_conc_method'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_chrom.volume_pooled_fractions
_item_description.description
; The total volume of all the fractions pooled to give the purified protein
solution.
;
_item.name '_pdbx_entity_src_gen_chrom.volume_pooled_fractions'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_type.code float
_item_units.code milliliters
save_
save__pdbx_entity_src_gen_chrom.yield_pooled_fractions
_item_description.description
; The yield in milligrams of protein recovered in the pooled fractions.
;
_item.name '_pdbx_entity_src_gen_chrom.yield_pooled_fractions'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_type.code float
_item_units.code milligrams
save_
save__pdbx_entity_src_gen_chrom.yield_method
_item_description.description
; The method used to determine the yield
;
_item.name '_pdbx_entity_src_gen_chrom.yield_method'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_entity_src_gen_chrom.post_treatment
_item_description.description
; Details of any post-chromatographic treatment of the protein sample.
;
_item.name '_pdbx_entity_src_gen_chrom.post_treatment'
_item.category_id pdbx_entity_src_gen_chrom
_item.mandatory_code no
_item_type.code text
save_
#############################
# PDBX_ENTITY_SRC_GEN_FRACT #
#############################
#
# _pdbx_entity_src_gen_fract.entry_id
# _pdbx_entity_src_gen_fract.entity_id
# _pdbx_entity_src_gen_fract.step_id
# _pdbx_entity_src_gen_fract.next_step_id
# _pdbx_entity_src_gen_fract.end_construct_id
# _pdbx_entity_src_gen_fract.robot_id
# _pdbx_entity_src_gen_fract.date
# _pdbx_entity_src_gen_fract.method
# _pdbx_entity_src_gen_fract.temperature
# _pdbx_entity_src_gen_fract.details
# _pdbx_entity_src_gen_fract.protein_location
# _pdbx_entity_src_gen_fract.protein_yield
# _pdbx_entity_src_gen_fract.protein_yield_method
#
save_pdbx_entity_src_gen_fract
_category.description
; This category contains details for the fraction steps used in
the overall protein production process. Examples of fractionation
steps are centrifugation and magnetic bead pull-down purification.
;
_category.id pdbx_entity_src_gen_fract
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_fract.entry_id'
'_pdbx_entity_src_gen_fract.entity_id'
'_pdbx_entity_src_gen_fract.step_id'
save_
save__pdbx_entity_src_gen_fract.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_fract.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_fract.entry_id'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_fract.entry_id'
save_
save__pdbx_entity_src_gen_fract.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_fract.entity_id uniquely identifies
each protein contained in the project target protein complex whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category. This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_fract.entity_id'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code yes
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_fract.entity_id'
save_
save__pdbx_entity_src_gen_fract.step_id
_item_description.description
; This item is the unique identifier for this fractionation step.
;
_item.name '_pdbx_entity_src_gen_fract.step_id'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_fract.next_step_id
_item_description.description
; This item unique identifier for the next production step. This allows
a workflow to have multiple entry points leading to a single product.
;
_item.name '_pdbx_entity_src_gen_fract.next_step_id'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_fract.end_construct_id
_item_description.description
; This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT
category. The referenced sequence is expected to be the amino
acid sequence of the expressed product after the fractionation
step.
;
_item.name '_pdbx_entity_src_gen_fract.end_construct_id'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code no
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_entity_src_gen_fract.end_construct_id'
save_
save__pdbx_entity_src_gen_fract.robot_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
;
_item.name '_pdbx_entity_src_gen_fract.robot_id'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_fract.robot_id'
save_
save__pdbx_entity_src_gen_fract.date
_item_description.description
; The date of this production step.
;
_item.name '_pdbx_entity_src_gen_fract.date'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_entity_src_gen_fract.method
_item_description.description
; This item describes the method of fractionation.
;
_item.name '_pdbx_entity_src_gen_fract.method'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
C 'Centrifugation'
M 'Magnetic beads'
P 'Phase separation'
save_
save__pdbx_entity_src_gen_fract.temperature
_item_description.description
; The temperature in degrees celsius at which the fractionation was performed.
;
_item.name '_pdbx_entity_src_gen_fract.temperature'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code yes
_item_type.code float
_item_units.code celsius
save_
save__pdbx_entity_src_gen_fract.details
_item_description.description
; String value containing details of the fractionation.
;
_item.name '_pdbx_entity_src_gen_fract.details'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_fract.protein_location
_item_description.description
; The fraction containing the protein of interest.
;
_item.name '_pdbx_entity_src_gen_fract.protein_location'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
S 'Supernatant'
P 'Pellet'
B 'Band in gradient'
M 'Magnetic beads'
A 'Aqueous phase'
L 'Lipid phase'
save_
save__pdbx_entity_src_gen_fract.protein_volume
_item_description.description
; The volume of the fraction containing the protein.
;
_item.name '_pdbx_entity_src_gen_fract.protein_volume'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code no
_item_type.code float
_item_units.code milliliters
save_
save__pdbx_entity_src_gen_fract.protein_yield
_item_description.description
; The yield in milligrams of protein from the fractionation.
;
_item.name '_pdbx_entity_src_gen_fract.protein_yield'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code yes
_item_type.code float
_item_units.code milligrams
save_
save__pdbx_entity_src_gen_fract.protein_yield_method
_item_description.description
; The method used to determine the yield
;
_item.name '_pdbx_entity_src_gen_fract.protein_yield_method'
_item.category_id pdbx_entity_src_gen_fract
_item.mandatory_code yes
_item_type.code text
save_
############################
# PDBX_ENTITY_SRC_GEN_PURE #
############################
#
# _pdbx_entity_src_gen_pure.entry_id
# _pdbx_entity_src_gen_pure.entity_id
# _pdbx_entity_src_gen_pure.next_step_id
# _pdbx_entity_src_gen_pure.date
# _pdbx_entity_src_gen_pure.conc_device_id
# _pdbx_entity_src_gen_pure.conc_details
# _pdbx_entity_src_gen_pure.conc_assay_method
# _pdbx_entity_src_gen_pure.protein_concentration
# _pdbx_entity_src_gen_pure.protein_yield
# _pdbx_entity_src_gen_pure.protein_purity
# _pdbx_entity_src_gen_pure.protein_oligomeric_state
# _pdbx_entity_src_gen_pure.storage_buffer_id
# _pdbx_entity_src_gen_pure.storage_temperature
#
# _pdbx_entity_src_gen_pure.summary
#
save_pdbx_entity_src_gen_pure
_category.description
; This category contains details for the final purified protein product. Note
that this category does not contain the amino acid sequence of the protein.
The sequence will be found in the ENTITY_POLY_SEQ entry with matching
entity_id.
Only one PDBX_ENTITY_SRC_GEN_PURE category is allowed per entity, hence there is
no step_id for this category.
;
_category.id pdbx_entity_src_gen_pure
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_pure.entry_id'
'_pdbx_entity_src_gen_pure.entity_id'
'_pdbx_entity_src_gen_pure.step_id'
save_
save__pdbx_entity_src_gen_pure.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_pure.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_pure.entry_id'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_pure.entry_id'
save_
save__pdbx_entity_src_gen_pure.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_pure.entity_id uniquely identifies
each protein contained in the project target complex proteins whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category. This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_pure.entity_id'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code yes
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_pure.entity_id'
save_
save__pdbx_entity_src_gen_pure.step_id
_item_description.description
; This item unique identifier the production step.
;
_item.name '_pdbx_entity_src_gen_pure.step_id'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_pure.product_id
_item_description.description
; When present, this item should be a globally unique identifier
that identifies the final product. It is envisaged that this
should be the same as and product code associated with the
sample and would provide the key by which information about
the production process may be extracted from the protein
production facility. For files describing the protein
production process (i.e. where _entity.type is 'P' or 'E')
this should have the same value as _entry.id
;
_item.name '_pdbx_entity_src_gen_pure.product_id'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code no
_item_type.code code
save_
save__pdbx_entity_src_gen_pure.date
_item_description.description
; The date of production step.
;
_item.name '_pdbx_entity_src_gen_pure.date'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_entity_src_gen_pure.conc_device_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
;
_item.name '_pdbx_entity_src_gen_pure.conc_device_id'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_pure.conc_device_id'
save_
save__pdbx_entity_src_gen_pure.conc_details
_item_description.description
; Details of the protein concentration procedure
;
_item.name '_pdbx_entity_src_gen_pure.conc_details'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_entity_src_gen_pure.conc_assay_method
_item_description.description
; The method used to measure the protein concentration
;
_item.name '_pdbx_entity_src_gen_pure.conc_assay_method'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_entity_src_gen_pure.protein_concentration
_item_description.description
; The final concentration of the protein.
;
_item.name '_pdbx_entity_src_gen_pure.protein_concentration'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code yes
_item_type.code float
_item_units.code mg_per_ml
save_
save__pdbx_entity_src_gen_pure.protein_yield
_item_description.description
; The yield of protein in milligrams.
;
_item.name '_pdbx_entity_src_gen_pure.protein_yield'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code no
_item_type.code float
_item_units.code milligrams
save_
save__pdbx_entity_src_gen_pure.protein_purity
_item_description.description
; The purity of the protein (percent).
;
_item.name '_pdbx_entity_src_gen_pure.protein_purity'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code no
_item_type.code float
# _item_units.code percent
save_
save__pdbx_entity_src_gen_pure.protein_oligomeric_state
_item_description.description
; The oligomeric state of the protein. Monomeric is 1, dimeric 2, etc.
;
_item.name '_pdbx_entity_src_gen_pure.protein_oligomeric_state'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code no
_item_type.code int
save_
save__pdbx_entity_src_gen_pure.storage_buffer_id
_item_description.description
; This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category.
The referenced buffer is that in which the protein was stored.
;
_item.name '_pdbx_entity_src_gen_pure.storage_buffer_id'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_buffer.id'
_item_linked.child_name '_pdbx_entity_src_gen_pure.storage_buffer_id'
save_
save__pdbx_entity_src_gen_pure.storage_temperature
_item_description.description
; The temperature in degrees celsius at which the protein was stored.
;
_item.name '_pdbx_entity_src_gen_pure.storage_temperature'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code no
_item_type.code float
_item_units.code celsius
save_
save__pdbx_entity_src_gen_pure.summary
_item_description.description
; Summary of the details of protein purification method used to obtain the final
protein product. This description should include any lysis, fractionation,
proteolysis, refolding, chromatography used as well as the method used the
characterize the final product.
;
_item.name '_pdbx_entity_src_gen_pure.summary'
_item.category_id pdbx_entity_src_gen_pure
_item.mandatory_code no
_item_type.code text
save_
#################################
# PDBX_ENTITY_SRC_GEN_CHARACTER #
#################################
#
# _pdbx_entity_src_gen_character.entry_id
# _pdbx_entity_src_gen_character.entity_id
# _pdbx_entity_src_gen_character.step_id
# _pdbx_entity_src_gen_character.robot_id
# _pdbx_entity_src_gen_character.date
# _pdbx_entity_src_gen_character.method
# _pdbx_entity_src_gen_character.value
# _pdbx_entity_src_gen_character.details
#
save_pdbx_entity_src_gen_character
_category.description
; This category contains details of protein characterisation. It
refers to the characteristion of the product of a specific
step.
;
_category.id pdbx_entity_src_gen_character
_category.mandatory_code no
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'entity_group'
'pdbx_group'
loop_
_category_key.name
'_pdbx_entity_src_gen_character.entry_id'
'_pdbx_entity_src_gen_character.entity_id'
'_pdbx_entity_src_gen_character.step_id'
save_
save__pdbx_entity_src_gen_character.entry_id
_item_description.description
; The value of _pdbx_entity_src_gen_character.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_character.entry_id'
_item.category_id pdbx_entity_src_gen_character
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_entity_src_gen_character.entry_id'
save_
save__pdbx_entity_src_gen_character.entity_id
_item_description.description
; The value of _pdbx_entity_src_gen_character.entity_id uniquely identifies
each protein contained in the project target complex proteins whose
structure is to be determined. This data item is a pointer to _entity.id
in the ENTITY category. This item may be a site dependent bar code.
;
_item.name '_pdbx_entity_src_gen_character.entity_id'
_item.category_id pdbx_entity_src_gen_character
_item.mandatory_code yes
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_entity_src_gen_character.entity_id'
save_
save__pdbx_entity_src_gen_character.step_id
_item_description.description
; This item is the unique identifier for the step whose product
has been characterised.
;
_item.name '_pdbx_entity_src_gen_character.step_id'
_item.category_id pdbx_entity_src_gen_character
_item.mandatory_code yes
_item_type.code int
save_
save__pdbx_entity_src_gen_character.robot_id
_item_description.description
; This data item is a pointer to pdbx_robot_system.id
in the PDBX_ROBOT_SYSTEM category.
;
_item.name '_pdbx_entity_src_gen_character.robot_id'
_item.category_id pdbx_entity_src_gen_character
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_entity_src_gen_character.robot_id'
save_
save__pdbx_entity_src_gen_character.date
_item_description.description
; The date of characterisation step.
;
_item.name '_pdbx_entity_src_gen_character.date'
_item.category_id pdbx_entity_src_gen_character
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_entity_src_gen_character.method
_item_description.description
; The method used for protein characterisation.
;
_item.name '_pdbx_entity_src_gen_character.method'
_item.category_id pdbx_entity_src_gen_character
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case 'Dynamic light scattering'
'Mass spectrometry'
save_
save__pdbx_entity_src_gen_character.result
_item_description.description
; The result from this method of protein characterisation.
;
_item.name '_pdbx_entity_src_gen_character.result'
_item.category_id pdbx_entity_src_gen_character
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_entity_src_gen_character.details
_item_description.description
; Any details associated with this method of protein characterisation.
;
_item.name '_pdbx_entity_src_gen_character.details'
_item.category_id pdbx_entity_src_gen_character
_item.mandatory_code no
_item_type.code text
save_
##################
# PDBX_CONSTRUCT #
##################
#
# _pdbx_construct.entry_id
# _pdbx_construct.id
# _pdbx_construct.name
# _pdbx_construct.class
# _pdbx_construct.type
# _pdbx_construct.seq
# _pdbx_construct.date
# _pdbx_construct.details
# _pdbx_construct.robot_id
# _pdbx_construct.ref_db_code
# _pdbx_construct.ref_db_name
# _pdbx_construct.ref_db_align_beg
# _pdbx_construct.ref_db_align_end
# _pdbx_construct.flag_align
# _pdbx_construct.flag_diff
#
save_pdbx_construct
_category.description
; Data items in the PDBX_CONSTRUCT category specify a sequence of
nucleic acids or amino acids. It is a catch-all that may be used to
provide details of sequences known to be relevant to the project as well
as primers, plasmids, proteins and such like that are either used or
produced during the protein production process. Molecules described
here are not necessarily complete, so for instance it would be
possible to include either a complete plasmid or just its insert.
This category may be considered as an abbreviated form of _entity where
the molecules described are not required to appear in the final co-ordinates.
Note that the details provided here all pertain to a single entry as defined
at deposition. It is anticipated that _pdbx_construct.id would also be
composed of a sequence that is unique within a given site prefixed by a code
that identifies that site and would, therefore, be GLOBALLY unique. Thus
this category could also be used locally to store details about the different
constructs used during protein production without reference to the entry_id
(which only becomes a meaningful concept during deposition).
;
_category.id pdbx_construct
_category.mandatory_code no
loop_
_category_key.name '_pdbx_construct.id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
'protein_production_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - hypothetical example
;
;
_pdbx_construct.entry_id 111000111
_pdbx_construct.id 1
_pdbx_construct.type DNA
_pdbx_construct.entity_id 1
_pdbx_construct.seq
; gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc
gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg
caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg
# - - - - data truncated for brevity - - - -
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_construct.entry_id
_item_description.description
; The value of _pdbx_construct.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_construct.entry_id'
_item.category_id pdbx_construct
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_construct.entry_id'
save_
save__pdbx_construct.id
_item_description.description
; The value of _pdbx_construct.id must uniquely identify a record
in the PDBX_CONSTRUCT list and should be arranged so that it is
composed of a site-speicific prefix combined with a value that is
unique within a given site.Note that this item need not be a
number; it can be any unique identifier.
;
loop_
_item.name '_pdbx_construct.id'
_item.category_id pdbx_construct
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_construct.name
_item_description.description
; _pdbx_construct.name provides a placeholder for the local name
of the construct, for example the plasmid name if this category
is used to list plasmids.
;
loop_
_item.name '_pdbx_construct.name'
_item.category_id pdbx_construct
_item.mandatory_code yes
_item_type.code line
save_
save__pdbx_construct.organisation
_item_description.description
; _pdbx_construct.organisation describes the organisation in which
the _pdbx_construct.id is unique. This will normally be the lab
in which the constrcut originated. It is envisaged that this item
will permit a globally unique identifier to be constructed in cases
where this is not possible from the _pdbx_construct.id alone.
;
loop_
_item.name '_pdbx_construct.organisation'
_item.category_id pdbx_construct
_item.mandatory_code yes
_item_type.code line
save_
save__pdbx_construct.entity_id
_item_description.description
; In cases where the construct IS found in the co-ordinates then this
item provides a pointer to _entity.id in the ENTITY category for
the corresponding molecule.
;
_item.name '_pdbx_construct.entity_id'
_item.category_id pdbx_construct
_item.mandatory_code no
_item_linked.parent_name '_entity.id'
_item_linked.child_name '_pdbx_construct.entity_id'
save_
save__pdbx_construct.robot_id
_item_description.description
; In cases where the sequence has been determined by a robot this
data item provides a pointer to pdbx_robot_system.id in the
PDBX_ROBOT_SYSTEM category for the robot responsible
;
_item.name '_pdbx_construct.robot_id'
_item.category_id pdbx_construct
_item.mandatory_code no
_item_linked.parent_name '_pdbx_robot_system.id'
_item_linked.child_name '_pdbx_construct.robot_id'
save_
save__pdbx_construct.date
_item_description.description
; The date that the sequence was determined.
;
_item.name '_pdbx_construct.date'
_item.category_id pdbx_construct
_item.mandatory_code no
_item_type.code yyyy-mm-dd:hh:mm
loop_
_item_examples.case '2003-12-25'
'2003-12-25:09:00'
save_
save__pdbx_construct.details
_item_description.description
; Additional details about the construct that cannot be
represented in the category _pdbx_construct_feature.
;
_item.name '_pdbx_construct.details'
_item.category_id pdbx_construct
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_construct.class
_item_description.description
; The primary function of the construct. This should be considered
as a guideline only.
;
_item.name '_pdbx_construct.class'
_item.category_id pdbx_construct
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
plasmid
protein
insert
primer
transcript
save_
save__pdbx_construct.type
_item_description.description
; The type of nucleic acid sequence in the construct. Note that
to find all the DNA molecules it is necessary to search for
DNA + cDNA and for RNA, RNA + mRNA + tRNA.
;
_item.name '_pdbx_construct.type'
_item.category_id pdbx_construct
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
DNA
RNA
cDNA
mRNA
tRNA
protein
save_
save__pdbx_construct.seq
_item_description.description
; sequence expressed as string of one-letter base codes or one
letter amino acid codes. Unusual residues may be represented
either using the appropriate one letter code wild cards or
by the three letter code in parentheses.
;
_item.name '_pdbx_construct.seq'
_item.category_id pdbx_construct
_item.mandatory_code yes
_item_type.code text
_item_examples.case
; gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc
gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg
caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg
;
save_
###########################
# PDBX_CONSTRUCT_FEATURE #
###########################
#
# _pdbx_construct_feature.id
# _pdbx_construct_feature.entry_id
# _pdbx_construct_feature.entity_id
# _pdbx_construct_feature.construct_id
# _pdbx_construct_feature.start_seq
# _pdbx_construct_feature.end_seq
# _pdbx_construct_feature.type
# _pdbx_construct_feature.details
#
save_pdbx_construct_feature
_category.description
; Data items in the PDBX_CONSTRUCT_FEATURE category may be used to
specify various properties of a nucleic acid sequence used during
protein production.
;
_category.id pdbx_construct_feature
_category.mandatory_code no
loop_
_category_key.name '_pdbx_construct_feature.construct_id'
'_pdbx_construct_feature.id'
loop_
_category_group.id 'inclusive_group'
'entity_group'
'protein_production_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - vector pUC28
;
;
loop_
_pdbx_construct_feature.id
_pdbx_construct_feature.entry_id
_pdbx_construct_feature.construct_id
_pdbx_construct_feature.start_seq
_pdbx_construct_feature.end_seq
_pdbx_construct_feature.type
_pdbx_construct_feature.details
1 111000111 1 . . .
"pKK84-1 ClaI 5260bp 5247..5247 ptac11 TaqI-TaqI 192bp, -35 trp promoter -> pEA300 5452bp"
2 111000111 1 . . .
"pKK84-1 1..5246 5246bp ClaI = AT^CGAT TaqI = T^CGA cgact..."
3 111000111 1 5247 5436 .
"ptac11 190bp ...cat TaqI = T^CGA ClaI = AT^CGAT"
4 111000111 1 5437 5450 .
"pKK84-1 5247..5260 14bp"
5 111000111 1 . . misc_binding
"SIT unique EcoRI-ClaI-HindIII-BamHI-PvuII"
6 111000111 1 . . rep_origin
"ORI E. coli pMB1 (ColE1 and pBR322)"
7 111000111 1 . . promoter
"PRO E. coli trp"
8 111000111 1 . . CDS
"ANT E. coli beta-lactamase gene (bla) ampicillin resistance gene (apr/amp)"
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_construct_feature.id
_item_description.description
; The value of _pdbx_construct_feature.id must uniquely
identify a record in the PDBX_CONSTRUCT_FEATURE list.
Note that this item need not be a number; it can be any unique
identifier.
;
loop_
_item.name '_pdbx_construct_feature.id'
_item.category_id pdbx_construct_feature
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_construct_feature.construct_id
_item_description.description
; The value of _pdbx_construct_feature.construct_id uniquely
identifies the construct with which the feature is
associated. This is a pointer to _pdbx_construct.id
This item may be a site dependent bar code.
;
_item.name '_pdbx_construct_feature.construct_id'
_item.category_id pdbx_construct_feature
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_construct.id'
_item_linked.child_name '_pdbx_construct_feature.construct_id'
save_
save__pdbx_construct_feature.entry_id
_item_description.description
; The value of _pdbx_construct_feature.entry_id uniquely identifies
a sample consisting of one or more proteins whose structure is
to be determined. This is a pointer to _entry.id. This item may
be a site dependent bar code.
;
_item.name '_pdbx_construct_feature.entry_id'
_item.category_id pdbx_construct
_item.mandatory_code yes
_item_linked.parent_name '_entry.id'
_item_linked.child_name '_pdbx_construct_feature.entry_id'
save_
save__pdbx_construct_feature.start_seq
_item_description.description
; The sequence position at which the feature begins
;
_item.name '_pdbx_construct_feature.start_seq'
_item.category_id pdbx_construct_feature
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__pdbx_construct_feature.end_seq
_item_description.description
; The sequence position at which the feature ends
;
_item.name '_pdbx_construct_feature.end_seq'
_item.category_id pdbx_construct_feature
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__pdbx_construct_feature.type
_item_description.description
; The type of the feature
;
_item.name '_pdbx_construct_feature.type'
_item.category_id pdbx_construct_feature
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_construct_feature.details
_item_description.description
; Details that describe the feature
;
_item.name '_pdbx_construct_feature.details'
_item.category_id pdbx_construct_feature
_item.mandatory_code no
_item_type.code text
save_
#####################
# PDBX_ROBOT_SYSTEM #
#####################
#
# _pdbx_robot_system.id
# _pdbx_robot_system.model
# _pdbx_robot_system.type
# _pdbx_robot_system.manufacturer
#
save_pdbx_robot_system
_category.description
; The details about each robotic system used to collect data for this
project.
;
_category.id pdbx_robot_system
_category.mandatory_code no
_category_key.name '_pdbx_robot_system.id'
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'pdbx_group'
save_
save__pdbx_robot_system.id
_item_description.description
; Assign a numerical ID to each instrument.
;
_item.name '_pdbx_robot_system.id'
_item.category_id pdbx_robot_system
_item.mandatory_code no
_item_type.code code
save_
save__pdbx_robot_system.model
_item_description.description
; The model of the robotic system.
;
_item.name '_pdbx_robot_system.model'
_item.category_id pdbx_robot_system
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_robot_system.type
_item_description.description
; The type of robotic system used for in the production pathway.
;
_item.name '_pdbx_robot_system.type'
_item.category_id pdbx_robot_system
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_robot_system.manufacturer
_item_description.description
; The name of the manufacturer of the robotic system.
;
_item.name '_pdbx_robot_system.manufacturer'
_item.category_id pdbx_robot_system
_item.mandatory_code no
_item_type.code line
save_
#################
## PDB_BUFFER ##
#################
#
# _pdbx_buffer.id
# _pdbx_buffer.name
# _pdbx_buffer.details
# _pdbx_buffer_components.id
# _pdbx_buffer_components.buffer_id
# _pdbx_buffer_components.name
# _pdbx_buffer_components.volume
# _pdbx_buffer_components.conc
# _pdbx_buffer_components.details
# _pdbx_buffer_components.conc_units
# _pdbx_buffer_components.isotopic_labeling
#
save_pdbx_buffer
_category.description
; Data items in the PDBX_BUFFER category
record details of the sample buffer.
;
_category.id pdbx_buffer
_category.mandatory_code no
_category_key.name '_pdbx_buffer.id'
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'pdbx_group'
save_
save__pdbx_buffer.id
_item_description.description
; The value of _pdbx_buffer.id must
uniquely identify the sample buffer.
;
_item.name '_pdbx_buffer.id'
_item.category_id pdbx_buffer
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_buffer.name
_item_description.description
; The name of each buffer.
;
_item.name '_pdbx_buffer.name'
_item.category_id pdbx_buffer
_item.mandatory_code no
_item_type.code line
_item_examples.case 'Acetic acid'
save_
save__pdbx_buffer.details
_item_description.description
; Any additional details to do with buffer.
;
_item.name '_pdbx_buffer.details'
_item.category_id pdbx_buffer
_item.mandatory_code no
_item_type.code text
_item_examples.case 'aerated'
save_
###############################
## PDBX_BUFFER_COMPONENTS ##
###############################
#
# _pdbx_buffer_components.id
# _pdbx_buffer_components.buffer_id
# _pdbx_buffer_components.name
# _pdbx_buffer_components.volume
# _pdbx_buffer_components.conc
# _pdbx_buffer_components.details
# _pdbx_buffer_components.conc_units
# _pdbx_buffer_components.isotopic_labeling
#
save_pdbx_buffer_components
_category.description
; Constituents of buffer in sample
;
_category.id pdbx_buffer_components
_category.mandatory_code no
loop_
_category_key.name
'_pdbx_buffer_components.buffer_id'
'_pdbx_buffer_components.id'
loop_
_category_group.id 'inclusive_group'
'protein_production_group'
'pdbx_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;loop_
_pdbx_buffer_components.buffer_id
_pdbx_buffer_components.id
_pdbx_buffer_components.name
_pdbx_buffer_components.volume
_pdbx_buffer_components.conc
_pdbx_buffer_components.details
1 1 'NaCl' '0.200 ' '4 ' .
1 2 'Acetic Acid' '0.047 ' '100' .
1 3 'water' '0.700 ' 'neat' .
;
save_
save__pdbx_buffer_components.id
_item_description.description
; The value of _pdbx_buffer_components.id must
uniquely identify a component of the buffer.
;
_item.name '_pdbx_buffer_components.id'
_item.category_id pdbx_buffer_components
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_buffer_components.buffer_id
_item_description.description
; This data item is a pointer to _pdbx_buffer.id in the BUFFER category.
;
_item.name '_pdbx_buffer_components.buffer_id'
_item.category_id pdbx_buffer_components
_item.mandatory_code yes
_item_linked.parent_name '_pdbx_buffer.id'
_item_linked.child_name '_pdbx_buffer_components.buffer_id'
save_
save__pdbx_buffer_components.name
_item_description.description
; The name of each buffer component.
;
_item.name '_pdbx_buffer_components.name'
_item.category_id pdbx_buffer_components
_item.mandatory_code no
_item_type.code line
_item_examples.case 'Acetic acid'
save_
save__pdbx_buffer_components.volume
_item_description.description
; The volume of buffer component.
;
_item.name '_pdbx_buffer_components.volume'
_item.category_id pdbx_buffer_components
_item.mandatory_code no
_item_type.code code
_item_examples.case 0.200
save_
save__pdbx_buffer_components.conc
_item_description.description
; The millimolar concentration of buffer component.
;
_item.name '_pdbx_buffer_components.conc'
_item.category_id pdbx_buffer_components
_item.mandatory_code no
_item_type.code code
_item_examples.case 200
save_
save__pdbx_buffer_components.details
_item_description.description
; Any additional details to do with buffer composition.
;
_item.name '_pdbx_buffer_components.details'
_item.category_id pdbx_buffer_components
_item.mandatory_code no
_item_type.code text
_item_examples.case 'pH adjusted with NaOH'
save_
#
save__pdbx_buffer_components.conc_units
_item_description.description
; The concentration units of the component.
;
_item.name '_pdbx_buffer_components.conc_units'
_item.category_id pdbx_buffer_components
_item.mandatory_code no
_item_type.code code
loop_
_item_examples.case
'mg/mL for mg per milliliter'
'mM for millimolar'
'% for percent by volume'
loop_
_item_enumeration.value
_item_enumeration.detail
'%' 'percent by volume'
'mM' 'millimolar'
'mg/mL' 'mg per milliliter'
'M' 'molar'
'g/L' 'grams per liter'
save_
save__pdbx_buffer_components.isotopic_labeling
_item_description.description
; The isotopic composition of each component, including
the % labeling level, if known. For example:
1. Uniform (random) labeling with 15N: U-15N
2. Uniform (random) labeling with 13C, 15N at known labeling
levels: U-95% 13C;U-98% 15N
3. Residue selective labeling: U-95% 15N-Thymine
4. Site specific labeling: 95% 13C-Ala18,
5. Natural abundance labeling in an otherwise uniformly labled
biomolecule is designated by NA: U-13C; NA-K,H
;
_item.name '_pdbx_buffer_components.isotopic_labeling'
_item.category_id pdbx_buffer_components
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
'U-15N'
'U-13C'
'U-15N,13C'
'U-2H'
'other'
save_
### EOF mmcif_pdbx-def-6.dic
###########################################################################
#
# File: mmcif_iims-def-2.dic
#
# PDB Extension Dictionary for 3-Dimensional
# Electron Microscopy
#
# Definition Section 2
#
#
###########################################################################
##
###
# Please note the data items listed below are not for the PDB
# but are intended solely for the EM database
# _em_entity_assembly.ebi_organism_scientific
# _em_entity_assembly.ebi_organism_common
# _em_entity_assembly.ebi_strain
# _em_entity_assembly.ebi_tissue
# _em_entity_assembly.ebi_cell
# _em_entity_assembly.ebi_organelle
# _em_entity_assembly.ebi_cellular_location
# _em_entity_assembly.ebi_engineered
# _em_entity_assembly.ebi_expression_system
# _em_entity_assembly.ebi_expression_system_plasmid
###
#
# categories
#
# EM_ASSEMBLY
# _em_assembly.id
# _em_assembly.entry_id
# _em_assembly.name
# _em_assembly.aggregation_state
# _em_assembly.composition
# _em_assembly.num_components
# _em_assembly.mol_wt_exp
# _em_assembly.mol_wt_theo
# _em_assembly.mol_wt_method
# _em_assembly.details
# EM_ENTITY_ASSEMBLY
# _em_entity_assembly.id
# _em_entity_assembly.assembly_id
# _em_entity_assembly.type
# _em_entity_assembly.name
# _em_entity_assembly.details
# _em_entity_assembly.go_id
# _em_entity_assembly.ipr_id
# _em_entity_assembly.synonym
# EM_ENTITY_ASSEMBLY_LIST
# _em_entity_assembly_list.id
# _em_entity_assembly_list.entity_id
# _em_entity_assembly_list.entity_assembly_id
# _em_entity_assembly_list.oligomeric_details
# _em_entity_assembly_list.number_of_copies
# EM_VIRUS_ENTITY
# _em_virus_entity.id
# _em_virus_entity.virus_host_category
# _em_virus_entity.virus_host_species
# _em_virus_entity.virus_host_growth_cell
# _em_virus_entity.virus_type
# _em_virus_entity.virus_isolate
# _em_virus_entity.ictvdb_id
# _em_virus_entity.entity_assembly_id
# _em_virus_entity.enveloped
# _em_virus_entity.empty
# EM_ICOS_VIRUS_SHELLS
# _em_icos_virus_shells.virus_entity_id
# _em_icos_virus_shells.id
# _em_icos_virus_shells.shell_diameter
# _em_icos_virus_shells.triangulation_num
# EM_SAMPLE_PREPARATION
# _em_sample_preparation.entry_id
# _em_sample_preparation.id
# _em_sample_preparation.ph
# _em_sample_preparation.buffer_id
# _em_sample_preparation.sample_concentration
# _em_sample_preparation.2d_crystal_grow_id
# _em_sample_preparation.support_id
# EM_SAMPLE_SUPPORT
# _em_sample_support.id
# _em_sample_support.film_material
# _em_sample_support.method
# _em_sample_support.grid_material
# _em_sample_support.grid_mesh_size
# _em_sample_support.grid_type
# _em_sample_support.pretreatment
# _em_sample_support.details
# _em_sample_support.citation_id
# EM_2D_CRYSTAL_GROW
# _em_2d_crystal_grow.id
# _em_2d_crystal_grow.method
# _em_2d_crystal_grow.apparatus
# _em_2d_crystal_grow.atmosphere
# _em_2d_crystal_grow.pH
# _em_2d_crystal_grow.temp
# _em_2d_crystal_grow.time
# _em_2d_crystal_grow.buffer_id
# _em_2d_crystal_grow.details
# _em_2d_crystal_grow.number_2d_crystals
# _em_2d_crystal_grow.mean_2d_crystal_size
# _em_2d_crystal_grow.citation_id
# EM_BUFFER
# _em_buffer.id
# _em_buffer.name
# _em_buffer.details
# EM_BUFFER_COMPONENTS
# _em_buffer_components.id
# _em_buffer_components.buffer_id
# _em_buffer_components.name
# _em_buffer_components.volume
# _em_buffer_components.conc
# _em_buffer_components.details
# EM_VITRIFICATION
# _em_vitrification.entry_id
# _em_vitrification.id
# _em_vitrification.sample_preparation_id
# _em_vitrification.cryogen_name
# _em_vitrification.humidity
# _em_vitrification.temp
# _em_vitrification.instrument
# _em_vitrification.method
# _em_vitrification.time_resolved_state
# _em_vitrification.citation_id
# _em_vitrification.details
# EM_IMAGING
# _em_imaging.entry_id
# _em_imaging.id
# _em_imaging.sample_support_id
# _em_imaging.detector_id
# _em_imaging.scans_id
# _em_imaging.microscope_model
# _em_imaging.specimen_holder_type
# _em_imaging.specimen_holder_model
# _em_imaging.details
# _em_imaging.date
# _em_imaging.accelerating_voltage
# _em_imaging.illumination_mode
# _em_imaging.mode
# _em_imaging.nominal_cs
# _em_imaging.nominal_defocus_min
# _em_imaging.nominal_defocus_max
# _em_imaging.tilt_angle_min
# _em_imaging.tilt_angle_max
# _em_imaging.nominal_magnification
# _em_imaging.calibrated_magnification
# _em_imaging.electron_source
# _em_imaging.electron_dose
# _em_imaging.energy_filter
# _em_imaging.energy_window
# _em_imaging.citation_id
# _em_imaging.temperature
# _em_imaging.detector_distance
# _em_imaging.recording_temperature_minimum
# _em_imaging.recording_temperature_maximum
# EM_DETECTOR
# _em_detector.entry_id
# _em_detector.id
# _em_detector.details
# _em_detector.type
# _em_detector.detective_quantum_efficiency
# EM_IMAGE_SCANS
# _em_image_scans.entry_id
# _em_image_scans.id
# _em_image_scans.number_digital_images
# _em_image_scans.details
# _em_image_scans.scanner_model
# _em_image_scans.sampling_size
# _em_image_scans.od_range
# _em_image_scans.quant_bit_size
# _em_image_scans.citation_id
# EM_2D_PROJECTION_SELECTION
# _em_2d_projection_selection.entry_id
# _em_2d_projection_selection.num_particles
# _em_2d_projection_selection.software_name
# _em_2d_projection_selection.method
# _em_2d_projection_selection.details
# _em_2d_projection_selection.citation_id
# EM_EULER_ANGLE_DISTRIBUTION
# _em_euler_angle_distribution.id
# _em_euler_angle_distribution.entry_id
# _em_euler_angle_distribution.details
# _em_euler_angle_distribution.alpha
# _em_euler_angle_distribution.beta
# _em_euler_angle_distribution.gamma
# EM_3D_RECONSTRUCTION
# _em_3d_reconstruction.entry_id
# _em_3d_reconstruction.id
# _em_3d_reconstruction.method
# _em_3d_reconstruction.citation_id
# _em_3d_reconstruction.details
# _em_3d_reconstruction.resolution
# _em_3d_reconstruction.resolution_method
# _em_3d_reconstruction.magnification_calibration
# _em_3d_reconstruction.ctf_correction_method
# _em_3d_reconstruction.nominal_pixel_size
# _em_3d_reconstruction.actual_pixel_size
# EM_3D_FITTING
# _em_3d_fitting.id
# _em_3d_fitting.entry_id
# _em_3d_fitting.method
# _em_3d_fitting.target_criteria
# _em_3d_fitting.software_name
# _em_3d_fitting.details
# _em_3d_fitting.overall_b_value
# _em_3d_fitting.ref_space
# _em_3d_fitting.ref_protocol
# EM_3D_FITTING_LIST
# _em_3d_fitting_list.id
# _em_3d_fitting_list.3d_fitting_id
# _em_3d_fitting_list.pdb_entry_id
# _em_3d_fitting_list.pdb_chain_id
#################
## EM_ASSEMBLY ##
#################
save_em_assembly
_category.description
; Data items in the EM_ASSEMBLY category record details
about the type of complex assembly that describes the
nature of the sample studied.
;
_category.id em_assembly
_category.mandatory_code no
loop_
_category_key.name
'_em_assembly.id'
'_em_assembly.entry_id'
loop_
_category_group.id
'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
; _em_assembly.id 1
_em_assembly.entry_id 1DYL
_em_assembly.name virus
_em_assembly.aggregation_state icosahedral
_em_assembly.composition virus
_em_assembly.num_components 1
_em_assembly.mol_wt_exp .
_em_assembly.mol_wt_theo .
_em_assembly.mol_wt_method .
_em_assembly.details .
;
save_
save__em_assembly.id
_item_description.description
; The value of _em_assembly.id must uniquely identify
a collection of observed complexes.
;
_item.name '_em_assembly.id'
_item.category_id em_assembly
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_entity_assembly.assembly_id'
_item_linked.parent_name '_em_assembly.id'
save_
save__em_assembly.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_em_assembly.entry_id'
_item.category_id em_assembly
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_assembly.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_assembly.name
_item_description.description
; The name of the assembly of observed complexes.
;
_item.name '_em_assembly.name'
_item.category_id em_assembly
_item.mandatory_code no
_item_type.code line
save_
save__em_assembly.aggregation_state
_item_description.description
; A description of the aggregation state of the assembly.
;
_item.name '_em_assembly.aggregation_state'
_item.category_id em_assembly
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'SINGLE PARTICLE'
'INDIVIDUAL STRUCTURE'
'2D-CRYSTAL'
ICOSAHEDRAL
HELICAL
FILAMENT
'HELICAL FILAMENTS'
TISSUE
save_
save__em_assembly.composition
_item_description.description
; The known composition of the assembly.
;
_item.name '_em_assembly.composition'
_item.category_id em_assembly
_item.mandatory_code no
_item_type.code line
save_
save__em_assembly.num_components
_item_description.description
; The number of components of the biological assembly.
;
_item.name '_em_assembly.num_components'
_item.category_id em_assembly
_item.mandatory_code no
_item_type.code int
save_
save__em_assembly.mol_wt_exp
_item_description.description
; The value (in megadaltons) of the experimentally
determined molecular weight of the assembly.
;
_item.name '_em_assembly.mol_wt_exp'
_item.category_id em_assembly
_item.mandatory_code no
_item_type.code float
_item_units.code megadaltons
save_
save__em_assembly.mol_wt_theo
_item_description.description
; The value (in megadaltons) of the theoretically
determined molecular weight of the assembly.
;
_item.name '_em_assembly.mol_wt_theo'
_item.category_id em_assembly
_item.mandatory_code no
_item_type.code float
_item_units.code megadaltons
save_
save__em_assembly.mol_wt_method
_item_description.description
; The method used in determining
the molecular weight.
;
_item.name '_em_assembly.mol_wt_method'
_item.category_id em_assembly
_item.mandatory_code no
_item_type.code text
save_
save__em_assembly.details
_item_description.description
; A description of any additional details
describing the observed sample.
;
_item.name '_em_assembly.details'
_item.category_id em_assembly
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
; This structure was preferentially oriented (end-on)on the grid.
;
; The structure was monodisperse.
;
save_
########################
## EM_ENTITY_ASSEMBLY ##
########################
save_em_entity_assembly
_category.description
; Data items in the EM_ENTITY_ASSEMBLY category
record details about each component of
the complex.
;
_category.id em_entity_assembly
_category.mandatory_code no
loop_
_category_key.name
'_em_entity_assembly.id'
'_em_entity_assembly.assembly_id'
loop_
_category_group.id
'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
; _em_entity_assembly.id 1
_em_entity_assembly.assembly_id 1
_em_entity_assembly.type VIRUS
;
save_
save__em_entity_assembly.id
_item_description.description
; The value of _em_entity_assembly.id must uniquely identify
each of the components of the complex.
;
_item.name '_em_entity_assembly.id'
_item.category_id em_entity_assembly
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_virus_entity.entity_assembly_id'
_item_linked.parent_name '_em_entity_assembly.id'
save_
save__em_entity_assembly.assembly_id
_item_description.description
; This data item is a pointer to _em_assembly.id in the
ASSEMBLY category.
;
_item.name '_em_entity_assembly.assembly_id'
_item.category_id em_entity_assembly
_item.mandatory_code yes
_item_type.code code
save_
save__em_entity_assembly.type
_item_description.description
; A description of types of components of the
assembly of the biological structure.
;
_item.name '_em_entity_assembly.type'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
VIRUS
PROTEIN
'NUCLEIC ACID'
LIGAND
LABEL
'CELLULAR COMPONENT'
save_
save__em_entity_assembly.name
_item_description.description
; The name of the component of the observed assembly.
;
_item.name '_em_entity_assembly.name'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code text
save_
save__em_entity_assembly.details
_item_description.description
; Additional details about the component.
;
_item.name '_em_entity_assembly.details'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code text
save_
save__em_entity_assembly.ebi_organism_scientific
_item_description.description
; The species of the natural organism from which the component
was obtained.
;
_item.name '_em_entity_assembly.ebi_organism_scientific'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code text
save_
save__em_entity_assembly.ebi_organism_common
_item_description.description
; The common name of the species of the natural organism from which
the component was obtained.
;
_item.name '_em_entity_assembly.ebi_organism_common'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code text
save_
save__em_entity_assembly.ebi_strain
_item_description.description
; The strain of the natural organism from which the component was
obtained, if relevant.
;
_item.name '_em_entity_assembly.ebi_strain'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'DH5a'
'BMH 71-18'
save_
save__em_entity_assembly.ebi_tissue
_item_description.description
; The tissue of the natural organism from which the component was
obtained.
;
_item.name '_em_entity_assembly.ebi_tissue'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'heart'
'liver'
'eye lens'
save_
save__em_entity_assembly.ebi_cell
_item_description.description
; The cell from which the component was
obtained.
;
_item.name '_em_entity_assembly.ebi_cell'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'CHO'
'HELA'
'3T3'
save_
save__em_entity_assembly.ebi_organelle
_item_description.description
; The organelle from which the component was
obtained.
;
_item.name '_em_entity_assembly.ebi_organelle'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'golgi'
'mitochondrion'
'cytoskeleton'
save_
save__em_entity_assembly.ebi_cellular_location
_item_description.description
; The cellular location of the component.
;
_item.name '_em_entity_assembly.ebi_cellular_location'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'cytoplasm'
'endoplasmic reticulum'
'plasma membrane'
save_
save__em_entity_assembly.ebi_engineered
_item_description.description
; A flag to indicate whether the component is engineered.
;
_item.name '_em_entity_assembly.ebi_engineered'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
YES
NO
save_
save__em_entity_assembly.ebi_expression_system
_item_description.description
; The expression system used to produce the component.
;
_item.name '_em_entity_assembly.ebi_expression_system'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'eschericia coli'
'saccharomyces cerevisiae'
save_
save__em_entity_assembly.ebi_expression_system_plasmid
_item_description.description
; The plasmid used in the expression system used to produce the component.
;
_item.name '_em_entity_assembly.ebi_expression_system_plasmid'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'pBR322'
'pMB9'
save_
save__em_entity_assembly.go_id
_item_description.description
; The Gene Ontology (GO) identifier for the component.
The GO id is the appropriate identifier used by the Gene Ontology
Consortium. Reference: Nature Genetics vol 25:25-29 (2000).
;
_item.name '_em_entity_assembly.go_id'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'GO:0005876'
'GO:0015630'
save_
save__em_entity_assembly.ipr_id
_item_description.description
; The InterPro (IPR) identifier for the component.
The IPR id is the appropriate identifier used by the Interpro Resource.
Reference: Nucleic Acid Research vol 29(1):37-40(2001).
;
_item.name '_em_entity_assembly.ipr_id'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'001304'
'002353'
save_
save__em_entity_assembly.synonym
_item_description.description
; Alternative name of the component.
;
_item.name '_em_entity_assembly.synonym'
_item.category_id em_entity_assembly
_item.mandatory_code no
_item_type.code line
_item_examples.case 'FADV-1'
save_
#############################
## EM_ENTITY_ASSEMBLY_LIST ##
#############################
save_em_entity_assembly_list
_category.description
; Data items in the EM_ENTITY_ASSEMBLY_LIST category record details
of the structural elements in each component.
;
_category.id em_entity_assembly_list
_category.mandatory_code no
loop_
_category_key.name
'_em_entity_assembly_list.entity_assembly_id'
'_em_entity_assembly_list.id'
'_em_entity_assembly_list.entity_id'
loop_
_category_group.id 'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - microtubule
;
;
loop_
_em_entity_assembly_list.entity_assembly_id
_em_entity_assembly_list.id
_em_entity_assembly_list.entity_id
_em_entity_assembly_list.oligomeric_details
_em_entity_assembly_list.number_of_copies
1 1 1 'DIMER' 2
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__em_entity_assembly_list.id
_item_description.description
; The value of _em_entity_assembly_list.id must uniquely identify
the component.
;
_item.name '_em_entity_assembly_list.id'
_item.category_id em_entity_assembly_list
_item.mandatory_code yes
_item_type.code code
save_
save__em_entity_assembly_list.entity_id
_item_description.description
; A pointer to entity id.
;
_item.name '_em_entity_assembly_list.entity_id'
_item.category_id em_entity_assembly_list
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_entity_assembly_list.entity_id'
_item_linked.parent_name '_entity.id'
save_
save__em_entity_assembly_list.entity_assembly_id
_item_description.description
; This data item is a pointer to _em_entity_assembly.id in
the ENTITY_ASSEMBLY category.
;
_item.name '_em_entity_assembly_list.entity_assembly_id'
_item.category_id em_entity_assembly_list
_item.mandatory_code yes
_item_type.code code
save_
save__em_entity_assembly_list.oligomeric_details
_item_description.description
; The oligomeric state of the entity.
;
_item.name '_em_entity_assembly_list.oligomeric_details'
_item.category_id em_entity_assembly_list
_item.mandatory_code no
_item_type.code line
save_
save__em_entity_assembly_list.number_of_copies
_item_description.description
; The number of copies of the entity.
;
_item.name '_em_entity_assembly_list.number_of_copies'
_item.category_id em_entity_assembly_list
_item.mandatory_code no
_item_type.code int
save_
#####################
## EM_VIRUS_ENTITY ##
#####################
save_em_virus_entity
_category.description
; Data items in the EM_VIRUS_ENTITY category record details
of the icosahedral virus.
;
_category.id em_virus_entity
_category.mandatory_code no
loop_
_category_key.name
'_em_virus_entity.id'
'_em_virus_entity.entity_assembly_id'
loop_
_category_group.id 'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
; loop_
_em_virus_entity.id
_em_virus_entity.virus_host_category
_em_virus_entity.virus_host_species
_em_virus_entity.virus_type
_em_virus_entity.virus_isolate
_em_virus_entity.ictvdb_id
_em_virus_entity.entity_assembly_id
_em_virus_entity.enveloped
_em_virus_entity.empty
1 'VERTERBRATES' 'HOMO SAPIENS' 'VIRUS' 'STRAIN' '00.073.0.01.023' 1 'YES' 'NO'
;
save_
save__em_virus_entity.id
_item_description.description
; Is the unique identifier for VIRUS_ENTITY category.
;
_item.name '_em_virus_entity.id'
_item.category_id em_virus_entity
_item.mandatory_code yes
_item_type.code code
save_
save__em_virus_entity.virus_host_category
_item_description.description
; The host category description for the virus.
;
_item.name '_em_virus_entity.virus_host_category'
_item.category_id em_virus_entity
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
ALGAE
ARCHAEA
'BACTERIA(EUBACTERIA)'
FUNGI
INVERTEBRATES
'PLANTAE (HIGHER PLANTS)'
PROTOZOA
VERTEBRATES
save_
save__em_virus_entity.virus_host_species
_item_description.description
; The host species from which the virus was isolated.
;
_item.name '_em_virus_entity.virus_host_species'
_item.category_id em_virus_entity
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'homo sapiens'
'gallus gallus'
save_
save__em_virus_entity.virus_host_growth_cell
_item_description.description
; The host cell from which the virus was isolated.
;
_item.name '_em_virus_entity.virus_host_growth_cell'
_item.category_id em_virus_entity
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'HELA'
'CHO'
save_
save__em_virus_entity.virus_type
_item_description.description
; The type of virus.
;
_item.name '_em_virus_entity.virus_type'
_item.category_id em_virus_entity
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
VIRION
SATELLITE
PRION
VIROID
'VIRUS-LIKE PARTICLE'
save_
save__em_virus_entity.virus_isolate
_item_description.description
; The isolate from which the virus was obtained.
;
_item.name '_em_virus_entity.virus_isolate'
_item.category_id em_virus_entity
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
STRAIN
SEROTYPE
SEROCOMPLEX
SUBSPECIES
SPECIES
save_
save__em_virus_entity.ictvdb_id
_item_description.description
; The International Committee on Taxonomy of Viruses
(ICTV) Taxon Identifier is the Virus Code used throughout the
ICTV database (ICTVdb). The ICTVdb id is the appropriate
identifier used by the International Committee on Taxonomy of Viruses
Resource. Reference: Virus Taxonomy, Academic Press (1999).
ISBN:0123702003.
;
_item.name '_em_virus_entity.ictvdb_id'
_item.category_id em_virus_entity
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'01.0.2.0.001'
'01.0.2.0.002'
save_
save__em_virus_entity.entity_assembly_id
_item_description.description
; This data item is a pointer to _em_virus_entity.id in the
ENTITY_ASSEMBLY category.
;
_item.name '_em_virus_entity.entity_assembly_id'
_item.category_id em_virus_entity
_item.mandatory_code yes
_item_type.code code
save_
save__em_virus_entity.enveloped
_item_description.description
; Flag to indicate if the virus is enveloped or not.
;
_item.name '_em_virus_entity.enveloped'
_item.category_id em_virus_entity
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
YES
NO
save_
save__em_virus_entity.empty
_item_description.description
; Flag to indicate if the virus is empty or not.
;
_item.name '_em_virus_entity.empty'
_item.category_id em_virus_entity
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
YES
NO
save_
save__em_virus_entity.details
_item_description.description
; Additional details about this virus entity
;
_item.name '_em_virus_entity.details'
_item.category_id em_virus_entity
_item.mandatory_code no
_item_type.code text
save_
##########################
## EM_ICOS_VIRUS_SHELLS ##
##########################
save_em_icos_virus_shells
_category.description
; Data items in the EM_ICOS_VIRUS_SHELLS category record details
of the viral shell number, diameter of each shell and triangulation number.
;
_category.id em_icos_virus_shells
_category.mandatory_code no
loop_
_category_key.name
'_em_icos_virus_shells.virus_entity_id'
'_em_icos_virus_shells.id'
loop_
_category_group.id
'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
; loop_
_em_icos_virus_shells.virus_entity_id
_em_icos_virus_shells.id
_em_icos_virus_shells.shell_diameter
_em_icos_virus_shells.triangulation_num
1 1 400 4
;
save_
save__em_icos_virus_shells.virus_entity_id
_item_description.description
; The value of _em_icos_virus_shells.virus_entity_id is
a pointer to _em_virus_entity.id in the VIRUS_ENTITY
category.
;
_item.name '_em_icos_virus_shells.virus_entity_id'
_item.category_id em_icos_virus_shells
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_icos_virus_shells.virus_entity_id'
_item_linked.parent_name '_em_virus_entity.id'
save_
save__em_icos_virus_shells.id
_item_description.description
; The value of _em_em_icos_virus_shells.id must uniquely identify
the number and diameter of each virus protein shell and its
triangulation number.
;
_item.name '_em_icos_virus_shells.id'
_item.category_id em_icos_virus_shells
_item.mandatory_code yes
_item_type.code code
save_
save__em_icos_virus_shells.shell_diameter
_item_description.description
; The value of the diameter (in angstroms) for each
protein shell of the virus.
;
_item.name '_em_icos_virus_shells.shell_diameter'
_item.category_id em_icos_virus_shells
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__em_icos_virus_shells.triangulation_num
_item_description.description
; The triangulation number (T number) is a geometric and abstract
concept that does not correspond to the structural components of
an individul virus.
It refers to the organisation of the geometric figure.
The triangulation number, T is given by the following relationship:
T= h*2 + hk +k*2, where h and k are positive integers which define the
position of the five-fold vertex on the original hexagonal net.
;
_item.name '_em_icos_virus_shells.triangulation_num'
_item.category_id em_icos_virus_shells
_item.mandatory_code no
_item_type.code int
_item_examples.case 4
save_
###########################
## EM_SAMPLE_PREPARATION ##
###########################
save_em_sample_preparation
_category.description
; Data items in the EM_SAMPLE_PREPARATION category
record details of sample conditions prior to loading
onto grid support.
;
_category.id em_sample_preparation
_category.mandatory_code no
loop_
_category_key.name
'_em_sample_preparation.id'
'_em_sample_preparation.entry_id'
loop_
_category_group.id
'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;
_em_sample_preparation.entry_id 1DYL
_em_sample_preparation.id 1
_em_sample_preparation.ph 7.6
_em_sample_preparation.buffer_id 1
_em_sample_preparation.sample_concentration 5
_em_sample_preparation.2d_crystal_grow_id .
_em_sample_preparation.support.id 1
;
save_
save__em_sample_preparation.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_em_sample_preparation.entry_id'
_item.category_id em_sample_preparation
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_sample_preparation.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_sample_preparation.id
_item_description.description
; The value of _em_sample_preparation.id must
uniquely identify the sample preparation.
;
_item.name '_em_sample_preparation.id'
_item.category_id em_sample_preparation
_item.mandatory_code yes
_item_type.code code
save_
save__em_sample_preparation.ph
_item_description.description
; The pH value of the observed sample buffer.
;
_item.name '_em_sample_preparation.ph'
_item.category_id em_sample_preparation
_item.mandatory_code no
_item_type.code float
save_
save__em_sample_preparation.buffer_id
_item_description.description
; This data item is a pointer to _em_buffer.id in the
BUFFER category.
;
_item.name '_em_sample_preparation.buffer_id'
_item.category_id em_sample_preparation
_item.mandatory_code no
_item_type.code code
save_
save__em_sample_preparation.sample_concentration
_item_description.description
; The value of the concentration (mg/mL for mg per milliliter)
of the complex in the sample.
;
_item.name '_em_sample_preparation.sample_concentration'
_item.category_id em_sample_preparation
_item.mandatory_code no
_item_type.code float
_item_units.code mg_per_ml
save_
save__em_sample_preparation.2d_crystal_grow_id
_item_description.description
; This data item is a pointer to _em_2d_crystal_grow.id
in the 2D_CRYSTAL_GROW category.
;
_item.name '_em_sample_preparation.2d_crystal_grow_id'
_item.category_id em_sample_preparation
_item.mandatory_code no
_item_type.code code
save_
save__em_sample_preparation.support_id
_item_description.description
; This data item is a pointer to _em_sample_support.id
in the EM_SAMPLE_SUPPORT category.
;
_item.name '_em_sample_preparation.support_id'
_item.category_id em_sample_preparation
_item.mandatory_code no
_item_type.code code
save_
#######################
## EM_SAMPLE_SUPPORT ##
#######################
save_em_sample_support
_category.description
; Data items in the EM_SAMPLE_SUPPORT category record details
of the electron microscope grid type, grid support film and pretreatment
of whole before sample is applied
;
_category.id em_sample_support
_category.mandatory_code no
_category_key.name '_em_sample_support.id'
loop_
_category_group.id
'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;
_em_sample_support.id 1
_em_sample_support.film_material 'HOLEY CARBON'
_em_sample_support.method .
_em_sample_support.grid_material COPPER
_em_sample_support.grid_mesh_size 400
_em_sample_support.grid_type MESH
_em_sample_support.pretreatment 'GLOW DISCHARGE'
_em_sample_support.details .
_em_sample_support.citation_id 2
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__em_sample_support.id
_item_description.description
; The value of _em_sample_support.id must uniquely identify
the sample support.
;
_item.name '_em_sample_support.id'
_item.category_id em_sample_support
_item.mandatory_code yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_em_imaging.sample_support_id' '_em_sample_support.id'
'_em_sample_preparation.support_id' '_em_sample_support.id'
save_
save__em_sample_support.film_material
_item_description.description
; The support material covering the em grid.
;
_item.name '_em_sample_support.film_material'
_item.category_id em_sample_support
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
CARBON
'FORMVAR PLUS CARBON'
'CELLULOSE ACETATE PLUS CARBON'
'PARLODION PLUS CARBON'
'HOLEY CARBON'
save_
save__em_sample_support.method
_item_description.description
; A description of the method used to produce the support film.
;
_item.name '_em_sample_support.method'
_item.category_id em_sample_support
_item.mandatory_code no
_item_type.code text
_item_examples.case '1%formvar in chloroform cast on distilled water'
save_
save__em_sample_support.grid_material
_item_description.description
; The name of the material from which the grid is made.
;
_item.name '_em_sample_support.grid_material'
_item.category_id em_sample_support
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
COPPER
COPPER/PALLADIUM
COPPER/RHODIUM
GOLD
NICKEL
PLATINUM
TUNGSTEN
TITANIUM
MOLYBDENUM
save_
save__em_sample_support.grid_mesh_size
_item_description.description
; The value of the mesh size (per inch) of the em grid.
;
_item.name '_em_sample_support.grid_mesh_size'
_item.category_id em_sample_support
_item.mandatory_code no
_item_type.code int
_item_examples.case 400
save_
save__em_sample_support.grid_type
_item_description.description
; A description of the grid type.
;
_item.name '_em_sample_support.grid_type'
_item.category_id em_sample_support
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
SLOT
APERTURE
DIAMOND
HEXAGONAL
save_
save__em_sample_support.pretreatment
_item_description.description
; A description of the grid plus support film pretreatment.
;
_item.name '_em_sample_support.pretreatment'
_item.category_id em_sample_support
_item.mandatory_code no
_item_type.code text
_item_examples.case 'glow-discharged for 30 sec in argon'
save_
save__em_sample_support.details
_item_description.description
; A description of any additional details concerning the sample support.
;
_item.name '_em_sample_support.details'
_item.category_id em_sample_support
_item.mandatory_code no
_item_type.code text
_item_examples.case
'This grid plus sample was kept at -170 deg C for a month before use'
save_
save__em_sample_support.citation_id
_item_description.description
; This data item is a pointer to _citation.id
in the CITATION category.
;
_item.name '_em_sample_support.citation_id'
_item.category_id em_sample_support
_item.mandatory_code no
_item_linked.child_name '_em_sample_support.citation_id'
_item_linked.parent_name '_citation.id'
_item_type.code code
save_
##########################
## EM_2D_CRYSTAL_GROW ##
##########################
save_em_2d_crystal_grow
_category.description
; Data items in the EM_2D_CRYSTAL_GROW category
record details of growth conditions for 2d crystal samples.
;
_category.id em_2d_crystal_grow
_category.mandatory_code no
_category_key.name '_em_2d_crystal_grow.id'
loop_
_category_group.id
'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1AT9 and laboratory records for the
structure corresponding to PDB entry 1DYL
;
; _em_2d_crystal_grow.id 1
_em_2d_crystal_grow.method .
_em_2d_crystal_grow.apparatus .
_em_2d_crystal_grow.atmosphere 'room air'
_em_2d_crystal_grow.pH 5.2
_em_2d_crystal_grow.temp 18
_em_2d_crystal_grow.time .
_em_2d_crystal_grow.buffer_id 2
_em_2d_crystal_grow.details 'on grid'
_em_2d_crystal_grow.number_2d_crystals 129
_em_2d_crystal_grow.mean_2d_crystal_size .
_em_2d_crystal_grow.citation_id 2
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__em_2d_crystal_grow.id
_item_description.description
; The value of _em_2d_crystal_grow.crystal_id
must uniquely identify the sample 2d crystal.
;
_item.name '_em_2d_crystal_grow.id'
_item.category_id em_2d_crystal_grow
_item.mandatory_code yes
_item_type.code code
save_
save__em_2d_crystal_grow.method
_item_description.description
; The method used for growing the crystals.
;
_item.name '_em_2d_crystal_grow.method'
_item.category_id em_2d_crystal_grow
_item.mandatory_code no
_item_type.code line
_item_examples.case 'lipid monolayer'
save_
save__em_2d_crystal_grow.apparatus
_item_description.description
; The type of the apparatus used for growing the crystals.
;
_item.name '_em_2d_crystal_grow.apparatus'
_item.category_id em_2d_crystal_grow
_item.mandatory_code no
_item_type.code line
_item_examples.case 'Langmuir trough'
save_
save__em_2d_crystal_grow.atmosphere
_item_description.description
; The type of atmosphere in which crystals were grown.
;
_item.name '_em_2d_crystal_grow.atmosphere'
_item.category_id em_2d_crystal_grow
_item.mandatory_code no
_item_type.code line
_item_examples.case 'room air'
save_
save__em_2d_crystal_grow.pH
_item_description.description
; the pH value used for growing the crystals.
;
_item.name '_em_2d_crystal_grow.pH'
_item.category_id em_2d_crystal_grow
_item.mandatory_code no
_item_type.code float
_item_examples.case 4.7
save_
save__em_2d_crystal_grow.temp
_item_description.description
; The value of the temperature in degrees Kelvin used for
growing the crystals.
;
_item.name '_em_2d_crystal_grow.temp'
_item.category_id em_2d_crystal_grow
_item.mandatory_code no
_item_type.code float
_item_units.code kelvins
_item_examples.case 293
save_
save__em_2d_crystal_grow.time
_item_description.description
; The length of time required to grow the crystals.
;
_item.name '_em_2d_crystal_grow.time'
_item.category_id em_2d_crystal_grow
_item.mandatory_code no
_item_type.code line
_item_examples.case 'approximately 2 days'
save_
save__em_2d_crystal_grow.buffer_id
_item_description.description
; This data item is a pointer to _em_buffer.id in the
BUFFER category.
;
_item.name '_em_2d_crystal_grow.buffer_id'
_item.category_id em_2d_crystal_grow
_item.mandatory_code no
_item_type.code code
save_
save__em_2d_crystal_grow.details
_item_description.description
; Any additional items concerning 2d crystal growth.
;
_item.name '_em_2d_crystal_grow.details'
_item.category_id em_2d_crystal_grow
_item.mandatory_code no
_item_type.code text
save_
save__em_2d_crystal_grow.number_2d_crystals
_item_description.description
; The number of 2d crystals imaged.
;
_item.name '_em_2d_crystal_grow.number_2d_crystals'
_item.category_id em_2d_crystal_grow
_item.mandatory_code no
_item_type.code int
save_
save__em_2d_crystal_grow.mean_2d_crystal_size
_item_description.description
; The approximate size (microns squared) of 2d crystals imaged.
;
_item.name '_em_2d_crystal_grow.mean_2d_crystal_size'
_item.category_id em_2d_crystal_grow
_item.mandatory_code no
_item_type.code float
_item_units.code microns_squared
save_
save__em_2d_crystal_grow.citation_id
_item_description.description
; This data item is a pointer to _citation.id
in the CITATION category.
;
_item.name '_em_2d_crystal_grow.citation_id'
_item.category_id em_2d_crystal_grow
_item.mandatory_code no
_item_linked.child_name '_em_2d_crystal_grow.citation_id'
_item_linked.parent_name '_citation.id'
_item_type.code code
save_
###############
## EM_BUFFER ##
###############
save_em_buffer
_category.description
; Data items in the BUFFER category
record details of the sample buffer.
;
_category.id em_buffer
_category.mandatory_code no
_category_key.name '_em_buffer.id'
loop_
_category_group.id 'inclusive_group'
'em_group'
save_
save__em_buffer.id
_item_description.description
; The value of _em_buffer.id must
uniquely identify the sample buffer.
;
_item.name '_em_buffer.id'
_item.category_id em_buffer
_item.mandatory_code yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_em_2d_crystal_grow.buffer_id' '_em_buffer.id'
'_em_sample_preparation.buffer_id' '_em_buffer.id'
'_em_buffer_components.buffer_id' '_em_buffer.id'
save_
save__em_buffer.name
_item_description.description
; The name of the buffer.
;
_item.name '_em_buffer.name'
_item.category_id em_buffer
_item.mandatory_code no
_item_type.code line
_item_examples.case 'Acetic acid'
save_
save__em_buffer.details
_item_description.description
; Any additional details to do with buffer.
;
_item.name '_em_buffer.details'
_item.category_id em_buffer
_item.mandatory_code no
_item_type.code text
_item_examples.case 'aerated'
save_
##########################
## EM_BUFFER_COMPONENTS ##
##########################
save_em_buffer_components
_category.description
; Constituents of buffer in sample
;
_category.id em_buffer_components
_category.mandatory_code no
loop_
_category_key.name
'_em_buffer_components.buffer_id'
'_em_buffer_components.id'
loop_
_category_group.id 'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;loop_
_em_buffer_components.buffer_id
_em_buffer_components.id
_em_buffer_components.name
_em_buffer_components.volume
_em_buffer_components.conc
_em_buffer_components.details
1 1 'NaCl' '0.200 ' '4 ' .
1 2 'Acetic Acid' '0.047 ' '100' .
1 3 'water' '0.700 ' 'neat' .
;
save_
save__em_buffer_components.id
_item_description.description
; The value of _em_buffer_components.id must
uniquely identify a component of the buffer.
;
_item.name '_em_buffer_components.id'
_item.category_id em_buffer_components
_item.mandatory_code yes
_item_type.code code
save_
save__em_buffer_components.buffer_id
_item_description.description
; This data item is a pointer to _em_buffer.id in the BUFFER category.
;
_item.name '_em_buffer_components.buffer_id'
_item.category_id em_buffer_components
_item.mandatory_code yes
_item_type.code code
save_
save__em_buffer_components.name
_item_description.description
; The name of each buffer component.
;
_item.name '_em_buffer_components.name'
_item.category_id em_buffer_components
_item.mandatory_code no
_item_type.code line
_item_examples.case 'Acetic acid'
save_
save__em_buffer_components.volume
_item_description.description
; The volume of buffer component.
;
_item.name '_em_buffer_components.volume'
_item.category_id em_buffer_components
_item.mandatory_code no
_item_type.code code
_item_examples.case 0.200
save_
save__em_buffer_components.conc
_item_description.description
; The millimolar concentration of buffer component.
;
_item.name '_em_buffer_components.conc'
_item.category_id em_buffer_components
_item.mandatory_code no
_item_type.code code
_item_examples.case 200
save_
save__em_buffer_components.details
_item_description.description
; Any additional details to do with buffer composition.
;
_item.name '_em_buffer_components.details'
_item.category_id em_buffer_components
_item.mandatory_code no
_item_type.code text
_item_examples.case 'pH adjusted with NaOH'
save_
######################
## EM_VITRIFICATION ##
######################
save_em_vitrification
_category.description
; Data items in the EM_VITRIFICATION category
record details about the method and cryogen used in
rapid freezing of the sample on the grid prior to its
insertion in the electron microscope
;
_category.id em_vitrification
_category.mandatory_code no
loop_
_category_key.name
'_em_vitrification.id'
'_em_vitrification.entry_id'
loop_
_category_group.id 'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;
_em_vitrification.entry_id 1DYL
_em_vitrification.id 1
_em_vitrification.sample_preparation_id 1
_em_vitrification.cryogen_name "ETHANE"
_em_vitrification.humidity 90
_em_vitrification.temp 95
_em_vitrification.instrument .
_em_vitrification.method "PLUNGE VITRIFICATION"
_em_vitrification.time_resolved_state .
_em_vitrification.citation_id 1
_em_vitrification.details
; SAMPLES WERE PREPARED AS THIN
LAYERS OF VITREOUS ICE AND
MAINTAINED AT NEAR LIQUID NITROGEN
TEMPERATURE IN THE ELECTRON MICROSCOPE
WITH A GATAN 626-0300 CRYOTRANSFER
HOLDER.
;
;
save_
save__em_vitrification.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_em_vitrification.entry_id'
_item.category_id em_vitrification
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_vitrification.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_vitrification.id
_item_description.description
; The value of _em_vitrification.id must uniquely identify
the vitrification procedure.
;
_item.name '_em_vitrification.id'
_item.category_id em_vitrification
_item.mandatory_code yes
_item_type.code code
save_
save__em_vitrification.sample_preparation_id
_item_description.description
; This data item is a pointer to _em_sample_preparation.id in the
EM_SAMPLE_PREPARATION category.
;
_item.name '_em_vitrification.sample_preparation_id'
_item.category_id em_vitrification
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_em_vitrification.sample_preparation_id'
_item_linked.parent_name '_em_sample_preparation.id'
save_
save__em_vitrification.cryogen_name
_item_description.description
; This is the name of the cryogen.
;
_item.name '_em_vitrification.cryogen_name'
_item.category_id em_vitrification
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
HELIUM
NITROGEN
PROPANE
ETHANE
METHANE
'FREON 22'
'FREON 12'
save_
save__em_vitrification.humidity
_item_description.description
; The humidity (%) in the vicinity of the vitrification process.
;
_item.name '_em_vitrification.humidity'
_item.category_id em_vitrification
_item.mandatory_code no
_item_type.code line
_item_examples.case 90
save_
save__em_vitrification.temp
_item_description.description
; The temperature (in degrees Kelvin) at which vitrification took place.
;
_item.name '_em_vitrification.temp'
_item.category_id em_vitrification
_item.mandatory_code no
_item_type.code float
_item_units.code kelvins
_item_examples.case 4.2
save_
save__em_vitrification.instrument
_item_description.description
; The type of instrument used in the vitrification process.
;
_item.name '_em_vitrification.instrument'
_item.category_id em_vitrification
_item.mandatory_code no
_item_type.code line
_item_examples.case 'Reichert plunger'
save_
save__em_vitrification.method
_item_description.description
; The procedure for vitrification.
;
_item.name '_em_vitrification.method'
_item.category_id em_vitrification
_item.mandatory_code no
_item_type.code text
_item_examples.case 'blot for 2 seconds before plunging'
save_
save__em_vitrification.time_resolved_state
_item_description.description
; The length of time after an event effecting the sample that
vitrification was induced and a description of the event.
;
_item.name '_em_vitrification.time_resolved_state'
_item.category_id em_vitrification
_item.mandatory_code no
_item_type.code text
_item_examples.case '30 msec after spraying with effector''
save_
save__em_vitrification.citation_id
_item_description.description
; This data item is a pointer to _citation.id in the
CITATION category.
;
_item.name '_em_vitrification.citation_id'
_item.category_id em_vitrification
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_em_vitrification.citation_id'
_item_linked.parent_name '_citation.id'
save_
save__em_vitrification.details
_item_description.description
; Any additional details relating to vitrification.
;
_item.name '_em_vitrification.details'
_item.category_id em_vitrification
_item.mandatory_code no
_item_type.code text
_item_examples.case 'argon atmosphere'
save_
################
## EM_IMAGING ##
################
save_em_imaging
_category.description
; Data items in the EM_IMAGING category record details about
the parameters used in imaging the sample in the electron microscope.
;
_category.id em_imaging
_category.mandatory_code no
loop_
_category_key.name
'_em_imaging.entry_id'
'_em_imaging.id'
loop_
_category_group.id 'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;
_em_imaging.entry_id 1DYL
_em_imaging.id 1
_em_imaging.sample_support_id 1
_em_imaging.microscope_model 'FEI/PHILIPS CM200 FEG'
_em_imaging.specimen_holder_type 'cryotransfer'
_em_imaging.specimen_holder_model 'gatan 626-0300'
_em_imaging.details .
_em_imaging.date 1998-15-06
_em_imaging.accelerating_voltage 200
_em_imaging.illumination_mode 'bright field'
_em_imaging.mode 'low dose'
_em_imaging.nominal_cs 2.0
_em_imaging.nominal_defocus_min 975
_em_imaging.nominal_defocus_max 7600
_em_imaging.tilt_angle_min 0
_em_imaging.tilt_angle_max 0
_em_imaging.nominal_magnification 50000
_em_imaging.calibrated_magnification .
_em_imaging.electron_source 'FEG'
_em_imaging.electron_dose .
_em_imaging.energy_filter .
_em_imaging.energy_window .
_em_imaging.citation_id 1
_em_imaging.temperature 95
_em_imaging.detector_distance .
_em_imaging.recording_temp_range .
;
save_
save__em_imaging.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_em_imaging.entry_id'
_item.category_id em_imaging
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_imaging.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_imaging.id
_item_description.description
; The value of _em_imaging.id must uniquely identify
each imaging experiment.
;
_item.name '_em_imaging.id'
_item.category_id em_imaging
_item.mandatory_code yes
_item_type.code code
save_
save__em_imaging.sample_support_id
_item_description.description
; This data item is a pointer to _em_sample_support.id in
the EM_SAMPLE_SUPPORT category.
;
_item.name '_em_imaging.sample_support_id'
_item.category_id em_imaging
_item.mandatory_code yes
_item_type.code code
save_
save__em_imaging.detector_id
_item_description.description
; The value of _em_imaging.detector_id must uniquely identify
the type of detector used in the experiment.
;
_item.name '_em_imaging.detector_id'
_item.category_id em_imaging
_item.mandatory_code yes
_item_type.code code
save_
save__em_imaging.scans_id
_item_description.description
; The value of _em_imaging.scans_id must uniquely identify
the image_scans used in the experiment.
;
_item.name '_em_imaging.scans_id'
_item.category_id em_imaging
_item.mandatory_code yes
_item_type.code code
save_
save__em_imaging.microscope_model
_item_description.description
; The name of the model of microscope.
;
_item.name '_em_imaging.microscope_model'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'HITACHI H8100'
'HITACHI HF2000'
'HITACHI HF2000-UHR'
'HITACHI H9000-UHR'
'HITACHI H9000-NAR'
'HITACHI 300KEV FEG'
'HITACHI HU1250'
'HITACHI H-1500'
'JEOL 2000EX'
'JEOL 2010HT'
'JEOL 2010UHR'
'JEOL 2010F'
'JEOL 3010HT'
'JEOL 3010UHR'
'JEOL KYOTO-3000SFF'
'JEOL 4000EX'
'JEOL HAREM'
'JEOL ARM-1000'
'JEOL KYOTO-1000'
'JEOL ARM-1250'
'FEI/PHILIPS CM120T'
'FEI/PHILIPS CM200T'
'FEI/PHILIPS CM20/ST'
'FEI/PHILIPS CM20/SOPHIE'
'FEI/PHILIPS CM200FEG/ST'
'FEI/PHILIPS CM20/UT'
'FEI/PHILIPS CM200FEG/UT'
'FEI/PHILIPS CM30/T'
'FEI/PHILIPS CM300FEG/T'
'FEI/PHILIPS CM300FEG/HE'
'FEI/PHILIPS CM30/ST'
'FEI/PHILIPS CM300FEG/ST'
'FEI/PHILIPS CM300FEG/UT'
'FEI TECNAI 12'
'FEI TECNAI 20'
'FEI TECNAI F20'
'FEI TECNAI F30'
'FEI MORGAGNI'
save_
save__em_imaging.specimen_holder_type
_item_description.description
; The type of specimen holder used during imaging.
;
_item.name '_em_imaging.specimen_holder_type'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code line
_item_examples.case 'cryo'
save_
save__em_imaging.specimen_holder_model
_item_description.description
; The name of the model of specimen holder used during imaging.
;
_item.name '_em_imaging.specimen_holder_model'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
'GATAN HELIUM'
'GATAN LIQUID NITROGEN'
OTHER
save_
save__em_imaging.details
_item_description.description
; Any additional imaging details.
;
_item.name '_em_imaging.details'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code text
_item_examples.case 'weak beam illumination'
save_
save__em_imaging.date
_item_description.description
; Date (YYYY-MM-DD) of imaging experiment or the date at which
a series of experiments began.
;
_item.name '_em_imaging.date'
_item.category_id em_imaging
_item.mandatory_code no
# _item_type.code yyyy-mm-dd
_item_type.code line
_item_examples.case '2001-05-08'
save_
save__em_imaging.accelerating_voltage
_item_description.description
; A value of accelerating voltage (in kV) used for imaging.
;
_item.name '_em_imaging.accelerating_voltage'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code int
_item_units.code kilovolts
_item_examples.case 300
save_
save__em_imaging.illumination_mode
_item_description.description
; The mode of illumination.
;
_item.name '_em_imaging.illumination_mode'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'FLOOD BEAM'
'FLOOD BEAM LOW DOSE'
'SPOT SCAN'
OTHER
save_
save__em_imaging.mode
_item_description.description
; The mode of imaging.
;
_item.name '_em_imaging.mode'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'BRIGHT FIELD'
'DARK FIELD'
DIFFRACTION
OTHER
save_
save__em_imaging.nominal_cs
_item_description.description
; The spherical aberration coefficient (Cs) in millimetres,
of the objective lens.
;
_item.name '_em_imaging.nominal_cs'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code float
_item_units.code millimetres
_item_examples.case 1.4
save_
save__em_imaging.nominal_defocus_min
_item_description.description
; The minimum defocus value of the objective lens (in nanometres) used
to obtain the recorded images.
;
_item.name '_em_imaging.nominal_defocus_min'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code float
_item_units.code nanometres
_item_examples.case 975
save_
save__em_imaging.nominal_defocus_max
_item_description.description
; The maximum defocus value of the objective lens (in nanometres) used
to obtain the recorded images.
;
_item.name '_em_imaging.nominal_defocus_max'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code float
_item_units.code nanometres
_item_examples.case 7600
save_
save__em_imaging.tilt_angle_min
_item_description.description
; The minimum angle at which the specimen was tilted to obtain
recorded images.
;
_item.name '_em_imaging.tilt_angle_min'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_examples.case 0
save_
save__em_imaging.tilt_angle_max
_item_description.description
; The maximum angle at which the specimen was tilted to obtain
recorded images.
;
_item.name '_em_imaging.tilt_angle_max'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_examples.case 60
save_
save__em_imaging.nominal_magnification
_item_description.description
; The magnification indicated by the microscope readout.
;
_item.name '_em_imaging.nominal_magnification'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code int
_item_examples.case 60000
save_
save__em_imaging.calibrated_magnification
_item_description.description
; The magnification value obtained for a known standard just
prior to, during or just after the imaging experiment.
;
_item.name '_em_imaging.calibrated_magnification'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code int
_item_examples.case 61200
save_
save__em_imaging.electron_source
_item_description.description
; The source of electrons. The electron gun.
;
_item.name '_em_imaging.electron_source'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'FIELD EMISSION GUN'
LAB6
'TUNGSTEN HAIRPIN'
'SCHOTTKY FIELD EMISSION GUN'
OTHER
save_
save__em_imaging.electron_dose
_item_description.description
; The electron dose received by the specimen (electrons per square angstrom).
;
_item.name '_em_imaging.electron_dose'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code float
_item_units.code electrons_angstrom_squared
_item_examples.case 0.9
save_
save__em_imaging.energy_filter
_item_description.description
; The type of energy filter spectrometer apparatus.
;
_item.name '_em_imaging.energy_filter'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code line
_item_examples.case 'FEI'
save_
save__em_imaging.energy_window
_item_description.description
; The energy filter range in electron volts (eV)set by spectrometer.
;
_item.name '_em_imaging.energy_window'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code line
_item_units.code electron_volts
_item_examples.case '0 - 15'
save_
save__em_imaging.citation_id
_item_description.description
; This data item is a pointer to _citation.id in
the CITATION category.
;
_item.name '_em_imaging.citation_id'
_item.category_id em_imaging
_item.mandatory_code no
_item_linked.child_name '_em_imaging.citation_id'
_item_linked.parent_name '_citation.id'
_item_type.code code
save_
save__em_imaging.temperature
_item_description.description
; The mean specimen stage temperature (degrees Kelvin) during imaging
in the microscope.
;
_item.name '_em_imaging.temperature'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code float
_item_units.code kelvins
save_
save__em_imaging.detector_distance
_item_description.description
; The camera length (in millimetres). The camera length is the
product of the objective focal length and the combined magnification
of the intermediate and projector lenses when the microscope is
operated in the diffraction mode.
;
_item.name '_em_imaging.detector_distance'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code float
_item_units.code millimetres
save_
save__em_imaging.recording_temperature_minimum
_item_description.description
; The specimen temperature minimum (degrees Kelvin) for the duration
of imaging.
;
_item.name '_em_imaging.recording_temperature_minimum'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code float
_item_units.code kelvins
save_
save__em_imaging.recording_temperature_maximum
_item_description.description
; The specimen temperature maximum (degrees Kelvin) for the duration
of imaging.
;
_item.name '_em_imaging.recording_temperature_maximum'
_item.category_id em_imaging
_item.mandatory_code no
_item_type.code float
_item_units.code kelvins
save_
#################
## EM_DETECTOR ##
#################
save_em_detector
_category.description
; Data items in the EM_DETECTOR category record details
of the image detector type.
;
_category.id em_detector
_category.mandatory_code no
loop_
_category_key.name
'_em_detector.entry_id'
'_em_detector.id'
loop_
_category_group.id 'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;
_em_detector.entry_id 1DYL
_em_detector.id 1
_em_detector.details .
_em_detector.type 'KODAK SO163 FILM'
_em_detector.detective_quantum_efficiency .
;
save_
save__em_detector.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_em_detector.entry_id'
_item.category_id em_detector
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_detector.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_detector.id
_item_description.description
; The value of _em_detector.id must uniquely identify
the detector used for imaging.
;
_item.name '_em_detector.id'
_item.category_id em_detector
_item.mandatory_code yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_em_imaging.detector_id' '_em_detector.id'
save_
save__em_detector.details
_item_description.description
; Any additional information about the detection system.
;
_item.name '_em_detector.details'
_item.category_id em_detector
_item.mandatory_code no
_item_type.code text
save_
save__em_detector.type
_item_description.description
; The detector type used for recording images.
Usually film or CCD camera.
;
_item.name '_em_detector.type'
_item.category_id em_detector
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case
'KODAK SO163 FILM'
'GATAN 673'
'GATAN 676'
'GATAN 692'
'GATAN 794'
'GATAN 1000'
'GATAN 4000'
'TVIPS BIOCAM'
'TVIPS TEMCAM F214'
'TVIPS TEMCAM F224'
'TVIPS FASTSCAN F114'
PROSCAN
AMT
save_
save__em_detector.detective_quantum_efficiency
_item_description.description
; The detective_quantum_efficiency (DQE)is defined as the
square of the signal-to-noise ratio in the recording device
divided by the square of the signal-to-ratio in the electron beam:
(SIGNAL/NOISE)2 recording device
DQE = -------------------------------
(SIGNAL/NOISE)2 electron beam
A DQE value of 1 indicates a perfect recorder. "DQE = 0.25" menas
that the signal-to-noise ratio is reduced by half in the
recording step.
(0.5)**2
DQE = --------- = 0.25.
(1.0)**2
;
_item.name '_em_detector.detective_quantum_efficiency'
_item.category_id em_detector
_item.mandatory_code no
_item_type.code float
_item_examples.case 0.25
save_
####################
## EM_IMAGE_SCANS ##
####################
save_em_image_scans
_category.description
; Data items in the EM_IMAGE_SCANS category record details
of the image scanning device (microdensitometer)
and parameters for digitization of the image.
;
_category.id em_image_scans
_category.mandatory_code no
loop_
_category_key.name
'_em_image_scans.entry_id'
'_em_image_scans.id'
loop_
_category_group.id 'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;
_em_image_scans.entry_id 1DYL
_em_image_scans.id 2
_em_image_scans.number_digital_images 48
_em_image_scans.details .
_em_image_scans.scanner_model .
_em_image_scans.sampling_size .
_em_image_scans.od_range .
_em_image_scans.quant_bit_number .
_em_image_scans.citation_id 1
;
save_
save__em_image_scans.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the
ENTRY category.
;
_item.name '_em_image_scans.entry_id'
_item.category_id em_image_scans
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_image_scans.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_image_scans.id
_item_description.description
; The value of _em_image_scans.id must uniquely identify
the images scanned.
;
_item.name '_em_image_scans.id'
_item.category_id em_image_scans
_item.mandatory_code yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_em_imaging.scans_id' '_em_image_scans.id'
save_
save__em_image_scans.number_digital_images
_item_description.description
; The number of images scanned and digitised.
;
_item.name '_em_image_scans.number_digital_images'
_item.category_id em_image_scans
_item.mandatory_code no
_item_type.code int
save_
save__em_image_scans.details
_item_description.description
; Any additional details about scanning images.
;
_item.name '_em_image_scans.details'
_item.category_id em_image_scans
_item.mandatory_code no
_item_type.code text
save_
save__em_image_scans.scanner_model
_item_description.description
; The scanner model.
;
_item.name '_em_image_scans.scanner_model'
_item.category_id em_image_scans
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
'ZEISS SCAI'
'EMIL 10'
OPTRONICS
'PERKIN ELMER'
TEMSCAN
OTHER
save_
save__em_image_scans.sampling_size
_item_description.description
; The sampling step size (microns) set on the scanner.
;
_item.name '_em_image_scans.sampling_size'
_item.category_id em_image_scans
_item.mandatory_code no
_item_type.code float
_item_units.code microns
save_
save__em_image_scans.od_range
_item_description.description
; The optical density range (OD=-log 10 transmission).
To the eye OD=1 appears light grey and OD=3 is opaque.
;
_item.name '_em_image_scans.od_range'
_item.category_id em_image_scans
_item.mandatory_code no
_item_type.code float
_item_examples.case 1.4
save_
save__em_image_scans.quant_bit_size
_item_description.description
; The number of bits per pixel.
;
_item.name '_em_image_scans.quant_bit_size'
_item.category_id em_image_scans
_item.mandatory_code no
_item_type.code int
_item_examples.case 8
save_
save__em_image_scans.citation_id
_item_description.description
; This data item is a pointer to _citation.id
in the CITATION category.
;
_item.name '_em_image_scans.citation_id'
_item.category_id em_image_scans
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_em_image_scans.citation_id'
_item_linked.parent_name '_citation.id'
save_
################################
## EM_2D_PROJECTION_SELECTION ##
################################
save_em_2d_projection_selection
_category.description
; Data items in the EM_2D_PROJECTION_SELECTION category
record details of images from scanned micrographs and the
number of particles selected from a scanned set of micrographs.
;
_category.id em_2d_projection_selection
_category.mandatory_code no
_category_key.name '_em_2d_projection_selection.entry_id'
loop_
_category_group.id 'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;
_em_2d_projection_selection.entry_id 1
_em_2d_projection_selection.number_particles 5267
_em_2d_projection_selection.software_name 1
_em_2d_projection_selection.method 'INTERACTIVE'
_em_2d_projection_selection.details .
_em_2d_projection_selection.citation_id 1
;
save_
save__em_2d_projection_selection.entry_id
_item_description.description
; The value of _em_2d_projection_selection.entry_id points to
the ENTRY category.
;
_item.name '_em_2d_projection_selection.entry_id'
_item.category_id em_2d_projection_selection
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_2d_projection_selection.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_2d_projection_selection.num_particles
_item_description.description
; The number of particles selected from the projection set of images.
;
_item.name '_em_2d_projection_selection.num_particles'
_item.category_id em_2d_projection_selection
_item.mandatory_code no
_item_type.code int
_item_examples.case 840
save_
save__em_2d_projection_selection.software_name
_item_description.description
; This data item is a pointer to _software.name in the
SOFTWARE category.
;
_item.name '_em_2d_projection_selection.software_name'
_item.category_id em_2d_projection_selection
_item.mandatory_code no
_item_type.code line
# _item_linked.child_name '_em_2d_projection_selection.software_name'
# _item_linked.parent_name '_software.name'
save_
save__em_2d_projection_selection.method
_item_description.description
; The method used for selecting observed assemblies.
;
_item.name '_em_2d_projection_selection.method'
_item.category_id em_2d_projection_selection
_item.mandatory_code no
_item_type.code text
_item_examples.case 'particles picked interactively from monitor'
save_
save__em_2d_projection_selection.details
_item_description.description
; Any additional details used for selecting observed assemblies.
;
_item.name '_em_2d_projection_selection.details'
_item.category_id em_2d_projection_selection
_item.mandatory_code no
_item_type.code text
_item_examples.case
'negative monitor contrast facilitated particle picking'
save_
save__em_2d_projection_selection.citation_id
_item_description.description
; This data item is a pointer to _citation.id in the
CITATION category.
;
_item.name '_em_2d_projection_selection.citation_id'
_item.category_id em_2d_projection_selection
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_em_2d_projection_selection.citation_id'
_item_linked.parent_name '_citation.id'
save_
#################################
## EM_EULER_ANGLE_DISTRIBUTION ##
#################################
save_em_euler_angle_distribution
_category.description
; Data items in the EM_EULER_ANGLE_DISTRIBUTION category
record details of assignment of Euler angles for projection
sets of particles.
;
_category.id em_euler_angle_distribution
_category.mandatory_code no
loop_
_category_key.name
'_em_euler_angle_distribution.id'
'_em_euler_angle_distribution.entry_id'
loop_
_category_group.id 'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;
_em_euler_angle_distribution.entry_id 1DYL
_em_euler_angle_distribution.id 1
_em_euler_angle_distribution.details .
_em_euler_angle_distribution.alpha .
_em_euler_angle_distribution.beta .
_em_euler_angle_distribution.gamma .
;
save_
save__em_euler_angle_distribution.id
_item_description.description
; The value of _em_euler_angle_distribution.id must
uniquely identify the euler angle assignments of
the projection set used in the final reconstruction.
;
_item.name '_em_euler_angle_distribution.id'
_item.category_id em_euler_angle_distribution
_item.mandatory_code yes
_item_type.code code
save_
save__em_euler_angle_distribution.entry_id
_item_description.description
; The value of _em_euler_angle_distribution.entry_id is a pointer
to the ENTRY category.
;
_item.name '_em_euler_angle_distribution.entry_id'
_item.category_id em_euler_angle_distribution
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_euler_angle_distribution.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_euler_angle_distribution.details
_item_description.description
; Any additional details of the euler angles distribution and assignment.
;
_item.name '_em_euler_angle_distribution.details'
_item.category_id em_euler_angle_distribution
_item.mandatory_code no
_item_type.code text
save_
save__em_euler_angle_distribution.alpha
_item_description.description
; The euler-alpha angle assignment.
;
_item.name '_em_euler_angle_distribution.alpha'
_item.category_id em_euler_angle_distribution
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_examples.case 90
save_
save__em_euler_angle_distribution.beta
_item_description.description
; The euler-beta angle assignment.
;
_item.name '_em_euler_angle_distribution.beta'
_item.category_id em_euler_angle_distribution
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_examples.case 90
save_
save__em_euler_angle_distribution.gamma
_item_description.description
; The euler-gamma angle assignment.
;
_item.name '_em_euler_angle_distribution.gamma'
_item.category_id em_euler_angle_distribution
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_examples.case 0
save_
##########################
## EM_3D_RECONSTRUCTION ##
##########################
save_em_3d_reconstruction
_category.description
; Data items in the EM_3D_RECONSTRUCTION category
record details of the 3D reconstruction procedure from 2D projections.
;
_category.id em_3d_reconstruction
_category.mandatory_code no
loop_
_category_key.name
'_em_3d_reconstruction.entry_id'
'_em_3d_reconstruction.id'
loop_
_category_group.id 'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;
_em_3d_reconstruction.entry_id 1DYL
_em_3d_reconstruction.id 1
_em_3d_reconstruction.method 'CROSS-COMMON LINES'
_em_3d_reconstruction.citation_id 1
_em_3d_reconstruction.details .
_em_3d_reconstruction.resolution 9
_em_3d_reconstruction.resolution_method .
_em_3d_reconstruction.ctf_correction_method .
_em_3d_reconstruction.nominal_pixel_size 2.64
_em_3d_reconstruction.actual_pixel_size 2.52
;
save_
save__em_3d_reconstruction.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_em_3d_reconstruction.entry_id'
_item.category_id em_3d_reconstruction
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_3d_reconstruction.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_3d_reconstruction.id
_item_description.description
; The value of _em_3d_reconstruction.id must
uniquely identify the 3d reconstruction.
;
_item.name '_em_3d_reconstruction.id'
_item.category_id em_3d_reconstruction
_item.mandatory_code yes
_item_type.code code
save_
save__em_3d_reconstruction.method
_item_description.description
; The algorithm method used for the 3d-reconstruction.
;
_item.name '_em_3d_reconstruction.method'
_item.category_id em_3d_reconstruction
_item.mandatory_code no
_item_type.code text
_item_examples.case 'cross-common lines'
save_
save__em_3d_reconstruction.citation_id
_item_description.description
; This data item is a pointer to _citation.id in the
CITATION category.
;
_item.name '_em_3d_reconstruction.citation_id'
_item.category_id em_3d_reconstruction
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_em_3d_reconstruction.citation_id'
_item_linked.parent_name '_citation.id'
save_
save__em_3d_reconstruction.details
_item_description.description
; Any additional details used in the 3d reconstruction.
;
_item.name '_em_3d_reconstruction.details'
_item.category_id em_3d_reconstruction
_item.mandatory_code no
_item_type.code text
save_
save__em_3d_reconstruction.resolution
_item_description.description
; The final resolution (in angstroms)of the 3d reconstruction.
;
_item.name '_em_3d_reconstruction.resolution'
_item.category_id em_3d_reconstruction
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__em_3d_reconstruction.resolution_method
_item_description.description
; The method used to determine the final resolution
of the 3d reconstruction.
The Fourier Shell Correlation criterion as a measure of
resolution is based on the concept of splitting the (2D)
data set into two halves; averaging each and comparing them
using the Fourier Ring Correlation (FRC) technique.
;
_item.name '_em_3d_reconstruction.resolution_method'
_item.category_id em_3d_reconstruction
_item.mandatory_code no
_item_type.code text
_item_examples.case 'FSC at 0.5 cut-off'
save_
save__em_3d_reconstruction.magnification_calibration
_item_description.description
; The magnification calibration method for the 3d reconstruction.
;
_item.name '_em_3d_reconstruction.magnification_calibration'
_item.category_id em_3d_reconstruction
_item.mandatory_code no
_item_type.code text
save_
save__em_3d_reconstruction.ctf_correction_method
_item_description.description
; The CTF-correction method.
The Contrast Transfer Function CTF compensation for low contrast
specimens (e.g. frozen-hydrated), for which phase contrast is the only
significant mechanism, then higher defocus levels must be used to
achieve any significant transfer, and several images at different
focus levels must be combined to complete the information lost from
the transfer gaps of any one image. The CTF correction can be applied
to each extracted particle separately or to the whole micrograph after
digitisation. The simplest level of compensation is to reverse phases
at the negative lobes of the CTF.
;
_item.name '_em_3d_reconstruction.ctf_correction_method'
_item.category_id em_3d_reconstruction
_item.mandatory_code no
_item_type.code text
_item_examples.case 'CTF correction of each particle'
save_
save__em_3d_reconstruction.nominal_pixel_size
_item_description.description
; The nominal pixel size of the projection set of images.
;
_item.name '_em_3d_reconstruction.nominal_pixel_size'
_item.category_id em_3d_reconstruction
_item.mandatory_code no
_item_type.code float
save_
save__em_3d_reconstruction.actual_pixel_size
_item_description.description
; The actual pixel size of projection set of images.
;
_item.name '_em_3d_reconstruction.actual_pixel_size'
_item.category_id em_3d_reconstruction
_item.mandatory_code no
_item_type.code float
save_
###################
## EM_3D_FITTING ##
###################
save_em_3d_fitting
_category.description
; Data items in the 3D_FITTING category
record details of the method of fitting atomic
coordinates from a PDB file into a 3d-em
volume map file
;
_category.id em_3d_fitting
_category.mandatory_code no
loop_
_category_key.name
'_em_3d_fitting.id'
'_em_3d_fitting.entry_id'
loop_
_category_group.id
'em_group'
'inclusive_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
;
_em_3d_fitting.id 1
_em_3d_fitting.entry_id 1DYL
_em_3d_fitting.method AUTOMATIC
_em_3d_fitting.target_criteria R-FACTOR
_em_3d_fitting.software_name 1
_em_3d_fitting.over_all_b_value .
_em_3d_fitting.ref_space REAL
_em_3d_fitting.ref_protocol 'RIGID BODY REFINEMENT'
_em_3d_fitting.details
; THE CRYSTAL STRUCTURE OF THE CAPSID
PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359
(SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM
DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED
INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE
FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET
OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED
BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT
(CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT
CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563
ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE
AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5
SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222
ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN
DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE
PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS
GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER
OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY
THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE
DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE
MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE
ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE
HIGHEST PSEUDO TEMPERATURE FACTORS.
;
;
save_
save__em_3d_fitting.id
_item_description.description
; The value of _em_3d_fitting.id must uniquely identify
a fitting procedure of atomic coordinates
into 3dem reconstructed volume map.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_em_3d_fitting.id' em_3d_fitting yes
'_em_3d_fitting_list.3d_fitting_id' em_3d_fitting_list yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_em_3d_fitting_list.3d_fitting_id' '_em_3d_fitting.id'
_item_type.code code
save_
save__em_3d_fitting.entry_id
_item_description.description
; This data item is a pointer to _entry_id in
the ENTRY category.
;
_item.name '_em_3d_fitting.entry_id'
_item.category_id em_3d_fitting
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_3d_fitting.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_3d_fitting.method
_item_description.description
; The method used to fit atomic coordinates
into the 3dem reconstructed map.
;
_item.name '_em_3d_fitting.method'
_item.category_id em_3d_fitting
_item.mandatory_code no
_item_type.code line
save_
save__em_3d_fitting.target_criteria
_item_description.description
; The quality of fit of the atomic coordinates into the
3dem volume map.
;
_item.name '_em_3d_fitting.target_criteria'
_item.category_id em_3d_fitting
_item.mandatory_code no
_item_type.code text
_item_examples.case 'best visual fit using the program O'
save_
save__em_3d_fitting.software_name
_item_description.description
; This data item is a pointer to _software.name
in the category.
;
_item.name '_em_3d_fitting.software_name'
_item.category_id em_3d_fitting
_item.mandatory_code no
_item_type.code line
# _item_linked.child_name '_em_3d_fitting.software_name'
# _item_linked.parent_name '_software.name'
save_
save__em_3d_fitting.details
_item_description.description
; Any additional details regarding fitting of atomic
coordinates into the 3d-em volume.
;
_item.name '_em_3d_fitting.details'
_item.category_id em_3d_fitting
_item.mandatory_code no
_item_type.code text
_item_examples.case 'partial'
save_
save__em_3d_fitting.overall_b_value
_item_description.description
; The overall B (temperature factor) value for the 3d-em volume.
;
_item.name '_em_3d_fitting.overall_b_value'
_item.category_id em_3d_fitting
_item.mandatory_code no
_item_type.code float
save_
save__em_3d_fitting.ref_space
_item_description.description
; A flag to indicate whether fitting was carried out in real
or reciprocal refinement space.
;
_item.name '_em_3d_fitting.ref_space'
_item.category_id em_3d_fitting
_item.mandatory_code no
_item_type.code line
loop_
_item_enumeration.value
REAL
RECIPROCAL
save_
save__em_3d_fitting.ref_protocol
_item_description.description
; The type of protocol used in the refinement.
;
_item.name '_em_3d_fitting.ref_protocol'
_item.category_id em_3d_fitting
_item.mandatory_code no
_item_type.code text
_item_examples.case 'rigid body'
save_
########################
## EM_3D_FITTING_LIST ##
########################
save_em_3d_fitting_list
_category.description
; Data items in the 3D_FITTING_LIST category
lists the methods of fitting atomic coordinates from a PDB file
into a 3d-em volume map file
;
_category.id em_3d_fitting_list
_category.mandatory_code no
loop_
_category_key.name
'_em_3d_fitting_list.id'
'_em_3d_fitting_list.3d_fitting_id'
loop_
_category_group.id
'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1DYL and laboratory records for the
structure corresponding to PDB entry 1DYL
;
; _em_3d_fitting_list.id 1
_em_3d_fitting_list.fitting_id l
_em_3d_fitting_list.pdb_entry_id 1VCQ
_em_3d_fitting_list.pdb_chain_id .
;
save_
save__em_3d_fitting_list.id
_item_description.description
; This data item is a unique identifier.
;
_item.name '_em_3d_fitting_list.id'
_item.category_id em_3d_fitting_list
_item.mandatory_code yes
_item_type.code code
save_
save__em_3d_fitting_list.3d_fitting_id
_item_description.description
; The value of _em_3d_fitting_list.3d_fitting_id is a pointer
to _em_3d_fitting.id in the 3d_fitting category
;
_item.name '_em_3d_fitting_list.3d_fitting_id'
_item.mandatory_code yes
save_
save__em_3d_fitting_list.pdb_entry_id
_item_description.description
; The PDB code for the entry used in fitting.
;
_item.name '_em_3d_fitting_list.pdb_entry_id'
_item.category_id em_3d_fitting_list
_item.mandatory_code no
_item_type.code line
save_
save__em_3d_fitting_list.pdb_chain_id
_item_description.description
; The chain id for the entry used in fitting.
;
_item.name '_em_3d_fitting_list.pdb_chain_id'
_item.category_id em_3d_fitting_list
_item.mandatory_code no
_item_type.code code
save_
#############################
## EM_ELECTRON_DIFFRACTION ##
#############################
save_em_electron_diffraction
_category.description
; Data items in the EM_ELECTRON_DIFFRACTION category
record details about the electron diffraction data
from the electron crystallography experiment.
;
_category.id em_electron_diffraction
_category.mandatory_code no
loop_
_category_key.name
'_em_electron_diffraction.id'
'_em_electron_diffraction.entry_id'
loop_
_category_group.id
'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1TUB and laboratory records for the
structure corresponding to PDB entry 1TUB
;
;
_em_electron_diffraction.entry_id 1TUB
_em_electron_diffraction.id 1
_em_electron_diffraction.num_structure_factors 12000
_em_electron_diffraction.num_diff_patterns .
_em_electron_diffraction.details .
;
save_
save__em_electron_diffraction.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_em_electron_diffraction.entry_id'
_item.category_id em_electron_diffraction
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_electron_diffraction.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_electron_diffraction.id
_item_description.description
; The value of _electron_diffraction.id must
uniquely identify the electron diffraction experiment.
;
_item.name '_em_electron_diffraction.id'
_item.category_id em_electron_diffraction
_item.mandatory_code yes
_item_type.code code
save_
save__em_electron_diffraction.num_structure_factors
_item_description.description
; The number of structure factors from the electron diffraction experiment.
;
_item.name '_em_electron_diffraction.num_structure_factors'
_item.category_id em_electron_diffraction
_item.mandatory_code no
_item_type.code int
_item_examples.case '12000'
save_
save__em_electron_diffraction.num_diff_patterns
_item_description.description
; The number of diffraction patterns used from the electron
diffraction experiment.
;
_item.name '_em_electron_diffraction.num_diff_patterns'
_item.category_id em_electron_diffraction
_item.mandatory_code no
_item_type.code int
save_
save__em_electron_diffraction.details
_item_description.description
; Details of the electron diffraction experiment
;
_item.name '_em_electron_diffraction.details'
_item.category_id em_electron_diffraction
_item.mandatory_code yes
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
1
; THE MODEL WAS DERIVED USING ELECTRON DIFFRACTION
AND IMAGE DATA FROM TWO DIMENSIONAL CRYSTALS OF TUBULIN
INDUCED BY THE PRESENCE OF ZN++ IONS.
WHAT FOLLOWS ARE THE COORDINATES FOR THE AB-TUBULIN DIMER
BOUND TO TAXOL AS OBTAINED BY ELECTRON CRYSTALLOGRAPHY OF
ZINC-INDUCED SHEETS. THIS IS THE UNREFINED MODEL, BUILT
INTO A RAW DENSITY MAP WHERE THE RESOLUTION IN THE PLANE
OF THE SHEET WAS 3.7 ANGSTROMS AND THAT PERPENDICULAR TO
THE SHEET ABOUT 4.8 ANGSTROMS. THE MODEL DOES NOT CONTAIN
MOST OF THE C-TERMINAL RESIDUES OF EITHER MONOMER WHICH
WERE DISORDERED IN THE MAP. THE LOOP BETWEEN HELIX H1 AND
STRAND S2, AND THAT BETWEEN H2 AND S3 ARE PRESENT FOR
COMPLETENESS BUT WERE BUILT INTO VERY WEAK DENSITY.
GIVEN THE LIMITED RESOLUTION OF THE MAP, THE CONFORMATION
OF THE SIDE CHAINS, ESPECIALLY THOSE CORRESPONDING TO
RESIDUES ON THE SURFACE OF THE DIMER, MUST BE TAKEN
CAUTIOUSLY. IN ADDITION, BECAUSE THIS IS AN UNREFINED
MODEL, CERTAIN GEOMETRY ERRORS MAY STILL BE PRESENT IN THE
STRUCTURE. PLEASE TAKE THIS INTO ACCOUNT WHEN
INTERPRETING YOUR OWN DATA BASED ON THE PRESENT TUBULIN
STRUCTURE. ALTHOUGH THE POSITION OF RESIDUES (WITH THE
EXCEPTION OF THOSE IN THE LOOPS MENTIONED ABOVE) SHOULD
NOT CHANGE SIGNIFICANTLY UPON REFINEMENT, DRAWING
INFORMATION AT THE LEVEL OF SIDE CHAIN CONFORMATION IS
CLEARLY NOT ADVISED. FINALLY, PLEASE NOTICE THAT THE
TAXOID IN THE MODEL IS THE TAXOL DERIVATIVE TAXOTERE.
;
save_
###################################
## EM_ELECTRON_DIFFRACTION_PHASE ##
###################################
save_em_electron_diffraction_phase
_category.description
; data items in the em_electron_diffraction_phase category
record details about the phase information
from the electron diffraction experiment.
;
_category.id em_electron_diffraction_phase
_category.mandatory_code no
loop_
_category_key.name
'_em_electron_diffraction_phase.id'
'_em_electron_diffraction_phase.entry_id'
loop_
_category_group.id
'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; example 1 - based on pdb entry 1tub and laboratory records for the
structure corresponding to pdb entry 1tub
;
;
_em_electron_diffraction_phase.entry_id 1TUB
_em_electron_diffraction_phase.id 1
_em_electron_diffraction_phase.d_res_low 5.0
_em_electron_diffraction_phase.d_res_high 4.0
_em_electron_diffraction_phase.residual .
_em_electron_diffraction_phase.highest_resolution_shell_error .
_em_electron_diffraction_phase.overall_error .
_em_electron_diffraction_phase.rejection_criteria_error .
;
save_
save__em_electron_diffraction_phase.entry_id
_item_description.description
; this data item is a pointer to _entry.id in the entry category.
;
_item.name '_em_electron_diffraction_phase.entry_id'
_item.category_id em_electron_diffraction_phase
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_electron_diffraction_phase.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_electron_diffraction_phase.id
_item_description.description
; the value of _electron_diffraction_phase.id must
uniquely identify the electron diffraction phase experiment.
;
_item.name '_em_electron_diffraction_phase.id'
_item.category_id em_electron_diffraction_phase
_item.mandatory_code yes
_item_type.code code
save_
save__em_electron_diffraction_phase.d_res_high
_item_description.description
; the highest resolution d-value for the electron diffraction experiment.
;
_item.name '_em_electron_diffraction_phase.d_res_high'
_item.category_id em_electron_diffraction_phase
_item.mandatory_code no
_item_type.code int
_item_examples.case '5.0'
save_
save__em_electron_diffraction_phase.residual
_item_description.description
; the phase residual value for the electron diffraction experiment.
;
_item.name '_em_electron_diffraction_phase.residual'
_item.category_id em_electron_diffraction_phase
_item.mandatory_code no
_item_type.code int
save_
save__em_electron_diffraction_phase.highest_resolution_shell_error
_item_description.description
; the highest resolution shell error in degrees.
;
_item.name '_em_electron_diffraction_phase.highest_resolution_shell_error'
_item.category_id em_electron_diffraction_phase
_item.mandatory_code no
_item_type.code int
save_
save__em_electron_diffraction_phase.overall_error
_item_description.description
; the overall phase error in degrees.
;
_item.name '_em_electron_diffraction_phase.overall_error'
_item.category_id em_electron_diffraction_phase
_item.mandatory_code no
_item_type.code int
save_
save__em_electron_diffraction_phase.rejection_criteria_error
_item_description.description
; the rejection criteria (phase error) in degrees.
;
_item.name '_em_electron_diffraction_phase.rejection_criteria_error'
_item.category_id em_electron_diffraction_phase
_item.mandatory_code no
_item_type.code int
save_
#####################################
## EM_ELECTRON_DIFFRACTION_PATTERN ##
#####################################
save_em_electron_diffraction_pattern
_category.description
; data items in the em_electron_diffraction_pattern category
record details about the pattern information
from the electron diffraction experiment.
;
_category.id em_electron_diffraction_pattern
_category.mandatory_code no
loop_
_category_key.name
'_em_electron_diffraction_pattern.id'
'_em_electron_diffraction_pattern.entry_id'
loop_
_category_group.id
'inclusive_group'
'em_group'
loop_
_category_examples.detail
_category_examples.case
; example 1 - based on pdb entry 1tub and laboratory records for the
structure corresponding to pdb entry 1tub
;
;
_em_electron_diffraction_pattern.entry_id 1TUB
_em_electron_diffraction_pattern.id 1
_em_electron_diffraction_pattern.num_patterns_by_tilt_angle 1
_em_electron_diffraction_pattern.num_images_by_tilt_angle 4
_em_electron_diffraction_pattern.tilt_angle .
;
save_
save__em_electron_diffraction_pattern.entry_id
_item_description.description
; this data item is a pointer to _entry.id in the entry category.
;
_item.name '_em_electron_diffraction_pattern.entry_id'
_item.category_id em_electron_diffraction_pattern
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_em_electron_diffraction_pattern.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__em_electron_diffraction_pattern.id
_item_description.description
; the value of _electron_diffraction_pattern.id must
uniquely identify the electron diffraction pattern experiment.
;
_item.name '_em_electron_diffraction_pattern.id'
_item.category_id em_electron_diffraction_pattern
_item.mandatory_code yes
_item_type.code code
save_
save__em_electron_diffraction_pattern.num_patterns_by_tilt_angle
_item_description.description
; the number of diffraction patterns by tilt angle.
;
_item.name '_em_electron_diffraction_pattern.num_patterns_by_tilt_angle'
_item.category_id em_electron_diffraction_pattern
_item.mandatory_code no
_item_type.code int
_item_examples.case '1'
save_
save__em_electron_diffraction_pattern.num_images_by_tilt_angle
_item_description.description
; the number of images by tilt angle.
;
_item.name '_em_electron_diffraction_pattern.num_images_by_tilt_angle'
_item.category_id em_electron_diffraction_pattern
_item.mandatory_code no
_item_type.code int
_item_examples.case '4'
save_
save__em_electron_diffraction_pattern.tilt_angle
_item_description.description
; the tilt angle at which the diffraction pattern was obtained.
;
_item.name '_em_electron_diffraction_pattern.tilt_angle'
_item.category_id em_electron_diffraction_pattern
_item.mandatory_code no
_item_type.code int
save_
### EOF mmcif_iims-def-2.dic
###########################################################################
#
# File: mmcif_pdbx-def-8.dic
#
# PDB Exchange Data Dictionary
#
# This data dictionary contains definitions used by wwPDB for data exchange
# and data processing.
#
# Definition Section 8
#
#
###########################################################################
####################
## RCSB_TABLEINFO ##
####################
save_rcsb_tableinfo
_category.description
;
;
_category.id rcsb_tableinfo
_category.mandatory_code no
loop_
_category_key.name '_rcsb_tableinfo.tablename'
loop_
_category_group.id 'inclusive_group'
'rcsb_group'
_category_examples.case
;
loop_
_rcsb_tableinfo.tablename
_rcsb_tableinfo.description
_rcsb_tableinfo.type
_rcsb_tableinfo.table_serial_no
_rcsb_tableinfo.group_name
_rcsb_tableinfo.WWW_Selection_Criteria
_rcsb_tableinfo.WWW_Report_Criteria
summary 'summary data' 1 1 STRUCTURE 1 1
# ...
;
save_
save__rcsb_tableinfo.tablename
_item_description.description
; SQL table name.
;
_item.name '_rcsb_tableinfo.tablename'
_item.category_id rcsb_tableinfo
_item.mandatory_code yes
_item_type.code code30
_item_examples.case 'structure_summary'
save_
save__rcsb_tableinfo.description
_item_description.description
; SQL table description.
;
_item.name '_rcsb_tableinfo.description'
_item.category_id rcsb_tableinfo
_item.mandatory_code yes
_item_type.code text
_item_examples.case 'Table of solvent coordinates'
save_
save__rcsb_tableinfo.type
_item_description.description
; SQL table type.
;
_item.name '_rcsb_tableinfo.type'
_item.category_id rcsb_tableinfo
_item.mandatory_code yes
_item_type.code int
_item_examples.case '0=general, 1=coordinate, 2=derived, 3=schema'
save_
save__rcsb_tableinfo.table_serial_no
_item_description.description
; SQL table serial number.
;
_item.name '_rcsb_tableinfo.table_serial_no'
_item.category_id rcsb_tableinfo
_item.mandatory_code yes
_item_type.code int
_item_examples.case '1,2,3,4,...'
save_
save__rcsb_tableinfo.column_serial_no
_item_description.description
; SQL column serial number.
;
_item.name '_rcsb_tableinfo.column_serial_no'
_item.category_id rcsb_tableinfo
_item.mandatory_code yes
_item_type.code int
_item_examples.case '1,2,3,4,...'
save_
save__rcsb_tableinfo.group_name
_item_description.description
; SQL table group name..
;
_item.name '_rcsb_tableinfo.group_name'
_item.category_id rcsb_tableinfo
_item.mandatory_code yes
_item_type.code line
_item_examples.case 'STRUCTURE FEATURES, SOURCE ORGANISM'
save_
save__rcsb_tableinfo.WWW_Selection_Criteria
_item_description.description
; SQL table visibility in WWW selection querires.
;
_item.name '_rcsb_tableinfo.WWW_Selection_Criteria'
_item.category_id rcsb_tableinfo
_item.mandatory_code yes
_item_type.code int
_item_examples.case '0=no, 1=yes'
save_
save__rcsb_tableinfo.WWW_Report_Criteria
_item_description.description
; SQL table visibility in WWW reports queries.
;
_item.name '_rcsb_tableinfo.WWW_Report_Criteria'
_item.category_id rcsb_tableinfo
_item.mandatory_code yes
_item_type.code int
_item_examples.case '0=no, 1=yes'
save_
#####################
## RCSB_COLUMNINFO ##
#####################
save_rcsb_columninfo
_category.description
;
;
_category.id rcsb_columninfo
_category.mandatory_code no
loop_
_category_key.name '_rcsb_columninfo.tablename'
'_rcsb_columninfo.columnname'
loop_
_category_group.id 'inclusive_group'
'rcsb_group'
_category_examples.case
;
loop_
_rcsb_columninfo.tablename
_rcsb_columninfo.columnname
_rcsb_columninfo.description
_rcsb_columninfo.example
_rcsb_columninfo.type
_rcsb_columninfo.table_serial_no
_rcsb_columninfo.column_serial_no
_rcsb_columninfo.WWW_Selection_Criteria
_rcsb_columninfo.WWW_Report_Criteria
summary id 'id code' 'id1, id2' 1 1 1 1 1
# ...
;
save_
save__rcsb_columninfo.columnname
_item_description.description
; SQL column name.
;
_item.name '_rcsb_columninfo.columnname'
_item.category_id rcsb_columninfo
_item.mandatory_code yes
_item_type.code code30
_item_examples.case 'id'
save_
save__rcsb_columninfo.tablename
_item_description.description
; SQL table name.
;
_item.name '_rcsb_columninfo.tablename'
_item.category_id rcsb_columninfo
_item.mandatory_code yes
_item_type.code code30
_item_examples.case 'structure_summary'
save_
save__rcsb_columninfo.description
_item_description.description
; SQL column description.
;
_item.name '_rcsb_columninfo.description'
_item.category_id rcsb_columninfo
_item.mandatory_code yes
_item_type.code text
_item_examples.case 'Table of solvent coordinates'
save_
save__rcsb_columninfo.example
_item_description.description
; SQL column example.
;
_item.name '_rcsb_columninfo.example'
_item.category_id rcsb_columninfo
_item.mandatory_code yes
_item_type.code text
_item_examples.case 'Table of solvent coordinates'
save_
save__rcsb_columninfo.type
_item_description.description
; SQL column type.
;
_item.name '_rcsb_columninfo.type'
_item.category_id rcsb_columninfo
_item.mandatory_code yes
_item_type.code int
_item_examples.case
;1:integer, 2:float, 3:string-single-left, 4:string-single-right, 5:string-multi-left,
6:string-multi-right, 7:angle, 8:boolean, 9:single character,
10:author or atom name column, 11: Date
;
save_
save__rcsb_columninfo.table_serial_no
_item_description.description
; SQL table serial number.
;
_item.name '_rcsb_columninfo.table_serial_no'
_item.category_id rcsb_columninfo
_item.mandatory_code yes
_item_type.code int
_item_examples.case '1,2,3,4,...'
save_
save__rcsb_columninfo.column_serial_no
_item_description.description
; SQL column serial number.
;
_item.name '_rcsb_columninfo.column_serial_no'
_item.category_id rcsb_columninfo
_item.mandatory_code yes
_item_type.code int
_item_examples.case '1,2,3,4,...'
save_
save__rcsb_columninfo.WWW_Selection_Criteria
_item_description.description
; SQL column visibility in WWW selection querires.
;
_item.name '_rcsb_columninfo.WWW_Selection_Criteria'
_item.category_id rcsb_columninfo
_item.mandatory_code yes
_item_type.code int
_item_examples.case '0=no, 1=yes'
save_
save__rcsb_columninfo.WWW_Report_Criteria
_item_description.description
; SQL column visibility in WWW reports queries.
;
_item.name '_rcsb_columninfo.WWW_Report_Criteria'
_item.category_id rcsb_columninfo
_item.mandatory_code yes
_item_type.code int
_item_examples.case '0=no, 1=yes'
save_
##
### EOF mmcif_pdbx-def-8.dic
###########################################################################
#
# File: mmcif_pdbx-def-9.dic
#
# PDB Exchange Data Dictionary
#
# This data dictionary contains definitions used by RCSB for describing
# derived data and computation.
#
# Definition Section 9
#
#
###########################################################################
#################
## PDBX_DOMAIN ##
#################
save_pdbx_domain
_category.description
; Data items in the PDBX_DOMAIN category record information
about domain definitions.
A domain need not correspond to a completely polypeptide chain;
it can be composed of one more more segments in a single chain,
or by segments from more than one chain.
;
_category.id pdbx_domain
_category.mandatory_code no
_category_key.name '_pdbx_domain.id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'pdbx_erf_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_pdbx_domain.id
_pdbx_domain.details
d1 'Chains A, B'
d2 'Asym_id D Residues 1-134'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_domain.details
_item_description.description
; A description of special aspects of the structural elements that
comprise a domain.
;
_item.name '_pdbx_domain.details'
_item.category_id pdbx_domain
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The loop between residues 18 and 23.
;
save_
save__pdbx_domain.id
_item_description.description
; The value of _pdbx_domain.id must uniquely identify a
record in the PDBX_DOMAIN list.
Note that this item need not be a number; it can be any unique
identifier.
;
_item.name '_pdbx_domain.id'
_item.category_id pdbx_domain
_item.mandatory_code yes
_item_type.code code
save_
#######################
## PDBX_DOMAIN_RANGE ##
#######################
save_pdbx_domain_range
_category.description
; Data items in the PDBX_DOMAIN_RANGE category identify the
beginning and ending points of polypeptide chain segments
that form all or part of a domain.
;
_category.id pdbx_domain_range
_category.mandatory_code no
loop_
_category_key.name '_pdbx_domain_range.domain_id'
'_pdbx_domain_range.beg_label_alt_id'
'_pdbx_domain_range.beg_label_asym_id'
'_pdbx_domain_range.beg_label_comp_id'
'_pdbx_domain_range.beg_label_seq_id'
'_pdbx_domain_range.end_label_alt_id'
'_pdbx_domain_range.end_label_asym_id'
'_pdbx_domain_range.end_label_comp_id'
'_pdbx_domain_range.end_label_seq_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'pdbx_erf_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_pdbx_domain_range.domain_id
_pdbx_domain_range.beg_label_alt_id
_pdbx_domain_range.beg_label_asym_id
_pdbx_domain_range.beg_label_comp_id
_pdbx_domain_range.beg_label_seq_id
_pdbx_domain_range.end_label_alt_id
_pdbx_domain_range.end_label_asym_id
_pdbx_domain_range.end_label_comp_id
_pdbx_domain_range.end_label_seq_id
d1 . A PRO 1 . A GLY 29
d1 . B PRO 31 . B GLY 59
d1 . C PRO 61 . B GLY 89
d2 . D PRO 91 . D GLY 119
d2 . E PRO 121 . E GLY 149
d2 . F PRO 151 . F GLY 179
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_domain_range.beg_label_alt_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_pdbx_domain_range.beg_label_alt_id'
_item.category_id pdbx_domain_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.beg_label_alt_id'
_item_linked.parent_name '_atom_site.label_alt_id'
save_
save__pdbx_domain_range.beg_label_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.beg_label_asym_id'
_item.category_id pdbx_domain_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.beg_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
save_
save__pdbx_domain_range.beg_label_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.beg_label_comp_id'
_item.category_id pdbx_domain_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.beg_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
save_
save__pdbx_domain_range.beg_label_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.beg_label_seq_id'
_item.category_id pdbx_domain_range
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_pdbx_domain_range.beg_label_seq_id'
_item_linked.parent_name '_atom_site.label_seq_id'
save_
save__pdbx_domain_range.beg_auth_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.beg_auth_asym_id'
_item.category_id pdbx_domain_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.beg_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
save_
save__pdbx_domain_range.beg_auth_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.beg_auth_comp_id'
_item.category_id pdbx_domain_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.beg_auth_comp_id'
_item_linked.parent_name '_atom_site.auth_comp_id'
save_
save__pdbx_domain_range.beg_auth_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain begins.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.beg_auth_seq_id'
_item.category_id pdbx_domain_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.beg_auth_seq_id'
_item_linked.parent_name '_atom_site.auth_seq_id'
save_
save__pdbx_domain_range.domain_id
_item_description.description
; This data item is a pointer to _pdbx_domain.id in the
PDBX_DOMAIN category.
;
_item.name '_pdbx_domain_range.domain_id'
_item.category_id pdbx_domain_range
_item.mandatory_code yes
_item_linked.child_name '_pdbx_domain_range.domain_id'
_item_linked.parent_name '_pdbx_domain.id'
save_
save__pdbx_domain_range.end_label_alt_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_pdbx_domain_range.end_label_alt_id'
_item.category_id pdbx_domain_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.end_label_alt_id'
_item_linked.parent_name '_atom_site.label_alt_id'
save_
save__pdbx_domain_range.end_label_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.end_label_asym_id'
_item.category_id pdbx_domain_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.end_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
save_
save__pdbx_domain_range.end_label_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.end_label_comp_id'
_item.category_id pdbx_domain_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.end_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
save_
save__pdbx_domain_range.end_label_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.end_label_seq_id'
_item.category_id pdbx_domain_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.end_label_seq_id'
_item_linked.parent_name '_atom_site.label_seq_id'
save_
save__pdbx_domain_range.end_auth_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.end_auth_asym_id'
_item.category_id pdbx_domain_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.end_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
save_
save__pdbx_domain_range.end_auth_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.end_auth_comp_id'
_item.category_id pdbx_domain_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.end_auth_comp_id'
_item_linked.parent_name '_atom_site.auth_comp_id'
save_
save__pdbx_domain_range.end_auth_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the domain ends.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_domain_range.end_auth_seq_id'
_item.category_id pdbx_domain_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_domain_range.end_auth_seq_id'
_item_linked.parent_name '_atom_site.auth_seq_id'
save_
#########################
## PDBX_SEQUENCE_RANGE ##
#########################
save_pdbx_sequence_range
_category.description
; Data items in the PDBX_SEQUENCE_RANGE category identify the
beginning and ending points of polypeptide sequence segments.
;
_category.id pdbx_sequence_range
_category.mandatory_code no
loop_
_category_key.name '_pdbx_sequence_range.seq_range_id'
'_pdbx_sequence_range.beg_label_alt_id'
'_pdbx_sequence_range.beg_label_asym_id'
'_pdbx_sequence_range.beg_label_comp_id'
'_pdbx_sequence_range.beg_label_seq_id'
'_pdbx_sequence_range.end_label_alt_id'
'_pdbx_sequence_range.end_label_asym_id'
'_pdbx_sequence_range.end_label_comp_id'
'_pdbx_sequence_range.end_label_seq_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'pdbx_erf_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_pdbx_sequence_range.seq_range_id
_pdbx_sequence_range.beg_label_alt_id
_pdbx_sequence_range.beg_label_asym_id
_pdbx_sequence_range.beg_label_comp_id
_pdbx_sequence_range.beg_label_seq_id
_pdbx_sequence_range.end_label_alt_id
_pdbx_sequence_range.end_label_asym_id
_pdbx_sequence_range.end_label_comp_id
_pdbx_sequence_range.end_label_seq_id
s1 . A PRO 1 . A GLY 29
s2 . D PRO 91 . D GLY 119
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_sequence_range.beg_label_alt_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_pdbx_sequence_range.beg_label_alt_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.beg_label_alt_id'
_item_linked.parent_name '_atom_site.label_alt_id'
save_
save__pdbx_sequence_range.beg_label_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.beg_label_asym_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.beg_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
save_
save__pdbx_sequence_range.beg_label_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.beg_label_comp_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.beg_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
save_
save__pdbx_sequence_range.beg_label_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.beg_label_seq_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_pdbx_sequence_range.beg_label_seq_id'
_item_linked.parent_name '_atom_site.label_seq_id'
save_
save__pdbx_sequence_range.beg_auth_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.beg_auth_asym_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.beg_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
save_
save__pdbx_sequence_range.beg_auth_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.beg_auth_comp_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.beg_auth_comp_id'
_item_linked.parent_name '_atom_site.auth_comp_id'
save_
save__pdbx_sequence_range.beg_auth_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range begins.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.beg_auth_seq_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.beg_auth_seq_id'
_item_linked.parent_name '_atom_site.auth_seq_id'
save_
save__pdbx_sequence_range.seq_range_id
_item_description.description
; This data item is an identifier for a sequence range.
;
_item.name '_pdbx_sequence_range.seq_range_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_sequence_range.end_label_alt_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_pdbx_sequence_range.end_label_alt_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.end_label_alt_id'
_item_linked.parent_name '_atom_site.label_alt_id'
save_
save__pdbx_sequence_range.end_label_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.end_label_asym_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.end_label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
save_
save__pdbx_sequence_range.end_label_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.end_label_comp_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.end_label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
save_
save__pdbx_sequence_range.end_label_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.end_label_seq_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.end_label_seq_id'
_item_linked.parent_name '_atom_site.label_seq_id'
save_
save__pdbx_sequence_range.end_auth_asym_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.end_auth_asym_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.end_auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
save_
save__pdbx_sequence_range.end_auth_comp_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.end_auth_comp_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.end_auth_comp_id'
_item_linked.parent_name '_atom_site.auth_comp_id'
save_
save__pdbx_sequence_range.end_auth_seq_id
_item_description.description
; A component of the identifier for the monomer at which this
segment of the sequence range ends.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_sequence_range.end_auth_seq_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_sequence_range.end_auth_seq_id'
_item_linked.parent_name '_atom_site.auth_seq_id'
save_
########################
## PDBX_FEATURE_ENTRY ##
########################
save_pdbx_feature_entry
_category.description
; Data items in the PDBX_FEATURE_ENTRY category records
information about properties pertaining to this
structure entry.
;
_category.id pdbx_feature_entry
_category.mandatory_code no
_category_key.name '_pdbx_feature_entry.id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'pdbx_erf_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Gene Ontology data by entry
;
;
loop_
_pdbx_feature_entry.id
_pdbx_feature_entry.feature_name
_pdbx_feature_entry.feature
_pdbx_feature_entry.feature_type
_pdbx_feature_entry.feature_assigned_by
_pdbx_feature_entry.feature_citation_id
1 'molecular function' 'DNA binding activity'
value GO GO
2 'biological process' 'regulation of transcription, DNA-dependent'
value GO GO
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_feature_entry.id
_item_description.description
; The value of _pdbx_feature_entry.id uniquely identifies a
feature in the PDBX_FEATURE_ENTRY category.
;
_item.name '_pdbx_feature_entry.id'
_item.category_id pdbx_feature_entry
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_feature_entry.feature_name
_item_description.description
; _pdbx_feature_entry.feature_name identifies a feature
by name.
;
_item.name '_pdbx_feature_entry.feature_name'
_item.category_id pdbx_feature_entry
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_entry.feature_type
_item_description.description
; _pdbx_feature_entry.feature_type identifies the
type of feature.
;
_item.name '_pdbx_feature_entry.feature_type'
_item.category_id pdbx_feature_entry
_item.mandatory_code yes
_item_type.code text
loop_
_item_enumeration.value 'value' 'uri'
save_
save__pdbx_feature_entry.feature
_item_description.description
; The value of _pdbx_feature_entry.feature_name.
;
_item.name '_pdbx_feature_entry.feature'
_item.category_id pdbx_feature_entry
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_entry.feature_identifier
_item_description.description
; _pdbx_feature_entry.feature_identifier is an
additional identifier used to identify or
accession this feature.
;
_item.name '_pdbx_feature_entry.feature_identifier'
_item.category_id pdbx_feature_entry
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_feature_entry.feature_assigned_by
_item_description.description
; _pdbx_feature_entry.feature_assigned_by identifies
the individual, organization or program that
assigned the feature.
;
_item.name '_pdbx_feature_entry.feature_assigned_by'
_item.category_id pdbx_feature_entry
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_entry.feature_citation_id
_item_description.description
; _pdbx_feature_entry.feature_citation_id is a
reference to a citation in the CITATION category
;
_item.name '_pdbx_feature_entry.feature_citation_id'
_item.category_id pdbx_feature_entry
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_entry.feature_citation_id'
_item_linked.parent_name '_citation.id'
save_
save__pdbx_feature_entry.feature_software_id
_item_description.description
; _pdbx_feature_entry.feature_software_id is a
reference to an application described in the
SOFTWARE category.
;
_item.name '_pdbx_feature_entry.feature_software_id'
_item.category_id pdbx_feature_entry
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_entry.feature_software_id'
_item_linked.parent_name '_software.name'
save_
#########################
## PDBX_FEATURE_DOMAIN ##
#########################
save_pdbx_feature_domain
_category.description
; Data items in the PDBX_FEATURE_DOMAIN category records
information about properties pertaining to this structure
domain.
;
_category.id pdbx_feature_domain
_category.mandatory_code no
_category_key.name '_pdbx_feature_domain.id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'pdbx_erf_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - SCOP data for PDB Entry 1KIP domain d1kipa_
;
;
loop_
_pdbx_feature_domain.id
_pdbx_feature_domain.domain_id
_pdbx_feature_domain.feature_name
_pdbx_feature_domain.feature
_pdbx_feature_domain.feature_type
_pdbx_feature_domain.feature_assigned_by
_pdbx_feature_domain.feature_citation_id
1 'd1kipa_' class 'All beta proteins'
value SCOP scop
2 'd1kipa_' fold 'Immunoglobulin-like beta-sandwich'
value SCOP scop
3 'd1kipa_' superfamily 'Immunoglobulin'
value SCOP scop
4 'd1kipa_' family 'V set domains (antibody variable domain-like)'
value SCOP scop
5 'd1kipa_' domain 'Immunoglobulin light chain kappa variable domain'
value SCOP scop
6 'd1kipa_' species 'Mouse (Mus musculus), cluster 4'
value SCOP scop
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_feature_domain.id
_item_description.description
; The value of _pdbx_feature_domain.id uniquely identifies
a feature in the PDBX_FEATURE_DOMAIN category.
;
_item.name '_pdbx_feature_domain.id'
_item.category_id pdbx_feature_domain
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_feature_domain.domain_id
_item_description.description
; The value of _pdbx_feature_domain.id references a domain
definition in category PDBX_DOMAIN.
;
_item.name '_pdbx_feature_domain.domain_id'
_item.category_id pdbx_feature_domain
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_feature_domain.domain_id'
_item_linked.parent_name '_pdbx_domain.id'
save_
save__pdbx_feature_domain.feature_name
_item_description.description
; _pdbx_feature_domain.feature_name identifies a feature
by name.
;
_item.name '_pdbx_feature_domain.feature_name'
_item.category_id pdbx_feature_domain
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_domain.feature_type
_item_description.description
; _pdbx_feature_domain.feature_type identifies the
type of feature.
;
_item.name '_pdbx_feature_domain.feature_type'
_item.category_id pdbx_feature_domain
_item.mandatory_code yes
_item_type.code text
loop_
_item_enumeration.value 'value' 'uri'
save_
save__pdbx_feature_domain.feature
_item_description.description
; The value of _pdbx_feature_domain.feature_name.
;
_item.name '_pdbx_feature_domain.feature'
_item.category_id pdbx_feature_domain
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_domain.feature_identifier
_item_description.description
; _pdbx_feature_domain.feature_identifier is an
additional identifier used to identify or
accession this feature.
;
_item.name '_pdbx_feature_domain.feature_identifier'
_item.category_id pdbx_feature_domain
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_feature_domain.feature_assigned_by
_item_description.description
; _pdbx_feature_domain.feature_assigned_by identifies
the individual, organization or program that
assigned the feature.
;
_item.name '_pdbx_feature_domain.feature_assigned_by'
_item.category_id pdbx_feature_domain
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_domain.feature_citation_id
_item_description.description
; _pdbx_feature_domain.feature_citation_id is a
reference to a citation in the CITATION category.
;
_item.name '_pdbx_feature_domain.feature_citation_id'
_item.category_id pdbx_feature_domain
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_domain.feature_citation_id'
_item_linked.parent_name '_citation.id'
save_
save__pdbx_feature_domain.feature_software_id
_item_description.description
; _pdbx_feature_domain.feature_software_id is a
reference to an application described in the
SOFTWARE category.
;
_item.name '_pdbx_feature_domain.feature_software_id'
_item.category_id pdbx_feature_domain
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_domain.feature_software_id'
_item_linked.parent_name '_software.name'
save_
#################################
## PDBX_FEATURE_SEQUENCE_RANGE ##
#################################
save_pdbx_feature_sequence_range
_category.description
; Data items in the PDBX_FEATURE_SEQUENCE_RANGE category
records information about properties pertaining to
this structure sequence_range.
;
_category.id pdbx_feature_sequence_range
_category.mandatory_code no
_category_key.name '_pdbx_feature_sequence_range.id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'pdbx_erf_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Secondary structure computed by program DSSP.
;
;
loop_
_pdbx_feature_sequence_range.id
_pdbx_feature_sequence_range.seq_range_id
_pdbx_feature_sequence_range.feature_name
_pdbx_feature_sequence_range.feature
_pdbx_feature_sequence_range.feature_type
_pdbx_feature_sequence_range.feature_assigned_by
_pdbx_feature_sequence_range.feature_software_id
1 H1 'secondary structure' '4-helix (alpha-helix)'
value DSSP DSSP
2 T1 'secondary structure' 'hydrogen-bonded turn in beta-ladder'
value DSSP DSSP
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_feature_sequence_range.id
_item_description.description
; The value of _pdbx_feature_sequence_range.id uniquely identifies
a feature in the PDBX_FEATURE_SEQUENCE_RANGE category
;
_item.name '_pdbx_feature_sequence_range.id'
_item.category_id pdbx_feature_sequence_range
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_feature_sequence_range.seq_range_id
_item_description.description
; The value of _pdbx_feature_sequence_range.seq_range_id
references a sequence_range definition in category
PDBX_SEQUENCE_RANGE.
;
_item.name '_pdbx_feature_sequence_range.seq_range_id'
_item.category_id pdbx_feature_sequence_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_feature_sequence_range.seq_range_id'
_item_linked.parent_name '_pdbx_sequence_range.seq_range_id'
save_
save__pdbx_feature_sequence_range.feature_name
_item_description.description
; _pdbx_feature_sequence_range.feature_name identifies a feature
by name.
;
_item.name '_pdbx_feature_sequence_range.feature_name'
_item.category_id pdbx_feature_sequence_range
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_sequence_range.feature_type
_item_description.description
; _pdbx_feature_sequence_range.feature_type identifies the
type of feature.
;
_item.name '_pdbx_feature_sequence_range.feature_type'
_item.category_id pdbx_feature_sequence_range
_item.mandatory_code yes
_item_type.code text
loop_
_item_enumeration.value 'value' 'uri'
save_
save__pdbx_feature_sequence_range.feature
_item_description.description
; The value of _pdbx_feature_sequence_range.feature_name.
;
_item.name '_pdbx_feature_sequence_range.feature'
_item.category_id pdbx_feature_sequence_range
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_sequence_range.feature_identifier
_item_description.description
; _pdbx_feature_sequence_range.feature_identifier is an
additional identifier used to identify or
accession this feature.
;
_item.name '_pdbx_feature_sequence_range.feature_identifier'
_item.category_id pdbx_feature_sequence_range
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_feature_sequence_range.feature_assigned_by
_item_description.description
; _pdbx_feature_sequence_range.feature_assigned_by identifies
the individual, organization or program that assigned
the feature.
;
_item.name '_pdbx_feature_sequence_range.feature_assigned_by'
_item.category_id pdbx_feature_sequence_range
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_sequence_range.feature_citation_id
_item_description.description
; _pdbx_feature_sequence_range.feature_citation_id is a
reference to a citation in the CITATION category
;
_item.name '_pdbx_feature_sequence_range.feature_citation_id'
_item.category_id pdbx_feature_sequence_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_sequence_range.feature_citation_id'
_item_linked.parent_name '_citation.id'
save_
save__pdbx_feature_sequence_range.feature_software_id
_item_description.description
; _pdbx_feature_sequence_range.feature_software_id is a
reference to an application descripted in the
SOFTWARE category.
;
_item.name '_pdbx_feature_sequence_range.feature_software_id'
_item.category_id pdbx_feature_sequence_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_sequence_range.feature_software_id'
_item_linked.parent_name '_software.name'
save_
###########################
## PDBX_FEATURE_ASSEMBLY ##
###########################
save_pdbx_feature_assembly
_category.description
; Data items in the PDBX_FEATURE_ASSEMBLY category records
information about properties pertaining to this
structural assembly.
;
_category.id pdbx_feature_assembly
_category.mandatory_code no
_category_key.name '_pdbx_feature_assembly.id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'pdbx_erf_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Biological process for functional assembly
;
;
loop_
_pdbx_feature_assembly.id
_pdbx_feature_assembly.assembly_id
_pdbx_feature_assembly.feature_name
_pdbx_feature_assembly.feature
_pdbx_feature_assembly.feature_type
_pdbx_feature_assembly.feature_assigned_by
_pdbx_feature_assembly.feature_citation_id
1 b1 'biological process' 'nitrogen metabolism' value GO GO
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_feature_assembly.id
_item_description.description
; The value of _pdbx_feature_assembly.id uniquely identifies a
feature in the PDBX_FEATURE_ASSEMBLY category.
;
_item.name '_pdbx_feature_assembly.id'
_item.category_id pdbx_feature_assembly
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_feature_assembly.assembly_id
_item_description.description
; The value of _pdbx_feature_assembly.assembly_id references an
assembly definition in category STRUCT_BIOL
;
_item.name '_pdbx_feature_assembly.assembly_id'
_item.category_id pdbx_feature_assembly
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_feature_assembly.assembly_id'
_item_linked.parent_name '_struct_biol.id'
save_
save__pdbx_feature_assembly.feature_name
_item_description.description
; _pdbx_feature_assembly.feature_name identifies a feature
by name.
;
_item.name '_pdbx_feature_assembly.feature_name'
_item.category_id pdbx_feature_assembly
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_assembly.feature_type
_item_description.description
; _pdbx_feature_assembly.feature_type identifies the
type of feature.
;
_item.name '_pdbx_feature_assembly.feature_type'
_item.category_id pdbx_feature_assembly
_item.mandatory_code yes
_item_type.code text
loop_
_item_enumeration.value 'value' 'uri'
save_
save__pdbx_feature_assembly.feature
_item_description.description
; The value of _pdbx_feature_assembly.feature_name.
;
_item.name '_pdbx_feature_assembly.feature'
_item.category_id pdbx_feature_assembly
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_assembly.feature_identifier
_item_description.description
; _pdbx_feature_assembly_range.feature_identifier is an
additional identifier used to identify or
accession this feature.
;
_item.name '_pdbx_feature_assembly.feature_identifier'
_item.category_id pdbx_feature_assembly
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_feature_assembly.feature_assigned_by
_item_description.description
; _pdbx_feature_assembly.feature_assigned_by identifies
the individual, organization or program that assigned
the feature.
;
_item.name '_pdbx_feature_assembly.feature_assigned_by'
_item.category_id pdbx_feature_assembly
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_assembly.feature_citation_id
_item_description.description
; _pdbx_feature_assembly.feature_citation_id is a
reference to a citation in the CITATION category
;
_item.name '_pdbx_feature_assembly.feature_citation_id'
_item.category_id pdbx_feature_assembly
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_assembly.feature_citation_id'
_item_linked.parent_name '_citation.id'
save_
save__pdbx_feature_assembly.feature_software_id
_item_description.description
; _pdbx_feature_assembly.feature_software_id is a
reference to an application described in the
SOFTWARE category.
;
_item.name '_pdbx_feature_assembly.feature_software_id'
_item.category_id pdbx_feature_assembly
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_assembly.feature_software_id'
_item_linked.parent_name '_software.name'
save_
##########################
## PDBX_FEATURE_MONOMER ##
##########################
save_pdbx_feature_monomer
_category.description
; Data items in the PDBX_FEATURE_MONOMER category records
information about properties pertaining to particular
monomers in this structure.
;
_category.id pdbx_feature_monomer
_category.mandatory_code no
_category_key.name '_pdbx_feature_monomer.id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
'pdbx_erf_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_pdbx_feature_monomer.id
_pdbx_feature_monomer.label_alt_id
_pdbx_feature_monomer.label_asym_id
_pdbx_feature_monomer.label_comp_id
_pdbx_feature_monomer.label_seq_id
_pdbx_feature_monomer.feature_name
_pdbx_feature_monomer.feature
_pdbx_feature_monomer.feature_type
_pdbx_feature_monomer.feature_assigned_by
_pdbx_feature_monomer.feature_citation_id
1 . A ASP 1 'SASA' 129.4 value POPS pops
1 . A ILE 2 'SASA' 35.5 value POPS pops
1 . A VAL 3 'SASA' 87.2 value POPS pops
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__pdbx_feature_monomer.id
_item_description.description
; The value of _pdbx_feature_monomer.id uniquely identifies
a feature in the PDBX_FEATURE_MONOMER category.
;
_item.name '_pdbx_feature_monomer.id'
_item.category_id pdbx_feature_monomer
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_feature_monomer.feature_name
_item_description.description
; _pdbx_feature_monomer.feature_name identifies a feature
by name.
;
_item.name '_pdbx_feature_monomer.feature_name'
_item.category_id pdbx_feature_monomer
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_monomer.feature_type
_item_description.description
; _pdbx_feature_monomer.feature_type identifies the
type of feature.
;
_item.name '_pdbx_feature_monomer.feature_type'
_item.category_id pdbx_feature_monomer
_item.mandatory_code yes
_item_type.code text
loop_
_item_enumeration.value 'value' 'uri'
save_
save__pdbx_feature_monomer.feature
_item_description.description
; The value of _pdbx_feature_monomer.feature_name.
;
_item.name '_pdbx_feature_monomer.feature'
_item.category_id pdbx_feature_monomer
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_monomer.feature_identifier
_item_description.description
; _pdbx_feature_monomer.feature_identifier is an
additional identifier used to identify or
accession this feature.
;
_item.name '_pdbx_feature_monomer.feature_identifier'
_item.category_id pdbx_feature_monomer
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_feature_monomer.feature_assigned_by
_item_description.description
; _pdbx_feature_monomer.feature_assigned_by identifies
the individual, organization or program that
assigned the feature.
;
_item.name '_pdbx_feature_monomer.feature_assigned_by'
_item.category_id pdbx_feature_monomer
_item.mandatory_code yes
_item_type.code text
save_
save__pdbx_feature_monomer.feature_citation_id
_item_description.description
; _pdbx_feature_monomer.feature_citation_id is a
reference to a citation in the CITATION category.
;
_item.name '_pdbx_feature_monomer.feature_citation_id'
_item.category_id pdbx_feature_monomer
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_monomer.feature_citation_id'
_item_linked.parent_name '_citation.id'
save_
save__pdbx_feature_monomer.feature_software_id
_item_description.description
; _pdbx_feature_monomer.feature_software_id is a
reference to an application described in the
SOFTWARE category.
;
_item.name '_pdbx_feature_monomer.feature_software_id'
_item.category_id pdbx_feature_monomer
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_monomer.feature_software_id'
_item_linked.parent_name '_software.name'
save_
##
save__pdbx_feature_monomer.label_alt_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_sites_alt.id in the
ATOM_SITES_ALT category.
;
_item.name '_pdbx_feature_monomer.label_alt_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_feature_monomer.label_alt_id'
_item_linked.parent_name '_atom_site.label_alt_id'
save_
save__pdbx_feature_monomer.label_asym_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_feature_monomer.label_asym_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_feature_monomer.label_asym_id'
_item_linked.parent_name '_atom_site.label_asym_id'
save_
save__pdbx_feature_monomer.label_comp_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_feature_monomer.label_comp_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_feature_monomer.label_comp_id'
_item_linked.parent_name '_atom_site.label_comp_id'
save_
save__pdbx_feature_monomer.label_seq_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_feature_monomer.label_seq_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_pdbx_feature_monomer.label_seq_id'
_item_linked.parent_name '_atom_site.label_seq_id'
save_
save__pdbx_feature_monomer.auth_asym_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
;
_item.name '_pdbx_feature_monomer.auth_asym_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_monomer.auth_asym_id'
_item_linked.parent_name '_atom_site.auth_asym_id'
save_
save__pdbx_feature_monomer.auth_comp_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
;
_item.name '_pdbx_feature_monomer.auth_comp_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_monomer.auth_comp_id'
_item_linked.parent_name '_atom_site.auth_comp_id'
save_
save__pdbx_feature_monomer.auth_seq_id
_item_description.description
; A component of the identifier for the monomer.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
;
_item.name '_pdbx_feature_monomer.auth_seq_id'
_item.category_id pdbx_sequence_range
_item.mandatory_code no
_item_type.code code
_item_linked.child_name '_pdbx_feature_monomer.auth_seq_id'
_item_linked.parent_name '_atom_site.auth_seq_id'
save_
##
## End of file: mmcif_pdbx-def-9.dic
##
###########################################################################
#
# File: mmcif_pdbx-def-10.dic
#
# PDB Exchange Data Dictionary
#
# This data dictionary contains preliminary extensions for describing
# macromolecular powder diffraction experiments.
#
# Definition Section 10
#
#
###########################################################################
save__diffrn_radiation.pdbx_analyzer
_item_description.description
; Indicates the method used to obtain monochromatic radiation.
_diffrn_radiation.monochromator describes the primary beam
monochromator (pre-specimen monochromation).
_diffrn_radiation.pdbx_analyzer specifies the
post-diffraction analyser (post-specimen) monochromation.
Note that monochromators may have either 'parallel' or
'antiparallel' orientation. It is assumed that the
geometry is parallel unless specified otherwise.
In a parallel geometry, the position of the monochromator
allows the incident beam and the final post-specimen
and post-monochromator beam to be as close to parallel
as possible. In a parallel geometry, the diffracting
planes in the specimen and monochromator will be parallel
when 2*theta(monochromator) is equal to 2*theta (specimen).
For further discussion see R. Jenkins and R. Snyder,
Introduction to X-ray Powder Diffraction, Wiley (1996),
pp. 164-5.
;
_item.name '_diffrn_radiation.pdbx_analyzer'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'GE(111)'
'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite (0001)'
'Si (111), antiparallel'
_item_aliases.dictionary cif_pd.dic
_item_aliases.version 1.0
_item_aliases.alias_name '_pd_instr_monochr_post_spec'
save_
save_pdbx_exptl_pd
_category.description
; Data items in the pdbx_exptl_pd record information about
powder sample preparations.
;
_category.id pdbx_exptl_pd
_category.mandatory_code no
_category_key.name '_pdbx_exptl_pd.entry_id'
loop_
_category_group.id 'inclusive_group'
'pdbx_group'
save_
save__pdbx_exptl_pd.entry_id
_item_description.description
; The value of _pdbx_exptl_pd.entry_id uniquely identifies a
record in the PDBX_EXPTL_PD category.
;
_item.name '_pdbx_exptl_pd.entry_id'
_item.category_id pdbx_exptl_pd
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_exptl_pd.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__pdbx_exptl_pd.spec_preparation_pH
_item_description.description
; The pH at which the powder sample was prepared.
;
_item.name '_pdbx_exptl_pd.spec_preparation_pH'
_item.category_id pdbx_exptl_pd
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__pdbx_exptl_pd.spec_preparation_pH_range
_item_description.description
; The range of pH values at which the sample was prepared. Used when
a point estimate of pH is not appropriate.
;
_item.name '_pdbx_exptl_pd.spec_preparation_pH_range'
_item.category_id pdbx_exptl_pd
_item.mandatory_code no
_item_type.code line
loop_
_item_examples.case '5.6 - 6.4'
save_
save__pdbx_exptl_pd.spec_preparation
_item_description.description
; A description of preparation steps for producing the
diffraction specimen from the sample. Include any procedures
related to grinding, sieving, spray drying, etc.
;
_item.name '_pdbx_exptl_pd.spec_preparation'
_item.category_id pdbx_exptl_pd
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case 'POLYCRYSTAL SLURRY'
'wet grinding in acetone'
'sieved through a 44 micron (325 mesh/inch) sieve'
'spray dried in water with 1% clay'
_item_aliases.dictionary cif_pd.dic
_item_aliases.version 1.0
_item_aliases.alias_name '_pd_spec_preparation'
save_
save__refine.pdbx_pd_number_of_powder_patterns
_item_description.description
; The total number of powder patterns used.
;
_item.name '_refine.pdbx_pd_number_of_powder_patterns'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine.pdbx_pd_number_of_points
_item_description.description
; The total number of data points in the processed diffractogram.
;
_item.name '_refine.pdbx_pd_number_of_points'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
_item_aliases.dictionary cif_pd.dic
_item_aliases.version 1.0
_item_aliases.alias_name '_pd_proc_number_of_points'
save_
save__refine.pdbx_pd_meas_number_of_points
_item_description.description
; The total number of points in the measured
diffractogram.
;
_item.name '_refine.pdbx_pd_meas_number_of_points'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
_item_aliases.dictionary cif_pd.dic
_item_aliases.version 1.0
_item_aliases.alias_name '_pd_meas_number_of_points'
save_
save__refine.pdbx_pd_proc_ls_prof_R_factor
_item_description.description
; Rietveld/Profile fit R factors.
Note that the R factor computed for Rietveld refinements
using the extracted reflection intensity values (often
called the Rietveld or Bragg R factor, R~B~) is not properly
a profile R factor.
pdbx_pd_proc_ls_prof_R_factor, often called R~p~, is an
unweighted fitness metric for the agreement between the
observed and computed diffraction patterns
R~p~ = sum~i~ | I~obs~(i) - I~calc~(i) |
/ sum~i~ ( I~obs~(i) )
Note that in the above equations,
w(i) is the weight for the ith data point
I~obs~(i) is the observed intensity for the ith data
point, sometimes referred to as y~i~(obs) or
y~oi~.
I~calc~(i) is the computed intensity for the ith data
point with background and other corrections
applied to match the scale of the observed dataset,
sometimes referred to as y~i~(calc) or
y~ci~.
n is the total number of data points (see _refine.pdbx_pd_number_of_points)
less the number of data points excluded from the refinement.
p is the total number of refined parameters.
;
_item.name '_refine.pdbx_pd_proc_ls_prof_R_factor'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_aliases.dictionary cif_pd.dic
_item_aliases.version 1.0
_item_aliases.alias_name '_pd_proc_ls_prof_R_factor'
save_
save__refine.pdbx_pd_proc_ls_prof_wR_factor
_item_description.description
; Rietveld/Profile fit R factors.
Note that the R factor computed for Rietveld refinements
using the extracted reflection intensity values (often
called the Rietveld or Bragg R factor, R~B~) is not properly
a profile R factor.
pdbx_pd_proc_ls_prof_wR_factor often called R~wp~, is a
weighted fitness metric for the agreement between the
observed and computed diffraction patterns
R~wp~ = SQRT {
sum~i~ ( w(i) [ I~obs~(i) - I~calc~(i) ]^2^ )
/ sum~i~ ( w(i) [I~obs~(i)]^2^ ) }
Note that in the above equations,
w(i) is the weight for the ith data point
I~obs~(i) is the observed intensity for the ith data
point, sometimes referred to as y~i~(obs) or
y~oi~.
I~calc~(i) is the computed intensity for the ith data
point with background and other corrections
applied to match the scale of the observed dataset,
sometimes referred to as y~i~(calc) or
y~ci~.
n is the total number of data points (see _refine.pdbx_pd_number_of_points)
less the number of data points excluded from the refinement.
p is the total number of refined parameters.
;
_item.name '_refine.pdbx_pd_proc_ls_prof_wR_factor'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
_item_aliases.dictionary cif_pd.dic
_item_aliases.version 1.0
_item_aliases.alias_name '_pd_proc_ls_prof_wR_factor'
save_
save__refine.pdbx_pd_Marquardt_correlation_coeff
_item_description.description
; The correlation coefficient between the observed and
calculated structure factors for reflections included in
the refinement. This correlation factor is found in the
fitting using the Levenberg-Marquardt algorithm to search
for the minimum value of chisquare. Almost all computer
codes for Rietveld refinement employ the Gauss-Newton algorithm
to find parameters which minimize the weighted sum of squares
of the residuals.
A description of the equations is given on
http://www.water.hut.fi/~tkarvone/fr_org_s.htm
;
_item.name '_refine.pdbx_pd_Marquardt_correlation_coeff'
_item.category_id refine
_item.mandatory_code no
_item_type.code float
save_
save__refine.pdbx_pd_Fsqrd_R_factor
_item_description.description
; Residual factor R for reflections that satisfy the resolution
limits established by _refine.ls_d_res_high and
_refine.ls_d_res_low and the observation limit established by
_reflns.observed_criterion.
sum|F~obs~**2 - F~calc~**2|
R = ---------------------
sum|F~obs~**2|
F~obs~ = the observed structure-factor amplitudes
F~calc~ = the calculated structure-factor amplitudes
sum is taken over the specified reflections
;
_item.name '_refine.pdbx_pd_Fsqrd_R_factor'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
_item_type.code float
save_
save__refine.pdbx_pd_ls_matrix_band_width
_item_description.description
; The least squares refinement "band matrix" approximation to the full matrix.
;
_item.name '_refine.pdbx_pd_ls_matrix_band_width'
_item.category_id refine
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
### EOF mmcif_pdbx-def-10.dic
#######################
## PDBX_SOLN_SCATTER ##
#######################
save_pdbx_soln_scatter
_category.description
; Data items in the PDBX_SOLN_SCATTER category record details about a
solution scattering experiment
;
_category.id pdbx_soln_scatter
_category.mandatory_code no
loop_
_category_key.name
'_pdbx_soln_scatter.entry_id'
'_pdbx_soln_scatter.id'
loop_
_category_group.id
'inclusive_group'
'solution_scattering_group'
loop_
_category_examples.detail
_category_examples.case
; Example 1 - based on PDB entry 1HAQ
;
; loop_
_pdbx_soln_scatter.entry_id
_pdbx_soln_scatter.id
_pdbx_soln_scatter.type
_pdbx_soln_scatter.source_type
_pdbx_soln_scatter.source_class
_pdbx_soln_scatter.source_beamline
_pdbx_soln_scatter.source_beamline_instrument
_pdbx_soln_scatter.detector_specific
_pdbx_soln_scatter.detector_type
_pdbx_soln_scatter.temperature
_pdbx_soln_scatter.pH
_pdbx_soln_scatter.num_time_frames
_pdbx_soln_scatter.concentration_range
_pdbx_soln_scatter.buffer_name
_pdbx_soln_scatter.mean_guiner_radius
_pdbx_soln_scatter.mean_guiner_radius_esd
_pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration
_pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration_esd
_pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration
_pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration_eds
_pdbx_soln_scatter.protein_length
1HAQ 1 x-ray 'SRS BEAMLINE 2.1' 'synchrotron' '2.1' . . '500-channel quadrant'
288 . 10 '0.7 - 14' tris
11.1 0.4 4.4 0.2 1.7 0.1 40
1HAQ 2 neutron 'ILL' 'neutron source' . 'D11, D22' . 'area'
. . . '0.4 - 9.6' 'PBS in 99.9% D2O'
11.3 0.4 3.9 0.2 1.51 0.06 '37.0 - 39.0'
1HAQ 3 neutron 'ISIS' 'neutron source' 'Pulsed Neutron' 'LOQ' . 'AREA (TIME-OF-FLIGHT)'
. . . '3.7, 6.1' 'PBS in 99.9% D2O'
11.7 0.5 . . . . 40.0
;
save_
save__pdbx_soln_scatter.entry_id
_item_description.description
; This data item is a pointer to _entry.id in the ENTRY category.
;
_item.name '_pdbx_soln_scatter.entry_id'
_item.category_id pdbx_soln_scatter
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_soln_scatter.entry_id'
_item_linked.parent_name '_entry.id'
save_
save__pdbx_soln_scatter.id
_item_description.description
; The value of _pdbx_soln_scatter.id must
uniquely identify the sample in the category PDBX_SOLN_SCATTER
;
_item.name '_pdbx_soln_scatter.id'
_item.category_id pdbx_soln_scatter
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_soln_scatter.type
_item_description.description
; The type of solution scattering experiment carried out
;
_item.name '_pdbx_soln_scatter.type'
_item.category_id pdbx_soln_scatter
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
'x-ray'
'neutron'
'modelling'
save_
save__pdbx_soln_scatter.source_beamline
_item_description.description
; The beamline name used for the experiment
;
_item.name '_pdbx_soln_scatter.source_beamline'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_soln_scatter.source_beamline_instrument
_item_description.description
; The instrumentation used on the beamline
;
_item.name '_pdbx_soln_scatter.source_beamline_instrument'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_soln_scatter.detector_type
_item_description.description
; The general class of the radiation detector.
;
_item.name '_pdbx_soln_scatter.detector_type'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_soln_scatter.detector_specific
_item_description.description
; The particular radiation detector. In general this will be a
manufacturer, description, model number or some combination of
these.
;
_item.name '_pdbx_soln_scatter.detector_specific'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_soln_scatter.source_type
_item_description.description
; The make, model, name or beamline of the source of radiation.
;
_item.name '_pdbx_soln_scatter.source_type'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code text
save_
save__pdbx_soln_scatter.source_class
_item_description.description
; The general class of the radiation source.
;
_item.name '_pdbx_soln_scatter.source_class'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
'neutron source'
'synchrotron'
save_
save__pdbx_soln_scatter.num_time_frames
_item_description.description
; The number of time frame solution scattering images used.
;
_item.name '_pdbx_soln_scatter.num_time_frames'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code int
save_
save__pdbx_soln_scatter.sample_pH
_item_description.description
; The pH value of the buffered sample.
;
_item.name '_pdbx_soln_scatter.sample_pH'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code float
save_
save__pdbx_soln_scatter.temperature
_item_description.description
; The temperature in kelvins at which the experiment
was conducted
;
_item.name '_pdbx_soln_scatter.temperature'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code kelvins
save_
save__pdbx_soln_scatter.concentration_range
_item_description.description
; The concentration range (mg/mL) of the complex in the
sample used in the solution scattering experiment to
determine the mean radius of structural elongation.
;
_item.name '_pdbx_soln_scatter.concentration_range'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code line
_item_units.code mg_per_ml
_item_examples.case '0.7 - 14'
save_
save__pdbx_soln_scatter.buffer_name
_item_description.description
; The name of the buffer used for the sample in the solution scattering
experiment.
;
_item.name '_pdbx_soln_scatter.buffer_name'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code line
_item_examples.case 'acetic acid'
save_
save__pdbx_soln_scatter.mean_guiner_radius
_item_description.description
; The mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q gives the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see: O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
;
_item.name '_pdbx_soln_scatter.mean_guiner_radius'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_units.code nanometres
_item_type.code float
_item_related.related_name '_pdbx_soln_scatter.mean_guiner_radius_esd'
_item_related.function_code associated_esd
save_
save__pdbx_soln_scatter.mean_guiner_radius_esd
_item_description.description
; The estimated standard deviation for the
mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q give the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see:
O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
;
_item.name '_pdbx_soln_scatter.mean_guiner_radius_esd'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code float
_item_units.code nanometres
_item_related.related_name '_pdbx_soln_scatter.mean_guiner_radius'
_item_related.function_code associated_value
save_
save__pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration
_item_description.description
;
The minimum mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q give the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see:
O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
;
_item.name '_pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code float
_item_units.code nanometres
_item_related.related_name '_pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration_esd'
_item_related.function_code associated_esd
save_
save__pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration_esd
_item_description.description
;
The estimated standard deviation for the
minimum mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q give the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see:
O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
;
_item.name '_pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration_esd'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code float
_item_units.code nanometres
_item_related.related_name '_pdbx_soln_scatter.min_mean_cross_sectional_radii_gyration'
_item_related.function_code associated_value
save_
save__pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration
_item_description.description
; The maximum mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q give the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see:
O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
;
_item.name '_pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code float
_item_units.code nanometres
_item_related.related_name '_pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration_esd'
_item_related.function_code associated_esd
save_
save__pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration_esd
_item_description.description
;
The estimated standard deviation for the
minimum mean radius of structural elongation of the sample.
In a given solute-solvent contrast, the radius of gyration
R_G is a measure of structural elongation if the internal
inhomogeneity of scattering densities has no effect. Guiner
analysis at low Q give the R_G and the forward scattering at
zero angle I(0).
lnl(Q) = lnl(0) - R_G^2Q^2/3
where
Q = 4(pi)sin(theta/lamda)
2theta = scattering angle
lamda = wavelength
The above expression is valid in a QR_G range for extended
rod-like particles. The relative I(0)/c values ( where
c = sample concentration) for sample measurements in a
constant buffer for a single sample data session, gives the
relative masses of the protein(s) studied when referenced
against a standard.
see:
O.Glatter & O.Kratky, (1982). Editors of "Small angle
X-ray Scattering, Academic Press, New York.
O.Kratky. (1963). X-ray small angle scattering with
substances of biological interest in diluted solutions.
Prog. Biophys. Chem., 13, 105-173.
G.D.Wignall & F.S.Bates, (1987). The small-angle approximation
of X-ray and neutron scatter from rigid rods of non-uniform
cross section and finite length. J.Appl. Crystallog., 18, 452-460.
If the structure is elongated, the mean radius of gyration
of the cross-sectional structure R_XS and the mean cross sectional
intensity at zero angle [I(Q).Q]_Q->0 is obtained from
ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2
;
_item.name '_pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration_esd'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code float
_item_units.code nanometres
_item_related.related_name '_pdbx_soln_scatter.max_mean_cross_sectional_radii_gyration'
_item_related.function_code associated_value
save_
save__pdbx_soln_scatter.protein_length
_item_description.description
;
The length (or range) of the protein sample under study.
If the solution structure is approximated as an elongated elliptical
cyclinder the the length L is determined from,
L = sqrt [12( (R_G)^2 - (R_XS)^2 ) ]
The length should also be given by
L = pi I(0) / [ I(Q).Q]_Q->0
;
_item.name '_pdbx_soln_scatter.protein_length'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code line
save_
save__pdbx_soln_scatter.data_reduction_software_list
_item_description.description
; A list of the software used in the data reduction
;
_item.name '_pdbx_soln_scatter.data_reduction_software_list'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code text
_item_examples.case 'OTOKO'
save_
save__pdbx_soln_scatter.data_analysis_software_list
_item_description.description
; A list of the software used in the data analysis
;
_item.name '_pdbx_soln_scatter.data_analysis_software_list'
_item.category_id pdbx_soln_scatter
_item.mandatory_code no
_item_type.code text
_item_examples.case 'SCTPL5 GNOM'
save_
#############################
## PDBX_SOLN_SCATTER_MODEL ##
#############################
save_pdbx_soln_scatter_model
_category.description
; Data items in the PDBX_SOLN_SCATTER_MODEL category record details about the
homology model fitting to the solution scatter data.
;
_category.id pdbx_soln_scatter_model
_category.mandatory_code no
loop_
_category_key.name
'_pdbx_soln_scatter_model.id'
'_pdbx_soln_scatter_model.scatter_id'
loop_
_category_group.id
'inclusive_group'
'solution_scattering_group'
save_
save__pdbx_soln_scatter_model.scatter_id
_item_description.description
; This data item is a pointer to _pdbx_soln_scatter.id in the PDBX_SOLN_SCATTER category.
;
_item.name '_pdbx_soln_scatter_model.scatter_id'
_item.category_id pdbx_soln_scatter_model
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_pdbx_soln_scatter_model.scatter_id'
_item_linked.parent_name '_pdbx_soln_scatter.id'
save_
save__pdbx_soln_scatter_model.id
_item_description.description
; The value of _pdbx_soln_scatter_model.id must
uniquely identify the sample in the category PDBX_SOLN_SCATTER_MODEL
;
_item.name '_pdbx_soln_scatter_model.id'
_item.category_id pdbx_soln_scatter_model
_item.mandatory_code yes
_item_type.code code
save_
save__pdbx_soln_scatter_model.details
_item_description.description
; A description of any additional details concerning the experiment.
;
_item.name '_pdbx_soln_scatter_model.details'
_item.category_id pdbx_soln_scatter_model
_item.mandatory_code no
_item_type.code text
_item_examples.case
; Homology models were built for
the 17 SCR domains and energy minimisations were
performed to improve the connectivity in the fh model.
triantennary complex-type carbohydrate structures
(MAN3GLCNAC6GAL3FUC3NEUNAC1) were added to each of the
N-linked glycosylation sites. a library of linker peptide
conformations was used in domain modelling constrained
by the solution scattering fits. modelling with the
scattering data was also carried out by rotational
search methods. the x-ray and neutron scattering curve
I(Q) was calculated assuming a uniform scattering density
for the spheres using the debye equation as adapted to
spheres. x-ray curves were calculated from the hydrated
sphere models without corrections for wavelength spread or
beam divergence, while these corrections were applied for
the neutron curves but now using unhydrated models.
;
save_
save__pdbx_soln_scatter_model.method
_item_description.description
; A description of the methods used in the modelling
;
_item.name '_pdbx_soln_scatter_model.method'
_item.category_id pdbx_soln_scatter_model
_item.mandatory_code no
_item_type.code text
_item_examples.case
; Constrained scattering fitting of homology models
;
save_
save__pdbx_soln_scatter_model.software_list
_item_description.description
; A list of the software used in the modeeling
;
_item.name '_pdbx_soln_scatter_model.software_list'
_item.category_id pdbx_soln_scatter_model
_item.mandatory_code no
_item_type.code text
_item_examples.case
; INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI
;
save_
save__pdbx_soln_scatter_model.software_author_list
_item_description.description
; A list of the software authors
;
_item.name '_pdbx_soln_scatter_model.software_author_list'
_item.category_id pdbx_soln_scatter_model
_item.mandatory_code no
_item_type.code text
_item_examples.case
; MSI
;
save_
save__pdbx_soln_scatter_model.entry_fitting_list
_item_description.description
; A list of the entries used to fit the model
to the scattering data
;
_item.name '_pdbx_soln_scatter_model.entry_fitting_list'
_item.category_id pdbx_soln_scatter_model
_item.mandatory_code no
_item_type.code text
_item_examples.case
; PDB CODE 1HFI, 1HCC, 1HFH, 1VCC
;
save_
save__pdbx_soln_scatter_model.num_conformers_calculated
_item_description.description
; The number of model conformers calculated.
;
_item.name '_pdbx_soln_scatter_model.num_conformers_calculated'
_item.category_id pdbx_soln_scatter_model
_item.mandatory_code no
_item_type.code int
save_
save__pdbx_soln_scatter_model.num_conformers_submitted
_item_description.description
; The number of model conformers submitted in the entry
;
_item.name '_pdbx_soln_scatter_model.num_conformers_submitted'
_item.category_id pdbx_soln_scatter_model
_item.mandatory_code no
_item_type.code int
save_
save__pdbx_soln_scatter_model.conformer_selection_criteria
_item_description.description
; A description of the conformer selection criteria
used.
;
_item.name '_pdbx_soln_scatter_model.conformer_selection_criteria'
_item.category_id pdbx_soln_scatter_model
_item.mandatory_code no
_item_type.code text
_item_examples.case
; The modelled scattering curves were assessed by calculation of the
RG, RSX-1 and RXS-2 values in the same Q ranges
used in the experimental Guinier fits. models were
then ranked using a goodness-of-fit R-factor
defined by analogy with protein crystallography
and based on the experimental curves in the Q range
extending to 1.4 nm-1.
;
save_
##
##
./CBFlib-0.9.2.2/doc/Idiffrn_radiation.polarizn_source_norm.html 0000644 0000765 0000765 00000007273 11603702115 023125 0 ustar yaya yaya
(IUCr) CIF Definition save__diffrn_radiation.polarizn_source_norm
The angle in degrees, as viewed from the specimen, between
the normal to the polarization plane and the laboratory Y
axis as defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monochromater.
This differs from the value of
_diffrn_radiation.polarisn_norm
in that _diffrn_radiation.polarisn_norm refers to
polarization relative to the diffraction plane rather than
to the laboratory axis system.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane should be taken
as the XZ plane and the angle as 0.
See _diffrn_radiation.polarizn_source_ratio.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The value of _map.details should give a
description of special aspects of each map.
Example:
; Example 1 - Identifying an observed density map
and a calculated density map
;
loop_
_map.id
_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Data items in the ARRAY_DATA category are the containers for
the array data items described in the category ARRAY_STRUCTURE.
It is recognized that the data in this category needs to be used in
two distinct ways. During a data collection the lack of ancillary
data and timing constraints in processing data may dictate the
need to make a 'miniCBF' nothing more than an essential minimum
of information to record the results of the data collection. In that
case it is proper to use the ARRAY_DATA category as a
container for just a single image and a compacted, beam-line
dependent list of data collection parameter values. In such
a case, only the tags '_array_data.header_convention',
'_array_data.header_contents' and '_array_data.data' need be
populated.
For full processing and archiving, most of the tags in this
dictionary will need to be populated.
Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
_array_intensities.gain. If raw, uncorrected values
are presented (e.g. for calibration experiments), the
value of _array_intensities.linearity will be 'raw'
and _array_intensities.gain will not be used.
Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets of axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axes: one for the angular
direction and one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one
set.
Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection or the axes defining the
coordinate system of an image.
The location of each axis is specified by two vectors: the axis
itself, given by a unit vector in the direction of the axis, and
an offset to the base of the unit vector.
The vectors defining an axis are referenced to an appropriate
coordinate system. The axis vector, itself, is a dimensionless
unit vector. Where meaningful, the offset vector is given in
millimetres. In coordinate systems not measured in metres,
the offset is not specified and is taken as zero.
The available coordinate systems are:
The imgCIF standard laboratory coordinate system
The direct lattice (fractional atomic coordinates)
The orthogonal Cartesian coordinate system (real space)
The reciprocal lattice
An abstract orthogonal Cartesian coordinate frame
DIFFRN_GROUP
Categories that describe details of the diffraction experiment.
Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases but should not be used for new work.
Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the
diffraction data were measured.
Data items in the DIFFRN_RADIATION category describe
the radiation used for measuring diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
Data items in the DIFFRN_REFLN category record details about
the intensities in the diffraction data set
identified by _diffrn_refln.diffrn_id.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in the particular diffraction
data set identified by _diffrn_reflns.diffrn_id and
_diffrn_refln.frame_id
Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the
settings of axes for particular frames. Unspecified axes are
assumed to be at their zero points. If, for any given frame,
nonzero values apply for any of the data items in this category,
those values should be given explicitly in this category and not
simply inferred from values in DIFFRN_SCAN_AXIS.
A single frame may have more than one monitor value, and each
monitor value may be the result of integration over the entire
frame integration time given by the value of
_diffrn_scan_frame.integration_time
or many monitor values may be reported over shorter times given
by the value of _diffrn_scan_frame_monitor.integration_time. If
only one monitor value for a given monitor is collected during
the integration time of the frame, the value of
_diffrn_scan_frame_monitor.id may be
omitted.
Data items in the MAP category record
the details of a maps. Maps record values of parameters,
such as density, that are functions of position within
a cell or are functions of orthogonal coordinates in
three space.
A map may is composed of one or more map segments
specified in the MAP_SEGMENT category.
Data items in the VARIANT category record
the details about sets of variants of data items.
There is sometimes a need to allow for multiple versions of the
same data items in order to allow for refinements and corrections
to earlier assumptions, observations and calculations. In order
to allow data sets to contain more than one variant of the same
information, an optional ...variant data item as a pointer to
_variant.variant has been added to the key of every category,
as an implicit data item with a null (empty) default value.
All rows in a category with the same variant value are considered
to be related to one another and to all rows in other categories
with the same variant value. For a given variant, all such rows
are also considered to be related to all rows with a null variant
value, except that a row with a null variant value is for which
all other components of its key are identical to those entries
in another row with a non-null variant value is not related the
the rows with that non-null variant value. This behavior is
similar to the convention for identifying alternate conformers
in an atom list.
An optional role may be specified for a variant as the value of
_variant.role. Possible roles are null, "preferred",
"raw data", "unsuccessful trial".
Variants may carry an optional timestamp as the value of
_variant.timestamp.
Variants may be related to other variants from which they were
derived by the value of _variant.variant_of
Further details about the variant may be specified as the value
of _variant.details.
In order to allow variant information from multiple datasets to
be combined, _variant.diffrn_id and/or _variant.entry_id may
be used.
;
_dictionary.title cif_img.dic
_dictionary.version 1.6.3
_dictionary.datablock_id cif_img.dic
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
'map_group'
'inclusive_group'
; Categories that describe details of map data.
;
'variant_group'
'inclusive_group'
; Categories that describe details of map data.
;
##################
## SUB_CATEGORY ##
##################
loop_
_sub_category.id
_sub_category.description
'matrix'
; The collection of elements of a matrix.
;
'vector'
; The collection of elements of a vector.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
; Data items in the ARRAY_DATA category are the containers for
the array data items described in the category ARRAY_STRUCTURE.
It is recognized that the data in this category needs to be used in
two distinct ways. During a data collection the lack of ancillary
data and timing constraints in processing data may dictate the
need to make a 'miniCBF' nothing more than an essential minimum
of information to record the results of the data collection. In that
case it is proper to use the ARRAY_DATA category as a
container for just a single image and a compacted, beam-line
dependent list of data collection parameter values. In such
a case, only the tags '_array_data.header_convention',
'_array_data.header_contents' and '_array_data.data' need be
populated.
For full processing and archiving, most of the tags in this
dictionary will need to be populated.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
'_array_data.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and is
presented as hexadecimal data. The first character 'H' on the
data lines means hexadecimal. It could have been 'O' for octal
or 'D' for decimal. The second character on the line shows
the number of bytes in each word (in this case '4'), which then
requires eight hexadecimal digits per word. The third character
gives the order of octets within a word, in this case '<'
for the ordering 4321 (i.e. 'big-endian'). Alternatively, the
character '>' could have been used for the ordering 1234
(i.e. 'little-endian'). The block has a 'message digest'
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id_array_data.binary_id_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 2
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
This example shows a single image in a miniCBF, provided by
E. Eikenberry. The entire CBF consists of one data block
containing one category and three tags. The CBFlib
program convert_miniCBF and a suitable template file
can be used to convert this miniCBF to a full imgCIF
file.
;
;
###CBF: VERSION 1.5
# CBF file written by CBFlib v0.7.8
data_insulin_pilatus6m
_array_data.header_convention SLS_1.0
_array_data.header_contents
;
# Detector: PILATUS 6M SN: 60-0001
# 2007/Jun/17 15:12:36.928
# Pixel_size 172e-6 m x 172e-6 m
# Silicon sensor, thickness 0.000320 m
# Exposure_time 0.995000 s
# Exposure_period 1.000000 s
# Tau = 194.0e-09 s
# Count_cutoff 1048575 counts
# Threshold_setting 5000 eV
# Wavelength 1.2398 A
# Energy_range (0, 0) eV
# Detector_distance 0.15500 m
# Detector_Voffset -0.01003 m
# Beam_xy (1231.00, 1277.00) pixels
# Flux 22487563295 ph/s
# Filter_transmission 0.0008
# Start_angle 13.0000 deg.
# Angle_increment 1.0000 deg.
# Detector_2theta 0.0000 deg.
# Polarization 0.990
# Alpha 0.0000 deg.
# Kappa 0.0000 deg.
# Phi 0.0000 deg.
# Chi 0.0000 deg.
# Oscillation_axis X, CW
# N_oscillations 1
;
_array_data.data
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_BYTE_OFFSET"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 6247567
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
X-Binary-Element-Byte-Order: LITTLE_ENDIAN
Content-MD5: 8wO6i2+899lf5iO8QPdgrw==
X-Binary-Number-of-Elements: 6224001
X-Binary-Size-Fastest-Dimension: 2463
X-Binary-Size-Second-Dimension: 2527
X-Binary-Size-Padding: 4095
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
If not given, it defaults to 1.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code implicit
_item_default.value 1
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id, should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-ID, the value of _array_data.binary_id
should be equal to the value given for X-Binary-ID.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
'\n--CIF-BINARY-FORMAT-SECTION--' (including the
required initial '\n--').
The Content-Type may be any of the discrete types permitted
in RFC 2045; 'application/octet-stream' is recommended
for diffraction images in the ARRAY_DATA category.
Note: When appropriate in other categories, e.g. for
photographs of crystals, more precise types, such as
'image/jpeg', 'image/tiff', 'image/png', etc. should be used.
If an octet stream was compressed, the compression should
be specified by the parameter
'conversions="X-CBF_PACKED"'
or the parameter
'conversions="X-CBF_CANONICAL"'
or the parameter
'conversions="X-CBF_BYTE_OFFSET"'
or the parameter
'conversions="X-CBF_BACKGROUND_OFFSET_DELTA"'
If the parameter
'conversions="X-CBF_PACKED"'
is given it may be further modified with the parameters
'"uncorrelated_sections"'
or
'"flat"'
If the '"uncorrelated_sections"' parameter is
given, each section will be compressed without using
the prior section for averaging.
If the '"flat"' parameter is given, each the
image will be treated as one long row.
Note that the X-CBF_CANONICAL and X-CBF_PACKED are
slower but more efficient compressions that the others.
The X-CBF_BYTE_OFFSET compression is a good compromise
between speed and efficiency for ordinary diffraction
images. The X-CBF_BACKGROUND_OFFSET_DELTA compression
is oriented towards sparse data, such as masks and
tables of replacement pixel values for images with
overloaded spots.
The Content-Transfer-Encoding may be 'BASE64',
'Quoted-Printable', 'X-BASE8', 'X-BASE10',
'X-BASE16' or 'X-BASE32K', for an imgCIF or 'BINARY'
for a CBF. The octal, decimal and hexadecimal transfer
encodings are provided for convenience in debugging and
are not recommended for archiving and data interchange.
In a CIF, one of the parameters 'charset=us-ascii',
'charset=utf-8' or 'charset=utf-16' may be used on the
Content-Transfer-Encoding to specify the character set
used for the external presentation of the encoded data.
If no charset parameter is given, the character set of
the enclosing CIF is assumed. In any case, if a BOM
flag is detected (FE FF for big-endian UTF-16, FF FE for
little-endian UTF-16 or EF BB BF for UTF-8) is detected,
the indicated charset will be assumed until the end of the
encoded data or the detection of a different BOM. The
charset of the Content-Transfer-Encoding is not the character
set of the encoded data, only the character set of the
presentation of the encoded data and should be respecified
for each distinct STAR string.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In an imgCIF file,
the encoded binary data ends with the terminating boundary
delimiter '\n--CIF-BINARY-FORMAT-SECTION----'
in the currently effective charset or with the '\n; '
that terminates the STAR string.
In a CBF, the raw binary data begins after an empty line
terminating the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of
the message size or in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. An adjustment is made for
the deprecated binary formats in which eight bytes of binary
header are used for the compression type. In this case,
the eight bytes used for the compression type are subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is 'unsigned 32-bit integer'.
An MD5 message digest may, optionally, be used. The 'RSA Data
Security, Inc. MD5 Message-Digest Algorithm' should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is 'X-BASE8', 'X-BASE10' or
'X-BASE16', the data are presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ('big-
endian') or 1234... ('little-endian'). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as '==' for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is 'H', 'O' or 'D' for hexadecimal, octal or
decimal, n is the number of octets per word and d is '<'
or '>' for the '...4321' and '1234...' octet orderings,
respectively. The '==' padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hexadecimal, octal and decimal formats only,
comments beginning with '#' are permitted to improve
readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three: c1, c2, c3. The resulting 24 bits
are broken into four six-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order four bits of the second octet [(c1 & 3)<<4 | (c2>>4)],
then the bottom four bits of the second octet followed by the
high-order two bits of the last octet [(c2 & 15)<<2 | (c3>>6)],
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
With short groups of octets padded on the right with one '='
if c3 is missing, and with '==' if both c2 and c3 are missing.
X-BASE32K encoding is similar to BASE64 encoding, except that
sets of 15 octets are encoded as sets of 8 16-bit unicode
characters, by breaking the 120 bits into 8 15-bit quantities.
256 is added to each 15 bit quantity to bring it into a
printable uncode range. When encoding, zero padding is used
to fill out the last 15 bit quantity. If 8 or more bits of
padding are used, a single equals sign (hexadecimal 003D) is
appended. Embedded whitespace and newlines are introduced
to produce lines of no more than 80 characters each. On
decoding, all printable ascii characters and ascii whitespace
characters are ignored except for any trailing equals signs.
The number of trailing equals signs indicated the number of
trailing octets to be trimmed from the end of the decoded data.
(see Georgi Darakev, Vassil Litchev, Kostadin Z. Mitev, Herbert
J. Bernstein, 'Efficient Support of Binary Data in the XML
Implementation of the NeXus File Format',absract W0165,
ACA Summer Meeting, Honolulu, HI, July 2006).
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32...38,
42, 48...57, 59, 60, 62, 64...126 and the octet is not a ';'
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
'wrapped' with a terminating '=' (i.e. the MIME conventions
for an implicit line terminator are never used).
The "X-Binary-Element-Byte-Order" can specify either
'"BIG_ENDIAN"' or '"LITTLE_ENDIAN"' byte order of the imaage
data. Only LITTLE_ENDIAN is recommended. Processors
may treat BIG_ENDIAN as a warning of data that can
only be processed by special software.
The "X-Binary-Number-of-Elements" specifies the number of
elements (not the number of octets) in the decompressed, decoded
image.
The optional "X-Binary-Size-Fastest-Dimension" specifies the
number of elements (not the number of octets) in one row of the
fastest changing dimension of the binary data array. This
information must be in the MIME header for proper operation of
some of the decompression algorithms.
The optional "X-Binary-Size-Second-Dimension" specifies the
number of elements (not the number of octets) in one column of
the second-fastest changing dimension of the binary data array.
This information must be in the MIME header for proper operation
of some of the decompression algorithms.
The optional "X-Binary-Size-Third-Dimension" specifies the
number of sections for the third-fastest changing dimension of
the binary data array.
The optional "X-Binary-Size-Padding" specifies the size in
octets of an optional padding after the binary array data and
before the closing flags for a binary section.
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
save__array_data.header_contents
_item_description.description
; This item is an text field for use in minimal CBF files to carry
essential header information to be kept with image data
in _array_data.data when the tags that normally carry the
structured metadata for the image have not been populated.
Normally this data item should not appear when the full set
of tags have been populated and _diffrn_data_frame.details
appears.
;
_item.name '_array_data.header_contents'
_item.category_id array_data
_item.mandatory_code no
_item_type.code text
save_
save__array_data.header_convention
_item_description.description
; This item is an identifier for the convention followed in
constructing the contents of _array_data.header_contents
The permitted values are of the of an image creator identifier
followed by an underscore and a version string. To avoid
confusion about conventions, all creator identifiers
should be registered with the IUCr and the conventions
for all identifiers and versions should be posted on
the MEDSBIO.org web site.
;
_item.name '_array_data.header_convention'
_item.category_id array_data
_item.mandatory_code no
_item_type.code code
save_
save__array_data.variant
_item_description.description
; The value of _array_data.variant gives the variant
to which the given array_data row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_data.variant'
_item.category_id array_data
_item.mandatory_code no
_item_type.code code
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
; Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
'_array_element_size.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code implicit
_item_type.code code
save_
save__array_element_size.index
_item_description.description
; This item is a pointer to _array_structure_list.index in
the ARRAY_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
; The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__array_element_size.variant
_item_description.description
; The value of _array_element_size.variant gives the variant
to which the given array_element_size row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_element_size.variant'
_item.category_id array_element_size
_item.mandatory_code no
_item_type.code code
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
; Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
_array_intensities.gain. If raw, uncorrected values
are presented (e.g. for calibration experiments), the
value of _array_intensities.linearity will be 'raw'
and _array_intensities.gain will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
'_array_intensities.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id_array_intensities.linearity_array_intensities.gain_array_intensities.overload_array_intensities.undefined_value_array_intensities.pixel_fast_bin_size_array_intensities.pixel_slow_bin_size_array_intensities.pixel_binning_method
image_1 linear 1.2 655535 0 2 2 hardware
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
; Detector 'gain'. The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
; The estimated standard deviation in detector 'gain'.
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
; The intensity linearity scaling method used to convert
from the raw intensity to the stored element value:
'linear' is linear.
'offset' means that the value defined by
_array_intensities.offset should be added to each
element value.
'scaling' means that the value defined by
_array_intensities.scaling should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by _array_intensities.scaling is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
'logarithmic_scaled' means that the logarithm base 10 of
raw intensities multiplied by _array_intensities.scaling
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and calculating 10
to the power of this number.
'raw' means that the data are a set of raw values straight
from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
; The value defined by _array_intensities.offset should
be added to each element value.
;
'scaling'
; The value defined by _array_intensities.scaling should be
multiplied with each element value.
;
'scaling_offset'
; The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
; The square root of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
;
'logarithmic_scaled'
; The logarithm base 10 of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
_array_intensities.scaling and calculating 10 to the
power of this number.
;
'raw'
; The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data-fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
; Offset value to add to array element values in the manner
described by the item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
; The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.pixel_fast_bin_size
_item_description.description
; The value of _array_intensities.pixel_fast_bin_size specifies
the number of pixels that compose one element in the direction
of the most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_fast_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_slow_bin_size
_item_description.description
; The value of _array_intensities.pixel_slow_bin_size specifies
the number of pixels that compose one element in the direction
of the second most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_slow_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_binning_method
_item_description.description
; The value of _array_intensities.pixel_binning_method specifies
the method used to derive array elements from multiple pixels.
;
_item.name '_array_intensities.pixel_binning_method'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'hardware'
; The element intensities were derived from the raw data of one
or more pixels by used of hardware in the detector, e.g. by use
of shift registers in a CCD to combine pixels into super-pixels.
;
'software'
; The element intensities were derived from the raw data of more
than one pixel by use of software.
;
'combined'
; The element intensities were derived from the raw data of more
than one pixel by use of both hardware and software, as when
hardware binning is used in one direction and software in the
other.
;
'none'
; In the both directions, the data has not been binned. The
number of pixels is equal to the number of elements.
When the value of _array_intensities.pixel_binning_method is
'none' the values of _array_intensities.pixel_fast_bin_size
and _array_intensities.pixel_slow_bin_size both must be 1.
;
'unspecified'
; The method used to derive element intensities is not specified.
;
_item_default.value 'unspecified'
save_
save__array_intensities.scaling
_item_description.description
; Multiplicative scaling value to be applied to array data
in the manner described by item
_array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.undefined_value
_item_description.description
; A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.variant
_item_description.description
; The value of _array_intensities.variant gives the variant
to which the given array_intensities row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_intensities.variant'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code code
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
; Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data that may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
loop_
_category_key.name '_array_structure.id'
'_array_structure.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
; The order of bytes for integer values which require more
than 1 byte.
(IBM-PC's and compatibles and DEC VAXs use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. DEC Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
; The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
; The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
; Type of data-compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'byte_offset'
; Using the 'byte_offset' compression scheme as per A. Hammersley
and the CBFlib manual, section 3.3.3
;
'canonical'
; Using the 'canonical' compression scheme (International Tables
for Crystallography Volume G, Section 5.6.3.1) and CBFlib
manual section 3.3.1
;
'none'
; Data are stored in normal format as defined by
_array_structure.encoding_type and
_array_structure.byte_order.
;
'packed'
; Using the 'packed' compression scheme, a CCP4-style packing
as per J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
'packed_v2'
; Using the 'packed' compression scheme, version 2, as per
J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
save_
save__array_structure.compression_type_flag
_item_description.description
; Flags modifying the type of data-compression method used to
compress the arraydata.
;
_item.name '_array_structure.compression_type_flag'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'uncorrelated_sections'
; When applying packed or packed_v2 compression on an array with
uncorrelated sections, do not average in points from the prior
section.
;
'flat'
; When applying packed or packed_v2 compression on an array with
treat the entire image as a single line set the maximum number
of bits for an offset to 65 bits.
The flag is included for compatibility with software prior to
CBFlib_0.7.7, and should not be used for new data sets.
;
save_
save__array_structure.encoding_type
_item_description.description
; Data encoding of a single element of array data.
The type 'unsigned 1-bit integer' is used for
packed Booleans arrays for masks. Each element
of the array corresponds to a single bit
packed in unsigned 8-bit data.
In several cases, the IEEE format is referenced.
See IEEE Standard 754-1985 (IEEE, 1985).
Ref: IEEE (1985). IEEE Standard for Binary Floating-Point
Arithmetic. ANSI/IEEE Std 754-1985. New York: Institute of
Electrical and Electronics Engineers.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 1-bit integer'
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
This item has been made implicit and given a default value of 1
as a convenience in writing miniCBF files. Normally an
explicit name with useful content should be used.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure implicit
'_array_data.array_id' array_data implicit
'_array_structure_list.array_id' array_structure_list implicit
'_array_intensities.array_id' array_intensities implicit
'_diffrn_data_frame.array_id' diffrn_data_frame implicit
_item_default.value 1
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
save__array_structure.variant
_item_description.description
; The value of _array_structure.variant gives the variant
to which the given array_structure row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_structure.variant'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code code
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
; Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
'_array_structure_list.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left to right (increasing) in the
first dimension and bottom to top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differs
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the 'poise' of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
; The number of elements stored in the array structure in
this dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
; Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
; Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
; Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
; Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
; Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.variant
_item_description.description
; The value of _array_structure_list.variant gives the variant
to which the given array_structure_list row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_structure_list.variant'
_item.category_id array_structure_list
_item.mandatory_code no
_item_type.code code
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
; Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets of axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axes: one for the angular
direction and one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one
set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
'_array_structure_list_axis.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes in the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
; The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to
_array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list_axis.angle
_item_description.description
; The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified for this case.
See _array_structure_list_axis.angular_pitch.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement
_item_description.description
; The setting of the specified axis as a decimal fraction of
the axis unit vector for the first data point of the array
index with the corresponding value of
_array_structure_list.axis_set_id.
If the index is specified as 'increasing', this will be the
centre of the pixel with index value 1. If the index is
specified as 'decreasing', this will be the centre of the
pixel with maximum index value.
;
_item.name '_array_structure_list_axis.fract_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis as a decimal fraction of the
axis unit vector.
;
_item.name
'_array_structure_list_axis.fract_displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
; The pixel-centre-to-pixel-centre distance for a one-step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans
or for uncoupled angular scans at a constant radius
(cylindrical scans) and should not be specified for cases
in which the angle between pixels (rather than the distance
between pixels) is uniform.
See _array_structure_list_axis.angle_increment.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
; The radial distance from one 'cylinder' of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of _array_structure_list_axis.displacement_increment.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.reference_angle
_item_description.description
; The value of _array_structure_list_axis.reference_angle
specifies the setting of the angle of this axis used for
determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the
value of _array_structure_list.angle.
;
_item.name '_array_structure_list_axis.reference_angle'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.reference_displacement
_item_description.description
; The value of _array_structure_list_axis.reference_displacement
specifies the setting of the displacement of this axis used
for determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the value
of _array_structure_list.displacement.
;
_item.name '_array_structure_list_axis.reference_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.variant
_item_description.description
; The value of _array_structure_list_axis.variant gives the variant
to which the given array_structure_list_axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_structure_list_axis.variant'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_type.code code
save_
########
# AXIS #
########
save_AXIS
_category.description
; Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection or the axes defining the
coordinate system of an image.
The location of each axis is specified by two vectors: the axis
itself, given by a unit vector in the direction of the axis, and
an offset to the base of the unit vector.
The vectors defining an axis are referenced to an appropriate
coordinate system. The axis vector, itself, is a dimensionless
unit vector. Where meaningful, the offset vector is given in
millimetres. In coordinate systems not measured in metres,
the offset is not specified and is taken as zero.
The available coordinate systems are:
The imgCIF standard laboratory coordinate system
The direct lattice (fractional atomic coordinates)
The orthogonal Cartesian coordinate system (real space)
The reciprocal lattice
An abstract orthogonal Cartesian coordinate frame
For consistency in this discussion, we call the three coordinate
system axes X, Y and Z. This is appropriate for the imgCIF
standard laboratory coordinate system, and last two Cartesian
coordinate systems, but for the direct lattice, X corresponds
to a, Y to b and Z to c, while for the reciprocal lattice,
X corresponds to a*, Y to b* and Z to c*.
For purposes of visualization, all the coordinate systems are
taken as right-handed, i.e., using the convention that the extended
thumb of a right hand could point along the first (X) axis, the
straightened pointer finger could point along the second (Y) axis
and the middle finger folded inward could point along the third (Z)
axis.
THE IMGCIF STANDARD LABORATORY COORDINATE SYSTEM
The imgCIF standard laboratory coordinate system is a right-handed
orthogonal coordinate similar to the MOSFLM coordinate system,
but imgCIF puts Z along the X-ray beam, rather than putting X along the
X-ray beam as in MOSFLM.
The vectors for the imgCIF standard laboratory coordinate system
form a right-handed Cartesian coordinate system with its origin
in the sample or specimen. The origin of the axis system should,
if possible, be defined in terms of mechanically stable axes to be
be both in the sample and in the beam. If the sample goniometer or other
sample positioner has two axes the intersection of which defines a
unique point at which the sample should be mounted to be bathed
by the beam, that will be the origin of the axis system. If no such
point is defined, then the midpoint of the line of intersection
between the sample and the center of the beam will define the origin.
For this definition the sample positioning system will be set at
its initial reference position for the experiment.
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer or
sample positioning system if the sample positioning system has an axis
that intersects the origin and which form an angle of more than 22.5
degrees with the beam axis.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
If the conditions for the X-axis can be met, the coordinate system
will be based on the goniometer or other sample positioning system
and the beam and not on the orientation of the detector, gravity etc.
The vectors necessary to specify all other axes are given by sets of
three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right-handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to but significantly
different from the choice in MOSFLM (Leslie & Powell, 2004). In MOSFLM,
X is along the X-ray beam (the CBF/imgCIF Z axis) and Z is along the
rotation axis.
In some experimental techniques, there is no goniometer or the principal
axis of the goniometer is at a small acute angle with respect to
the source axis. In such cases, other reference axes are needed
to define a useful coordinate system. The order of priority in
defining directions in such cases is to use the detector, then
gravity, then north.
If the X-axis cannot be defined as above, then the
direction (not the origin) of the X-axis should be parallel to the axis
of the primary detector element corresponding to the most rapidly
varying dimension of that detector element's data array, with its
positive sense corresponding to increasing values of the index for
that dimension. If the detector is such that such a direction cannot
be defined (as with a point detector) or that direction forms an
angle of less than 22.5 degrees with respect to the source axis, then
the X-axis should be chosen so that if the Y-axis is chosen
in the direction of gravity, and the Z-axis is chosen to be along
the source axis, a right-handed orthogonal coordinate system is chosen.
In the case of a vertical source axis, as a last resort, the
X-axis should be chosen to point North.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam centre.
The location of the beam centre on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected millimetres from
the (0,0) corner of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, it is necessary to
specify the location of the beam centre on the detector in terms
of the origin of the detector, which is, of course, not coincident
with the centre of the sample.
The unit cell, reciprocal cell and crystallographic orthogonal
Cartesian coordinate system are defined by the CELL and the matrices
in the ATOM_SITES category.
THE DIRECT LATTICE (FRACTIONAL COORDINATES)
The direct lattice coordinate system is a system of fractional
coordinates aligned to the crystal, rather than to the laboratory.
This is a natural coordinate system for maps and atomic coordinates.
It is the simplest coordinate system in which to apply symmetry.
The axes are determined by the cell edges, and are not necessarily
othogonal. This coordinate system is not uniquely defined and
depends on the cell parameters in the CELL category and the
settings chosen to index the crystal.
Molecules in a crystal studied by X-ray diffracraction are organized
into a repeating regular array of unit cells. Each unit cell is defined
by three vectors, a, b and c. To quote from Drenth,
"The choice of the unit cell is not unique and therefore, guidelines
have been established for selecting the standard basis vectors and
the origin. They are based on symmetry and metric considerations:
"(1) The axial system should be right handed.
(2) The basis vectors should coincide as much as possible with
directions of highest symmetry."
(3) The cell taken should be the smallest one that satisfies
condition (2)
(4) Of all the lattice vectors, none is shorter than a.
(5) Of those not directed along a, none is shorter than b.
(6) Of those not lying in the ab plane, none is shorter than c.
(7) The three angles between the basis vectors a, b and c are
either all acute (<90\%) or all obtuse (≥90\%)."
These rules do not produce a unique result that is stable under
the assumption of experimental errors, and the the resulting cell
may not be primitive.
In this coordinate system, the vector (.5, .5, .5) is in the middle
of the given unit cell.
Grid coordinates are an important variation on fractional coordinates
used when working with maps. In imgCIF, the conversion from
fractional to grid coordinates is implicit in the array indexing
specified by _array_structure_list.dimension. Note that this
implicit grid-coordinate scheme is 1-based, not zero-based, i.e.
the origin of the cell for axes along the cell edges with no
specified _array_structure_list_axis.displacement will have
grid coordinates of (1,1,1), i.e. array indices of (1,1,1).
THE ORTHOGONAL CARTESIAN COORDINATE SYSTEM (REAL SPACE)
The orthogonal Cartesian coordinate system is a transformation of
the direct lattice to the actual physical coordinates of atoms in
space. It is similar to the laboratory coordinate system, but
is anchored to and moves with the crystal, rather than being
schored to the laboratory. The transformation from fractional
to orthogonal cartesian coordinates is given by the
_atom_sites.Cartn_transf_matrix[i][j] and
_atom_sites.Cartn_transf_vector[i]
tags. A common choice for the matrix of the transformation is
given in the 1992 PDB format document
| a b cos(\g) c cos(\b) |
| 0 b sin(\g) c (cos(\a) - cos(\b)cos(\g))/sin(\g) |
| 0 0 V/(a b sin(\g)) |
This is a convenient coordinate system in which to do fitting
of models to maps and in which to understand the chemistry of
a molecule.
THE RECIPROCAL LATTICE
The reciprocal lattice coordinate system is used for diffraction
intensitities. It is based on the reciprocal cell, the dual of the cell,
in which reciprocal cell edges are derived from direct cell faces:
a* = bc sin(\a)/V b* = ac sin(\b)/V c* = ab sin(\g)/V
cos(\a*) = (cos(\b) cos(\g) - cos(\a))/(sin(\b) sin(\g))
cos(\b*) = (cos(\a) cos(\g) - cos(\b))/(sin(\a) sin(\g))
cos(\g*) = (cos(\a) cos(\b) - cos(\g))/(sin(\a) sin(\b))
V = abc SQRT(1 - cos(\a)^2^
- cos(\b)^2^
- cos(\g)^2^
+ 2 cos(\a) cos(\b) cos(\g) )
In this form the dimensions of the reciprocal lattice are in reciprocal
\%Angstroms (\%A^-1^). A dimensionless form can be obtained by
multiplying by the wavelength. Reflections are commonly indexed against
this coordinate system as (h, k, l) triples.
References:
Drenth, J., "Introduction to basic crystallography." chapter
2.1 in Rossmann, M. G. and Arnold, E. "Crystallography of
biological macromolecules", Volume F of the IUCr's "International
tables for crystallography", Kluwer, Dordrecht 2001, pp 44 -- 63
Leslie, A. G. W. and Powell, H. (2004). MOSFLM v6.11.
MRC Laboratory of Molecular Biology, Hills Road, Cambridge, England.
http://www.CCP4.ac.uk/dist/X-windows/Mosflm/.
Stout, G. H. and Jensen, L. H., "X-ray structure determination",
2nd ed., Wiley, New York, 1989, 453 pp.
__, "PROTEIN DATA BANK ATOMIC COORDINATE AND BIBLIOGRAPHIC ENTRY
FORMAT DESCRIPTION," Brookhaven National Laboratory, February 1992.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
'_axis.variant'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
This example shows the axis specification of the axes of a kappa-
geometry goniometer [see Stout, G. H. & Jensen, L. H. (1989). X-ray
structure determination. A practical
guide, 2nd ed. p. 134. New York: Wiley Interscience].
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X axis. The next innermost axis, kappa,
is at a 50 degree angle to the X axis, pointed away from the source.
The innermost axis, phi, aligns with the X axis when omega and
phi are at their zero points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
X' = (T-omega) (T-kappa) (T-phi) X
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 -
This example shows the axis specification of the axes of a
detector, source and gravity. The order has been changed as a
reminder that the ordering of presentation of tokens is not
significant. The centre of rotation of the detector has been taken
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 3 -
This example show the axis specification of the axes for a map,
using fractional coordinates. Each cell edge has been divided
into a grid of 50 divisions in the ARRAY_STRUCTURE_LIST_AXIS
category. The map is using only the first octant of the grid
in the ARRAY_STRUCTURE_LIST category.
The fastest changing axis is the gris along A, then along B,
and the slowest is along C.
The map sampling is being done in the middle of each grid
division
;
;
loop_
_axis.id_axis.system_axis.vector[1]_axis.vector[2]_axis.vector[3]
CELL_A_AXIS fractional 1 0 0
CELL_B_AXIS fractional 0 1 0
CELL_C_AXIS fractional 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing CELL_A_AXIS
MAP 1 25 2 increasing CELL_B_AXIS
MAP 1 25 3 increasing CELL_C_AXIS
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.fract_displacement
_array_structure_list_axis.fract_displacement_increment
CELL_A_AXIS 0.01 0.02
CELL_B_AXIS 0.01 0.02
CELL_C_AXIS 0.01 0.02
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 4 -
This example show the axis specification of the axes for a map,
this time as orthogonal \%Angstroms, using the same coordinate system
as for the atomic coordinates. The map is sampling every 1.5
\%Angstroms (1.5e-7 millimeters) in a map segment 37.5 \%Angstroms on
a side.
;
;
loop_
_axis.id_axis.system_axis.vector[1]_axis.vector[2]_axis.vector[3]
X orthogonal 1 0 0
Y orthogonal 0 1 0
Z orthogonal 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing X
MAP 2 25 2 increasing Y
MAP 3 25 3 increasing Z
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
X 7.5e-8 1.5e-7
Y 7.5e-8 1.5e-7
Z 7.5e-8 1.5e-7
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.depends_on specifies the next outermost
axis upon which this axis depends.
This item is a pointer to _axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.equipment specifies the type of
equipment using the axis: 'goniometer', 'detector',
'gravity', 'source' or 'general'.
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.system
_item_description.description
; The value of _axis.system specifies the coordinate
system used to define the axis: 'laboratory', 'direct',
'orthogonal', 'reciprocal' or 'abstract'.
;
_item.name '_axis.system'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value laboratory
loop_
_item_enumeration.value
_item_enumeration.detail
laboratory
; the axis is referenced to the imgCIF standard laboratory Cartesian
coordinate system
;
direct
; the axis is referenced to the direct lattice
;
orthogonal
; the axis is referenced to the cell Cartesian orthogonal coordinates
;
reciprocal
; the axis is referenced to the reciprocal lattice
;
abstract
; the axis is referenced to abstract Cartesian cooridinate system
;
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: 'rotation' or 'translation' (or 'general' when
the type is not relevant, as for gravity).
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.variant
_item_description.description
; The value of _axis.variant gives the variant
to which the given axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_axis.variant'
_item.category_id axis
_item.mandatory_code no
_item_type.code code
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
; Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
'_diffrn_data_frame.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element are
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id.
;
;
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.center_fast
_item_description.description
; The value of _diffrn_data_frame.center_fast is
the fast index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_data_frame.center_units' along the fast
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement the current setting of detector
positioner given frame are used.
It is important to note that for measurements in millimetres,
the sense of the axis is used, rather than the sign of the
pixel-to-pixel increments.
;
_item.name '_diffrn_data_frame.center_fast'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_data_frame.center_slow
_item_description.description
; The value of _diffrn_data_frame.center_slow is
the slow index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_data_frame.center_units' along the slow
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement the current setting of detector
positioner given frame are used.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
;
_item.name '_diffrn_data_frame.center_slow'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_data_frame.center_units
_item_description.description
; The value of _diffrn_data_frame.center_units
specifies the units in which the values of
'_diffrn_data_frame.center_fast' and
'_diffrn_data_frame.center_slow'
are presented. The default is 'mm' for millimetres. The
alternatives are 'pixels' and 'bins'. In all cases the
center distances are measured from the center of the
first pixel, i.e. in a 2x2 binning, the measuring origin
is offset from the centers of the bins by one half pixel
towards the first pixel.
If 'bins' is specified, the data in
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size', and
'_array_intensities.pixel_binning_method'
is used to define the binning scheme.
;
_item.name '_diffrn_data_frame.center_units'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
mm 'millimetres'
pixels 'detector pixels'
bins 'detector bins'
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.id
_item_description.description
; The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
'_diffrn_scan_frame_monitor.frame_id'
diffrn_scan_frame_monitor
implicit
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
'_diffrn_scan_frame_monitor.frame_id'
'_diffrn_data_frame.id'
save_
save__diffrn_data_frame.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
This is an appropriate location in which to record
information from vendor headers as presented in those
headers, but it should never be used as a substitute
for providing the fully parsed information within
the appropriate imgCIF/CBF categories.
Normally, when a conversion from a miniCBF has been done
the data from '_array_data.header_convention'
should be transferred to this data item and
'_array_data.header_convention'
should be removed.
;
_item.name '_diffrn_data_frame.details'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_frame_data.details'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.4
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
;
HEADER_BYTES = 512;
DIM = 2;
BYTE_ORDER = big_endian;
TYPE = unsigned_short;
SIZE1 = 3072;
SIZE2 = 3072;
PIXEL_SIZE = 0.102588;
BIN = 2x2;
DETECTOR_SN = 901;
TIME = 29.945155;
DISTANCE = 200.000000;
PHI = 85.000000;
OSC_START = 85.000000;
OSC_RANGE = 1.000000;
WAVELENGTH = 0.979381;
BEAM_CENTER_X = 157.500000;
BEAM_CENTER_Y = 157.500000;
PIXEL SIZE = 0.102588;
OSCILLATION RANGE = 1;
EXPOSURE TIME = 29.9452;
TWO THETA = 0;
BEAM CENTRE = 157.5 157.5;
;
; Example of header information extracted from an ADSC Quantum
315 detector header by CBFlib_0.7.6. Image provided by Chris
Nielsen of ADSC from a data collection at SSRL beamline 1-5.
;
save_
save__diffrn_data_frame.variant
_item_description.description
; The value of _diffrn_data_frame.variant gives the variant
to which the given diffrn_data_frame row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_data_frame.variant'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code code
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
'_diffrn_detector.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'slow mode'
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detector(s) used to
measure the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
; The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of
_diffrn_detector.diffrn_id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
'_diffrn_scan_frame_monitor.detector_id'
_diffrn_scan_frame_monitor.detector_id yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
'_diffrn_scan_frame_monitor.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
; The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id.
The word 'positioner' is a general term used in
instrumentation design for devices that are used to change
the positions of portions of apparatus by linear
translation, rotation or combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__diffrn_detector.variant
_item_description.description
; The value of _diffrn_detector.variant gives the variant
to which the given diffrn_detector row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_detector.variant'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_type.code code
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
; Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
'_diffrn_detector_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named _diffrn_detector_axis.id
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_detector_axis.variant
_item_description.description
; The value of _diffrn_detector_axis.variant gives the variant
to which the given diffrn_detector_axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_detector_axis.variant'
_item.category_id diffrn_detector_axis
_item.mandatory_code no
_item_type.code code
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
; Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, giving more detailed information
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
is preferable to simply providing the centre of the
detector element.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
'_diffrn_detector_element.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square, in the pattern
1 2
*
3 4
Note that the beam centre is slightly displaced from each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4. For each element, the detector
face coordiate system, is assumed to have the fast axis
running from left to right and the slow axis running from
top to bottom with the origin at the top left corner.
;
;
loop_
_diffrn_detector_element.detector_id_diffrn_detector_element.id_diffrn_detector_element.reference_center_fast_diffrn_detector_element.reference_center_slow_diffrn_detector_element.reference_center_units
d1 d1_ccd_1 201.5 201.5 mm
d1 d1_ccd_2 -1.8 201.5 mm
d1 d1_ccd_3 201.6 -1.4 mm
d1 d1_ccd_4 -1.7 -1.5 mm
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.id
_item_description.description
; The value of _diffrn_detector_element.id must uniquely
identify each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
; This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_element.reference_center_fast
_item_description.description
; The value of _diffrn_detector_element.reference_center_fast is
the fast index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_detector_element.reference_center_units' along the fast
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value given whould be
representive of the beam center as determined from the ensemble
of settings.
It is important to note that for measurements in millimetres,
the sense of the axis is used, rather than the sign of the
pixel-to-pixel increments.
;
_item.name '_diffrn_detector_element.reference_center_fast'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_detector_element.reference_center_slow
_item_description.description
; The value of _diffrn_detector_element.reference_center_slow is
the slow index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_detector_element.reference_center_units' along the slow
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value givien whould be
representive of the beam center as determined from the ensemble
of settings.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
;
_item.name '_diffrn_detector_element.reference_center_slow'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_detector_element.reference_center_units
_item_description.description
; The value of _diffrn_detector_element.reference_center_units
specifies the units in which the values of
'_diffrn_detector_element.reference_center_fast' and
'_diffrn_detector_element.reference_center_slow'
are presented. The default is 'mm' for millimetres. The
alternatives are 'pixels' and 'bins'. In all cases the
center distances are measured from the center of the
first pixel, i.e. in a 2x2 binning, the measuring origin
is offset from the centers of the bins by one half pixel
towards the first pixel.
If 'bins' is specified, the data in
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size', and
'_array_intensities.pixel_binning_method'
is used to define the binning scheme.
;
_item.name '_diffrn_detector_element.reference_center_units'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
mm 'millimetres'
pixels 'detector pixels'
bins 'detector bins'
save_
save__diffrn_detector_element.variant
_item_description.description
; The value of _diffrn_detector_element.variant gives the variant
to which the given diffrn_detector_element row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_detector_element.variant'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code code
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the
diffraction data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
'_diffrn_measurement.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model X'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector
angle 22.5 degrees
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support
and orient the specimen.
If the value of _diffrn_measurement.device is not given,
it is implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to
measure the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'home-made'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity
measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
; The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during the collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
; The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id.
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
# _diffrn_measurement.sample_detector_distance
# _diffrn_measurement.sample_detector_voffset
save__diffrn_measurement.sample_detector_distance
_item_description.description
; The value of _diffrn_measurement.sample_detector_distance gives
the unsigned distance in millimetres from the sample to the
detector along the beam.
;
_item.name '_diffrn_measurement.sample_detector_distance'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
_item_type.code float
_item_units.code mm
save_
save__diffrn_measurement.sample_detector_voffset
_item_description.description
; The value of _diffrn_measurement.sample_detector_voffset gives
the signed distance in millimetres in the vertical
direction (positive for up) from the center of
the beam to the center of the detector.
;
_item.name '_diffrn_measurement.sample_detector_voffset'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . .
. .
_item_type.code float
_item_units.code mm
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
save__diffrn_measurement.variant
_item_description.description
; The value of _diffrn_measurement.variant gives the variant
to which the given diffrn_measurement row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_measurement.variant'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_type.code code
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
; Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
'_diffrn_measurement_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
; This data item is a pointer to _diffrn_measurement.device
in the DIFFRN_MEASUREMENT category.
;
_item.name
'_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_type.code text
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named _diffrn_measurement_axis.id,
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_measurement_axis.variant
_item_description.description
; The value of _diffrn_measurement_axis.variant gives the variant
to which the given diffrn_measurement_axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_measurement_axis.variant'
_item.category_id diffrn_measurement_axis
_item.mandatory_code no
_item_type.code code
save_
####################
# DIFFRN_RADIATION #
####################
save_DIFFRN_RADIATION
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used for measuring diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
loop_
_category_key.name '_diffrn_radiation.diffrn_id'
'_diffrn_radiation.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions of
photons in the XZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions
of photons in the YZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation degrees^2^ between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
direction of each photon in XZ plane times the deviations
of the direction of the same photon in the YZ plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons, this value is specified in
milliradians^2^, in which case a conversion would be needed.
To go from a value in milliradians^2^ to a value in
degrees^2^, multiply by 0.180^2^ and divide by \p^2^.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in \%Angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a
monochromator crystal is used, the material and the
indices of the Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarization ratio of the diffraction beam incident on the
crystal. This is the ratio of the perpendicularly polarized to
the parallel polarized component of the radiation. The
perpendicular component forms an angle of
_diffrn_radiation.polarisn_norm to the normal to the
diffraction plane of the sample (i.e. the plane containing
the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between
the normal to the polarization plane and the laboratory Y
axis as defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monochromater.
This differs from the value of
_diffrn_radiation.polarisn_norm
in that _diffrn_radiation.polarisn_norm refers to
polarization relative to the diffraction plane rather than
to the laboratory axis system.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane should be taken
as the XZ plane and the angle as 0.
See _diffrn_radiation.polarizn_source_ratio.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared)
of the electric vector in the plane of the normal to the
plane of polarization.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane is to be taken
as the XZ plane and the normal is parallel to the Y axis.
Thus, if there was complete polarization in the plane of
polarization, the value of
_diffrn_radiation.polarizn_source_ratio would be 1, and
for an unpolarized beam
_diffrn_radiation.polarizn_source_ratio would have a
value of 0.
If the X axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of 'MONOCHROMATOR' in the Denzo glossary, and values of near
1 should be expected for a bending-magnet source. However,
if the X axis were perpendicular to the polarization plane
(not a common choice), then the Denzo value would be the
negative of _diffrn_radiation.polarizn_source_ratio.
See http://www.hkl-xray.com for information on Denzo and
Otwinowski & Minor (1997).
This differs both in the choice of ratio and choice of
orientation from _diffrn_radiation.polarisn_ratio, which,
unlike _diffrn_radiation.polarizn_source_ratio, is
unbounded.
Reference: Otwinowski, Z. & Minor, W. (1997). 'Processing of
X-ray diffraction data collected in oscillation mode.' Methods
Enzymol. 276, 307-326.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly
recommended that this be given so that the
probe radiation is clearly specified.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'X-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for the probe
radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to
_diffrn_radiation_wavelength.id in the
DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.category_id diffrn_radiation
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_radiation.variant
_item_description.description
; The value of _diffrn_radiation.variant gives the variant
to which the given diffrn_radiation row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_radiation.variant'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code code
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
; This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
Data items in the DIFFRN_REFLN category record details about
the intensities in the diffraction data set
identified by _diffrn_refln.diffrn_id.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in the particular diffraction
data set identified by _diffrn_reflns.diffrn_id and
_diffrn_refln.frame_id
;
;
_category.id diffrn_refln
_category.mandatory_code no
loop_
_category_key.name '_diffrn_refln.diffrn_id'
'_diffrn_refln.id'
'_diffrn_refln.frame_id'
'_diffrn_refln.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
; This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_refln.variant
_item_description.description
; The value of _diffrn_refln.variant gives the variant
to which the given diffrn_refln row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_refln.variant'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
; Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
loop_
_category_key.name '_diffrn_scan.id'
'_diffrn_scan.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. In this example, three rotation axes and one translation axis
at nonzero values are specified, with one axis stepping. There is no
reason why more axes could not have been specified to step. Range
information has been specified, but note that it can be calculated from
the number of frames and the increment, so the data item
_diffrn_scan_axis.angle_range could be dropped.
Both the sweep data and the data for a single frame are specified.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
_diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
_diffrn_scan_frame.integration_time and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustments are made to
scan times and nonlinear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.angle_increment_diffrn_scan_frame_axis.displacement_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
; Example 2 - a more extensive example (R. M. Sweet, P. J. Ellis &
H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the goniometer.
This leads to a choice: either the axes of
the detector are defined at the origin, and then a Z setting of -240
is entered, or the axes are defined with the necessary Z offset.
In this case, the setting is used and the offset is left as zero.
This axis is called DETECTOR_Z.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm X 0.150mm, the centre of the first pixel is at (0.075,
0.075) in this coordinate system.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.displacement_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
; Example 3 - Example 2 revised for a spiral scan (R. M. Sweet,
P. J. Ellis & H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the
goniometer, as in Example 2 above, but in this example the
image plate is scanned in a spiral pattern from the outside edge in.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. The rotation axis is called ELEMENT_ROT and the
radial axis is called ELEMENT_RAD. A 150 micrometre radial pitch
and a 75 micrometre 'constant velocity' angular pitch are assumed.
Indexing is carried out first on the rotation axis and the radial axis
is made to be dependent on it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.angle_array_structure_list_axis.displacement_array_structure_list_axis.angular_pitch_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
; The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
; The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
; Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
_diffrn_scan_frame.integration_time, even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
; The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frame_id_end
_item_description.description
; The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frames
_item_description.description
; The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
save__diffrn_scan.variant
_item_description.description
; The value of _diffrn_scan.variant gives the variant
to which the given diffrn_scan row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan.variant'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code code
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
; Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
'_diffrn_scan_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
; The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.angle_start
_item_description.description
; The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
; The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
; The increment for each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_increment. The
sum of the values of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
; The increment after each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_rstrt_incr. The
sum of the values of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment
and _diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.angle for this
next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
; The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
; The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_increment.
The sum of the values of
_diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_rstrt_incr.
The sum of the values of
_diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.displacement
for this next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_angle.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_angle will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_angle (e.g.
the mean).
If not specified, the value defaults to zero.
;
_item.name '_diffrn_scan_axis.reference_angle'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_displacement.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_displacement will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_displacement (e.g.
the mean).
If not specified, the value defaults to to the value of
_diffrn_scan_axis.displacement.
;
_item.name '_diffrn_scan_axis.reference_displacement'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.variant
_item_description.description
; The value of _diffrn_scan_axis.variant gives the variant
to which the given diffrn_scan_axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_axis.variant'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_type.code code
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
; Data items in the DIFFRN_SCAN_FRAME category describe
the relationships of particular frames to scans.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
'_diffrn_scan_frame.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
; The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame.frame_number
_item_description.description
; The value of this data item is the number of the frame
within the scan, starting with 1. It is not necessarily
the same as the value of _diffrn_scan_frame.frame_id,
but it may be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
; The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of _diffrn_scan.integration_time.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame.variant
_item_description.description
; The value of _diffrn_scan_frame.variant gives the variant
to which the given diffrn_scan_frame row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_frame.variant'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code code
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
; Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the
settings of axes for particular frames. Unspecified axes are
assumed to be at their zero points. If, for any given frame,
nonzero values apply for any of the data items in this category,
those values should be given explicitly in this category and not
simply inferred from values in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
'_diffrn_scan_frame_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
; The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
; The increment for this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
; The increment after this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment and
_diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.angle for this next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.displacement for this next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be zero.
;
_item.name '_diffrn_scan_frame_axis.reference_angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be equal to
_diffrn_scan_frame_axis.displacement.
;
_item.name '_diffrn_scan_frame_axis.reference_displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.variant
_item_description.description
; The value of _diffrn_scan_frame_axis.variant gives the variant
to which the given diffrn_scan_frame_axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_frame_axis.variant'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_type.code code
save_
#############################
# DIFFRN_SCAN_FRAME_MONITOR #
#############################
save_DIFFRN_SCAN_FRAME_MONITOR
_category.description
; Data items in the DIFFRN_SCAN_FRAME_MONITOR category record
the values and details about each monitor for each frame of data
during a scan.
Each monitor value is uniquely identified by the combination of
the scan_id given by _diffrn_scan_frame.scan_id
the frame_id given by _diffrn_scan_frame_monitor.frame_id,
the monitor's detector_id given by
_diffrn_scan_frame_monitor.monitor_id,
and a 1-based ordinal given by _diffrn_scan_frame_monitor.id.
If there is only one frame for the scan, the value of
_diffrn_scan_frame_monitor.frame_id may be
omitted.
A single frame may have more than one monitor value, and each
monitor value may be the result of integration over the entire
frame integration time given by the value of
_diffrn_scan_frame.integration_time
or many monitor values may be reported over shorter times given
by the value of _diffrn_scan_frame_monitor.integration_time. If
only one monitor value for a given monitor is collected during
the integration time of the frame, the value of
_diffrn_scan_frame_monitor.id may be
omitted.
;
_category.id diffrn_data_frame_monitor
_category.mandatory_code no
loop_
_category_key.name '_diffrn_scan_frame_monitor.id'
'_diffrn_scan_frame_monitor.detector_id'
'_diffrn_scan_frame_monitor.scan_id'
'_diffrn_data_frame_monitor.frame_id'
'_diffrn_data_frame_monitor.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - The beam intensity for frame FRAME1 is being tracked
by a beamstop monitor detector BSM01, made from metal foil and
a PIN diode, locate 20 mm in front of a MAR345 detector and being
sampled every 2 seconds in a 20 second scan.
;
;
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
P6MB BSM01 'metal foil and PIN diode' 1
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
BSM01 MONITOR_Z
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
SCAN1 MONITOR_Z 0.0 0.0 0.0 -220.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_MONITOR
loop_
_diffrn_scan_frame_monitor.id_diffrn_scan_frame_monitor.detector_id_diffrn_scan_frame_monitor.scan_id_diffrn_data_frame_monitor.frame_id_diffrn_data_frame_monitor.integration_time_diffrn_data_frame_monitor.monitor_value
1 BSM01 SCAN1 FRAME1 2.0 23838345642
2 BSM01 SCAN1 FRAME1 2.0 23843170669
3 BSM01 SCAN1 FRAME1 2.0 23839478690
4 BSM01 SCAN1 FRAME1 2.0 23856642085
5 BSM01 SCAN1 FRAME1 2.0 23781717656
6 BSM01 SCAN1 FRAME1 2.0 23788850775
7 BSM01 SCAN1 FRAME1 2.0 23815576677
8 BSM01 SCAN1 FRAME1 2.0 23789299964
9 BSM01 SCAN1 FRAME1 2.0 23830195536
10 BSM01 SCAN1 FRAME1 2.0 23673082270
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
FRAME1 MONITOR_Z 0.0 -220.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
MONITOR_Z translation detector . 0 0 1 0 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan_frame_monitor.id
_item_description.description
; This item is an integer identifier which, along with
_diffrn_scan_frame_monitor.detector_id,
_diffrn_scan_frame_monitor.scan_id, and
_diffrn_data_frame_monitor.frame_id
should uniquely identify the monitor value being recorded
If _array_data.binary_id is not explicitly given,
it defaults to 1.
;
loop_
_item.name _diffrn_scan_frame_monitor.id
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code implicit
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__diffrn_scan_frame_monitor.detector_id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_scan_frame_monitor.detector_id'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_monitor.frame_id
_item_description.description
; This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_monitor.frame_id'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_monitor.integration_time
_item_description.description
; The precise time for integration of the monitor value given in
_diffrn_scan_frame_monitor.value
must be given in _diffrn_scan_frame_monitor.integration_time.
;
_item.name '_diffrn_scan_frame_monitor.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame_monitor.value
_item_description.description
; The value reported by the monitor detector should be given in
_diffrn_scan_frame_monitor.value.
The value is typed as float to allow of monitors for very intense beams
that cannot report all digits, but when available, all digits of the
monitor should be recorded.
;
_item.name '_diffrn_scan_frame_monitor.value'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame_monitor.variant
_item_description.description
; The value of _diffrn_scan_frame_monitor.variant gives the variant
to which the given diffrn_scan_frame_monitor row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_frame_monitor.variant'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code no
_item_type.code code
save_
#######
# MAP #
#######
save_MAP
_category.description
; Data items in the MAP category record
the details of a maps. Maps record values of parameters,
such as density, that are functions of position within
a cell or are functions of orthogonal coordinates in
three space.
A map may is composed of one or more map segments
specified in the MAP_SEGMENT category.
Examples are given in the MAP_SEGMENT category.
;
_category.id map
_category.mandatory_code no
loop_
_category_key.name '_map.id'
'_map.diffrn_id'
'_map.entry_id'
'_map.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'map_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.details
_item_description.description
; The value of _map.details should give a
description of special aspects of each map.
;
_item.name '_map.details'
_item.category_id map
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.diffrn_id
_item_description.description
; This item is a pointer to _diffrn.id in the
DIFFRN category.
;
_item.name '_map.diffrn_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.entry_id
_item_description.description
; This item is a pointer to _entry.id in the
ENTRY category.
;
_item.name '_map.entry_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.id
_item_description.description
; The value of _map.id must uniquely identify
each map for the given diffrn.id or entry.id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map.id' map yes
'_map_segment.id' map_segment yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_segment.id' '_map.id'
save_
save__map.variant
_item_description.description
; The value of _map.variant gives the variant
to which the given map row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_map.variant'
_item.category_id map
_item.mandatory_code no
_item_type.code code
save_
###############
# MAP_SEGMENT #
###############
save_MAP_SEGMENT
_category.description
; Data items in the MAP_SEGMENT category record
the details about each segment (section or brick) of a map.
;
_category.id map_segment
_category.mandatory_code no
loop_
_category_key.name '_map_segment.id'
'_map_segment.map_id'
'_map_segment.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'map_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map, each consisting of one
segment, both using the same array structure
and mask.
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
loop_
_map_segment.map_id
_map_segment.id
_map_segment.array_id
_map_segment.binary_id
_map_segment.mask_array_id
_map_segment.mask_binary_id
rho_calc rho_calc map_structure 1 mask_structure 1
rho_obs rho_obs map_structure 2 mask_structure 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map_segment.array_id
_item_description.description
; The value of _map_segment.array_id identifies the array
structure into which the map is organized.
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.array_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code code
save_
save__map_segment.binary_id
_item_description.description
; The value of _map_segment.binary_id distinguishes the particular
set of data organized according to _map_segment.array_id in
which the data values of the map are stored.
This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.mask_array_id
_item_description.description
; The value of _map_segment.mask_array_id, if given, the array
structure into which the mask for the map is organized. If no
value is given, then all elements of the map are valid. If a
value is given, then only elements of the map for which the
corresponding element of the mask is non-zero are valid. The
value of _map_segment.mask_array_id differs from the value of
_map_segment.array_id in order to permit the mask to be given
as, say, unsigned 8-bit integers, while the map is given as
a data type with more range. However, the two array structures
must be aligned, using the same axes in the same order with the
same displacements and increments
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.mask_array_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code code
save_
save__map_segment.mask_binary_id
_item_description.description
; The value of _map_segment.mask_binary_id identifies the
particular set of data organized according to
_map_segment.mask_array_id specifying the mask for the map.
This item is a pointer to _array_data.mask_binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.mask_binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.id
_item_description.description
; The value of _map_segment.id must uniquely
identify each segment of a map.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map_segment.id'
map_segment
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_data_frame.map_segment_id'
'_map_segment.id'
save_
save__map_segment.map_id
_item_description.description
; This item is a pointer to _map.id
in the MAP category.
;
_item.name '_map_segment.map_id'
_item.category_id map_segment
_item.mandatory_code yes
_item_type.code code
save_
save__map_segment.details
_item_description.description
; The value of _map_segment.details should give a
description of special aspects of each segment of a map.
;
_item.name '_map_segment.details'
_item.category_id map_segment
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
; Example to be provided
;
;
;
save_
save__map_segment.variant
_item_description.description
; The value of _map_segment.variant gives the variant
to which the given map segment is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_map_segment.variant'
_item.category_id map_segment
_item.mandatory_code no
_item_type.code code
save_
###########
# VARIANT #
###########
save_VARIANT
_category.description
; Data items in the VARIANT category record
the details about sets of variants of data items.
There is sometimes a need to allow for multiple versions of the
same data items in order to allow for refinements and corrections
to earlier assumptions, observations and calculations. In order
to allow data sets to contain more than one variant of the same
information, an optional ...variant data item as a pointer to
_variant.variant has been added to the key of every category,
as an implicit data item with a null (empty) default value.
All rows in a category with the same variant value are considered
to be related to one another and to all rows in other categories
with the same variant value. For a given variant, all such rows
are also considered to be related to all rows with a null variant
value, except that a row with a null variant value is for which
all other components of its key are identical to those entries
in another row with a non-null variant value is not related the
the rows with that non-null variant value. This behavior is
similar to the convention for identifying alternate conformers
in an atom list.
An optional role may be specified for a variant as the value of
_variant.role. Possible roles are null, "preferred",
"raw data", "unsuccessful trial".
Variants may carry an optional timestamp as the value of
_variant.timestamp.
Variants may be related to other variants from which they were
derived by the value of _variant.variant_of
Further details about the variant may be specified as the value
of _variant.details.
In order to allow variant information from multiple datasets to
be combined, _variant.diffrn_id and/or _variant.entry_id may
be used.
;
_category.id variant
_category.mandatory_code no
loop_
_category_key.name '_variant.variant'
'_variant.diffrn_id'
'_variant.entry_id'
loop_
_category_group.id 'inclusive_group'
'variant_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Distinguishing between a raw beam center and a refined beam
center inferred after indexing. Detector d1 is composed of
four CCD detector elements, each 200 mm by 200 mm, arranged
in a square, in the pattern
1 2
*
3 4
Note that the beam centre is slightly displaced from each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4. For each element, the detector
face coordiate system, is assumed to have the fast axis
running from left to right and the slow axis running from
top to bottom with the origin at the top left corner.
After indexing and refinement, the center is shifted by .2 mm
left and .1 mm down.
;
;
loop_
_variant.variant
_variant.role
_variant.timestamp
_variant.variant_of
_variant.details
. "raw data" 2007-08-03T23:20:00 . .
indexed "preferred" 2007-08-04T01:17:28 .
"indexed cell and refined beam center"
loop_
_diffrn_detector_element.detector_id_diffrn_detector_element.id_diffrn_detector_element.reference_center_fast_diffrn_detector_element.reference_center_slow_diffrn_detector_element.reference_center_units_diffrn_detector_element.variant
d1 d1_ccd_1 201.5 201.5 mm .
d1 d1_ccd_2 -1.8 201.5 mm .
d1 d1_ccd_3 201.6 -1.4 mm .
d1 d1_ccd_4 -1.7 -1.5 mm .
d1 d1_ccd_1 201.3 201.6 mm indexed
d1 d1_ccd_2 -2.0 201.6 mm indexed
d1 d1_ccd_3 201.3 -1.5 mm indexed
d1 d1_ccd_4 -1.9 -1.6 mm indexed
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__variant.details
_item_description.description
; A description of special aspects of the variant.
;
_item.name '_variant.details'
_item.category_id variant
_item.mandatory_code no
_item_type.code text
_item_examples.case
; indexed cell and refined beam center
;
save_
save__variant.role
_item_description.description
; The value of _variant.role specified a role
for this variant. Possible roles are null, "preferred",
"raw data", and "unsuccessful trial".
;
_item.name '_variant.role'
_item.category_id variant
_item.mandatory_code no
_item_type.code uline
loop_
_item_enumeration.value
_item_enumeration.detail
.
; A null value for _variant.role leaves the precise role of
the variant unspecified. No inference should be made that the variant
with the latest time stamp is preferred.
;
"preferred"
; A value of "preferred" indicates that rows of any categories specifying
this variant should be used in preference to rows with the same key
specifying other variants or the null variant. It is an error to specify
two variants that appear in the same category with the same key as being
preferred, but it is not an error to specify more than one variant as
preferred in other cases.
;
"raw data"
; A value of "raw data" indicates data prior to any corrections,
calculations or refinements. It is not necessarily an error for raw data
to also be a variant of an earlier variant. It may be replacement raw
data for earlier data believed to be erroneous.
;
"unsuccessful trial"
; A value of "unsuccessful trial" indicates data that should not be used
for further calculation.
;
save_
save__variant.timestamp
_item_description.description
; The date and time identifying a variant. This is not
necessarily the precise time of the measurement or calculation
of the individual related data items, but a timestamp that
reflects the order in which the variants were defined.
;
_item.name '_variant.timestamp'
_item.category_id variant
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__variant.variant
_item_description.description
; The value of _variant.variant must uniquely identify
each variant for the given diffraction experiment and/or entry
This item has been made implicit and given a default value of
null.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_variant.variant' variant implicit
'_variant.variant_of' variant implicit
'_array_data.variant' array_data implicit
'_array_element_size.variant' array_element_size implicit
'_array_intensities.variant' array_intensities implicit
'_array_structure.variant' array_structure implicit
'_array_structure_list.variant' array_structure_list
implicit
'_array_structure_list_axis.variant' array_structure_list_axis
implicit
'_axis.variant' axis implicit
'_diffrn_data_frame.variant' diffrn_data_frame implicit
'_diffrn_detector.variant' diffrn_detector implicit
'_diffrn_detector_axis.variant' diffrn_detector_axis
implicit
'_diffrn_detector_element.variant' diffrn_detector_element
implicit
'_diffrn_measurement.variant' diffrn_measurement implicit
'_diffrn_measurement_axis.variant' diffrn_measurement_axis
implicit
'_diffrn_radiation.variant' diffrn_radiation implicit
'_diffrn_refln.variant' diffrn_refln implicit
'_diffrn_scan.variant' diffrn_scan implicit
'_diffrn_scan_axis.variant' diffrn_scan_axis implicit
'_diffrn_scan_frame.variant' diffrn_scan_frame implicit
'_diffrn_scan_frame_axis.variant' diffrn_scan_frame_axis
implicit
'_diffrn_scan_frame_monitor.variant' diffrn_scan_frame_monitor
implicit
'_map.variant' map implicit
'_map_segment.variant' map_segment implicit
_item_default.value .
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.variant' '_variant.variant'
'_array_data.variant_of' '_variant.variant'
'_array_element_size.variant' '_variant.variant'
'_array_intensities.variant' '_variant.variant'
'_array_structure.variant' '_variant.variant'
'_array_structure_list.variant' '_variant.variant'
'_array_structure_list_axis.variant' '_variant.variant'
'_axis.variant' '_variant.variant'
'_diffrn_data_frame.variant' '_variant.variant'
'_diffrn_detector.variant' '_variant.variant'
'_diffrn_detector_axis.variant' '_variant.variant'
'_diffrn_detector_element.variant' '_variant.variant'
'_diffrn_measurement.variant' '_variant.variant'
'_diffrn_measurement_axis.variant' '_variant.variant'
'_diffrn_radiation.variant' '_variant.variant'
'_diffrn_refln.variant' '_variant.variant'
'_diffrn_scan.variant' '_variant.variant'
'_diffrn_scan_axis.variant' '_variant.variant'
'_diffrn_scan_frame.variant' '_variant.variant'
'_diffrn_scan_frame_axis.variant' '_variant.variant'
'_diffrn_scan_frame_monitor.variant' '_variant.variant'
'_map.variant' '_variant.variant'
'_map_segment.variant' '_variant.variant'
save_
save__variant.variant_of
_item_description.description
; The value of _variant.variant_of gives the variant
from which this variant was derived. If this value is not given,
the variant is assumed to be derived from the default null
variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_variant.variant_of'
_item.category_id variant
_item.mandatory_code no
_item_type.code code
save_
######################## DEPRECATED DATA ITEMS ########################
save__diffrn_detector_axis.id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_detector_axis.id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_element.center[1]
_item_description.description
; The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
Because of ambiguity about the setting used to determine this
center, use of this data item is deprecated. The data item
_diffrn_data_frame.center_fast
which is referenced to the detector coordinate system and not
directly to the laboratory coordinate system should be used
instead.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
; The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
Because of ambiguity about the setting used to determine this
center, use of this data item is deprecated. The data item
_diffrn_data_frame.center_slow
which is referenced to the detector coordinate system and not
directly to the laboratory coordinate system should be used
instead.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_measurement_axis.id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_measurement_axis.id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
######################### DEPRECATED CATEGORY #########################
#####################
# DIFFRN_FRAME_DATA #
#####################
save_DIFFRN_FRAME_DATA
_category.description
; Data items in the DIFFRN_FRAME_DATA category record
the details about each frame of data.
The items in this category are now in the
DIFFRN_DATA_FRAME category.
The items in the DIFFRN_FRAME_DATA category
are now deprecated. The items from this category
are provided as aliases in the 1.0 dictionary
or, in the case of _diffrn_frame_data.details,
in the 1.4 dictionary. THESE ITEMS SHOULD NOT
BE USED FOR NEW WORK.
The items from the old category are provided
in this dictionary for completeness
but should not be used or cited. To avoid
confusion, the example has been removed
and the redundant parent-child links to other
categories have been removed.
;
_category.id diffrn_frame_data
_category.mandatory_code no
loop_
_category_key.name '_diffrn_frame_data.id'
'_diffrn_frame_data.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
THE DIFFRN_FRAME_DATA category is deprecated and should not be used.
;
;
# EXAMPLE REMOVED #
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_frame_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.array_id'
_item.category_id diffrn_frame_data
_item.mandatory_code implicit
_item_type.code code
save_
save__diffrn_frame_data.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.binary_id'
_item.category_id diffrn_frame_data
_item.mandatory_code implicit
_item_type.code int
save_
save__diffrn_frame_data.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.detector_element_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.id
_item_description.description
; The value of _diffrn_frame_data.id must uniquely identify
each complete frame of data.
DEPRECATED -- DO NOT USE
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_frame_data.id' diffrn_frame_data yes
_item_type.code code
save_
save__diffrn_frame_data.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.details'
_item.category_id diffrn_frame_data
_item.mandatory_code no
_item_type.code text
save_
################ END DEPRECATED SECTION ###########
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive) ...
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items (case insensitive)...
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
point numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9]?[0-9]\
((T[0-2][0-9](:[0-5][0-9](:[0-5][0-9](.[0-9]+)?)?)?)?\
([+-][0-5][0-9]:[0-5][0-9]))?
;
;
Standard format for CIF date and time strings (see
http://www.iucr.org/iucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character 'T' followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
decimal fraction on the seconds of time.
Time is local time if no time-zone offset is given.
Note that this type extends the mmCIF yyyy-mm-dd type
but does not conform to the mmCIF yyyy-mm-dd:hh:mm
type that uses a ':' in place if the 'T' specified
by the IUCr standard. For reading, both forms should
be accepted, but for writing, only the IUCr form should
be used.
For maximal compatibility, the special time zone
indicator 'Z' (for 'zulu') should be accepted on
reading in place of '+00:00' for GMT.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2)^)'
'millimetres' 'millimetres (metres * 10^( -3)^)'
'nanometres' 'nanometres (metres * 10^( -9)^)'
'angstroms' '\%Angstroms (metres * 10^(-10)^)'
'picometres' 'picometres (metres * 10^(-12)^)'
'femtometres' 'femtometres (metres * 10^(-15)^)'
#
'reciprocal_metres' 'reciprocal metres (metres^(-1)^)'
'reciprocal_centimetres'
'reciprocal centimetres ((metres * 10^( -2)^)^(-1)^)'
'reciprocal_millimetres'
'reciprocal millimetres ((metres * 10^( -3)^)^(-1)^)'
'reciprocal_nanometres'
'reciprocal nanometres ((metres * 10^( -9)^)^(-1)^)'
'reciprocal_angstroms'
'reciprocal \%Angstroms ((metres * 10^(-10)^)^(-1)^)'
'reciprocal_picometres'
'reciprocal picometres ((metres * 10^(-12)^)^(-1)^)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9)^)^2^'
'angstroms_squared' '\%Angstroms squared (metres * 10^(-10)^)^2^'
'8pi2_angstroms_squared'
'8\p^2^ * \%Angstroms squared (metres * 10^(-10)^)^2^'
'picometres_squared' 'picometres squared (metres * 10^(-12)^)^2^'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9)^)^3^'
'angstroms_cubed' '\%Angstroms cubed (metres * 10^(-10)^)^3^'
'picometres_cubed' 'picometres cubed (metres * 10^(-12)^)^3^'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^( -9)^)^(-3)^)
;
'electrons_per_angstroms_cubed'
; electrons per \%Angstroms cubed (electrons/(metres * 10^(-10)^)^(-3)^)
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (electrons/(metres * 10^(-12)^)^(-3)^)
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'pixels_per_element' '(image) pixels per (array) element'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.6.3 2010-08-26
; Cummulative corrections from 1.6.0, 1, 2 drafts (HJB)
+ Move descriptive dictionary comments into
_datablock.description with catgeory tree described
+ add default _array_data.array_id value of 1
+ add option of CBF_BACKGROUND_OFFSET_DELTA compression
+ add VARIANT catgeory and tags
+ add DIFFRN_SCAN_FRAME_MONITOR category
;
1.5.4 2007-07-28
; Typographics corrections (HJB)
+ Corrected embedded degree characters to \%
+ Corrected embedded Aring to \%A
+ Added trailing ^ for a power
+ Removed 2 cases of a space after an underscore
in tag name.
;
1.5.3 2007-07-08
; Changes to support SLS miniCBF and suggestions
from the 24 May 07 BNL imgCIF workshop (HJB)
+ Added new data items
'_array_data.header_contents',
'_array_data.header_convention',
'_diffrn_data_frame.center_fast',
'_diffrn_data_frame.center_slow',
'_diffrn_data_frame.center_units',
'_diffrn_measurement.sample_detector_distance',
'_diffrn_measurement.sample_detector_voffset
+ Deprecated data items
'_diffrn_detector_element.center[1]',
'_diffrn_detector_element.center[2]'
+ Added comments and example on miniCBF
+ Changed all array_id data items to implicit
;
1.5.2 2007-05-06
; Further clarifications of the coordinate system. (HJB)
;
1.5.1 2007-04-26
; Improve defintion of X-axis to cover the case of no goniometer
and clean up more line folds (HJB)
;
1.5 2007-07-25
; This is a cummulative list of the changes proposed since the
imgCIF workshop in Hawaii in July 2006. It is the result
of contributions by H. J. Bernstein, A. Hammersley,
J. Wright and W. Kabsch.
2007-02-19 Consolidated changes (edited by HJB)
+ Added new data items
'_array_structure.compression_type_flag',
'_array_structure_list_axis.fract_displacement',
'_array_structure_list_axis.displacement_increment',
'_array_structure_list_axis.reference_angle',
'_array_structure_list_axis.reference_displacement',
'_axis.system',
'_diffrn_detector_element.reference_center_fast',
'_diffrn_detector_element.reference_center_slow',
'_diffrn_scan_axis.reference_angle',
'_diffrn_scan_axis.reference_displacement',
'_map.details', '_map.diffrn_id',
'_map.entry_id', '_map.id',
'_map_segment.array_id', '_map_segment.binary_id',
'_map_segment.mask_array_id', '_map_segment.mask_binary_id',
'_map_segment.id', '_map_segment.map_id',
'_map_segment.details.
+ Change type of
'_array_structure.byte_order' and
'_array_structure.compression_type'
to ucode to make these values case-insensitive
+ Add values 'packed_v2' and 'byte_offset' to enumeration of values for
'_array_structure.compression_type'
+ Add to definitions for the binary data type to handle new compression
types, maps, and a variety of new axis types.
2007-07-25 Cleanup of typos for formal release (HJB)
+ Corrected text fields for reference_ tag descriptions that
were off by one column
+ Fix typos in comments listing fract_ tags
+ Changed name of release from 1.5_DRAFT to 1.5
+ Fix unclosed text fields in various map definitions
;
1.4 2006-07-04
; This is a change to reintegrate all changes made in the course of
publication of ITVG, by the RCSB from April 2005 through
August 2008 and changes for the 2006 imgCIF workshop in
Hawaii.
2006-07-04 Consolidated changes for the 2006 imgCIF workshop (edited by HJB)
+ Correct type of '_array_structure_list.direction' from 'int' to 'code'.
+ Added new data items suggested by CN
'_diffrn_data_frame.details'
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size and
'_array_intensities.pixel_binning_method
+ Added deprecated item for completeness
'_diffrn_frame_data.details'
+ Added entry for missing item in contents list
'_array_structure_list_axis.displacement'
+ Added new MIME type X-BASE32K based on work by VL, KM, GD, HJB
+ Correct description of MIME boundary delimiter to start in
column 1.
+ General cleanup of text fields to conform to changes for ITVG
by removing empty lines at start and finish of text field.
+ Amend example for ARRAY_INTENSITIES to include binning.
+ Add local copy of type specification (as 'code') for all children
of '_diffrn.id'.
+ For consistency, change all references to 'pi' to '\p' and all
references to 'Angstroms' to '\%Angstroms'.
+ Clean up all powers to use IUCr convention of '^power^', as in
'10^3^' for '10**3'.
+ Update 'yyyy-mm-dd' type regex to allow truncation from the right
and improve comments to explain handling of related mmCIF
'yyyy-mm-dd:hh:mm' type, and use of 'Z' for GMT time zone.
2005-03-08 and
2004-08-08 fixed cases where _item_units.code used
instead of _item_type.code (JDW)
2004-04-15 fixed item ordering in
_diffrn_measurement_axis.measurement_id
added sub_category 'vector' (JDW)
;
1.3.2 2005-06-25
; 2005-06-25 ITEM_TYPE_LIST: code, ucode, line, uline regexps updated
to those of current mmCIF; float modified by allowing integers
terminated by a point as valid. The 'time' part of
yyyy-mm-dd types made optional in the regexp. (BM)
2005-06-17 Minor corrections as for proofs for IT G Chapter 4.6
(NJA)
2005-02-21 Minor corrections to spelling and punctuation
(NJA)
2005-01-08 Changes as per Nicola Ashcroft.
+ Updated example 1 for DIFFRN_MEASUREMENT to agree with mmCIF.
+ Spelled out "micrometres" for "um" and "millimetres" for "mm".
+ Removed phrase "which may be stored" from ARRAY_STRUCTURE
description.
+ Removed unused 'byte-offsets' compressions and updated
cites to ITVG for '_array_structure.compression_type'.
(HJB)
;
1.3.1 2003-08-13
;
Changes as per Frances C. Bernstein.
+ Identify initials.
+ Adopt British spelling for centre in text.
+ Set \p and \%Angstrom and powers.
+ Clean up commas and unclear wordings.
+ Clean up tenses in history.
Changes as per Gotzon Madariaga.
+ Fix the ARRAY_DATA example to align '_array_data.binary_id'
and X-Binary-ID.
+ Add a range to '_array_intensities.gain_esd'.
+ In the example of DIFFRN_DETECTOR_ELEMENT,
'_diffrn_detector_element.id' and
'_diffrn_detector_element.detector_id' interchanged.
+ Fix typos for direction, detector and axes.
+ Clarify description of polarisation.
+ Clarify axes in '_diffrn_detector_element.center[1]'
'_diffrn_detector_element.center[2]'.
+ Add local item types for items that are pointers.
(HJB)
;
1.3.0 2003-07-24
;
Changes as per Brian McMahon.
+ Consistently quote tags embedded in text.
+ Clean up introductory comments.
+ Adjust line lengths to fit in 80 character window.
+ Fix several descriptions in AXIS category which
referred to '_axis.type' instead of the current item.
+ Fix erroneous use of deprecated item
'_diffrn_detector_axis.id' in examples for
DIFFRN_SCAN_AXIS.
+ Add deprecated items '_diffrn_detector_axis.id'
and '_diffrn_measurement_axis.id'.
(HJB)
;
1.2.4 2003-07-14
;
Changes as per I. David Brown.
+ Enhance descriptions in DIFFRN_SCAN_AXIS to make them less
dependent on the descriptions in DIFFRN_SCAN_FRAME_AXIS.
+ Provide a copy of the deprecated DIFFRN_FRAME_DATA
category for completeness.
(HJB)
;
1.2.3 2003-07-03
;
Cleanup to conform to ITVG.
+ Correct sign error in ..._cubed units.
+ Correct '_diffrn_radiation.polarisn_norm' range.
(HJB)
;
1.2.2 2003-03-10
;
Correction of typos in various DIFFRN_SCAN_AXIS descriptions.
(HJB)
;
1.2.1 2003-02-22
;
Correction of ATOM_ for ARRAY_ typos in various descriptions.
(HJB)
;
1.2 2003-02-07
;
Corrections to encodings (remove extraneous hyphens) remove
extraneous underscore in '_array_structure.encoding_type'
enumeration. Correct typos in items units list. (HJB)
;
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB.
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li.
;
1.1.1 2001-02-16
;
Several typo corrections by JW.
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS. (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME.
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to
'_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source',
'_diffrn_radiation.polarizn_source_norm',
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add '_diffrn_measurement.device' to category key.
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to
allow for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up. (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes. (JW)
+ Correct spelling of diffrn_measurement_axis in '_axis.id'
+ Correct ordering of uses of '_item.mandatory_code' and
'_item_default.value'.
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown. (HJB)
+ Add further comments on '\n' and '\t'.
+ Update ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Change 'meter' to 'metre' throughout.
+ Add missing enumerations to '_array_structure.compression_type'
and make 'none' the default.
+ Remove parent-child relationship between
'_array_structure_list.index' and '_array_structure_list.precedence'.
+ Improve alphabetization.
+ Fix '_array_intensities_gain.esd' related function.
+ Improve comments in AXIS.
+ Fix DIFFRN_FRAME_DATA example.
+ Remove erroneous DIFFRN_MEASUREMENT example.
+ Add '_diffrn_measurement_axis.id' to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data. (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors. (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for '_diffrn_scan.id' definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header. (HJB)
+ Restore '_diffrn_detector.diffrn_id' to DIFFRN_DETECTOR KEY.
+ Add AXIS category.
+ Bring in complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
from cif_mm.dic for clarity.
+ Change '_array_structure.encoding_type' from type code to uline and
added X-Binary-Element-Type to MIME header.
+ Add detector beam centre '_diffrn_detector_element.center[1]' and
'_diffrn_detector_element.center[2]'.
+ Correct item name of '_diffrn_refln.frame_id'.
+ Replace reference to '_array_intensities.undefined' by
'_array_intensities.undefined_value'.
+ Replace references to '_array_intensity.scaling' with
'_array_intensities.scaling'.
+ Add DIFFRN_SCAN... categories.
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft. (HJB)
+ Reflow comment lines over 80 characters and corrected typos.
+ Update examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF. (HJB)
+ Add binary type, which is a text field containing a variant on
MIME encoded data.
+ Change type of '_array_data.data' to binary and specify internal
structure of raw binary data.
+ Add '_array_data.binary_id', and make
'_diffrn_frame_data.binary_id' and '_array_intensities.binary_id'
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft. (JW)
+ Add category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes are made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA is renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE is renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for '_diffrn_frame_data.array_id' is changed from
'_array_structure_list.array_id' to '_array_structure.id'. Item
'_diffrn_detector.array_id' is deleted.
+ Add data item '_diffrn_frame_data.binary_id' to identify data
groups within a binary section. The formal identification of the
binary section is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version is adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley
(AH).
Modifications to the CBF draft. (JW)
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories
have been generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category
ARRAY_DATA. This departs from the CBF notion of data existing
in some special comment. In this description, data are handled as an
ordinary data item encapsulated in a character data type. Although
data this manner deviates from CIF conventions, it does not violate
any DDL 2.1 rules. DDL 2.1 regular expressions can be used to define
the binary representation which will permit some level of data
validation. In this version, the placeholder type code "any" has
been used. This translates to a regular expression which will match
any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary.
It may be possible to use the DDL 2.1 ITEM_STRUCTURE and
ITEM_STRUCTURE_LIST categories to provide the information that is
carried in by the ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By
moving the array structure to the DDL level it would be possible to
define an array type as well as a regular expression defining the
data format.
+ Multiple array sections can be properly handled within a single
datablock.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.2.3 #
# of 2001-07-04 #
# by Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook #
# #
# This dictionary was adapted from the imgCIF Workshop, held at BNL Oct 1997#
# and the Crystallographic Binary File Format Draft Proposal by Andy #
# Hammersley. The first DDL 2.1 Version was created by John Westbrook. #
# This version was drafted by Herbert J. Bernstein and incorporates comments #
# by I. David Brown, John Westbrook, Brian McMahon, Bob Sweet, Paul Ellis, #
# Harry Powell, Wilfred Li and others. #
##############################################################################
data_cif_img.dic
_dictionary.title cif_img.dic
_dictionary.version 1.2.3
_dictionary.datablock_id cif_img.dic
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.gain
# _array_intensities.gain_esd
# _array_intensities.linearity
# _array_intensities.offset
# _array_intensities.scaling
# _array_intensities.overload
# _array_intensities.undefined_value
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.encoding_type
# _array_structure.id
#
# category ARRAY_STRUCTURE_LIST
#
# _array_structure_list.axis_set_id
# _array_structure_list.array_id
# _array_structure_list.dimension
# _array_structure_list.direction
# _array_structure_list.index
# _array_structure_list.precedence
#
# category ARRAY_STRUCTURE_LIST_AXIS
#
# _array_structure_list_axis.axis_id
# _array_structure_list_axis.axis_set_id
# _array_structure_list_axis.angle
# _array_structure_list_axis.angle_increment
# _array_structure_list_axis.displacement_increment
# _array_structure_list_axis.angular_pitch
# _array_structure_list_axis.radial_pitch
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.type
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
#
# category DIFFRN_DATA_FRAME
#
# _diffrn_data_frame.array_id
# _diffrn_data_frame.binary_id
# _diffrn_data_frame.detector_element_id
# _diffrn_data_frame.id
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.id
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.axis_id
# _diffrn_detector_axis.detector_id
#
# category DIFFRN_DETECTOR_ELEMENT
#
# _diffrn_detector_element.center[1]
# _diffrn_detector_element.center[2]
# _diffrn_detector_element.id
# _diffrn_detector_element.detector_id
#
# category DIFFRN_MEASUREMENT
#
# _diffrn_measurement.diffrn_id
# _diffrn_measurement.details
# _diffrn_measurement.device
# _diffrn_measurement.device_details
# _diffrn_measurement.device_type
# _diffrn_measurement.id
# _diffrn_measurement.method
# _diffrn_measurement.number_of_axes
# _diffrn_measurement.specimen_support
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.axis_id
# _diffrn_measurement_axis.measurement_device
# _diffrn_measurement_axis.measurement_id
#
# category DIFFRN_RADIATION
#
# _diffrn_radiation.collimation
# _diffrn_radiation.diffrn_id
# _diffrn_radiation.div_x_source
# _diffrn_radiation.div_y_source
# _diffrn_radiation.div_x_y_source
# _diffrn_radiation.filter_edge'
# _diffrn_radiation.inhomogeneity
# _diffrn_radiation.monochromator
# _diffrn_radiation.polarisn_norm
# _diffrn_radiation.polarisn_ratio
# _diffrn_radiation.polarizn_source_norm
# _diffrn_radiation.polarizn_source_ratio
# _diffrn_radiation.probe
# _diffrn_radiation.type
# _diffrn_radiation.xray_symbol
# _diffrn_radiation.wavelength_id
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.date_end
# _diffrn_scan.date_start
# _diffrn_scan.integration_time
# _diffrn_scan.frame_id_start
# _diffrn_scan.frame_id_end
# _diffrn_scan.frames
#
# category DIFFRN_SCAN_AXIS
#
# _diffrn_scan_axis.axis_id
# _diffrn_scan_axis.angle_start
# _diffrn_scan_axis.angle_range
# _diffrn_scan_axis.angle_increment
# _diffrn_scan_axis.angle_rstrt_incr
# _diffrn_scan_axis.displacement_start
# _diffrn_scan_axis.displacement_range
# _diffrn_scan_axis.displacement_increment
# _diffrn_scan_axis.displacement_rstrt_incr
# _diffrn_scan_axis.scan_id
#
# category DIFFRN_SCAN_FRAME
#
# _diffrn_scan_frame.date
# _diffrn_scan_frame.frame_id
# _diffrn_scan_frame.frame_number
# _diffrn_scan_frame.integration_time
# _diffrn_scan_frame.scan_id
#
# category DIFFRN_SCAN_FRAME_AXIS
#
# _diffrn_scan_frame_axis.axis_id
# _diffrn_scan_frame_axis.angle
# _diffrn_scan_frame_axis.angle_increment
# _diffrn_scan_frame_axis.angle_rstrt_incr
# _diffrn_scan_frame_axis.displacement
# _diffrn_scan_frame_axis.displacement_increment
# _diffrn_scan_frame_axis.displacement_rstrt_incr
# _diffrn_scan_frame_axis.frame_id
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
;
Data items in the ARRAY_DATA category are the containers for
the array data items described in category ARRAY_STRUCTURE.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and
presented as hexadecimal data. The first character "H" on the
data lines means hexadecimal. It could have been "O" for octal
or "D" for decimal. The second character on the line shows
the number of bytes in each word (in this case "4"), which then
requires 8 hexadecimal digits per word. The third character
gives the order of octets within a word, in this case "<"
for the ordering 4321 (i.e. "big-endian"). Alternatively the
character ">" could have been used for the ordering 1234
(i.e. "little-endian"). The block has a "message digest"
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id_array_data.binary_id_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 1
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-Id, these values should be equal.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
"--CIF-BINARY-FORMAT-SECTION--" (including the
required initial "--").
The Content-Type may be any of the discrete types permitted
in RFC 2045; "application/octet-stream" is recommended.
If an octet stream was compressed, the compression should
be specified by the parameter 'conversions="x-CBF_PACKED"'
or the parameter 'conversions="x-CBF_CANONICAL"'.
The Content-Transfer-Encoding may be "BASE64",
"Quoted-Printable", "X-BASE8", "X-BASE10", or
"X-BASE16" for an imgCIF or "BINARY" for a CBF. The
octal, decimal and hexadecimal transfer encodings are
for convenience in debugging, and are not recommended
for archiving and data interchange.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In a CBF, the
raw binary data begins after an empty line terminating
the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of
the message size, nor in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. An adjustment is made for
the deprecated binary formats in which 8 bytes of binary
header are used for the compression type. In that case,
the 8 bytes used for the compression type is subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is "unsigned 32-bit integer".
An MD5 message digest may, optionally, be used. The "RSA Data
Security, Inc. MD5 Message-Digest Algorithm" should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is "X-BASE8", "X-BASE10", or
"X-BASE16", the data is presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ("big-
endian") or 1234... (little-endian). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as "==" for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is "H", "O", or "D" for hexadecimal, octal or
decimal, n is the number of octets per word. and d is "<"
for ">" for the "...4321" and "1234..." octet orderings
respectively. The "==" padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hex, octal and decimal formats, only, comments
beginning with "#" are permitted to improve readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three, c1, c2, c3. The resulting 24 bits
are broken into four 6-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order 4 bits of the second octet ((c1 & 3)<<4 | (c2>>4)),
then the bottom 4 bits of the second octet followed by the
high order two bits of the last octet ((c2 & 15)<<2 | (c3>>6)),
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
With short groups of octets padded on the right with one "="
if c3 is missing, and with "==" if both c2 and c3 are missing.
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32..38,
42, 48..57, 59..60, 62, 64..126 and the octet is not a ";"
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
"wrapped" with a terminating "=" (i.e. the MIME conventions
for an implicit line terminator are never used).
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
;
Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.index
_item_description.description
;
This item is a pointer to _array_structure_list.index in the
ARRAY_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
;
The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
;
Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The actual detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
'_array_intensities.gain'. If raw, uncorrected values
are presented (e.g for calibration experiments), the
value of '_array_intensities.linearity' will be 'raw'
and '_array_intensities.gain' will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id_array_intensities.linearity_array_intensities.gain_array_intensities.overload_array_intensities.undefined_value
image_1 linear 1.2 655535 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
;
Detector "gain". The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
;
The estimated standard deviation in detector "gain".
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
;
The intensity linearity scaling used from raw intensity
to the stored element value:
'linear' is obvious
'offset' means that the value defined by
'_array_intensities.offset' should be added to each
element value.
'scaling' means that the value defined by
'_array_intensities.scaling' should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by '_array_intensities.scaling' is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
'logarithmic_scaled' means that the logarithm based 10 of
raw intensities multiplied by '_array_intensities.scaling'
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and calculating 10
to the power of this number.
'raw' means that the data is the raw is a set of raw values
straight from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
;
The value defined by '_array_intensities.offset' should
be added to each element value.
;
'scaling'
;
The value defined by '_array_intensities.scaling' should be
multiplied with each element value.
;
'scaling_offset'
;
The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
;
The square root of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
;
'logarithmic_scaled'
;
The logarithm based 10 of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
'_array_intensities.scaling' and calculating 10 to the
power of this number.
;
'raw'
;
The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
;
Offset value to add to array element values in the manner
described by item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.scaling
_item_description.description
;
Multiplicative scaling value to be applied to array data
in the manner described by item _array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
;
The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.undefined_value
_item_description.description
;
A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
;
Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data which may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
_category_key.name '_array_structure.id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
;
The order of bytes for integer values which require more
than 1-byte.
(IBM-PC's and compatibles, and Dec-Vaxes use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. Dec-Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
;
The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
;
The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
;
Type of data compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code code
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'none'
;
Data are stored in normal format as defined by
'_array_structure.encoding_type' and
'_array_structure.byte_order'.
;
'byte_offsets'
;
Using the compression scheme defined in CBF definition
Section 5.0.
;
'packed'
;
Using the 'packed' compression scheme, a CCP4-style packing
(CBFlib section 3.3.2)
;
'canonical'
;
Using the 'canonical' compression scheme (CBFlib section
3.3.1)
;
save_
save__array_structure.encoding_type
_item_description.description
;
Data encoding of a single element of array data.
In several cases, the IEEE format is referenced.
See "IEEE Standard for Binary Floating-Point Arithmetic",
ANSI/IEEE Std 754-1985, the Institute of Electrical and
Electronics Engineers, Inc., NY 1985.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure yes
'_array_data.array_id' array_data yes
'_array_structure_list.array_id' array_structure_list yes
'_array_intensities.array_id' array_intensities yes
'_diffrn_data_frame.array_id' diffrn_data_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
;
Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left-to-right (increasing) in
first dimension and bottom-to-top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differ
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the "poise" of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
;
The number of elements stored in the array structure in this
dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
;
Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
;
Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
;
Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
;
Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
;
Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
;
Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axis, one for the angular
direction, one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
'_array_structure_list_axis.axis_set_id'
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
;
The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id .
This item is a pointer to _array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
save_
save__array_structure_list_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of '_array_structure_list.axis_set_id'. If the index is
specified as 'increasing' this will be the center of the
pixel with index value 1. If the index is specified as
'decreasing' this will be the center of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
;
The pixel-center-to-pixel-center increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified in that case.
See '_array_structure_list_axis.angular_pitch'.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
;
The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of '_array_structure_list.axis_set_id'. If the index is
specified as 'increasing' this will be the center of the
pixel with index value 1. If the index is specified as
'decreasing' this will be the center of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
;
The pixel-center-to-pixel-center increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
;
The pixel-center-to-pixel-center distance for a one step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans,
or for uncoupled angular scans at a constant radius
(cylindrical scan) and should not be specified for cases
in which the angle between pixels, rather than the distance
between pixels is uniform.
See '_array_structure_list_axis.angle_increment'.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
;
The radial distance from one "cylinder" of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of '_array_structure_list_axis.displacement_increment'.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
########
# AXIS #
########
save_AXIS
_category.description
;
Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection. The location of each
axis is specified by two vectors: the axis itself, given as a unit
vector, and an offset to the base of the unit vector. These vectors
are referenced to a right-handed laboratory coordinate system with
its origin in the sample or specimen:
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
These axes are based on the goniometer, not on the orientation of the
detector, gravity, etc. The vectors necessary to specify all other
axes are given by sets of three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to, but significantly
different from the choice in MOSFLM (Andrew G.W. Leslie, Harry Powell,
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH,UK
http://www.dl.ac.uk/CCP/CCP4/dist/x-windows/Mosflm/). In MOSFLM,
X is along the X-ray beam (our Z axis) and Z is along the rotation axis.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam center.
The location of the beam center on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected mm from the (0,0) corner
of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, we need to specify the
location of the beam center on the detector in terms of the origin of the
detector, which is, of course, not coincident with the center of the
sample.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows the axis specification of the axes of a kappa
geometry goniometer (See "X-Ray Structure Determination, A Practical
Guide", 2nd ed. by G. H. Stout, L. H. Jensen, Wiley Interscience,
1989, 453 pp, p 134.).
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X-axis. The next innermost axis, kappa,
is at a 50 degree angle to the X-axis, pointed away from the source.
The innermost axis, phi, aligns with the X-axis when omega and
phi are at their zero-points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
x' = (T-omega) (T-kappa) (T-phi) x
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
This example show the axis specification of the axes of a
detector, source and gravity. We have juggled the order as a
reminder that the ordering of presentation of tokens is not
significant. We have taken the center of rotation of the detector
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.type specifies the next outermost
axis upon which this axis depends.
This item is a pointer to axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.type specifies the type of equipment
using the axis: goniometer, detector, gravity, source
or general
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so that the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: rotation, translation (or general when the type is
not relevant, as for gravity)
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
;
Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases, but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element is
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id
;
;
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0.00
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
;
This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.id
_item_description.description
;
The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Need new example here.
;
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detectors used to measure
the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
;
The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of _diffrn_detector.diffrn_id
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
;
The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id
The word "positioner" is a general term used in instrumentation
design for devices that are used to change the positions of
portions of apparatus by linear translation, rotation, or
combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
;
Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
;
This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named '_diffrn_detector_axis.id'
which is now a deprecated name. The old name is
provided as an alias, but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
;
Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, the more detailed information provided
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
are preferable to simply providing the centre.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square. in the pattern
1 2
*
3 4
Note that the beam center is slightly off of each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4.
;
;
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id_diffrn_detector_element.center[1]_diffrn_detector_element.center[2]
d1 d1_ccd_1 201.5 -1.5
d1 d1_ccd_2 -1.8 -1.5
d1 d1_ccd_3 201.6 201.4
d1 d1_ccd_4 -1.7 201.5
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.center[1]
_item_description.description
;
The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
;
The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.id
_item_description.description
;
The value of _diffrn_detector_element.id must uniquely identify
each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
;
This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the diffraction
data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model x'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; Need new example here
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support and
orient the specimen.
If the value of _diffrn_measurement.device is not given, it is
implicitly equal to the value of _diffrn_measurement.diffrn_id
Either '_diffrn_measurement.device' or '_diffrn_measurement.id'
may be used to link to other categories. If the experimental
setup admits multiple devices, then '_diffrn_measurement.id'
is used to provide a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to measure
the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'homemade'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
;
The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of _diffrn_measurement.diffrn_id
Either '_diffrn_measurement.device' or '_diffrn_measurement.id'
may be used to link to other categories. If the experimental
setup admits multiple devices, then '_diffrn_measurement.id'
is used to provide a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
;
The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
;
Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
;
This data item is a pointer to _diffrn_measurement.device in
the DIFFRN_MEASUREMENT category.
;
_item.name '_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
;
This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named '_diffrn_measurement_axis.id'
which is now a deprecated name. The old name is
provided as an alias, but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0.00
_item.mandatory_code implicit
save_
####################
# DIFFRN_RADIATION #
####################
save_DIFFRN_RADIATION
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used in measuring diffraction intensities,
its collimation and monochromatisation before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
_category_key.name '_diffrn_radiation.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the esd of the directions of photons in the X-Z plane
around the mean source beam direction.
Note that some synchrotrons specify this value in milliradians,
in which case a conversion would be needed. To go from a
value in milliradians to a value in degrees, multiply by 0.180
and divide by Pi.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the esd of the directions of photons in the Y-Z plane
around the mean source beam direction.
Note that some synchrotrons specify this value in milliradians,
in which case a conversion would be needed. To go from a
value in milliradians to a value in degrees, multiply by 0.180
and divide by Pi.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation degrees**2 between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
directin of each photons in X-Z plane times the deviations
of the direction of the same photon in the Y-Z plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons specify this value in
milliradians**2, in which case a conversion would be needed.
To go from a value in milliradians**2 to a value in
degrees**2, multiply by 0.180**2 and divide by Pi**2.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a mono-
chromator crystal is used the material and the indices of the
Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarisation and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarisation ratio of the diffraction beam incident on the
crystal. It is the ratio of the perpendicularly polarised to the
parallel polarised component of the radiation. The perpendicular
component forms an angle of _diffrn_radiation.polarisn_norm to
the normal to the diffraction plane of the sample (i.e. the
plane containing the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
normal to the polarization plane and the laboratory Y axis as
defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monchromater.
This differs from the value of '_diffrn_radiation.polarisn_norm'
in that '_diffrn_radiation.polarisn_norm' refers to polarization
relative to the diffraction plane rather than to the laboratory
axis system.
In the case of an unpolarized beam, or a beam with true circular
polarization, in which no single plane of polarization can be
determined, the plane should be taken as the X-Z plane, and the
angle as 0.
See '_diffrn_radiation.polarizn_source_ratio'.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity (amplitude squared)
of the electric vector in the plane of polarization and In is
the intensity (amplitude squared) of the electric vector
in plane of the normal to the plane of polarization.
Thus, if we had complete polarization in the plane of
polarization, the value of
'_diffrn_radiation.polarizn_source_ratio' would
be 1, and an unpolarized beam would have a value of 0.
If the X-axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of "MONOCHROMATOR" in the Denzo glossary, and values of near
1 should be expected for a bending magnet source. However,
if the X-axis were, for some reason to be, say, perpendicular
to the polarization plane (not a common choice), then the
Denzo value would be the negative of
'_diffrn_radiation.polarizn_source_ratio'.
See http://www.hkl-xray.com for information on Denzo, and
Z. Otwinowski and W. Minor, " Processing of X-ray Diffraction
Data Collected in Oscillation Mode ", Methods in Enzymology,
Volume 276: Macromolecular Crystallography, part A, p.307-326,
1997,C.W. Carter, Jr. & R. M. Sweet, Eds., Academic Press.
This differs both in the choice of ratio and choice of
orientation from '_diffrn_radiation.polarisn_ratio', which,
unlike '_diffrn_radiation.polarizn_source_ratio', is unbounded.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly encouraged
that this field be specified so that the probe radiation
can be simply determined.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'x-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for probe radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to _diffrn_radiation_wavelength.id
in the DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.mandatory_code yes
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
;
This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
;
_category.id diffrn_refln
_category.mandatory_code no
_category_key.name '_diffrn_refln.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
;
This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
;
Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
_category_key.name '_diffrn_scan.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. We have specified three rotation axes and one translation axis
at non-zero values, with one axis stepping. There is no reason why
more axes could not have been specified to step. We have specified
range information, but note that it is redundant from the number of
frames and the increment, so we could drop the data item
_diffrn_scan_axis.angle_range .
We have specified both the sweep data and the data for a single frame.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
'_diffrn_scan.integration_time' and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
'_diffrn_scan_frame.integration_time' and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustements are made to
scan times and non-linear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.angle_increment_diffrn_scan_frame_axis.displacement_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
;
Example 2 - a more extensive example, R. M. Sweet, P. Ellis, H. Bernstein.
We place a detector 240 mm along the Z axis from the goniometer.
This presents us with a choice -- either we define the axes of
the detector at the origin, and then put a Z setting of -240 in
for the actual use, or we define the axes with the necessary Z-offset.
In this case we use the setting, and leave the offset as zero.
We call this axis DETECTOR_Z.
The axis for positioning the detector in the Y-direction depends
on the detector Z-axis. We call this axis, DETECTOR_Y.
The axis for positioning the dector in the X-direction depends
on the detector Y-axis (and therefore on the detector Z-axis).
We call this axis DETECTOR_X.
This detector may be rotated around the Y-axis. This rotation axis
depends on the three translation axies. We call it DETECTOR_PITCH.
We define a coordinate system on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm x 0.150mm, the center of the first pixel is at (0.075,
0.075) in this coordinate system.
;
;
###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.displacement_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
;
Example 3 - Example 2 revised for a spiral scan, R. M. Sweet,
P. Ellis, H. Bernstein.
We place a detector 240 mm along the Z axis from the goniometer,
as in Example 2, above, but in this example, the image plate is
scanned in a spiral pattern outside edge in.
The axis for positioning the detector in the Y-direction depends
on the detector Z-axis. We call this axis, DETECTOR_Y.
The axis for positioning the dector in the X-direction depends
on the detector Y-axis (and therefore on the detector Z-axis).
We call this axis DETECTOR_X.
This detector may be rotated around the Y-axis. This rotation axis
depends on the three translation axies. We call it DETECTOR_PITCH.
We define a coordinate system on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. Let us call rotation axis ELEMENT_ROT, and the
radial axis ELEMENT_RAD. We assume 150 um radial pitch and 75 um
'constant velocity' angular pitch.
We index first on the rotation axis and make the radial axis
dependent on
it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
;
###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.angle_array_structure_list_axis.displacement_array_structure_list_axis.angular_pitch_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
;
The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
;
The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
;
Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
'_diffrn_scan_frame.integration_time', even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
;
The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frame_id_end
_item_description.description
;
The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frames
_item_description.description
;
The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
;
The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
'_diffrn_scan.id'.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
'_diffrn_scan.id'.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.angle_start
_item_description.description
;
The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
;
The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
;
The increment for each step for the specified axis
in degrees. In general, this will agree with
'_diffrn_scan_frame_axis.angle_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
;
The increment after each step for the specified axis
in degrees. In general, this will agree with
'_diffrn_scan_frame_axis.angle_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
;
The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
;
The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
;
The increment for each step for the specified axis
in millimetres. In general, this will agree with
'_diffrn_scan_frame_axis.displacement_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
;
The increment for each step for the specified axis
in millimetres. In general, this will agree with
'_diffrn_scan_frame_axis.displacement_rstrt_incr', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
;
Data items in the DIFFRN_SCAN_FRAME category describe
the relationship of particular frames to scans.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
;
The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
save__diffrn_scan_frame.frame_number
_item_description.description
;
The value of this data item is the number of the frame within
the scan, starting with 1. It is not necessarily the same as
the value of _diffrn_scan_frame.frame_id, but may
be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
;
The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of '_diffrn_scan.integration_time'.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the settings
of axes for particular frames. Unspecified axes are assumed to be at
their zero points. If, for any given frame, non-zero values apply
for any of the data items in this category, those values should be
given explicitly in this category and not simply inferred from values
in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
;
The increment for this frame for angular setting of
the specified axis in degrees. The sum of the values
of '_diffrn_scan_frame_axis.angle' and
'_diffrn_scan_frame_axis.angle_increment' is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
;
The increment after this frame for angular setting of
the specified axis in degrees. The sum of the values
of '_diffrn_scan_frame_axis.angle' and
'_diffrn_scan_frame_axis.angle_increment' and
'_diffrn_scan_frame_axis.angle_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame, and should equal
'_diffrn_scan_frame_axis.angle' for that next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
;
The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
;
The increment for this frame for displacement setting of
the specified axis in millimetres. The sum of the values
of '_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
;
The increment for this frame for displacement setting of
the specified axis in millimetres. The sum of the values
of '_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' and
'_diffrn_scan_frame_axis.displacement_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame, and should equal
'_diffrn_scan_frame_axis.displacement' for that next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id .
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive)
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items (case insensitive)
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]\
(T[0-2][0-9]:[0-5][0-9]:[0-5][0-9](.[0-9]+)([+-][0-5][0-9]:[0-5][0-9]))
;
;
Standard format for CIF date and time strings (see
http://www.iucr.orgiucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character "T" followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
decimal fraction on the seconds of time.
Time is local time if no time-zone offset is given.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2))'
'millimetres' 'millimetres (metres * 10^( -3))'
'nanometres' 'nanometres (metres * 10^( -9))'
'angstroms' 'angstroms (metres * 10^(-10))'
'picometres' 'picometres (metres * 10^(-12))'
'femtometres' 'femtometres (metres * 10^(-15))'
#
'reciprocal_metres' 'reciprocal metres (metres^(-1))'
'reciprocal_centimetres' 'reciprocal centimetres ((metres * 10^( -2))^(-1))'
'reciprocal_millimetres' 'reciprocal millimetres ((metres * 10^( -3))^(-1))'
'reciprocal_nanometres' 'reciprocal nanometres ((metres * 10^( -9))^(-1))'
'reciprocal_angstroms' 'reciprocal angstroms ((metres * 10^(-10))^(-1))'
'reciprocal_picometres' 'reciprocal picometres ((metres * 10^(-12))^(-1))'
'reciprocal_metres' 'reciprocal metres (metres * 10^-1)'
'reciprocal_centimetres' 'reciprocal centimetres (metres * 10^( -2)^-1)'
'reciprocal_millimetres' 'reciprocal millimetres (metres * 10^( -3)^-1)'
'reciprocal_nanometres' 'reciprocal nanometres (metres * 10^( -9)^-1)'
'reciprocal_angstroms' 'reciprocal angstroms (metres * 10^(-10)^-1)'
'reciprocal_picometres' 'reciprocal picometres (metres * 10^(-12)^-1)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9))^2'
'angstroms_squared' 'angstroms squared (metres * 10^(-10))^2'
'8pi2_angstroms_squared' '8pi^2 * angstroms squared (metres * 10^(-10))^2'
'picometres_squared' 'picometres squared (metres * 10^(-12))^2'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9))^3'
'angstroms_cubed' 'angstroms cubed (metres * 10^(-10))^3'
'picometres_cubed' 'picometres cubed (metres * 10^(-12))^3'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^( -9))^(-3))
;
'electrons_per_angstroms_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^(-10))^(-3));
;
'electrons_per_picometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^(-12))^(-3));
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.2.3 2003-07-03
;
Cleanup to conform to ITVG.
+ Correct sign error in ..._cubed units.
+ Correct '_diffrn_radiation.polarisn_norm' range.
(HJB)
;
1.2.2 2003-03-10
;
Correction of typos in various DIFFRN_SCAN_AXIS descriptions.
(HJB)
;
1.2.1 2003-02-22
;
Correction of ATOM_ for ARRAY_ typos in various descriptions.
(HJB)
;
1.2 2003-02-07
;
Corrections to encodings (remove extraneous hyphens) remove
extraneous underscore in _array_structure.encoding_type
enumeration. Correct typos in items units list.
(HJB)
;
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li
;
1.1.1 2001-02-16
;
Several typo corrections by JW
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to '_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source', '_diffrn_radiation.polarizn_source_norm',
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add _diffrn_measurement.device to category key
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to allow
for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes (JW)
+ Correct spelling of diffrn_measurement_axis in _axis.id
+ Correct ordering of uses of _item.mandatory_code and _item_default.value
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown (HJB)
+ Added further comments on '\n' and '\t'
+ Updated ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Changed all spelling 'meter' to 'metre' throughout.
+ Added missing enumerations to _array_structure.compression_type
and made 'none' the default.
+ Removed parent-child relationship between _array_structure_list.index
and _array_structure_list.precedence .
+ Improve alphabetization.
+ Fix _array_intensities_gain.esd related function.
+ Improved comments in AXIS.
+ Fixed DIFFRN_FRAME_DATA example.
+ Removed erroneous DIFFRN_MEASUREMENT example.
+ Added _diffrn_measurement_axis.id to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for _diffrn_scan.id definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header (HJB)
+ Restored _diffrn_detector.diffrn_id to DIFFRN_DETECTOR KEY.
+ Added AXIS category.
+ Brought complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
in from cif_mm.dic for clarity.
+ changed _array_structure.encoding_type from type code to uline and
added X-Binary-Element-Type to MIME header.
+ added detector beam center _diffrn_detector_element.center[1] and
_diffrn_detector_element.center[2]
+ corrected item name of _diffrn_refln.frame_id
+ replace reference to _array_intensities.undefined by
_array_intensities.undefined_value
+ replace references to _array_intensity.scaling with
_array_intensities.scaling
+ added DIFFRN_SCAN... categories
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft (HJB)
+ Reflowed comment lines over 80 characters and corrected typos.
+ Updated examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF (HJB)
+ Added binary type, which is a text field containing a variant on
MIME encoded data.
+ Changed type of _array_data.data to binary and specified internal
structure of raw binary data.
+ Added _array_data.binary_id, and made
_diffrn_frame_data.binary_id and _array_intensities.binary_id
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft (JW):
+ Added category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes were made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA was renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE was renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for _diffrn_frame_data.array_id was changed from
array_structure_list.array_id to array_structure.id. Item
_diffrn_detector.array_id was deleted.
+ Added data item _diffrn_frame_data.binary_id to identify data groups
within a binary section. The formal identification of the binary section
is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version was adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley (AH).
Modifications to the CBF draft (JW):
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories have been
generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category ARRAY_DATA .
This departs from the CBF notion of data existing in some special comment.
In this description, data is handled as an ordinary data item encapsulated
in a character data type. Although handling binary data this manner
deviates from CIF conventions, it does not violate any DDL 2.1 rules.
DDL 2.1 regular expressions can be used to define the binary
representation which will permit some level of data validation. In
this version, the placeholder type code "any" has been used.
This translates to a regular expression which will match any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary. It
may be possible to use the DDL 2.1 ITEM_STRUCTURE and ITEM_STRUCTURE_LIST
categories to provide the information that is carried in by the
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By moving the array
structure to the DDL level it would be possible to define an array
type as well as a regular expression defining the data format.
+ Multiple array sections can be properly handled within a single datablock.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
./CBFlib-0.9.2.2/doc/CBFlib.txt 0000644 0000765 0000765 00001215111 11603702115 014167 0 ustar yaya yaya CBFlib
An API for CBF/imgCIF
Crystallographic Binary Files with ASCII Support
Version 0.9.2
12 February 2011
by
Paul J. Ellis
Stanford Synchrotron Radiation Laboratory
and
Herbert J. Bernstein
Bernstein + Sons
yaya at bernstein-plus-sons dot com
(c) Copyright 2006, 2007, 2008, 2011 Herbert J. Bernstein
----------------------------------------------------------------------
YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL.
ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS OF THE
LGPL.
----------------------------------------------------------------------
Before using this software, please read the
NOTICE
for important disclaimers and the IUCr Policy on the Use of the Crystallographic
Information File (CIF) and for other important information.
Work on imgCIF and CBFlib supported in part by the U. S. Department of
Energy (DOE) under grants ER63601-1021466-0009501 and
ER64212-1027708-0011962, by the U. S. National Science Foundation (NSF)
under grants DBI-0610407, DBI-0315281 and EF-0312612, the U. S. National
Institutes of Health (NIH) under grants 1R15GM078077 from NIGMS and
1R13RR023192 from NCRR and funding from the International Union for
Crystallographyn (IUCr). The content is solely the responsibility of the
authors and does not necessarily represent the official views of DOE, NSF,
NIH, NIGMS, NCRR or IUCr.
----------------------------------------------------------------------
Version History
Version Date By Description
0.1 Apr. 1998 PJE This was the first CBFlib release.
It supported binary CBF files using
binary strings.
0.2 Aug. 1998 HJB This release added ascii imgCIF
support using MIME-encoded binary
sections, added the option of MIME
headers for the binary strings was
well. MIME code adapted from mpack
1.5. Added hooks needed for DDL1-style
names without categories.
0.3 Sep. 1998 PJE This release cleaned up the changes
made for version 0.2, allowing
multi-threaded use of the code, and
removing dependence on the mpack
package.
0.4 Nov. 1998 HJB This release merged much of the
message digest code into the general
file reading and writing to reduce the
number of passes. More consistency
checking between the MIME header and
the binary header was introduced. The
size in the MIME header was adjusted
to agree with the version 0.2
documentation.
0.5 Dec. 1998 PJE This release greatly increased the
speed of processing by allowing for
deferred digest evaluation.
0.6 Jan. 1999 HJB This release removed the redundant
information (binary id, size,
compression id) from a binary header
when there is a MIME header, removed
the unused repeat argument, and made
the memory allocation for buffering
and tables with many rows sensitive to
the current memory allocation already
used.
0.6.1 Feb. 2001 HP (per This release fixed a memory leak due
HJB) to misallocation by size of cbf_handle
instead of cbf_handle_struct
0.7 Mar. 2001 PJE This release added high-level
instructions based on the imgCIF
dictionary version 1.1.
0.7.1 Mar. 2001 PJE The high-level functions were
revised to permit future expansion to
files with multiple images.
0.7.2 Apr. 2001 HJB This release adjusted cbf_cimple.c
to conform to cif_img.dic version
1.1.3
0.7.2.1 May 2001 PJE This release corrected an if nesting
error in the prior mod to
cbf_cimple.c.
0.7.3 Oct. 2002 PJE This release modified cbf_simple.c
to reorder image data on read so that
the indices are always increasing in
memory (this behavior was undefined
previously).
0.7.4 Jan 2004 HJB This release fixes a parse error for
quoted strings, adds code to get and
set character string types, and
removes compiler warnings
0.7.5 Apr 2006 HJB This release cleans up some compiler
warnings, corrects a parse error on
quoted strings with a leading blank as
adds the new routines for support of
aliases, dictionaries and real arrays,
higher level routines to get and set
pixel sizes, do cell computations, and
to set beam centers, improves support
for conversion of images, picking up
more data from headers.
0.7.6 Jul 2006 HJB This release reorganizes the kit
into two pieces:
CBFlib_0.7.6_Data_Files and
CBFlib_0.7.6. An optional local copy
of getopt is added. The 1.4 draft
dictionary has been added. cif2cbf
updated to support vcif2 validation.
convert_image and cif2cbf updated to
report text of error messages.
convert_image updated to support tag
and category aliases, default to adxv
images. convert_image and img updated
to support row-major images. Support
added for binning. API Support added
for validation, wide files and line
folding. Logic changed for beam center
reporting. Added new routines:
cbf_validate, cbf_get_bin_sizes,
cbf_set_bin_sizes,
cbf_find_last_typed_child,
cbf_compose_itemname,
cbf_set_cbf_logfile,
cbf_make_widefile, cbf_read_anyfile,
cbf_read_widefile,
cbf_write_local_file,
cbf_write_widefile, cbf_column_number,
cbf_blockitem_number, cbf_log,
cbf_check_category_tags,
cbf_set_beam_center
0.7.7 February 2007 HJB This release reflects changes for
base 32K support developed by G.
Darakev, and changes for support of
reals, 3d arrays, byte_offset
compression and J. P. Abrahams packed
compression made in consultation with
(in alphabetic order) E. Eikenberry,
A. Hammerley, W. Kabsch, M. Kobas, J.
Wright and others at PSI and ESRF in
January 2007, as well accumulated
changes fixing problems in release
0.7.6.
0.7.7.1 February 2007 HJB This release is a patch to 0.7.7 to
change the treatment of the byteorder
parameter from strcpy semantics to
return of a pointer to a string
constant. Our thanks to E. Eikenberry
for pointing out the problem.
0.7.7.2 February 2007 HJB This release is a patch to 0.7.7.1
to add testing for JPA packed
compression and to respect signs
declared in the MIME header.
0.7.7.3 April 2007 HJB This release is a patch to 0.7.7.3
to add f90 support for reading of CBF
byte-offset and packed compression, to
fix problems with gcc 4.4.1 and to
correct errors in multidimensional
packed compression.
0.7.7.4 May 2007 HJB Corrects in handling SLS detector
mincbfs and reorder dimensions versus
arrays for some f90 compilers as per
H. Powell.
0.7.7.5 May 2007 HJB Fix to cbf_get_image for bug
reported by F. Remacle, fixes for
windows builds as per J. Wright and F.
Remacle.
0.7.7.6 Jun 2007 HJB Fix to CBF byte-offset compression
writes, fix to Makefiles and m4 for
f90 test programs to allow adjustable
record length.
0.7.8 Jul 2007 HJB Release for full support of SLS data
files with updated convert_minicbf,
and support for gfortran from gcc 4.2.
0.7.8.1 Jul 2007 HJB Update to 0.7.8 release to fix
memory leaks reported by N. Sauter and
to update validation checks for recent
changes.
0.7.8.2 Dec 2007 CN, HJB Update to 0.7.8.1 to add ADSC jiffie
by Chris Nielsen, and to add ..._fs
and ..._sf macros.
0.7.9 Dec 2007 CN, HJB Identical to 0.7.8.2 except for a
cleanup of deprecated examples, e.g.
diffrn_frame_data
0.7.9.1 Jan 2008 CN, HJB Update to 0.7.8.2 to add inverse
ADSC jiffie by Chris Nielsen, to clean
up problems in handling maps for
RasMol.
0.8.0 Jul 2008 GT, HJB Cleanup of 0.7.9.1 to start 0.8
series.
0.8.1 Jul 2009 EZ, CN, Release with EZ's 2008 DDLm support
PC, GW, using JH's PyCifRW, also cbff f95
JH, HJB wrapper code, PC's java bindings.
0.9.1 Aug 2010 PC, EE, Release with EE's Dectris template
JLM, NS, software, also with vcif3, new
EZ, HJB arvai_test, sequence_match.
0.9.2 Feb 2011 PC, EE, New default release with updated
JLM, NS, pycbf, tiff support, removal of
EZ, HJB default use of PyCifRW to avoid Fedora
license issue.
----------------------------------------------------------------------
Known Problems
The example program tiff2cbf needs the enviroment variable LD_LIBRARY_PATH
set to the location of the lib directory in CBFlib_0.9.2, unless a system
install of tiff-3.9.4-rev-6Feb11 has been done.
Due to license issues, PyCifRW is not included with default releases of
CBFlib. Users can download PyCifRW separately.
There are some issues with Peter Chang's lastest java wrapper under the
CBFlib 0.9.2 release. Until they are resolved, the CBFlib 0.8.1 release
should be used for Java applications.
This version does not have support for predictor compression.
Code is needed to support array sub-sections.
Foreword
In order to work with CBFlib, you need:
* the source code, in the form of a "gzipped" tar, CBFlib_0.9.2.tar.gz;
and
* the test data:
* CBFlib_0.9.2_Data_Files_Input.tar.gz (17 MB) a "gzipped" tar of
the input data files needed to test the API;
* CBFlib_0.9.2_Data_Files_Output.tar.gz (36 MB) a "gzipped" tar of
the output data files needed to test the API, or, if space is at
a premium;
* CBFlib_0.9.2_Data_Files_Output_Sigs_Only.tar.gz (1 KB) is a
"gzipped" tar of only the MD5 signatures of the output data files
needed to test the API.
If your system has the program wget, you only need the source code. The
download of the other tar balls will be handled automatically.
Be careful about space. A full build and test can use 350 MB or more. If
space is tight, be sure to read the instructions below on using only the
signatures of the test files.
Uncompress and unpack :
* gunzip < CBFlib_0.9.2.tar.gz | tar xvf -
To run the test programs, you will also need Paul Ellis's sample MAR345
image, example.mar2300, Chris Nielsen's sample ADSC Quantum 315 image,
mb_LP_1_001.img, and Eric Eikenberry's SLS sample Pilatus 6m image,
insulin_pilatus6m, as sample data. In addition there are is a PDB mmCIF
file, 9ins.cif, and 3 special test files testflatin.cbf,
testflatpackedin.cbf and testrealin.cbf. All these files will be dowloaded
and extracted by the Makefile from CBFlib_0.9.2_Data_Files_Input. Do not
download copies into the top level directory.
Thare are various sample Makefiles for common configurations. The
Makefile_OSX samples is for systems with gfortran from prior to the
release of gcc 4.2. For the most recent gfortran, use Makefile_OSX_gcc42.
All the Makefiles are generated from m4/Makefile.m4.
The Makefiles use GNU make constructs, such as ifeq and ifneq. If you need
to use a different version of make, you will need to edit out the
conditionals
The operation of the Makefiles is sensitive to the following environment
variables:
* CBFLIB_USE_PYCIFRW If you define this environment variable, you may
rebuild the Makefiles to include James Hester's PyCifRW. The process
under bash is:
export CBFLIB_USE_PYCIFRW=yes
cd CBFlib_0.9.2
touch m4/Makefile.m4
make Makefiles
* CBF_DONT_USE_LONG_LONG If you define this environment variable, use of
the long long data type in CBFlib is replaced by use of a struct. The
Makefiles do not need to be rebuilt. Makefile_MINGW does not use the
long long data type even without defining this variable.
* NOFORTRAN If you define this environment variable, use of the fortran
compiler is suppressed.
If necessary, adjust the definition of CC and C++ and other defintions in
Makefile to point to your compilers. Set the definition of CFLAGS to an
appropriate value for your C and C++ compilers, the definition of F90C to
point to your Fortan-90/95 compiler, and the definitions of F90FLAGS and
F90LDFLAGS to approriate values for your Fortan-90/95 compilers, and then
make all
make tests
or, if space is at a premium:
make all
make tests_sigs_only
If you do not have a fortran compiler, you will need edit the Makefile or
to define the variable NOFORTRAN, either in the Makefile or in the
environment
We have included examples of CBF/imgCIF files produced by CBFlib in the
test data CBFlib_0.9.2_Data_Files_Output.tar.gz, the current best draft of
the CBF Extensions Dictionary, and of Andy Hammersley's CBF definition,
updated to become a DRAFT CBF/ImgCIF DEFINITION.
CBFlib 0.9.2 includes a program, tiff2cbf, to convert from tiff files to
CBF files, that requires an augmented version of tiff-3.9.4 called
tiff-3.9.4-rev-6Feb11, that installs into the CBFlib_0.9.2 directory. If a
system copy is desired, download and install
http://downloads.sf.net/cbflib/tiff-3.9.4-rev-6Feb11.tar.gz
----------------------------------------------------------------------
Contents
* 1. Introduction
* 2. Function descriptions
* 2.1 General description
* 2.1.1 CBF handles
* 2.1.2 CBF goniometer handles
* 2.1.3 CBF detector handles
* 2.1.4 Return values
* 2.2 Reading and writing files containing binary sections
* 2.2.1 Reading binary sections
* 2.2.2 Writing binary sections
* 2.2.3 Summary of reading and writing files containing binary
sections
* 2.2.4 Ordering of array indices
* 2.3 Low-level function prototypes
* 2.3.1 cbf_make_handle
* 2.3.2 cbf_free_handle
* 2.3.3 cbf_read_file, cbf_read_widefile
* 2.3.4 cbf_write_file, cbf_write_widefile
* 2.3.5 cbf_new_datablock, cbf_new_saveframe
* 2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
* 2.3.7 cbf_new_category
* 2.3.8 cbf_force_new_category
* 2.3.9 cbf_new_column
* 2.3.10 cbf_new_row
* 2.3.11 cbf_insert_row
* 2.3.12 cbf_delete_row
* 2.3.13 cbf_set_datablockname, cbf_set_saveframename
* 2.3.14 cbf_reset_datablocks
* 2.3.15 cbf_reset_datablock, cbf_reset_saveframe
* 2.3.16 cbf_reset_category
* 2.3.17 cbf_remove_datablock, cbf_remove_saveframe
* 2.3.18 cbf_remove_category
* 2.3.19 cbf_remove_column
* 2.3.20 cbf_remove_row
* 2.3.21 cbf_rewind_datablock
* 2.3.22 cbf_rewind_category, cbf_rewind_saveframe,
cbf_rewind_blockitem
* 2.3.23 cbf_rewind_column
* 2.3.24 cbf_rewind_row
* 2.3.25 cbf_next_datablock
* 2.3.26 cbf_next_category, cbf_next_saveframe,
cbf_next_blockitem
* 2.3.27 cbf_next_column
* 2.3.28 cbf_next_row
* 2.3.29 cbf_find_datablock
* 2.3.30 cbf_find_category, cbf_find_saveframe,
cbf_find_blockitem
* 2.3.31 cbf_find_column
* 2.3.32 cbf_find_row
* 2.3.33 cbf_find_nextrow
* 2.3.34 cbf_count_datablocks
* 2.3.35 cbf_count_categories, cbf_count_saveframes,
cbf_count_blockitems
* 2.3.36 cbf_count_columns
* 2.3.37 cbf_count_rows
* 2.3.38 cbf_select_datablock
* 2.3.39 cbf_select_category, cbf_select_saveframe,
cbf_select_blockitem
* 2.3.40 cbf_select_column
* 2.3.41 cbf_select_row
* 2.3.42 cbf_datablock_name
* 2.3.43 cbf_category_name
* 2.3.44 cbf_column_name, cbf_set_column_name
* 2.3.45 cbf_row_number
* 2.3.46 cbf_get_value, cbf_require_value
* 2.3.47 cbf_set_value
* 2.3.48 cbf_get_typeofvalue
* 2.3.49 cbf_set_typeofvalue
* 2.3.50 cbf_get_integervalue, cbf_require_integervalue
* 2.3.51 cbf_set_integervalue
* 2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
* 2.3.53 cbf_set_doublevalue
* 2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims,
cbf_get_integerarrayparameters_wdims_fs,
cbf_get_integerarrayparameters_wdims_sf
cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims,
cbf_get_realarrayparameters_wdims_fs,
cbf_get_realarrayparameters_wdims_sf
* 2.3.55 cbf_get_integerarray, cbf_get_realarray
* 2.3.56 cbf_set_integerarray,
cbf_set_integerarray_wdims,
cbf_set_integerarray_wdims_fs,
cbf_set_integerarray_wdims_sf,
cbf_set_realarray,
cbf_set_realarray_wdims, cbf_set_realarray_wdims_fs,
cbf_set_realarray_wdims_sf
* 2.3.57 cbf_failnez
* 2.3.58 cbf_onfailnez
* 2.3.59 cbf_require_datablock
* 2.3.60 cbf_require_category
* 2.3.61 cbf_require_column
* 2.3.62 cbf_require_column_value
* 2.3.63 cbf_require_column_integervalue
* 2.3.64 cbf_require_column_doublevalue
* 2.3.65 cbf_get_local_integer_byte_order,
cbf_get_local_real_byte_order, cbf_get_local_real_format
* 2.3.66 cbf_get_dictionary, cbf_set_dictionary,
cbf_require_dictionary
* 2.3.67 cbf_convert_dictionary
* 2.3.68 cbf_find_tag, cbf_find_local_tag
* 2.3.69 cbf_find_category_root, cbf_set_category_root,
cbf_require_category_root
* 2.3.70 cbf_find_tag_root, cbf_set_tag_root,
cbf_require_tag_root
* 2.3.71 cbf_find_tag_category, cbf_set_tag_category
* 2.4 High-level function prototypes (new for version 0.7)
* 2.4.1 cbf_read_template
* 2.4.2 cbf_get_diffrn_id, cbf_require_diffrn_id
* 2.4.3 cbf_set_diffrn_id
* 2.4.4 cbf_get_crystal_id
* 2.4.5 cbf_set_crystal_id
* 2.4.6 cbf_get_wavelength
* 2.4.7 cbf_set_wavelength
* 2.4.8 cbf_get_polarization
* 2.4.9 cbf_set_polarization
* 2.4.10 cbf_get_divergence
* 2.4.11 cbf_set_divergence
* 2.4.12 cbf_count_elements
* 2.4.13 cbf_get_element_id
* 2.4.14 cbf_get_gain
* 2.4.15 cbf_set_gain
* 2.4.16 cbf_get_overload
* 2.4.17 cbf_set_overload
* 2.4.18 cbf_get_integration_time
* 2.4.19 cbf_set_integration_time
* 2.4.20 cbf_get_time
* 2.4.21 cbf_set_time
* 2.4.22 cbf_get_date
* 2.4.23 cbf_set_date
* 2.4.24 cbf_set_current_time
* 2.4.25 cbf_get_image_size, cbf_get_image_size_fs,
cbf_get_image_size_fs,
cbf_get_3d_image_size, cbf_get_3d_image_size_fs,
cbf_get_3d_image_size_sf
* 2.4.26 cbf_get_image, cbf_get_image_fs, cbf_get_image_sf,
cbf_get_real_image, cbf_get_real_image_fs,
cbf_get_real_image_sf,
cbf_get_3d_image, cbf_get_3d_image_fs,
cbf_get_3d_image_sf,
cbf_get_real_3d_image, cbf_get_real_3d_image_fs,
cbf_get_real_3d_image_sf
* 2.4.27 cbf_set_image, cbf_set_image_fs, cbf_set_image_sf,
cbf_set_real_image, cbf_set_real_image_fs,
cbf_set_real_image_sf,
cbf_set_3d_image, cbf_set_3d_image, cbf_set_3d_image,
cbf_set_real_3d_image, cbf_set_real_3d_image_fs,
cbf_set_real_3d_image_sf
* 2.4.28 cbf_get_axis_setting
* 2.4.29 cbf_set_axis_setting
* 2.4.30 cbf_construct_goniometer
* 2.4.31 cbf_free_goniometer
* 2.4.32 cbf_get_rotation_axis
* 2.4.33 cbf_get_rotation_range
* 2.4.34 cbf_rotate_vector
* 2.4.35 cbf_get_reciprocal
* 2.4.36 cbf_construct_detector,
cbf_construct_reference_detector,
cbf_require_reference_detector
* 2.4.37 cbf_free_detector
* 2.4.38 cbf_get_beam_center, cbf_get_beam_center_fs,
cbf_get_beam_center_sf,
cbf_set_beam_center, cbf_set_beam_center_fs,
cbf_set_beam_center_sf,
cbf_set_reference_beam_center,
cbf_set_reference_beam_center_fs,
cbf_set_reference_beam_center_sf
* 2.4.39 cbf_get_detector_distance
* 2.4.40 cbf_get_detector_normal
* 2.4.41 cbf_get_detector_axis_slow,
cbf_get_detector_axis_fast, cbf_get_detector_axes,
cbf_get_detector_axes_fs, cbf_get_detector_axes_sf
* 2.4.42 cbf_get_pixel_coordinates,
cbf_get_pixel_coordinates_fs, cbf_get_pixel_coordinates_sf
* 2.4.43 cbf_get_pixel_normal, cbf_get_pixel_normal_fs,
cbf_get_pixel_normal_sf
* 2.4.44 cbf_get_pixel_area, cbf_get_pixel_area_fs,
cbf_get_pixel_area_sf
* 2.4.45 cbf_get_pixel_size, cbf_get_pixel_size_fs,
cbf_get_pixel_size_sf
* 2.4.46 cbf_set_pixel_size, cbf_set_pixel_size_fs,
cbf_set_pixel_size_sf
* 2.4.47 cbf_get_inferred_pixel_size,
cbf_get_inferred_pixel_size_fs,
cbf_get_inferred_pixel_size_sf
* 2.4.48 cbf_get_unit_cell
* 2.4.49 cbf_set_unit_cell
* 2.4.50 cbf_get_reciprocal_cell
* 2.4.51 cbf_set_reciprocal_cell
* 2.4.52 cbf_compute_cell_volume
* 2.4.53 cbf_compute_reciprocal_cell
* 2.4.54 cbf_get_orientation_matrix,
cbf_set_orientation_matrix
* 2.4.55 cbf_get_bin_sizes, cbf_set_bin_sizes
* 2.5 F90 function interfaces
* 2.5.1 FCB_ATOL_WCNT
* 2.5.2 FCB_CI_STRNCMPARR
* 2.5.3 FCB_EXIT_BINARY
* 2.5.4 FCB_NBLEN_ARRAY
* 2.5.5 FCB_NEXT_BINARY
* 2.5.6 FCB_OPEN_CIFIN
* 2.5.7 FCB_PACKED: FCB_DECOMPRESS_PACKED_I2,
FCB_DECOMPRESS_PACKED_I4, FCB_DECOMPRESS_PACKED_3D_I2,
FCB_DECOMPRESS_PACKED_3D_I4
* 2.5.8 FCB_READ_BITS
* 2.5.9 FCB_READ_BYTE
* 2.5.10 FCB_READ_IMAGE_I2, FCB_READ_IMAGE_I4,
FCB_READ_IMAGE_3D_I2, FCB_READ_IMAGE_3D_I4
* 2.5.11 FCB_READ_LINE
* 2.5.12 FCB_READ_XDS_I2
* 2.5.13 FCB_SKIP_WHITESPACE
* 3. File format
* 3.1 General description
* 3.2 Format of the binary sections
* 3.2.1 Format of imgCIF binary sections
* 3.2.2 Format of CBF binary sections
* 3.3 Compression schemes
* 3.3.1 Canonical-code compression
* 3.3.2 CCP4-style compression
* 3.3.3 Byte_offset compression
* 4. Installation
* 5. Example programs
1. Introduction
CBFlib (Crystallographic Binary File library) is a library of ANSI-C
functions providing a simple mechanism for accessing Crystallographic
Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The
CBFlib API is loosely based on the CIFPARSE API for mmCIF files. Like
CIFPARSE, CBFlib does not perform any semantic integrity checks; rather it
simply provides functions to create, read, modify and write CBF binary
data files and imgCIF ASCII data files.
Starting with version 0.7.7, an envolving FCBlib (Fortran Crystallographic
Binary library) has been added. As of this release it includes code for
reading byte-offset and packed compression image files created by CBFlib.
2. Function descriptions
2.1 General description
Almost all of the CBFlib functions receive a value of type cbf_handle (a
CBF handle) as the first argument. Several of the high-level CBFlib
functions dealing with geometry receive a value of type cbf_goniometer (a
handle for a CBF goniometer object) or cbf_detector (a handle for a CBF
detector object).
All functions return an integer equal to 0 for success or an error code
for failure.
2.1.1 CBF handles
CBFlib permits a program to use multiple CBF objects simultaneously. To
identify the CBF object on which a function will operate, CBFlib uses a
value of type cbf_handle.
All functions in the library except cbf_make_handle expect a value of type
cbf_handle as the first argument.
The function cbf_make_handle creates and initializes a new CBF handle.
The function cbf_free_handle destroys a handle and frees all memory
associated with the corresponding CBF object.
2.1.2 CBF goniometer handles
To represent the goniometer used to orient a sample, CBFlib uses a value
of type cbf_goniometer.
A goniometer object is created and initialized from a CBF object using the
function cbf_construct_goniometer.
The function cbf_free_goniometer destroys a goniometer handle and frees
all memory associated with the corresponding object.
2.1.3 CBF detector handles
To represent a detector surface mounted on a positioning system, CBFlib
uses a value of type cbf_detector.
A goniometer object is created and initialized from a CBF object using one
of the functions cbf_construct_detector, cbf_construct_reference_detector
or cbf_require_reference_detector.
The function cbf_free_detector destroys a detector handle and frees all
memory associated with the corresponding object.
2.1.4 Return values
All of the CBFlib functions return 0 on success and an error code on
failure. The error codes are:
CBF_FORMAT The file format is invalid
CBF_ALLOC Memory allocation failed
CBF_ARGUMENT Invalid function argument
CBF_ASCII The value is ASCII (not binary)
CBF_BINARY The value is binary (not ASCII)
CBF_BITCOUNT The expected number of bits does
not match the actual number written
CBF_ENDOFDATA The end of the data was reached
before the end of the array
CBF_FILECLOSE File close error
CBF_FILEOPEN File open error
CBF_FILEREAD File read error
CBF_FILESEEK File seek error
CBF_FILETELL File tell error
CBF_FILEWRITE File write error
CBF_IDENTICAL A data block with the new name
already exists
CBF_NOTFOUND The data block, category, column or
row does not exist
CBF_OVERFLOW The number read cannot fit into the
destination argument. The destination has
been set to the nearest value.
CBF_UNDEFINED The requested number is not defined (e.g. 0/0; new for
version 0.7).
CBF_NOTIMPLEMENTED The requested functionality is not yet implemented (New
for version 0.7).
If more than one error has occurred, the error code is the logical OR of
the individual error codes.
2.2 Reading and writing files containing binary sections
2.2.1 Reading binary sections
The current version of CBFlib only decompresses a binary section from disk
when requested by the program.
When a file containing one or more binary sections is read, CBFlib saves
the file pointer and the position of the binary section within the file
and then jumps past the binary section. When the program attempts to
access the binary data, CBFlib sets the file position back to the start of
the binary section and then reads the data.
For this scheme to work:
1. The file must be a random-access file opened in binary mode (fopen ( ,"
rb")).
2. The program must not close the file. CBFlib will close the file using
fclose ( ) when it is no longer needed.
At present, this also means that a program cant read a file and then write
back to the same file. This restriction will be eliminated in a future
version.
When reading an imgCIF vs a CBF, the difference is detected automatically.
2.2.2 Writing binary sections
When a program passes CBFlib a binary value, the data is compressed to a
temporary file. If the CBF object is subsequently written to a file, the
data is simply copied from the temporary file to the output file.
The output file can be of any type. If the program indicates to CBFlib
that the file is a random-access and readable, CBFlib will conserve disk
space by closing the temporary file and using the output file as the
location at which the binary value is stored.
For this option to work:
1. The file must be a random-access file opened in binary update mode
(fopen ( , "w+b")).
2. The program must not close the file. CBFlib will close the file using
fclose ( ) when it is no longer needed.
If this option is not used:
1. CBFlib will continue using the temporary file.
2. CBFlib will not close the file. This is the responsibility of the main
program.
2.2.3 Summary of reading and writing files containing binary sections
1. Open disk files to read using the mode "rb".
2. If possible, open disk files to write using the mode "w+b" and tell
CBFlib that it can use the file as a buffer.
3. Do not close any files read by CBFlib or written by CBFlib with
buffering turned on.
4. Do not attempt to read from a file, then write to the same file.
2.2.4 Ordering of array indices
There are two major conventions in the ordering of array indices:
* fs: Fast to slow. The first array index (the one numbered "1") is the
one for which the values of that index change "fastest". That is, as
we move forward in memory, the value of this index changes more
rapidly than any other.
* sf: Slow to fast. The first array index (the one numbered "1") is the
one for which the values of that index change "slowest". That is as we
move forward in memory, the value of this index changes more slowly
than any other.
During the development of CBFlib, both conventions have been used. In
order to avoid confusion, the functions for which array indices are used
are available in three forms: a default version which may used either one
convention or the other, a form in which the name of the function has an
"_fs" suffix for the fast to slow convention and a form in which the name
of the function has a "_sf" suffix for the slow to fast convention.
Designers of applications are advised to use one of the two suffix
conventions. There is no burden on performance for using one convention or
the other. The differences are resolved at compile time by use of
preprocessor macros.
----------------------------------------------------------------------
----------------------------------------------------------------------
2.3 Low-level function prototypes
2.3.1 cbf_make_handle
PROTOTYPE
#include "cbf.h"
int cbf_make_handle (cbf_handle *handle);
DESCRIPTION
cbf_make_handle creates and initializes a new internal CBF object. All
other CBFlib functions operating on this object receive the CBF handle as
the first argument.
ARGUMENTS
handle Pointer to a CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.2 cbf_free_handle
----------------------------------------------------------------------
2.3.2 cbf_free_handle
PROTOTYPE
#include "cbf.h"
int cbf_free_handle (cbf_handle handle);
DESCRIPTION
cbf_free_handle destroys the CBF object specified by the handle and frees
all associated memory.
ARGUMENTS
handle CBF handle to free.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.1 cbf_make_handle
----------------------------------------------------------------------
2.3.3 cbf_read_file, cbf_read_widefile
PROTOTYPE
#include "cbf.h"
int cbf_read_file (cbf_handle handle, FILE *file, int flags);
int cbf_read_widefile (cbf_handle handle, FILE *file, int flags);
DESCRIPTION
cbf_read_file reads the CBF or CIF file file into the CBF object specified
by handle, using the CIF 1.0 convention of 80 character lines.
cbf_read_widefile reads the CBF or CIF file file into the CBF object
specified by handle, using the CIF 1.1 convention of 2048 character lines.
A warning is issued to stderr for ascii lines over the limit. No test is
performed on binary sections.
Validation is performed in three ways levels: during the lexical scan,
during the parse, and, if a dictionary was converted, against the value
types, value enumerations, categories and parent-child relationships
specified in the dictionary.
flags controls the interpretation of binary section headers, the parsing
of brackets constructs and the parsing of treble-quoted strings.
MSG_DIGEST: Instructs CBFlib to check that the digest of
the binary section matches any header digest
value. If the digests do not match, the call
will return CBF_FORMAT. This evaluation and
comparison is delayed (a "lazy" evaluation) to
ensure maximal processing efficiency. If an
immediately evaluation is required, see
MSG_DIGESTNOW, below.
MSG_DIGESTNOW: Instructs CBFlib to check that the digest of
the binary section matches any header digeste
value. If the digests do not match, the call
will return CBF_FORMAT. This evaluation and
comparison is performed during initial parsing
of the section to ensure timely error reporting
at the expense of processing efficiency. If a
more efficient delayed ("lazy") evaluation is
required, see MSG_DIGEST, above.
MSG_DIGESTWARN: Instructs CBFlib to check that the digest of
the binary section matches any header digeste
value. If the digests do not match, a warning
message will be sent to stderr, but processing
will attempt to continue. This evaluation and
comparison is first performed during initial
parsing of the section to ensure timely error
reporting at the expense of processing
efficiency. An mismatch of the message digest
usually indicates a serious error, but it is
sometimes worth continuing processing to try to
isolate the cause of the error. Use this option
with caution.
MSG_NODIGEST: Do not check the digest (default).
PARSE_BRACKETS: Accept DDLm bracket-delimited
[item,item,...item] or {item,item,...item} or
(item,item,...item) constructs as valid,
stripping non-quoted embedded whitespace and
comments. These constructs may span multiple
lines.
PARSE_LIBERAL_BRACKETS: Accept DDLm bracket-delimited
[item,item,...item] or {item,item,...item} or
(item,item,...item) constructs as valid,
stripping embedded non-quoted, non-separating
whitespace and comments. These constructs may
span multiple lines. In this case, whitespace
may be used as an alternative to the comma.
PARSE_TRIPLE_QUOTES: Accept DDLm triple-quoted
"""item,item,...item""" or
'''item,item,...item''' constructs as valid,
stripping embedded whitespace and comments.
These constructs may span multiple lines. If
this flag is set, then ''' will not be
interpreted as a quoted apoptrophe and """ will
not be interpreted as a quoted double quote mark
and
PARSE_NOBRACKETS: Do not accept DDLm bracket-delimited
[item,item,...item] or {item,item,...item} or
(item,item,...item) constructs as valid,
stripping non-quoted embedded whitespace and
comments. These constructs may span multiple
lines.
PARSE_NOTRIPLE_QUOTES: No not accept DDLm triple-quoted
"""item,item,...item""" or
'''item,item,...item''' constructs as valid,
stripping embedded whitespace and comments.
These constructs may span multiple lines. If
this flag is set, then ''' will be interpreted
as a quoted apostrophe and """ will be
interpreted as a quoted double quote mark.
CBFlib defers reading binary sections as long as possible. In the current
version of CBFlib, this means that:
1. The file must be a random-access file opened in binary mode (fopen ( ,
"rb")).
2. The program must not close the file. CBFlib will close the file using
fclose ( ) when it is no longer needed.
These restrictions may change in a future release.
ARGUMENTS
handle CBF handle.
file Pointer to a file descriptor.
headers Controls interprestation of binary section headers.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.4 cbf_write_file
----------------------------------------------------------------------
2.3.4 cbf_write_file
PROTOTYPE
#include "cbf.h"
int cbf_write_file (cbf_handle handle, FILE *file, int readable, int
ciforcbf, int flags, int encoding);
int cbf_write_widefile (cbf_handle handle, FILE *file, int readable, int
ciforcbf, int flags, int encoding);
DESCRIPTION
cbf_write_file writes the CBF object specified by handle into the file
file, following CIF 1.0 conventions of 80 character lines.
cbf_write_widefile writes the CBF object specified by handle into the file
file, following CIF 1.1 conventions of 2048 character lines. A warning is
issued to stderr for ascii lines over the limit, and an attempt is made to
fold lines to fit. No test is performed on binary sections.
If a dictionary has been provided, aliases will be applied on output.
Unlike cbf_read_file, the file does not have to be random-access.
If the file is random-access and readable, readable can be set to non-0 to
indicate to CBFlib that the file can be used as a buffer to conserve disk
space. If the file is not random-access or not readable, readable must be
0.
If readable is non-0, CBFlib will close the file when it is no longer
required, otherwise this is the responsibility of the program.
ciforcbf selects the format in which the binary sections are written:
CIF Write an imgCIF file.
CBF Write a CBF file (default).
flags selects the type of header used in CBF binary sections, selects
whether message digests are generated, and controls the style of output.
The value of flags can be a logical OR of any of:
MIME_HEADERS Use MIME-type headers (default).
MIME_NOHEADERS Use a simple ASCII headers.
MSG_DIGEST Generate message digests for binary data
validation.
MSG_NODIGEST Do not generate message digests (default).
PARSE_BRACKETS Do not convert bracketed strings to text fields
(default).
PARSE_LIBERAL_BRACKETS Do not convert bracketed strings to text fields
(default).
PARSE_NOBRACKETS Convert bracketed strings to text fields
(default).
PARSE_TRIPLE_QUOTES Do not convert triple-quoted strings to text
fields (default).
PARSE_NOTRIPLE_QUOTES Convert triple-quoted strings to text fields
(default).
PAD_1K Pad binary sections with 1023 nulls.
PAD_2K Pad binary sections with 2047 nulls.
PAD_4K Pad binary sections with 4095 nulls.
Note that on output, the types "prns&, "brcs" and "bkts" will be converted
to "text" fields if PARSE_NOBRACKETS has been set flags, and that the
types "tsqs" and "tdqs" will be converted to "text" fields if the flag
PARSE_NOTRIPLE_QUOTES has been set in the flags. It is an error to set
PARSE_NOBRACKETS and to set either PARSE_BRACKETS or
PARSE_LIBERAL_BRACKETS. It is an error to set both PARSE_NOTRIPLE_QUOTES
and PARSE_TRIPLE_QUOTES.
encoding selects the type of encoding used for binary sections and the
type of line-termination in imgCIF files. The value can be a logical OR of
any of:
ENC_BASE64 Use BASE64 encoding (default).
ENC_QP Use QUOTED-PRINTABLE encoding.
ENC_BASE8 Use BASE8 (octal) encoding.
ENC_BASE10 Use BASE10 (decimal) encoding.
ENC_BASE16 Use BASE16 (hexadecimal) encoding.
ENC_FORWARD For BASE8, BASE10 or BASE16 encoding, map bytes to words
forward (1234) (default on little-endian machines).
ENC_BACKWARD Map bytes to words backward (4321) (default on big-endian
machines).
ENC_CRTERM Terminate lines with CR.
ENC_LFTERM Terminate lines with LF (default).
ARGUMENTS
handle CBF handle.
file Pointer to a file descriptor.
readable If non-0: this file is random-access and readable and can be
used as a buffer.
ciforcbf Selects the format in which the binary sections are written
(CIF/CBF).
headers Selects the type of header in CBF binary sections and message
digest generation.
encoding Selects the type of encoding used for binary sections and the
type of line-termination in imgCIF files.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.3 cbf_read_file
----------------------------------------------------------------------
2.3.5 cbf_new_datablock, cbf_new_saveframe
PROTOTYPE
#include "cbf.h"
int cbf_new_datablock (cbf_handle handle, const char *datablockname);
int cbf_new_saveframe (cbf_handle handle, const char *saveframename);
DESCRIPTION
cbf_new_datablock creates a new data block with name datablockname and
makes it the current data block. cbf_new_saveframe creates a new save
frame with name saveframename within the current data block and makes the
new save frame the current save frame.
If a data block or save frame with this name already exists, the existing
data block or save frame becomes the current data block or save frame.
ARGUMENTS
handle CBF handle.
datablockname The name of the new data block.
saveframename The name of the new save frame.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.9 cbf_new_column
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.12 cbf_set_datablockname, cbf_set_saveframename
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
PROTOTYPE
#include "cbf.h"
int cbf_force_new_datablock (cbf_handle handle, const char
*datablockname);
int cbf_force_new_saveframe (cbf_handle handle, const char
*saveframename);
DESCRIPTION
cbf_force_new_datablock creates a new data block with name datablockname
and makes it the current data block. Duplicate data block names are
allowed. cbf_force_new_saveframe creates a new savew frame with name
saveframename and makes it the current save frame. Duplicate save frame
names are allowed.
Even if a save frame with this name already exists, a new save frame is
created and becomes the current save frame.
ARGUMENTS
handle CBF handle.
datablockname The name of the new data block.
saveframename The name of the new save frame.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.9 cbf_new_column
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.12 cbf_set_datablockname, cbf_set_saveframename
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.7 cbf_new_category
PROTOTYPE
#include "cbf.h"
int cbf_new_category (cbf_handle handle, const char *categoryname);
DESCRIPTION
cbf_new_category creates a new category in the current data block with
name categoryname and makes it the current category.
If a category with this name already exists, the existing category becomes
the current category.
ARGUMENTS
handle CBF handle.
categoryname The name of the new category.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.8 cbf_force_new_category
2.3.9 cbf_new_column
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.18 cbf_remove_category
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.8 cbf_force_new_category
PROTOTYPE
#include "cbf.h"
int cbf_force_new_category (cbf_handle handle, const char *categoryname);
DESCRIPTION
cbf_force_new_category creates a new category in the current data block
with name categoryname and makes it the current category. Duplicate
category names are allowed.
Even if a category with this name already exists, a new category of the
same name is created and becomes the current category. The allows for the
creation of unlooped tag/value lists drawn from the same category.
ARGUMENTS
handle CBF handle.
categoryname The name of the new category.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.7 cbf_new_category
2.3.9 cbf_new_column
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.18 cbf_remove_category
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.9 cbf_new_column
PROTOTYPE
#include "cbf.h"
int cbf_new_column (cbf_handle handle, const char *columnname);
DESCRIPTION
cbf_new_column creates a new column in the current category with name
columnname and makes it the current column.
If a column with this name already exists, the existing column becomes the
current category.
ARGUMENTS
handle CBF handle.
columnname The name of the new column.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.19 cbf_remove_column
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.10 cbf_new_row
PROTOTYPE
#include "cbf.h"
int cbf_new_row (cbf_handle handle);
DESCRIPTION
cbf_new_row adds a new row to the current category and makes it the
current row.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.9 cbf_new_column
2.3.11 cbf_insert_row
2.3.12 cbf_delete_row
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.11 cbf_insert_row
PROTOTYPE
#include "cbf.h"
int cbf_insert_row (cbf_handle handle, unsigned int rownumber);
DESCRIPTION
cbf_insert_row adds a new row to the current category. The new row is
inserted as row rownumber and existing rows starting from rownumber are
moved up by 1. The new row becomes the current row.
If the category has fewer than rownumber rows, the function returns
CBF_NOTFOUND.
The row numbers start from 0.
ARGUMENTS
handle CBF handle.
rownumber The row number of the new row.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.9 cbf_new_column
2.3.10 cbf_new_row
2.3.12 cbf_delete_row
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.12 cbf_delete_row
PROTOTYPE
#include "cbf.h"
int cbf_delete_row (cbf_handle handle, unsigned int rownumber);
DESCRIPTION
cbf_delete_row deletes a row from the current category. Rows starting from
rownumber +1 are moved down by 1. If the current row was higher than
rownumber, or if the current row is the last row, it will also move down
by 1.
The row numbers start from 0.
ARGUMENTS
handle CBF handle.
rownumber The number of the row to delete.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.18 cbf_remove_category
2.3.19 cbf_remove_column
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.13 cbf_set_datablockname, cbf_set_saveframename
PROTOTYPE
#include "cbf.h"
int cbf_set_datablockname (cbf_handle handle, const char *datablockname);
int cbf_set_saveframename (cbf_handle handle, const char *saveframename);
DESCRIPTION
cbf_set_datablockname changes the name of the current data block to
datablockname. cbf_set_saveframename changes the name of the current save
frame to saveframename.
If a data block or save frame with this name already exists (comparison is
case-insensitive), the function returns CBF_IDENTICAL.
ARGUMENTS
handle CBF handle.
datablockname The new data block name.
datablockname The new save frame name.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.14 cbf_reset_datablocks
2.3.15 cbf_reset_datablock, cbf_reset_saveframe
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.42 cbf_datablock_name
----------------------------------------------------------------------
2.3.14 cbf_reset_datablocks
PROTOTYPE
#include "cbf.h"
int cbf_reset_datablocks (cbf_handle handle);
DESCRIPTION
cbf_reset_datablocks deletes all categories from all data blocks.
The current data block does not change.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.15 cbf_reset_datablock, cbf_reset_saveframe
2.3.18 cbf_remove_category
----------------------------------------------------------------------
2.3.15 cbf_reset_datablock, cbf_reset_datablock
PROTOTYPE
#include "cbf.h"
int cbf_reset_datablock (cbf_handle handle);
int cbf_reset_saveframe (cbf_handle handle);
DESCRIPTION
cbf_reset_datablock deletes all categories from the current data block.
cbf_reset_saveframe deletes all categories from the current save frame.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.14 cbf_reset_datablocks
2.3.18 cbf_remove_category
----------------------------------------------------------------------
2.3.16 cbf_reset_category
PROTOTYPE
#include "cbf.h"
int cbf_reset_category (cbf_handle handle);
DESCRIPTION
cbf_reset_category deletes all columns and rows from current category.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.16 cbf_reset_category
2.3.19 cbf_remove_column
2.3.20 cbf_remove_row
----------------------------------------------------------------------
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
PROTOTYPE
#include "cbf.h"
int cbf_remove_datablock (cbf_handle handle);
int cbf_remove_saveframe (cbf_handle handle);
DESCRIPTION
cbf_remove_datablock deletes the current data block. cbf_remove_saveframe
deletes the current save frame.
The current data block becomes undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.18 cbf_remove_category
2.3.19 cbf_remove_column
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.18 cbf_remove_category
PROTOTYPE
#include "cbf.h"
int cbf_remove_category (cbf_handle handle);
DESCRIPTION
cbf_remove_category deletes the current category.
The current category becomes undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.19 cbf_remove_column
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.19 cbf_remove_column
PROTOTYPE
#include "cbf.h"
int cbf_remove_column (cbf_handle handle);
DESCRIPTION
cbf_remove_column deletes the current column.
The current column becomes undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.9 cbf_new_column
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.18 cbf_remove_category
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.20 cbf_remove_row
PROTOTYPE
#include "cbf.h"
int cbf_remove_row (cbf_handle handle);
DESCRIPTION
cbf_remove_row deletes the current row in the current category.
If the current row was the last row, it will move down by 1, otherwise, it
will remain the same.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.18 cbf_remove_category
2.3.19 cbf_remove_column
2.3.12 cbf_delete_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.21 cbf_rewind_datablock
PROTOTYPE
#include "cbf.h"
int cbf_rewind_datablock (cbf_handle handle);
DESCRIPTION
cbf_rewind_datablock makes the first data block the current data block.
If there are no data blocks, the function returns CBF_NOTFOUND.
The current category becomes undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.19 cbf_rewind_column
2.3.24 cbf_rewind_row
2.3.25 cbf_next_datablock
----------------------------------------------------------------------
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
PROTOTYPE
#include "cbf.h"
int cbf_rewind_category (cbf_handle handle);
int cbf_rewind_saveframe (cbf_handle handle);
int cbf_rewind_blockitem (cbf_handle handle, CBF_NODETYPE * type);
DESCRIPTION
cbf_rewind_category makes the first category in the current data block the
current category. cbf_rewind_saveframe makes the first saveframe in the
current data block the current saveframe. cbf_rewind_blockitem makes the
first blockitem (category or saveframe) in the current data block the
current blockitem. The type of the blockitem (CBF_CATEGORY or
CBF_SAVEFRAME) is returned in type.
If there are no categories, saveframes or blockitems the function returns
CBF_NOTFOUND.
The current column and row become undefined.
ARGUMENTS
handle CBF handle.
type CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.19 cbf_rewind_column
2.3.24 cbf_rewind_row
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
----------------------------------------------------------------------
2.3.23 cbf_rewind_column
PROTOTYPE
#include "cbf.h"
int cbf_rewind_column (cbf_handle handle);
DESCRIPTION
cbf_rewind_column makes the first column in the current category the
current column.
If there are no columns, the function returns CBF_NOTFOUND.
The current row is not affected.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.24 cbf_rewind_row
2.3.27 cbf_next_column
----------------------------------------------------------------------
2.3.24 cbf_rewind_row
PROTOTYPE
#include "cbf.h"
int cbf_rewind_row (cbf_handle handle);
DESCRIPTION
cbf_rewind_row makes the first row in the current category the current
row.
If there are no rows, the function returns CBF_NOTFOUND.
The current column is not affected.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.19 cbf_rewind_column
2.3.28 cbf_next_row
----------------------------------------------------------------------
2.3.25 cbf_next_datablock
PROTOTYPE
#include "cbf.h"
int cbf_next_datablock (cbf_handle handle);
DESCRIPTION
cbf_next_datablock makes the data block following the current data block
the current data block.
If there are no more data blocks, the function returns CBF_NOTFOUND.
The current category becomes undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
2.3.27 cbf_next_column
2.3.28 cbf_next_row
----------------------------------------------------------------------
2.3.26 cbf_next_category
PROTOTYPE
#include "cbf.h"
int cbf_next_category (cbf_handle handle);
DESCRIPTION
cbf_next_category makes the category following the current category in the
current data block the current category.
If there are no more categories, the function returns CBF_NOTFOUND.
The current column and row become undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.25 cbf_next_datablock
2.3.27 cbf_next_column
2.3.27 cbf_next_row
----------------------------------------------------------------------
2.3.27 cbf_next_column
PROTOTYPE
#include "cbf.h"
int cbf_next_column (cbf_handle handle);
DESCRIPTION
cbf_next_column makes the column following the current column in the
current category the current column.
If there are no more columns, the function returns CBF_NOTFOUND.
The current row is not affected.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.19 cbf_rewind_column
2.3.25 cbf_next_datablock
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
2.3.28 cbf_next_row
----------------------------------------------------------------------
2.3.28 cbf_next_row
PROTOTYPE
#include "cbf.h"
int cbf_next_row (cbf_handle handle);
DESCRIPTION
cbf_next_row makes the row following the current row in the current
category the current row.
If there are no more rows, the function returns CBF_NOTFOUND.
The current column is not affected.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.24 cbf_rewind_row
2.3.25 cbf_next_datablock
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
2.3.27 cbf_next_column
----------------------------------------------------------------------
2.3.29 cbf_find_datablock
PROTOTYPE
#include "cbf.h"
int cbf_find_datablock (cbf_handle handle, const char *datablockname);
DESCRIPTION
cbf_find_datablock makes the data block with name datablockname the
current data block.
The comparison is case-insensitive.
If the data block does not exist, the function returns CBF_NOTFOUND.
The current category becomes undefined.
ARGUMENTS
handle CBF handle.
datablockname The name of the data block to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.25 cbf_next_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.31 cbf_find_column
2.3.32 cbf_find_row
2.3.42 cbf_datablock_name
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.30 cbf_find_category
PROTOTYPE
#include "cbf.h"
int cbf_find_category (cbf_handle handle, const char *categoryname);
DESCRIPTION
cbf_find_category makes the category in the current data block with name
categoryname the current category.
The comparison is case-insensitive.
If the category does not exist, the function returns CBF_NOTFOUND.
The current column and row become undefined.
ARGUMENTS
handle CBF handle.
categoryname The name of the category to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
2.3.29 cbf_find_datablock
2.3.31 cbf_find_column
2.3.32 cbf_find_row
2.3.43 cbf_category_name
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.31 cbf_find_column
PROTOTYPE
#include "cbf.h"
int cbf_find_column (cbf_handle handle, const char *columnname);
DESCRIPTION
cbf_find_column makes the columns in the current category with name
columnname the current column.
The comparison is case-insensitive.
If the column does not exist, the function returns CBF_NOTFOUND.
The current row is not affected.
ARGUMENTS
handle CBF handle.
columnname The name of column to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.19 cbf_rewind_column
2.3.27 cbf_next_column
2.3.29 cbf_find_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.32 cbf_find_row
2.3.44 cbf_column_name
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.32 cbf_find_row
PROTOTYPE
#include "cbf.h"
int cbf_find_row (cbf_handle handle, const char *value);
DESCRIPTION
cbf_find_row makes the first row in the current column with value value
the current row.
The comparison is case-sensitive.
If a matching row does not exist, the function returns CBF_NOTFOUND.
The current column is not affected.
ARGUMENTS
handle CBF handle.
value The value of the row to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.24 cbf_rewind_row
2.3.28 cbf_next_row
2.3.29 cbf_find_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.31 cbf_find_column
2.3.33 cbf_find_nextrow
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.33 cbf_find_nextrow
PROTOTYPE
#include "cbf.h"
int cbf_find_nextrow (cbf_handle handle, const char *value);
DESCRIPTION
cbf_find_nextrow makes the makes the next row in the current column with
value value the current row. The search starts from the row following the
last row found with cbf_find_row or cbf_find_nextrow, or from the current
row if the current row was defined using any other function.
The comparison is case-sensitive.
If no more matching rows exist, the function returns CBF_NOTFOUND.
The current column is not affected.
ARGUMENTS
handle CBF handle.
value the value to search for.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.24 cbf_rewind_row
2.3.28 cbf_next_row
2.3.29 cbf_find_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.31 cbf_find_column
2.3.32 cbf_find_row
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
----------------------------------------------------------------------
2.3.34 cbf_count_datablocks
PROTOTYPE
#include "cbf.h"
int cbf_count_datablocks (cbf_handle handle, unsigned int *datablocks);
DESCRIPTION
cbf_count_datablocks puts the number of data blocks in *datablocks .
ARGUMENTS
handle CBF handle.
datablocks Pointer to the destination data block count.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.35 cbf_count_categories, cbf_count_saveframes, cbf_count_blockitems
2.3.36 cbf_count_columns
2.3.37 cbf_count_rows
2.3.38 cbf_select_datablock
----------------------------------------------------------------------
2.3.35 cbf_count_categories
PROTOTYPE
#include "cbf.h"
int cbf_count_categories (cbf_handle handle, unsigned int *categories);
DESCRIPTION
cbf_count_categories puts the number of categories in the current data
block in *categories.
ARGUMENTS
handle CBF handle.
categories Pointer to the destination category count.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.34 cbf_count_datablocks
2.3.36 cbf_count_columns
2.3.37 cbf_count_rows
2.3.39 cbf_select_category, cbf_select_saveframe, cbf_select_blockitem
----------------------------------------------------------------------
2.3.36 cbf_count_columns
PROTOTYPE
#include "cbf.h"
int cbf_count_columns (cbf_handle handle, unsigned int *columns);
DESCRIPTION
cbf_count_columns puts the number of columns in the current category in
*columns.
ARGUMENTS
handle CBF handle.
columns Pointer to the destination column count.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.34 cbf_count_datablocks
2.3.35 cbf_count_categories, cbf_count_saveframes, cbf_count_blockitems
2.3.37 cbf_count_rows
2.3.40 cbf_select_column
----------------------------------------------------------------------
2.3.37 cbf_count_rows
PROTOTYPE
#include "cbf.h"
int cbf_count_rows (cbf_handle handle, unsigned int *rows);
DESCRIPTION
cbf_count_rows puts the number of rows in the current category in *rows .
ARGUMENTS
handle CBF handle.
rows Pointer to the destination row count.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.34 cbf_count_datablocks
2.3.35 cbf_count_categories, cbf_count_saveframes, cbf_count_blockitems
2.3.36 cbf_count_columns
2.3.41 cbf_select_row
----------------------------------------------------------------------
2.3.38 cbf_select_datablock
PROTOTYPE
#include "cbf.h"
int cbf_select_datablock (cbf_handle handle, unsigned int datablock);
DESCRIPTION
cbf_select_datablock selects data block number datablock as the current
data block.
The first data block is number 0.
If the data block does not exist, the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
datablock Number of the data block to select.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.34 cbf_count_datablocks
2.3.39 cbf_select_category, cbf_select_saveframe, cbf_select_blockitem
2.3.40 cbf_select_column
2.3.41 cbf_select_row
----------------------------------------------------------------------
2.3.39 cbf_select_category
PROTOTYPE
#include "cbf.h"
int cbf_select_category (cbf_handle handle, unsigned int category);
DESCRIPTION
cbf_select_category selects category number category in the current data
block as the current category.
The first category is number 0.
The current column and row become undefined.
If the category does not exist, the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
category Number of the category to select.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.35 cbf_count_categories, cbf_count_saveframes, cbf_count_blockitems
2.3.38 cbf_select_datablock
2.3.40 cbf_select_column
2.3.41 cbf_select_row
----------------------------------------------------------------------
2.3.40 cbf_select_column
PROTOTYPE
#include "cbf.h"
int cbf_select_column (cbf_handle handle, unsigned int column);
DESCRIPTION
cbf_select_column selects column number column in the current category as
the current column.
The first column is number 0.
The current row is not affected
If the column does not exist, the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
column Number of the column to select.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.36 cbf_count_columns
2.3.38 cbf_select_datablock
2.3.39 cbf_select_category, cbf_select_saveframe, cbf_select_blockitem
2.3.41 cbf_select_row
----------------------------------------------------------------------
2.3.41 cbf_select_row
PROTOTYPE
#include "cbf.h"
int cbf_select_row (cbf_handle handle, unsigned int row);
DESCRIPTION
cbf_select_row selects row number row in the current category as the
current row.
The first row is number 0.
The current column is not affected
If the row does not exist, the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
row Number of the row to select.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.37 cbf_count_rows
2.3.38 cbf_select_datablock
2.3.39 cbf_select_category, cbf_select_saveframe, cbf_select_blockitem
2.3.40 cbf_select_column
----------------------------------------------------------------------
2.3.42 cbf_datablock_name
PROTOTYPE
#include "cbf.h"
int cbf_datablock_name (cbf_handle handle, const char **datablockname);
DESCRIPTION
cbf_datablock_name sets *datablockname to point to the name of the current
data block.
The data block name will be valid as long as the data block exists and has
not been renamed.
The name must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
datablockname Pointer to the destination data block name pointer.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.29 cbf_find_datablock
----------------------------------------------------------------------
2.3.43 cbf_category_name
PROTOTYPE
#include "cbf.h"
int cbf_category_name (cbf_handle handle, const char **categoryname);
DESCRIPTION
cbf_category_name sets *categoryname to point to the name of the current
category of the current data block.
The category name will be valid as long as the category exists.
The name must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
categoryname Pointer to the destination category name pointer.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
----------------------------------------------------------------------
2.3.44 cbf_column_name, cbf_set_column_name
PROTOTYPE
#include "cbf.h"
int cbf_column_name (cbf_handle handle, const char **columnname);
int cbf_set_column_name (cbf_handle handle, const char *newcolumnname)
DESCRIPTION
cbf_column_name sets *columnname to point to the name of the current
column of the current category.
The column name will be valid as long as the column exists.
The name must not be modified by the program in any way.
cbf_set_column_name sets the name of the current column to newcolumnname
ARGUMENTS
handle CBF handle.
columnname Pointer to the destination column name pointer.
newcolumnname New column name pointer.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.31 cbf_find_column
----------------------------------------------------------------------
2.3.45 cbf_row_number
PROTOTYPE
#include "cbf.h"
int cbf_row_number (cbf_handle handle, unsigned int *row);
DESCRIPTION
cbf_row_number sets *row to the number of the current row of the current
category.
ARGUMENTS
handle CBF handle.
row Pointer to the destination row number.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.41 cbf_select_row
----------------------------------------------------------------------
2.3.46 cbf_get_value, cbf_require_value
PROTOTYPE
#include "cbf.h"
int cbf_get_value (cbf_handle handle, const char **value);
int cbf_require_value (cbf_handle handle, const char **value, const char
*defaultvalue );
DESCRIPTION
cbf_get_value sets *value to point to the ASCII value of the item at the
current column and row. cbf_require_value sets *value to point to the
ASCII value of the item at the current column and row, creating the data
item if necessary and initializing it to a copy of defaultvalue.
If the value is not ASCII, the function returns CBF_BINARY.
The value will be valid as long as the item exists and has not been set to
a new value.
The value must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
value Pointer to the destination value pointer.
defaultvalue Default value character string.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.47 cbf_set_value
PROTOTYPE
#include "cbf.h"
int cbf_set_value (cbf_handle handle, const char *value);
DESCRIPTION
cbf_set_value sets the item at the current column and row to the ASCII
value value.
ARGUMENTS
handle CBF handle.
value ASCII value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.53 cbf_set_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.48 cbf_get_typeofvalue
PROTOTYPE
#include "cbf.h"
int cbf_get_typeofvalue (cbf_handle handle, const char **typeofvalue);
DESCRIPTION
cbf_get_value sets *typeofvalue to point an ASCII descriptor of the value
of the item at the current column and row. The strings that may be
returned are:
"null" for a null value indicated by a "." or a "?"
"bnry" for a binary value
"word" for an unquoted string
"dblq" for a double-quoted string
"sglq" for a single-quoted string
"text" for a semicolon-quoted string (multiline text field)
"prns" for a parenthesis-bracketed string (multiline text field)
"brcs" for a brace-bracketed string (multiline text field)
"bkts" for a square-bracket-bracketed string (multiline text field)
"tsqs" for a treble-single-quote quoted string (multiline text field)
"tdqs" for a treble-double-quote quoted string (multiline text field)
Not all types are valid for all type of CIF files. In partcular the types
"prns", "brcs", "bkts" were introduced with DDLm and are not valid in DDL1
or DDL2 CIFS. The types "tsqs" and "tdqs" are not formally part of the CIF
syntax. A field for which no value has been set sets *typeofvalue to NULL
rather than to the string "null".
The typeofvalue must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
typeofvalue Pointer to the destination type-of-value string pointer.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.49 cbf_set_typeofvalue
PROTOTYPE
#include "cbf.h"
int cbf_set_typeofvalue (cbf_handle handle, const char *typeofvalue);
DESCRIPTION
cbf_set_typeofvalue sets the type of the item at the current column and
row to the type specified by the ASCII character string given by
typeofvalue. The strings that may be used are:
"null" for a null value indicated by a "." or a "?"
"bnry" for a binary value
"word" for an unquoted string
"dblq" for a double-quoted string
"sglq" for a single-quoted string
"text" for a semicolon-quoted string (multiline text field)
"prns" for a parenthesis-bracketed string (multiline text field)
"brcs" for a brace-bracketed string (multiline text field)
"bkts" for a square-bracket-bracketed string (multiline text field)
"tsqs" for a treble-single-quote quoted string (multiline text field)
"tdqs" for a treble-double-quote quoted string (multiline text field)
Not all types may be used for all values. Not all types are valid for all
type of CIF files. In partcular the types "prns", "brcs", "bkts" were
introduced with DDLm and are not valid in DDL1 or DDL2 CIFS. The types
"tsqs" and "tdqs" are not formally part of the CIF syntax. No changes may
be made to the type of binary values. You may not set the type of a string
that contains a single quote followed by a blank or a tab or which
contains multiple lines to "sglq". You may not set the type of a string
that contains a double quote followed by a blank or a tab or which
contains multiple lines to "dblq".
ARGUMENTS
handle CBF handle.
typeofvalue ASCII string for desired type of value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.51 cbf_set_integervalue
2.3.53 cbf_set_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.50 cbf_get_integervalue, cbf_require_integervalue
PROTOTYPE
#include "cbf.h"
int cbf_get_integervalue (cbf_handle handle, int *number);
int cbf_require_integervalue (cbf_handle handle, int *number, int
defaultvalue);
DESCRIPTION
cbf_get_integervalue sets *number to the value of the ASCII item at the
current column and row interpreted as a decimal integer.
cbf_require_integervalue sets *number to the value of the ASCII item at
the current column and row interpreted as a decimal integer, setting it to
defaultvalue if necessary.
If the value is not ASCII, the function returns CBF_BINARY.
ARGUMENTS
handle CBF handle.
number pointer to the number.
defaultvalue default number value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.51 cbf_set_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.51 cbf_set_integervalue
PROTOTYPE
#include "cbf.h"
int cbf_set_integervalue (cbf_handle handle, int number);
DESCRIPTION
cbf_set_integervalue sets the item at the current column and row to the
integer value number written as a decimal ASCII string.
ARGUMENTS
handle CBF handle.
number Integer value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.51 cbf_set_integervalue
2.3.53 cbf_set_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
PROTOTYPE
#include "cbf.h"
int cbf_get_doublevalue (cbf_handle handle, double *number);
int cbf_require_doublevalue (cbf_handle handle, double *number, double
defaultvalue);
DESCRIPTION
cbf_get_doublevalue sets *number to the value of the ASCII item at the
current column and row interpreted as a decimal floating-point number.
cbf_require_doublevalue sets *number to the value of the ASCII item at the
current column and row interpreted as a decimal floating-point number,
setting it to defaultvalue if necessary.
If the value is not ASCII, the function returns CBF_BINARY.
ARGUMENTS
handle CBF handle.
number Pointer to the destination number.
defaultvalue default number value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.53 cbf_set_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.53 cbf_set_doublevalue
PROTOTYPE
#include "cbf.h"
int cbf_set_doublevalue (cbf_handle handle, const char *format, double
number);
DESCRIPTION
cbf_set_doublevalue sets the item at the current column and row to the
floating-point value number written as an ASCII string with the format
specified by format as appropriate for the printf function.
ARGUMENTS
handle CBF handle.
format Format for the number.
number Floating-point value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims,
cbf_get_integerarrayparameters_wdims_fs,
cbf_get_integerarrayparameters_wdims_sf, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims,
cbf_get_realarrayparameters_wdims_fs, cbf_get_realarrayparameters_wdims_sf
PROTOTYPE
#include "cbf.h"
int cbf_get_integerarrayparameters (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, int *elsigned, int
*elunsigned, size_t *elements, int *minelement, int *maxelement);
int cbf_get_integerarrayparameters_wdims (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, int *elsigned, int
*elunsigned, size_t *elements, int *minelement, int *maxelement, const
char **byteorder, size_t *dimfast, size_t *dimmid, size_t *dimslow, size_t
*padding);
int cbf_get_integerarrayparameters_wdims_fs (cbf_handle handle, unsigned
int *compression, int *binary_id, size_t *elsize, int *elsigned, int
*elunsigned, size_t *elements, int *minelement, int *maxelement, const
char **byteorder, size_t *dimfast, size_t *dimmid, size_t *dimslow, size_t
*padding);
int cbf_get_integerarrayparameters_wdims_sf (cbf_handle handle, unsigned
int *compression, int *binary_id, size_t *elsize, int *elsigned, int
*elunsigned, size_t *elements, int *minelement, int *maxelement, const
char **byteorder, size_t *dimslow, size_t *dimmid, size_t *dimfast, size_t
*padding);
int cbf_get_realarrayparameters (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, size_t *elements);
int cbf_get_realarrayparameters_wdims (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, size_t *elements, const char
**byteorder, size_t *dimfast, size_t *dimmid, size_t *dimslow, size_t
*padding);
int cbf_get_realarrayparameters_wdims_fs (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, size_t *elements, const char
**byteorder, size_t *dimfast, size_t *dimmid, size_t *dimslow, size_t
*padding);
int cbf_get_realarrayparameters_wdims_sf (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, size_t *elements, const char
**byteorder, size_t *dimslow, size_t *dimmid, size_t *dimfast, size_t
*padding);
DESCRIPTION
cbf_get_integerarrayparameters sets *compression, *binary_id, *elsize,
*elsigned, *elunsigned, *elements, *minelement and *maxelement to values
read from the binary value of the item at the current column and row. This
provides all the arguments needed for a subsequent call to
cbf_set_integerarray, if a copy of the array is to be made into another
CIF or CBF. cbf_get_realarrayparameters sets *compression, *binary_id,
*elsize, *elements to values read from the binary value of the item at the
current column and row. This provides all the arguments needed for a
subsequent call to cbf_set_realarray, if a copy of the arry is to be made
into another CIF or CBF.
The variants cbf_get_integerarrayparameters_wdims,
cbf_get_integerarrayparameters_wdims_fs,
cbf_get_integerarrayparameters_wdims_sf,
cbf_get_realarrayparameters_wdims, cbf_get_realarrayparameters_wdims_fs,
cbf_get_realarrayparameters_wdims_sf set **byteorder, *dimfast, *dimmid,
*dimslow, and *padding as well, providing the additional parameters needed
for a subsequent call to cbf_set_integerarray_wdims or
cbf_set_realarray_wdims.
The value returned in *byteorder is a pointer either to the string
"little_endian" or to the string "big_endian". This should be the byte
order of the data, not necessarily of the host machine. No attempt should
be made to modify this string. At this time only "little_endian" will be
returned.
The values returned in *dimfast, *dimmid and *dimslow are the sizes of the
fastest changing, second fastest changing and third fastest changing
dimensions of the array, if specified, or zero, if not specified.
The value returned in *padding is the size of the post-data padding, if
any and if specified in the data header. The value is given as a count of
octets.
If the value is not binary, the function returns CBF_ASCII.
ARGUMENTS
handle CBF handle.
compression Compression method used.
elsize Size in bytes of each array element.
binary_id Pointer to the destination integer binary identifier.
elsigned Pointer to an integer. Set to 1 if the elements can be
read as signed integers.
elunsigned Pointer to an integer. Set to 1 if the elements can be
read as unsigned integers.
elements Pointer to the destination number of elements.
minelement Pointer to the destination smallest element.
maxelement Pointer to the destination largest element.
byteorder Pointer to the destination byte order.
dimfast Pointer to the destination fastest dimension.
dimmid Pointer to the destination second fastest dimension.
dimslow Pointer to the destination third fastest dimension.
padding Pointer to the destination padding size.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.55 cbf_get_integerarray, cbf_get_realarray
PROTOTYPE
#include "cbf.h"
int cbf_get_integerarray (cbf_handle handle, int *binary_id, void *array,
size_t elsize, int elsigned, size_t elements, size_t *elements_read);
int cbf_get_realarray (cbf_handle handle, int *binary_id, void *array,
size_t elsize, size_t elements, size_t *elements_read);
DESCRIPTION
cbf_get_integerarray reads the binary value of the item at the current
column and row into an integer array. The array consists of elements
elements of elsize bytes each, starting at array. The elements are signed
if elsigned is non-0 and unsigned otherwise. *binary_id is set to the
binary section identifier and *elements_read to the number of elements
actually read. cbf_get_realarray reads the binary value of the item at the
current column and row into a real array. The array consists of elements
elements of elsize bytes each, starting at array. *binary_id is set to the
binary section identifier and *elements_read to the number of elements
actually read.
If any element in the integer binary data cant fit into the destination
element, the destination is set the nearest possible value.
If the value is not binary, the function returns CBF_ASCII.
If the requested number of elements cant be read, the function will read
as many as it can and then return CBF_ENDOFDATA.
Currently, the destination array must consist of chars, shorts or ints
(signed or unsigned). If elsize is not equal to sizeof (char), sizeof
(short) or sizeof (int), for cbf_get_integerarray, or sizeof(double) or
sizeof(float), for cbf_get_realarray the function returns CBF_ARGUMENT.
An additional restriction in the current version of CBFlib is that values
too large to fit in an int are not correctly decompressed. As an example,
if the machine with 32-bit ints is reading an array containing a value
outside the range 0 .. 2^32-1 (unsigned) or -2^31 .. 2^31-1 (signed), the
array will not be correctly decompressed. This restriction will be removed
in a future release. For cbf_get_realarray, only IEEE format is supported.
No conversion to other floating point formats is done at this time.
ARGUMENTS
handle CBF handle.
binary_id Pointer to the destination integer binary identifier.
array Pointer to the destination array.
elsize Size in bytes of each destination array element.
elsigned Set to non-0 if the destination array elements are
signed.
elements The number of elements to read.
elements_read Pointer to the destination number of elements actually
read.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.56 cbf_set_integerarray,
cbf_set_integerarray_wdims, cbf_set_integerarray_wdims_fs,
cbf_set_integerarray_wdims_sf,
cbf_set_realarray,
cbf_set_realarray_wdims, cbf_set_realarray_wdims_fs,
cbf_set_realarray_wdims_sf
PROTOTYPE
#include "cbf.h"
int cbf_set_integerarray (cbf_handle handle, unsigned int compression, int
binary_id, void *array, size_t elsize, int elsigned, size_t elements);
int cbf_set_integerarray_wdims (cbf_handle handle, unsigned int
compression, int binary_id, void *array, size_t elsize, int elsigned,
size_t elements, const char *byteorder, size_t dimfast, size_t dimmid,
size_t dimslow, size_t padding);
int cbf_set_integerarray_wdims_fs (cbf_handle handle, unsigned int
compression, int binary_id, void *array, size_t elsize, int elsigned,
size_t elements, const char *byteorder, size_t dimfast, size_t dimmid,
size_t dimslow, size_t padding);
int cbf_set_integerarray_wdims_sf (cbf_handle handle, unsigned int
compression, int binary_id, void *array, size_t elsize, int elsigned,
size_t elements, const char *byteorder, size_t dimslow, size_t dimmid,
size_t dimfast, size_t padding);
int cbf_set_realarray (cbf_handle handle, unsigned int compression, int
binary_id, void *array, size_t elsize, size_t elements);
int cbf_set_realarray_wdims (cbf_handle handle, unsigned int compression,
int binary_id, void *array, size_t elsize, size_t elements, const char
*byteorder, size_t dimfast, size_t dimmid, size_t dimslow, size_t
padding);
int cbf_set_realarray_wdims_fs (cbf_handle handle, unsigned int
compression, int binary_id, void *array, size_t elsize, size_t elements,
const char *byteorder, size_t dimfast, size_t dimmid, size_t dimslow,
size_t padding);
int cbf_set_realarray_wdims_sf (cbf_handle handle, unsigned int
compression, int binary_id, void *array, size_t elsize, size_t elements,
const char *byteorder, size_t dimslow, size_t dimmid, size_t dimfast,
size_t padding);
DESCRIPTION
cbf_set_integerarray sets the binary value of the item at the current
column and row to an integer array. The array consists of elements
elements of elsize bytes each, starting at array. The elements are signed
if elsigned is non-0 and unsigned otherwise. binary_id is the binary
section identifier. cbf_set_realarray sets the binary value of the item at
the current column and row to an integer array. The array consists of
elements elements of elsize bytes each, starting at array. binary_id is
the binary section identifier.
The cbf_set_integerarray_wdims, cbf_set_integerarray_wdims_fs,
cbf_set_integerarray_wdims_sf, cbf_set_realarray_wdims,
cbf_set_realarray_wdims_fs and cbf_set_realarray_wdims_sf variants allow
the data header values of byteorder, dimfast, dimmid, dimslow and padding
to be set to the data byte order, the fastest, second fastest and third
fastest array dimensions and the size in byte of the post data padding to
be used.
The array will be compressed using the compression scheme specifed by
compression. Currently, the available schemes are:
CBF_CANONICAL Canonical-code compression (section 3.3.1)
CBF_PACKED CCP4-style packing (section 3.3.2)
CBF_PACKED_V2 CCP4-style packing, version 2 (section 3.3.2)
CBF_BYTE_OFFSET Simple "byte_offset" compression.
CBF_NONE No compression. NOTE: This scheme is by far the
slowest of the four and uses much more disk space. It is
intended for routine use with small arrays only. With
large arrays (like images) it should be used only for
debugging.
The values compressed are limited to 64 bits. If any element in the array
is larger than 64 bits, the value compressed is the nearest 64-bit value.
Currently, the source array must consist of chars, shorts or ints (signed
or unsigned), for cbf_set_integerarray, or IEEE doubles or floats for
cbf_set_realarray. If elsize is not equal to sizeof (char), sizeof (short)
or sizeof (int), the function returns CBF_ARGUMENT.
ARGUMENTS
handle CBF handle.
compression Compression method to use.
binary_id Integer binary identifier.
array Pointer to the source array.
elsize Size in bytes of each source array element.
elsigned Set to non-0 if the source array elements are signed.
elements: The number of elements in the array.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.53 cbf_set_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.57 cbf_failnez
DEFINITION
#include "cbf.h"
#define cbf_failnez(f) {int err; err = (f); if (err) return err; }
DESCRIPTION
cbf_failnez is a macro used for error propagation throughout CBFlib.
cbf_failnez executes the function f and saves the returned error value. If
the error value is non-0, cbf_failnez executes a return with the error
value as argument. If CBFDEBUG is defined, then a report of the error is
also printed to the standard error stream, stderr, in the form
CBFlib error f in "symbol"
where f is the decimal value of the error and symbol is the symbolic form.
ARGUMENTS
f Integer error value.
SEE ALSO
2.3.58 cbf_onfailnez
----------------------------------------------------------------------
2.3.58 cbf_onfailnez
DEFINITION
#include "cbf.h"
#define cbf_onfailnez(f,c) {int err; err = (f); if (err) {{c; }return err;
}}
DESCRIPTION
cbf_onfailnez is a macro used for error propagation throughout CBFlib.
cbf_onfailnez executes the function f and saves the returned error value.
If the error value is non-0, cbf_failnez executes first the statement c
and then a return with the error value as argument. If CBFDEBUG is
defined, then a report of the error is also printed to the standard error
stream, stderr, in the form
CBFlib error f in "symbol"
where f is the decimal value of the error and symbol is the symbolic form.
ARGUMENTS
f integer function to execute.
c statement to execute on failure.
SEE ALSO
* 2.3.57 cbf_failnez
----------------------------------------------------------------------
2.3.59 cbf_require_datablock
PROTOTYPE
#include "cbf.h"
int cbf_require_datablock (cbf_handle handle, const char
*datablockname);
DESCRIPTION
cbf_require_datablock makes the data block with name datablockname the
current data block, if it exists, or creates it if it does not.
The comparison is case-insensitive.
The current category becomes undefined.
ARGUMENTS
handle CBF handle.
datablockname The name of the data block to find or create.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.25 cbf_next_datablock
2.3.29 cbf_find_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.31 cbf_find_column
2.3.32 cbf_find_row
2.3.42 cbf_datablock_name
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.60 cbf_require_category
PROTOTYPE
#include "cbf.h"
int cbf_require_category (cbf_handle handle, const char *categoryname);
DESCRIPTION
cbf_rewuire_category makes the category in the current data block with
name categoryname the current category, if it exists, or creates the
catagory if it does not exist.
The comparison is case-insensitive.
The current column and row become undefined.
ARGUMENTS
handle CBF handle.
categoryname The name of the category to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
2.3.29 cbf_find_datablock
2.3.31 cbf_find_column
2.3.32 cbf_find_row
2.3.43 cbf_category_name
2.3.59 cbf_require_datablock
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.61 cbf_require_column
PROTOTYPE
#include "cbf.h"
int cbf_require_column (cbf_handle handle, const char *columnname);
DESCRIPTION
cbf_require_column makes the columns in the current category with name
columnname the current column, if it exists, or creates it if it does
not.
The comparison is case-insensitive.
The current row is not affected.
ARGUMENTS
handle CBF handle.
columnname The name of column to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.19 cbf_rewind_column
2.3.27 cbf_next_column
2.3.29 cbf_find_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.32 cbf_find_row
2.3.44 cbf_column_name, cbf_set_column_name
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
----------------------------------------------------------------------
2.3.62 cbf_require_column_value
PROTOTYPE
#include "cbf.h"
int cbf_require_column_value (cbf_handle handle, const char *columnname,
const char **value, const char *defaultvalue);
DESCRIPTION
cbf_require_column_doublevalue sets *value to the ASCII item at the
current row for the column given with the name given by *columnname, or
to the string given by defaultvalue if the item cannot be found.
ARGUMENTS
handle CBF handle.
columnname Name of the column containing the number.
value pointer to the location to receive the value.
defaultvalue Value to use if the requested column and value cannot
be found.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.63 cbf_require_column_integervalue
PROTOTYPE
#include "cbf.h"
int cbf_require_column_integervalue (cbf_handle handle, const char
*columnname, int *number, const int defaultvalue);
DESCRIPTION
cbf_require_column_doublevalue sets *number to the value of the ASCII
item at the current row for the column given with the name given by
*columnname, with the value interpreted as an integer number, or to the
number given by defaultvalue if the item cannot be found.
ARGUMENTS
handle CBF handle.
columnname Name of the column containing the number.
number pointer to the location to receive the integer value.
defaultvalue Value to use if the requested column and value cannot
be found.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.64 cbf_require_column_doublevalue
PROTOTYPE
#include "cbf.h"
int cbf_require_column_doublevalue (cbf_handle handle, const char
*columnname, double *number, const double defaultvalue);
DESCRIPTION
cbf_require_column_doublevalue sets *number to the value of the ASCII
item at the current row for the column given with the name given by
*columnname, with the value interpreted as a decimal floating-point
number, or to the number given by defaultvalue if the item cannot be
found.
ARGUMENTS
handle CBF handle.
columnname Name of the column containing the number.
number pointer to the location to receive the floating-point
value.
defaultvalue Value to use if the requested column and value cannot
be found.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
----------------------------------------------------------------------
2.3.65 cbf_get_local_integer_byte_order, cbf_get_local_real_byte_order,
cbf_get_local_real_format
PROTOTYPE
#include "cbf.h"
int cbf_get_local_integer_byte_order (char ** byte_order);
int cbf_get_local_real_byte_order (char ** byte_order);
int cbf_get_local_real_format (char ** real_format );
DESCRIPTION
cbf_get_local_integer_byte_order returns the byte order of integers on
the machine on which the API is being run in the form of a character
string returned as the value pointed to by byte_order.
cbf_get_local_real_byte_order returns the byte order of reals on the
machine on which the API is being run in the form of a character string
returned as the value pointed to by byte_order.
cbf_get_local_real_format returns the format of floats on the machine on
which the API is being run in the form of a character string returned as
the value pointed to by real_format. The strings returned must not be
modified in any way.
The values returned in byte_order may be the strings "little_endian" or
"big-endian". The values returned in real_format may be the strings
"ieee 754-1985" or "other". Additional values may be returned by future
versions of the API.
ARGUMENTS
byte_order pointer to the returned string
real_format pointer to the returned string
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.66 cbf_get_dictionary, cbf_set_dictionary, cbf_require_dictionary
PROTOTYPE
#include "cbf.h"
int cbf_get_dictionary (cbf_handle handle, cbf_handle * dictionary);
int cbf_set_dictionary (cbf_handle handle, cbf_handle dictionary_in);
int cbf_require_dictionary (cbf_handle handle, cbf_handle * dictionary)
DESCRIPTION
cbf_get_dictionary sets *dictionary to the handle of a CBF which has
been associated with the CBF handle by cbf_set_dictionary.
cbf_set_dictionary associates the CBF handle dictionary_in with handle
as its dictionary. cbf_require_dictionary sets *dictionary to the handle
of a CBF which has been associated with the CBF handle by
cbf_set_dictionary or creates a new empty CBF and associates it with
handle, returning the new handle in *dictionary.
ARGUMENTS
handle CBF handle.
dictionary Pointer to CBF handle of dictionary.
dictionary_in CBF handle of dcitionary.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.67 cbf_convert_dictionary
PROTOTYPE
#include "cbf.h"
int cbf_convert_dictionary (cbf_handle handle, cbf_handle dictionary )
DESCRIPTION
cbf_convert_dictionary converts dictionary as a DDL1 or DDL2 dictionary
to a CBF dictionary of category and item properties for handle, creating
a new dictionary if none exists or layering the definitions in
dictionary onto the existing dictionary of handle if one exists.
If a CBF is read into handle after calling cbf_convert_dictionary, then
the dictionary will be used for validation of the CBF as it is read.
ARGUMENTS
handle CBF handle.
dictionary CBF handle of dictionary.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.68 cbf_find_tag, cbf_find_local_tag
PROTOTYPE
#include "cbf.h"
int cbf_find_tag (cbf_handle handle, const char *tag)
int cbf_find_local_tag (cbf_handle handle, const char *tag)
DESCRIPTION
cbf_find_tag searches all of the CBF handle for the CIF tag given by the
string tag and makes it the current tag. The search does not include the
dictionary, but does include save frames as well as categories.
The string tag is the complete tag in either DDL1 or DDL2 format,
starting with the leading underscore, not just a category or column.
ARGUMENTS
handle CBF handle.
tag CIF tag.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.69 cbf_find_category_root, cbf_set_category_root,
cbf_require_category_root
PROTOTYPE
#include "cbf.h"
int cbf_find_category_root (cbf_handle handle, const char* categoryname,
const char** categoryroot);
int cbf_set_category_root (cbf_handle handle, const char*
categoryname_in, const char*categoryroot);
int cbf_require_category_root (cbf_handle handle, const char*
categoryname, const char** categoryroot);
DESCRIPTION
cbf_find_category_root sets *categoryroot to the root category of which
categoryname is an alias. cbf_set_category_root sets categoryname_in as
an alias of categoryroot in the dictionary associated with handle,
creating the dictionary if necessary. cbf_require_category_root sets
*categoryroot to the root category of which categoryname is an alias, if
there is one, or to the value of categoryname, if categoryname is not an
alias.
A returned categoryroot string must not be modified in any way.
ARGUMENTS
handle CBF handle.
categoryname category name which may be an alias.
categoryroot pointer to a returned category root name.
categoryroot_in input category root name.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.70 cbf_find_tag_root, cbf_set_tag_root, cbf_require_tag_root
PROTOTYPE
#include "cbf.h"
int cbf_find_tag_root (cbf_handle handle, const char* tagname, const
char** tagroot);
int cbf_set_tag_root (cbf_handle handle, const char* tagname, const
char*tagroot_in);
int cbf_require_tag_root (cbf_handle handle, const char* tagname, const
char** tagroot);
DESCRIPTION
cbf_find_tag_root sets *tagroot to the root tag of which tagname is an
alias. cbf_set_tag_root sets tagname as an alias of tagroot_in in the
dictionary associated with handle, creating the dictionary if necessary.
cbf_require_tag_root sets *tagroot to the root tag of which tagname is
an alias, if there is one, or to the value of tagname, if tagname is not
an alias.
A returned tagroot string must not be modified in any way.
ARGUMENTS
handle CBF handle.
tagname tag name which may be an alias.
tagroot pointer to a returned tag root name.
tagroot_in input tag root name.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.71 cbf_find_tag_category, cbf_set_tag_category
PROTOTYPE
#include "cbf.h"
int cbf_find_tag_category (cbf_handle handle, const char* tagname, const
char** categoryname);
int cbf_set_tag_category (cbf_handle handle, const char* tagname, const
char* categoryname_in);
DESCRIPTION
cbf_find_tag_category sets categoryname to the category associated with
tagname in the dictionary associated with handle. cbf_set_tag_category
upddates the dictionary associated with handle to indicated that tagname
is in category categoryname_in.
ARGUMENTS
handle CBF handle.
tagname tag name.
categoryname pointer to a returned category name.
categoryname_in input category name.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
----------------------------------------------------------------------
2.4 High-level function prototypes
2.4.1 cbf_read_template
PROTOTYPE
#include "cbf_simple.h"
int cbf_read_template (cbf_handle handle, FILE *file);
DESCRIPTION
cbf_read_template reads the CBF or CIF file file into the CBF object
specified by handle and selects the first datablock as the current
datablock.
ARGUMENTS
handle Pointer to a CBF handle.
file Pointer to a file descriptor.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.2 cbf_get_diffrn_id, cbf_require_diffrn_id
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_diffrn_id (cbf_handle handle, const char **diffrn_id);
int cbf_require_diffrn_id (cbf_handle handle, const char **diffrn_id,
const char *default_id)
DESCRIPTION
cbf_get_diffrn_id sets *diffrn_id to point to the ASCII value of the
"diffrn.id" entry. cbf_require_diffrn_id also sets *diffrn_id to point
to the ASCII value of the "diffrn.id" entry, but, if the "diffrn.id"
entry does not exist, it sets the value in the CBF and in*diffrn_id to
the character string given by default_id, creating the category and
column is necessary.
The diffrn_id will be valid as long as the item exists and has not been
set to a new value.
The diffrn_id must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
diffrn_id Pointer to the destination value pointer.
default_id Character string default value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.3 cbf_set_diffrn_id
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_diffrn_id (cbf_handle handle, const char *diffrn_id);
DESCRIPTION
cbf_set_diffrn_id sets the "diffrn.id" entry of the current datablock to
the ASCII value diffrn_id.
This function also changes corresponding "diffrn_id" entries in the
"diffrn_source", "diffrn_radiation", "diffrn_detector" and
"diffrn_measurement" categories.
ARGUMENTS
handle CBF handle.
diffrn_id ASCII value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.4 cbf_get_crystal_id
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_crystal_id (cbf_handle handle, const char **crystal_id);
DESCRIPTION
cbf_get_crystal_id sets *crystal_id to point to the ASCII value of the
"diffrn.crystal_id" entry.
If the value is not ASCII, the function returns CBF_BINARY.
The value will be valid as long as the item exists and has not been set
to a new value.
The value must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
crystal_id Pointer to the destination value pointer.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.5 cbf_set_crystal_id
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_crystal_id (cbf_handle handle, const char *crystal_id);
DESCRIPTION
cbf_set_crystal_id sets the "diffrn.crystal_id" entry to the ASCII value
crystal_id.
ARGUMENTS
handle CBF handle.
crystal_id ASCII value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.6 cbf_get_wavelength
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_wavelength (cbf_handle handle, double *wavelength);
DESCRIPTION
cbf_get_wavelength sets *wavelength to the current wavelength in AA.
ARGUMENTS
handle CBF handle.
wavelength Pointer to the destination.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.7 cbf_set_wavelength
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_wavelength (cbf_handle handle, double wavelength);
DESCRIPTION
cbf_set_wavelength sets the current wavelength in AA to wavelength.
ARGUMENTS
handle CBF handle.
wavelength Wavelength in AA.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.8 cbf_get_polarization
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_polarization (cbf_handle handle, double
*polarizn_source_ratio, double *polarizn_source_norm);
DESCRIPTION
cbf_get_polarization sets *polarizn_source_ratio and
*polarizn_source_norm to the corresponding source polarization
parameters.
Either destination pointer may be NULL.
ARGUMENTS
handle CBF handle.
polarizn_source_ratio Pointer to the destination
polarizn_source_ratio.
polarizn_source_norm Pointer to the destination
polarizn_source_norm.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.9 cbf_set_polarization
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_polarization (cbf_handle handle, double
polarizn_source_ratio, double polarizn_source_norm);
DESCRIPTION
cbf_set_polarization sets the source polarization to the values
specified by polarizn_source_ratio and polarizn_source_norm.
ARGUMENTS
handle CBF handle.
polarizn_source_ratio New value of polarizn_source_ratio.
polarizn_source_norm New value of polarizn_source_norm.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.10 cbf_get_divergence
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_divergence (cbf_handle handle, double *div_x_source, double
*div_y_source, double *div_x_y_source);
DESCRIPTION
cbf_get_divergence sets *div_x_source, *div_y_source and *div_x_y_source
to the corresponding source divergence parameters.
Any of the destination pointers may be NULL.
ARGUMENTS
handle CBF handle.
div_x_source Pointer to the destination div_x_source.
div_y_source Pointer to the destination div_y_source.
div_x_y_source Pointer to the destination div_x_y_source.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.11 cbf_ set_divergence
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_divergence (cbf_handle handle, double div_x_source, double
div_y_source, double div_x_y_source);
DESCRIPTION
cbf_set_divergence sets the source divergence parameters to the values
specified by div_x_source, div_y_source and div_x_y_source.
ARGUMENTS
handle CBF handle.
div_x_source New value of div_x_source.
div_y_source New value of div_y_source.
div_x_y_source New value of div_x_y_source.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.12 cbf_count_elements
PROTOTYPE
#include "cbf_simple.h"
int cbf_count_elements (cbf_handle handle, unsigned int *elements);
DESCRIPTION
cbf_count_elements sets *elements to the number of detector elements.
ARGUMENTS
handle CBF handle.
elements Pointer to the destination count.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.13 cbf_get_element_id
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_element_id (cbf_handle handle, unsigned int element_number,
const char **element_id);
DESCRIPTION
cbf_get_element_id sets *element_id to point to the ASCII value of the
element_number'th "diffrn_data_frame.detector_element_id" entry,
counting from 0.
If the detector element does not exist, the function returns
CBF_NOTFOUND.
The element_id will be valid as long as the item exists and has not been
set to a new value.
The element_id must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
element_id Pointer to the destination.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.14 cbf_get_gain
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_gain (cbf_handle handle, unsigned int element_number, double
*gain, double *gain_esd);
DESCRIPTION
cbf_get_gain sets *gain and *gain_esd to the corresponding gain
parameters for element number element_number.
Either of the destination pointers may be NULL.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
gain Pointer to the destination gain.
gain_esd Pointer to the destination gain_esd.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.15 cbf_ set_gain
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_gain (cbf_handle handle, unsigned int element_number, double
gain, double gain_esd);
DESCRIPTION
cbf_set_gain sets the gain of element number element_number to the
values specified by gain and gain_esd.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
gain New gain value.
gain_esd New gain_esd value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.16 cbf_get_overload
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_overload (cbf_handle handle, unsigned int element_number,
double *overload);
DESCRIPTION
cbf_get_overload sets *overload to the overload value for element number
element_number.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
overload Pointer to the destination overload.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.17 cbf_ set_overload
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_overload (cbf_handle handle, unsigned int element_number,
double overload);
DESCRIPTION
cbf_set_overload sets the overload value of element number
element_number to overload.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
overload New overload value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.18 cbf_get_integration_time
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_integration_time (cbf_handle handle, unsigned int reserved,
double *time);
DESCRIPTION
cbf_get_integration_time sets *time to the integration time in seconds.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
time Pointer to the destination time.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.19 cbf_set_integration_time
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_integration_time (cbf_handle handle, unsigned int reserved,
double time);
DESCRIPTION
cbf_set_integration_time sets the integration time in seconds to the
value specified by time. The parameter reserved is presently unused and
should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
time Integration time in seconds.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.20 cbf_get_timestamp
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_timestamp (cbf_handle handle, unsigned int reserved, double
*time, int *timezone);
DESCRIPTION
cbf_get_timestamp sets *time to the collection timestamp in seconds
since January 1 1970. *timezone is set to timezone difference from UTC
in minutes. The parameter reserved is presently unused and should be set
to 0.
Either of the destination pointers may be NULL.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
time Pointer to the destination collection timestamp.
timezone Pointer to the destination timezone difference.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.21 cbf_set_timestamp
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_timestamp (cbf_handle handle, unsigned int reserved, double
time, int timezone, double precision);
DESCRIPTION
cbf_set_timestamp sets the collection timestamp in seconds since January
1 1970 to the value specified by time. The timezone difference from UTC
in minutes is set to timezone. If no timezone is desired, timezone
should be CBF_NOTIM EZONE. The parameter reserved is presently unused
and should be set to 0.
The precision of the new timestamp is specified by the value precision
in seconds. If precision is 0, the saved timestamp is assumed accurate
to 1 second.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
time Timestamp in seconds since January 1 1970.
timezone Timezone difference from UTC in minutes or CBF_NOTIMEZONE.
precision Timestamp precision in seconds.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.22 cbf_get_datestamp
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_datestamp (cbf_handle handle, unsigned int reserved, int
*year, int *month, int *day, int *hour, int *minute, double *second, int
*timezone);
DESCRIPTION
cbf_get_datestamp sets *year, *month, *day, *hour, *minute and *second
to the corresponding values of the collection timestamp. *timezone is
set to timezone difference from UTC in minutes. The parameter <
i>reserved is presently unused and should be set to 0.
Any of the destination pointers may be NULL.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
year Pointer to the destination timestamp year.
month Pointer to the destination timestamp month (1-12).
day Pointer to the destination timestamp day (1-31).
hour Pointer to the destination timestamp hour (0-23).
minute Pointer to the destination timestamp minute (0-59).
second Pointer to the destination timestamp second (0-60.0).
timezone Pointer to the destination timezone difference from UTC in
minutes.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.23 cbf_set_datestamp
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_datestamp (cbf_handle handle, unsigned int reserved, int
year, int month, int day, int hour, int minute, double second, int
timezone, double precision);
DESCRIPTION
cbf_set_datestamp sets the collection timestamp in seconds since January
1 1970 to the value specified by time. The timezone difference from UTC
in minutes is set to timezone. If no timezone is desired, timezone
should be CBF_NOTIM EZONE. The parameter reserved is presently unused
and should be set to 0.
The precision of the new timestamp is specified by the value precision
in seconds. If precision is 0, the saved timestamp is assumed accurate
to 1 second.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
time Timestamp in seconds since January 1 1970.
timezone Timezone difference from UTC in minutes or CBF_NOTIMEZONE.
precision Timestamp precision in seconds.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.24 cbf_set_current_timestamp
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_current_timestamp (cbf_handle handle, unsigned int reserved,
int timezone);
DESCRIPTION
cbf_set_current_timestamp sets the collection timestamp to the current
time. The timezone difference from UTC in minutes is set to timezone. If
no timezone is desired, timezone should be CBF_NOTIMEZONE. If no
timezone is used, the timest amp will be UTC. The parameter reserved is
presently unused and should be set to 0.
The new timestamp will have a precision of 1 second.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
timezone Timezone difference from UTC in minutes or CBF_NOTIMEZONE.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.25 cbf_get_image_size, cbf_get_image_size_fs, cbf_get_image_size_sf,
cbf_get_3d_image_size, cbf_get_3d_image_size_fs,
cbf_get_3d_image_size_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_image_size (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimslow, size_t *ndimfast);
int cbf_get_image_size_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimfast, size_t *ndimslow);
int cbf_get_image_size_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimslow, size_t *ndimfast);
int cbf_get_3d_image_size (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimslow, size_t *ndimmid, size_t
*ndimfast);
int cbf_get_3d_image_size_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimfast, size_t *ndimmid, size_t
*ndimslow);
int cbf_get_3d_image_size_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimslow, size_t *ndimmid, size_t
*ndimfast);
DESCRIPTION
cbf_get_image_size, cbf_get_image_size_fs and cbf_get_image_size_sf set
*ndimslow and *ndimfast to the slow and fast dimensions of the image
array for element number element_number. If the array is 1-dimensional,
*ndimslow will be set to the array size and *ndimfast will be set to 1.
If the array is 3-dimensional an error code will be returned.
cbf_get_3d_image_size, cbf_get_3d_image_size_fs and
cbf_get_3d_image_size_sf set *ndimslow, *ndimmid and *ndimfast to the
slowest, next fastest and fastest dimensions, respectively, of the 3D
image array for element number element_number. If the array is
1-dimensional, *ndimslow will be set to the array size and *ndimmid and
*ndimfast will be set to 1. If the array is 2-dimensional *ndimslow and
*ndimmid will be set as for a call to cbf_get_image_size and *ndimfast
will be set to 1.
The _fs calls give the dimensions in a fast-to-slow order. The calls
with no suffix and the calls _sf calls give the dimensions in
slow-to-fast order
Note that the ordering of dimensions is specified by values of the tag
_array_structure_list.precedence with a precedence of 1 for the fastest
dimension, 2 for the next slower, etc., which is opposite to the
ordering of the dimension arguments for these functions, except for the
ones with the _fs suffix..
Any of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
ndimslow Pointer to the destination slowest dimension.
ndimmid Pointer to the destination next faster dimension.
ndimfast Pointer to the destination fastest dimension.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.26 cbf_get_image, cbf_get_image_fs, cbf_get_image_sf,
cbf_get_real_image, cbf_get_real_image_fs, cbf_get_real_image_sf,
cbf_get_3d_image, cbf_get_3d_image_fs, cbf_get_3d_image_sf,
cbf_get_real_3d_image, cbf_get_real_3d_image_fs,
cbf_get_real_3d_image_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_image (cbf_handle handle, unsigned int reserved, unsigned
int element_number, void *array, size_t elsize, int elsign, size_t
ndimslow, size_t ndimfast);
int cbf_get_image_fs (cbf_handle handle, unsigned int reserved, unsigned
int element_number, void *array, size_t elsize, int elsign, size_t
ndimfast, size_t ndimslow);
int cbf_get_image_sf (cbf_handle handle, unsigned int reserved, unsigned
int element_number, void *array, size_t elsize, int elsign, size_t
ndimslow, size_t ndimfast);
int cbf_get_real_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimslow, size_t ndimfast);
int cbf_get_real_image_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimfast, size_t ndimslow);
int cbf_get_real_image_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimslow, size_t ndimfast);
int cbf_get_3d_image (cbf_handle handle, unsigned int reserved, unsigned
int element_number, void *array, size_t elsize, int elsign, size_t
ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_get_3d_image_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, int elsign,
size_t ndimfast, size_t ndimmid, size_t ndimslow);
int cbf_get_3d_image_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, int elsign,
size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_get_real_3d_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_get_real_3d_image_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimfast, size_t ndimmid, size_t ndimslow);
int cbf_get_real_3d_image_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimslow, size_t ndimmid, size_t ndimfast);
DESCRIPTION
cbf_get_image, cbf_get_image_fs and cbf_get_image_sf read the image
array for element number element_number into an array. The array
consists of ndimslow *ndimfast elements of elsize bytes each, starting
at array. The elements are signed if elsign is non-0 and unsigned
otherwise. cbf_get_real_image, cbf_get_real_image_fs and
cbf_get_real_image_sf read the image array of IEEE doubles or floats for
element number element_number into an array. A real array is always
signed. cbf_get_3d_image, cbf_get_3d_image_fs and cbf_get_3d_image_sf
read the 3D image array for element number element_number into an array.
The array consists of ndimslow *ndimmid *ndimfast elements of elsize
bytes each, starting at array. The elements are signed if elsign is
non-0 and unsigned otherwise. cbf_get_real_3d_image,
cbf_get_real_3d_image_fs, cbf_get_real_3d_image_sf reads the 3D image
array of IEEE doubles or floats for element number element_number into
an array. A real array is always signed.
The _fs calls give the dimensions in a fast-to-slow order. The calls
with no suffix and the calls _sf calls give the dimensions in
slow-to-fast order
The structure of the array as a 1-, 2- or 3-dimensional array should
agree with the structure of the array given in the ARRAY_STRUCTURE_LIST
category. If the array is 1-dimensional, ndimslow should be the array
size and ndimfast and, for the 3D calls, ndimmid, should be set to 1
both in the call and in the imgCIF data being processed. If the array is
2-dimensional and a 3D call is used, ndimslow and ndimmid should be the
array dimensions and ndimfast should be set to 1 both in the call and in
the imgCIF data being processed.
If any element in the binary data canOt fit into the destination
element, the destination is set the nearest possible value.
If the value is not binary, the function returns CBF_ASCII.
If the requested number of elements canOt be read, the function will
read as many as it can and then return CBF_ENDOFDATA.
Currently, the destination array must consist of chars, shorts or ints
(signed or unsigned) for cbf_get_image, or IEEE doubles or floats for
cbf_get_real_image. If elsize is not equal to sizeof (char), sizeof
(short), sizeof (int), sizeof(double) or sizeof(float), the function
returns CBF_ARGUMENT.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
array Pointer to the destination array.
elsize Size in bytes of each destination array element.
elsigned Set to non-0 if the destination array elements are
signed.
ndimslow Slowest array dimension.
ndimmid Next faster array dimension.
ndimfast Fastest array dimension.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.27 cbf_set_image, cbf_set_image_fs, cbf_set_image_sf,
cbf_set_real_image, cbf_set_real_image_fs, cbf_set_real_image_sf,
cbf_set_3d_image, cbf_set_3d_image, cbf_set_3d_image,
cbf_set_real_3d_image, cbf_set_real_3d_image_fs,
cbf_set_real_3d_image_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_image (cbf_handle handle, unsigned int reserved, unsigned
int element_number, unsigned int compression, void *array, size_t
elsize, int elsign, size_t ndimslow, size_t ndimfast);
int cbf_set_image_fs(cbf_handle handle, unsigned int reserved, unsigned
int element_number, unsigned int compression, void *array, size_t
elsize, int elsign, size_t ndimfast, size_t ndimslow);
int cbf_set_image_sf(cbf_handle handle, unsigned int reserved, unsigned
int element_number, unsigned int compression, void *array, size_t
elsize, int elsign, size_t ndimslow, size_t ndimfast);
int cbf_set_real_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimslow, size_t ndimfast);
int cbf_set_real_image_fs(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimfast, size_t ndimslow);
int cbf_set_real_image_sf(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimslow, size_t ndimfast);
int cbf_set_3d_image (cbf_handle handle, unsigned int reserved, unsigned
int element_number, unsigned int compression, void *array, size_t
elsize, int elsign, size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_set_3d_image_fs(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void *array,
size_t elsize, int elsign, size_t ndimfast, size_t ndimmid, size_t
ndimslow);
int cbf_set_3d_image_sf(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void *array,
size_t elsize, int elsign, size_t ndimslow, size_t ndimmid, size_t
ndimfast);
int cbf_set_real_3d_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_set_real_3d_image_fs(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimfast, size_t ndimmid, size_t ndimslow);
int cbf_set_real_3d_image_sf(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimslow, size_t ndimmid, size_t ndimfast);
DESCRIPTION
cbf_set_image, cbf_set_image_fs and cbf_set_image_sf write the image
array for element number element_number. The array consists of ndimfast
*ndimslow elements of elsize bytes each, starting at array. The elements
are signed if elsign is non-zero and unsigned otherwise.
cbf_set_real_image, cbf_set_real_image_fs and cbf_set_real_image_sf
write the image array for element number element_number. The array
consists of ndimfast *ndimslow IEEE double or float elements of elsize
bytes each, starting at array. cbf_set_3d_image, cbf_set_3d_image_fs and
cbf_set_3d_image_sf write the 3D image array for element number
element_number. The array consists of ndimfast *ndimmid *ndimslow
elements of elsize bytes each, starting at array. The elements are
signed if elsign is non-0 and unsigned otherwise. cbf_set_real_3d_image,
cbf_set_real_3d_image_fs and cbf_set_real_3d_image_sf writes the 3D
image array for element number element_number. The array consists of
ndimfast *ndimmid *ndimslow IEEE double or float elements of elsize
bytes each, starting at array.
The _fs calls give the dimensions in a fast-to-slow order. The calls
with no suffix and the calls _sf calls give the dimensions in
slow-to-fast order
If the array is 1-dimensional, ndimslow should be the array size and
ndimfast and, for the 3D calls, ndimmid, should be set to 1. If the
array is 2-dimensional and the 3D calls are used, ndimslow and ndimmid
should be used for the array dimensions and ndimfast should be set to 1.
The array will be compressed using the compression scheme specifed by
compression. Currently, the available schemes are:
CBF_CANONICAL Canonical-code compression (section 3.3.1)
CBF_PACKED CCP4-style packing (section 3.3.2)
CBF_PACKED_V2 CCP4-style packing, version 2 (section 3.3.2)
CBF_BYTE_OFFSET Simple "byte_offset" compression.
CBF_NONE No compression.
The values compressed are limited to 64 bits. If any element in the
array is larger than 64 bits, the value compressed is the nearest 64-bit
value.
Currently, the source array must consist of chars, shorts or ints
(signed or unsigned)for cbf_set_image, or IEEE doubles or floats for
cbf_set_real_image. If elsize is not equal to sizeof (short), sizeof
(int), sizeof(double) or sizeof(float), the function returns
CBF_ARGUMENT.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
compression Compression type.
array Pointer to the image array.
elsize Size in bytes of each image array element.
elsigned Set to non-0 if the image array elements are signed.
ndimslow Slowest array dimension.
ndimmid Second slowest array dimension.
ndimfast Fastest array dimension.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.28 cbf_get_axis_setting
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_axis_setting (cbf_handle handle, unsigned int reserved,
const char *axis_id, double *start, double *increment);
DESCRIPTION
cbf_get_axis_setting sets *start and *increment to the corresponding
values of the axis axis_id.
Either of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
axis_id Axis id.
start Pointer to the destination start value.
increment Pointer to the destination increment value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.29 cbf_set_axis_setting
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_axis_setting (cbf_handle handle, unsigned int reserved,
const char *axis_id, double start, double increment);
DESCRIPTION
cbf_set_axis_setting sets the starting and increment values of the axis
axis_id to start and increment.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
axis_id Axis id.
start Start value.
increment Increment value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.30 cbf_construct_goniometer
PROTOTYPE
#include "cbf_simple.h"
int cbf_construct_goniometer (cbf_handle handle, cbf_goniometer
*goniometer);
DESCRIPTION
cbf_construct_goniometer constructs a goniometer object using the
description in the CBF object handle and initialises the goniometer
handle *goniometer.
ARGUMENTS
handle CBF handle.
goniometer Pointer to the destination goniometer handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.31 cbf_free_goniometer
PROTOTYPE
#include "cbf_simple.h"
int cbf_free_goniometer (cbf_goniometer goniometer);
DESCRIPTION
cbf_free_goniometer destroys the goniometer object specified by
goniometer and frees all associated memory.
ARGUMENTS
goniometer Goniometer handle to free.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.32 cbf_get_rotation_axis
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_rotation_axis (cbf_goniometer goniometer, unsigned int
reserved, double *vector1, double *vector2, double *vector3);
DESCRIPTION
cbf_get_rotation_axis sets *vector1, *vector2, and *vector3 to the 3
components of the goniometer rotation axis used for the exposure.
Any of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
goniometer Goniometer handle.
reserved Unused. Any value other than 0 is invalid.
vector1 Pointer to the destination x component of the rotation
axis.
vector2 Pointer to the destination y component of the rotation
axis.
vector3 Pointer to the destination z component of the rotation
axis.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.33 cbf_get_rotation_range
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_rotation_range (cbf_goniometer goniometer, unsigned int
reserved, double *start, double *increment);
DESCRIPTION
cbf_get_rotation_range sets *start and *increment to the corresponding
values of the goniometer rotation axis used for the exposure.
Either of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
goniometer Goniometer handle.
reserved Unused. Any value other than 0 is invalid.
start Pointer to the destination start value.
increment Pointer to the destination increment value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.34 cbf_rotate_vector
PROTOTYPE
#include "cbf_simple.h"
int cbf_rotate_vector (cbf_goniometer goniometer, unsigned int reserved,
double ratio, double initial1, double initial2, double initial3, double
*final1, double *final2, double *final3);
DESCRIPTION
cbf_rotate_vector sets *final1, *final2, and *final3 to the 3 components
of the of the vector (initial1, initial2, initial3) after reorientation
by applying the goniometer rotations. The value ratio specif ies the
goniometer setting and varies from 0.0 at the beginning of the exposure
to 1.0 at the end, irrespective of the actual rotation range.
Any of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
goniometer Goniometer handle.
reserved Unused. Any value other than 0 is invalid.
ratio Goniometer setting. 0 = beginning of exposure, 1 = end.
initial1 x component of the initial vector.
initial2 y component of the initial vector.
initial3 z component of the initial vector.
vector1 Pointer to the destination x component of the final
vector.
vector2 Pointer to the destination y component of the final
vector.
vector3 Pointer to the destination z component of the final
vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.35 cbf_get_reciprocal
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_reciprocal (cbf_goniometer goniometer, unsigned int
reserved, double ratio, double wavelength, double real1, double real2,
double real3, double *reciprocal1, double *reciprocal2, double
*reciprocal3);
DESCRIPTION
cbf_get_reciprocal sets *reciprocal1, * reciprocal2, and * reciprocal3
to the 3 components of the of the reciprocal-space vector corresponding
to the real-space vector (real1, real2, real3). The reciprocal-space
vector is oriented to correspond to the goniometer setting with all axes
at 0. The value wavelength is the wavlength in AA and the value ratio
specifies the current goniometer setting and varies from 0.0 at the
beginning of the exposur e to 1.0 at the end, irrespective of the actual
rotation range.
Any of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
goniometer Goniometer handle.
reserved Unused. Any value other than 0 is invalid.
ratio Goniometer setting. 0 = beginning of exposure, 1 = end.
wavelength Wavelength in AA.
real1 x component of the real-space vector.
real2 y component of the real-space vector.
real3 z component of the real-space vector.
reciprocal1 Pointer to the destination x component of the
reciprocal-space vector.
reciprocal2 Pointer to the destination y component of the
reciprocal-space vector.
reciprocal3 Pointer to the destination z component of the
reciprocal-space vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.36 cbf_construct_detector, cbf_construct_reference_detector,
cbf_require_reference_detector
PROTOTYPE
#include "cbf_simple.h"
int cbf_construct_detector (cbf_handle handle, cbf_detector *detector,
unsigned int element_number);
int cbf_construct_reference_detector (cbf_handle handle, cbf_detector
*detector, unsigned int element_number);
int cbf_require_reference_detector (cbf_handle handle, cbf_detector
*detector, unsigned int element_number);
DESCRIPTION
cbf_construct_detector constructs a detector object for detector element
number element_number using the description in the CBF object handle and
initialises the detector handle *detector.
cbf_construct_reference_detector constructs a detector object for
detector element number element_number using the description in the CBF
object handle and initialises the detector handle *detector using the
reference settings of the axes. cbf_require_reference_detector is
similar, but try to force the creations of missing intermediate
categories needed to construct a detector object.
ARGUMENTS
handle CBF handle.
detector Pointer to the destination detector handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.37 cbf_free_detector
PROTOTYPE
#include "cbf_simple.h"
int cbf_free_detector (cbf_detector detector);
DESCRIPTION
cbf_free_detector destroys the detector object specified by detector and
frees all associated memory.
ARGUMENTS
detector Detector handle to free.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.38 cbf_get_beam_center, cbf_get_beam_center_fs, cbf_get_beam_center_sf,
cbf_set_beam_center, cbf_set_beam_center_fs, cbf_set_beam_center_sf,
set_reference_beam_center, set_reference_beam_center_fs,
set_reference_beam_center_fs
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_beam_center (cbf_detector detector, double *indexslow,
double *indexfast, double *centerslow, double *centerfast);
int cbf_get_beam_center_fs (cbf_detector detector, double *indexfast,
double *indexslow, double *centerfast, double *centerslow);
int cbf_get_beam_center_sf (cbf_detector detector, double *indexslow,
double *indexfast, double *centerslow, double *centerfast);
int cbf_set_beam_center (cbf_detector detector, double *indexslow,
double *indexfast, double *centerslow, double *centerfast);
int cbf_set_beam_center_fs (cbf_detector detector, double *indexfast,
double *indexslow, double *centerfast, double *centerslow);
int cbf_set_beam_center_sf (cbf_detector detector, double *indexslow,
double *indexfast, double *centerslow, double *centerfast);
int cbf_set_reference_beam_center (cbf_detector detector, double
*indexslow, double *indexfast, double *centerslow, double *centerfast);
int cbf_set_reference_beam_center_fs (cbf_detector detector, double
*indexfast, double *indexslow, double *centerfast, double *centerslow);
int cbf_set_reference_beam_center_sf (cbf_detector detector, double
*indexslow, double *indexfast, double *centerslow, double *centerfast);
DESCRIPTION
cbf_get_beam_center sets *centerfast and *centerslow to the
displacements in mm along the detector axes from pixel (0, 0) to the
point at which the beam intersects the detector and *indexfast and
*indexslow to the corresponding indices. cbf_set_beam_center sets the
offsets in the axis category for the detector element axis with
precedence 1 to place the beam center at the position given in mm by
*centerfast and *centerslow as the displacements in mm along the
detector axes from pixel (0, 0) to the point at which the beam
intersects the detector at the indices given *indexfast and *indexslow.
cbf_set_reference_beam_center sets the displacments in the
array_structure_list_axis category to place the beam center at the
position given in mm by *centerfast and *centerslow as the displacements
in mm along the detector axes from pixel (0, 0) to the point at which
the beam intersects the detector at the indices given by *indexfast and
*indexslow. In order to achieve consistent results, a reference detector
should be used for detector to have all axes at their reference
settings.
Note that the precedence 1 axis is the fastest axis, so that *centerfast
and *indexfast are the fast axis components of the center and
*centerslow and *indexslow are the slow axis components of the center.
The _fs calls give the displacments in a fast-to-slow order. The calls
with no suffix and the calls _sf calls give the displacements in
slow-to-fast order
Any of the destination pointers may be NULL for getting the beam center.
For setting the beam axis, either the indices of the center must not be
NULL.
The indices are non-negative for beam centers within the detector
surface, but the center for an axis with a negative increment will be
negative for a beam center within the detector surface.
For cbf_set_beam_center if the diffrn_data_frame category exists with a
row for the corresponding element id, the values will be set for
_diffrn_data_frame.center_fast and _diffrn_data_frame.center_slow in
millimetres and the value of _diffrn_data_frame.center_units will be set
to 'mm'.
For cbf_set_reference_beam_center if the diffrn_detector_element
category exists with a row for the corresponding element id, the values
will be set for _diffrn_detector_element.reference_center_fast and
_diffrn_detector_element.reference_center_slow in millimetres and the
value of _diffrn_detector_element.reference_units will be set to 'mm'.
ARGUMENTS
detector Detector handle.
indexfast Pointer to the destination fast index.
indexslow Pointer to the destination slow index.
centerfast Pointer to the destination displacement along the fast
axis.
centerslow Pointer to the destination displacement along the slow
axis.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.39 cbf_get_detector_distance
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_detector_distance (cbf_detector detector, double *distance);
DESCRIPTION
cbf_get_detector_distance sets *distance to the nearest distance from
the sample position to the detector plane.
ARGUMENTS
detector Detector handle.
distance Pointer to the destination distance.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.40 cbf_get_detector_normal
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_detector_normal (cbf_detector detector, double *normal1,
double *normal2, double *normal3);
DESCRIPTION
cbf_get_detector_normal sets *normal1, *normal2, and *normal3 to the 3
components of the of the normal vector to the detector plane. The vector
is normalized.
Any of the destination pointers may be NULL.
ARGUMENTS
detector Detector handle.
normal1 Pointer to the destination x component of the normal
vector.
normal2 Pointer to the destination y component of the normal
vector.
normal3 Pointer to the destination z component of the normal
vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.41 cbf_get_detector_axis_slow, cbf_get_detector_axis_slow,
cbf_get_detector_axes, cbf_get_detector_axes_fs, cbf_get_detector_axes_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_detector_axis_slow (cbf_detector detector, double
*slowaxis1, double *slowaxis2, double *slowaxis3);
int cbf_get_detector_axis_fast (cbf_detector detector, double
*fastaxis1, double *fastaxis2, double *fastaxis3);
int cbf_get_detector_axes (cbf_detector detector, double *slowaxis1,
double *slowaxis2, double *slowaxis3, double *fastaxis1, double
*fastaxis2, double *fastaxis3);
int cbf_get_detector_axes_fs (cbf_detector detector, double *fastaxis1,
double *fastaxis2, double *fastaxis3, double *slowaxis1, double
*slowaxis2, double *slowaxis3);
int cbf_get_detector_axes_sf (cbf_detector detector, double *slowaxis1,
double *slowaxis2, double *slowaxis3, double *fastaxis1, double
*fastaxis2, double *fastaxis3);
DESCRIPTION
cbf_get_detector_axis_slow sets *slowaxis1, *slowaxis2, and *slowaxis3
to the 3 components of the slow axis of the specified detector at the
current settings of all axes. cbf_get_detector_axis_slow sets
*fastaxis1, *fastaxis2, and *fastaxis3 to the 3 components of the fast
axis of the specified detector at the current settings of all axes.
cbf_get_detector_axes, cbf_get_detector_axes_fs and int
cbf_get_detector_axes_sf set *slowaxis1, *slowaxis2, and *slowaxis3 to
the 3 components of the slow axis and *fastaxis1, *fastaxis2, and
*fastaxis3 to the 3 components of the fast axis of the specified
detector at the current settings of all axes.
Any of the destination pointers may be NULL.
ARGUMENTS
detector Detector handle.
slowaxis1 Pointer to the destination x component of the slow axis
vector.
slowaxis2 Pointer to the destination y component of the slow axis
vector.
slowaxis3 Pointer to the destination z component of the slow axis
vector.
fastaxis1 Pointer to the destination x component of the fast axis
vector.
fastaxis2 Pointer to the destination y component of the fast axis
vector.
fastaxis3 Pointer to the destination z component of the fast axis
vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.42 cbf_get_pixel_coordinates, cbf_get_pixel_coordinates_fs,
cbf_get_pixel_coordinates_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_pixel_coordinates (cbf_detector detector, double indexslow,
double indexfast, double *coordinate1, double *coordinate2, double
*coordinate3);
int cbf_get_pixel_coordinates_fs (cbf_detector detector, double
indexfast, double indexslow, double *coordinate1, double *coordinate2,
double *coordinate3);
int cbf_get_pixel_coordinates_sf (cbf_detector detector, double
indexslow, double indexfast, double *coordinate1, double *coordinate2,
double *coordinate3);
DESCRIPTION
cbf_get_pixel_coordinates, cbf_get_pixel_coordinates_fs and
cbf_get_pixel_coordinates_sf ses *coordinate1, *coordinate2, and
*coordinate3 to the vector position of pixel (indexfast, indexslow) on
the detector surface. If indexslow and indexfast are integers then the
coordinates correspond to the center of a pixel.
Any of the destination pointers may be NULL.
ARGUMENTS
detector Detector handle.
indexslow Slow index.
indexfast Fast index.
coordinate1 Pointer to the destination x component.
coordinate2 Pointer to the destination y component.
coordinate3 Pointer to the destination z component.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.43 cbf_get_pixel_normal, cbf_get_pixel_normal_fs,
cbf_get_pixel_normal_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_pixel_normal (cbf_detector detector, double indexslow,
double indexfast, double *normal1, double *normal2, double *normal3);
int cbf_get_pixel_normal_fs (cbf_detector detector, double indexfast,
double indexslow, double *normal1, double *normal2, double *normal3);
int cbf_get_pixel_normal (cbf_detector detector, double indexslow,
double indexfast, double *normal1, double *normal2, double *normal3);
DESCRIPTION
cbf_get_detector_normal, cbf_get_pixel_normal_fs and
cbf_get_pixel_normal_sf set *normal1, *normal2, and *normal3 to the 3
components of the of the normal vector to the pixel at (indexfast,
indexslow). The vector is normalized.
Any of the destination pointers may be NULL.
ARGUMENTS
detector Detector handle.
indexslow Slow index.
indexfast Fast index.
normal1 Pointer to the destination x component of the normal
vector.
normal2 Pointer to the destination y component of the normal
vector.
normal3 Pointer to the destination z component of the normal
vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.44 cbf_get_pixel_area, cbf_get_pixel_area_fs, cbf_get_pixel_area_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_pixel_area (cbf_detector detector, double indexslow, double
indexfast, double *area, double *projected_area);
int cbf_get_pixel_area_fs(cbf_detector detector, double indexfast,
double indexslow, double *area, double *projected_area);
int cbf_get_pixel_area_sf(cbf_detector detector, double indexslow,
double indexfast, double *area, double *projected_area);
DESCRIPTION
cbf_get_pixel_area, cbf_get_pixel_area_fs and cbf_get_pixel_area_sf set
*area to the area of the pixel at (indexfast, indexslow) on the detector
surface and *projected_area to the apparent area of the pixel as viewed
from the sample position, with indexslow being the slow axis and
indexfast being the fast axis.
Either of the destination pointers may be NULL.
ARGUMENTS
detector Detector handle.
indexfast Fast index.
indexslow Slow index.
area Pointer to the destination area in mm2.
projected_area Pointer to the destination apparent area in mm2.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.45 cbf_get_pixel_size, cbf_get_pixel_size_fs, cbf_get_pixel_size_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_pixel_size (cbf_handle handle, unsigned int element_number,
int axis_number, double *psize);
int cbf_get_pixel_size_fs(cbf_handle handle, unsigned int
element_number, int axis_number, double *psize);
int cbf_get_pixel_size_sf(cbf_handle handle, unsigned int
element_number, int axis_number, double *psize);
DESCRIPTION
cbf_get_pixel_size and cbf_get_pixel_size_sf set *psize to point to the
double value in millimeters of the axis axis_number of the detector
element element_number. The axis_number is numbered from 1, starting
with the slowest axis. cbf_get_pixel_size_fs sets *psize to point to the
double value in millimeters of the axis axis_number of the detector
element element_number. The axis_number is numbered from 1, starting
with the fastest axis.
If a negative axis number is given, the order of axes is reversed, so
that -1 specifies the slowest axis for cbf_get_pixel_size_fs and the
fastest axis for cbf_get_pixel_size_sf.
If the pixel size is not given explcitly in the "array_element_size"
category, the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
axis_number The number of the axis, starting from 1 for the
fastest for cbf_get_pixel_size and
cbf_get_pixel_size_fs and the slowest for
cbf_get_pixel_size_sf.
psize Pointer to the destination pixel size.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.46 cbf_set_pixel_size, cbf_set_pixel_size_fs, cbf_set_pixel_size_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_pixel_size (cbf_handle handle, unsigned int element_number,
int axis_number, double psize);
int cbf_set_pixel_size_fs(cbf_handle handle, unsigned int
element_number, int axis_number, double psize);
int cbf_set_pixel_size_sf(cbf_handle handle, unsigned int
element_number, int axis_number, double psize);
DESCRIPTION
cbf_set_pixel_size and cbf_set_pixel_size_sf set the item in the
"e;size"e; column of the "array_structure_list" category at the
row which matches axis axis_number of the detector element
element_number converting the double pixel size psize from meters to
millimeters in storing it in the "size" column for the axis axis_number
of the detector element element_number. The axis_number is numbered from
1, starting with the slowest axis. cbf_set_pixel_size_fs sets the item
in the "e;size"e; column of the "array_structure_list" category
at the row which matches axis axis_number of the detector element
element_number converting the double pixel size psize from meters to
millimeters in storing it in the "size" column for the axis axis_number
of the detector element element_number. The axis_number is numbered from
1, starting with the fastest axis.
If a negative axis number is given, the order of axes is reversed, so
that -1 specifies the slowest axis for cbf_get_pixel_size_fs and the
fastest axis for cbf_get_pixel_size_sf.
If the "array_structure_list" category does not already exist, it is
created.
If the appropriate row in the "array_structure_list" catgeory does not
already exist, it is created.
If the pixel size is not given explcitly in the "array_element_size
category", the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
axis_number The number of the axis, fastest first, starting from
1.
psize The pixel size in millimeters.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.47 cbf_get_inferred_pixel_size, cbf_get_inferred_pixel_size_fs,
cbf_get_inferred_pixel_size_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_inferred_pixel_size (cbf_detector detector, int axis_number,
double *psize);
int cbf_get_inferred_pixel_size_fs(cbf_detector detector, int
axis_number, double *psize);
int cbf_get_inferred_pixel_size_sf(cbf_detector detector, int
axis_number, double *psize);
DESCRIPTION
cbf_get_inferred_pixel_size, cbf_get_inferred_pixel_size_sf set *psize
to point to the double value in millimeters of the pixel size for the
axis axis_number value. The slow index is treated as axis 1 and the next
faster index is treated as axis 2. cbf_get_inferred_pixel_size_fs sets
*psize to point to the double value in millimeters of the pixel size for
the axis axis_number value. The fast index is treated as axis 1 and the
next slower index is treated as axis 2.
If the axis number is negative, the axes are used in the reverse order
so that an axis_number of -1 indicates the fast axes in a call to
cbf_get_inferred_pixel_size or cbf_get_inferred_pixel_size_sf and
indicates the fast axis in a call to cbf_get_inferred_pixel_size_fs.
ARGUMENTS
detector Detector handle.
axis_number The number of the axis.
area Pointer to the destination pizel size in mm.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.48 cbf_get_unit_cell
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_unit_cell (cbf_handle handle, double cell[6], double
cell_esd[6] );
DESCRIPTION
cbf_get_unit_cell sets cell[0:2] to the double values of the cell edge
lengths a, b and c in AAngstroms, cell[3:5] to the double values of the
cell angles a, b and g in degrees, cell_esd[0:2] to the double values of
the estimated strandard deviations of the cell edge lengths a, b and c
in AAngstroms, cell_esd[3:5] to the double values of the estimated
standard deviations of the the cell angles a, b and g in degrees.
The values returned are retrieved from the first row of the "cell"
category. The value of "_cell.entry_id" is ignored.
cell or cell_esd may be NULL.
If cell is NULL, the cell parameters are not retrieved.
If cell_esd is NULL, the cell parameter esds are not retrieved.
If the "cell" category is present, but some of the values are missing,
zeros are returned for the missing values.
ARGUMENTS
handle CBF handle.
cell Pointer to the destination array of 6 doubles for the cell
parameters.
cell_esd Pointer to the destination array of 6 doubles for the cell
parameter esds.
RETURN VALUE
Returns an error code on failure or 0 for success. No errors is returned
for missing values if the "cell" category exists.
SEE ALSO
2.4.49 cbf_set_unit_cell
2.4.50 cbf_get_reciprocal_cell
2.4.51 cbf_set_reciprocal_cell
2.4.52 cbf_compute_cell_volume
2.4.53 cbf_compute_reciprocal_cell
----------------------------------------------------------------------
2.4.49 cbf_set_unit_cell
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_unit_cell (cbf_handle handle, double cell[6], double
cell_esd[6] );
DESCRIPTION
cbf_set_unit_cell sets the cell parameters to the double values given in
cell[0:2] for the cell edge lengths a, b and c in AAngstroms, the double
values given in cell[3:5] for the cell angles a, b and g in degrees, the
double values given in cell_esd[0:2] for the estimated strandard
deviations of the cell edge lengths a, b and c in AAngstroms, and the
double values given in cell_esd[3:5] for the estimated standard
deviations of the the cell angles a, b and g in degrees.
The values are placed in the first row of the "cell" category. If no
value has been given for "_cell.entry_id", it is set to the value of the
"diffrn.id" entry of the current data block.
cell or cell_esd may be NULL.
If cell is NULL, the cell parameters are not set.
If cell_esd is NULL, the cell parameter esds are not set.
If the "cell" category is not present, it is created. If any of the
necessary columns are not present, they are created.
ARGUMENTS
handle CBF handle.
cell Pointer to the array of 6 doubles for the cell parameters.
cell_esd Pointer to the array of 6 doubles for the cell parameter
esds.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.4.48 cbf_get_unit_cell
2.4.50 cbf_get_reciprocal_cell
2.4.51 cbf_set_reciprocal_cell
2.4.52 cbf_compute_cell_volume
2.4.53 cbf_compute_reciprocal_cell
----------------------------------------------------------------------
SEE ALSO
2.4.50 cbf_get_reciprocal_cell
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_reciprocal_cell (cbf_handle handle, double cell[6], double
cell_esd[6] );
DESCRIPTION
cbf_get_reciprocal_cell sets cell[0:2] to the double values of the
reciprocal cell edge lengths a*, b* and c* in AAngstroms-1, cell[3:5] to
the double values of the reciprocal cell angles a*, b* and g* in
degrees, cell_esd[0:2] to the double values of the estimated strandard
deviations of the reciprocal cell edge lengths a*, b* and c* in
AAngstroms-1, cell_esd[3:5] to the double values of the estimated
standard deviations of the the reciprocal cell angles a*, b* and g* in
degrees.
The values returned are retrieved from the first row of the "cell"
category. The value of "_cell.entry_id" is ignored.
cell or cell_esd may be NULL.
If cell is NULL, the reciprocal cell parameters are not retrieved.
If cell_esd is NULL, the reciprocal cell parameter esds are not
retrieved.
If the "cell" category is present, but some of the values are missing,
zeros are returned for the missing values.
ARGUMENTS
handle CBF handle.
cell Pointer to the destination array of 6 doubles for the
reciprocal cell parameters.
cell_esd Pointer to the destination array of 6 doubles for the
reciprocal cell parameter esds.
RETURN VALUE
Returns an error code on failure or 0 for success. No errors is returned
for missing values if the "cell" category exists.
SEE ALSO
2.4.48 cbf_get_unit_cell
2.4.49 cbf_set_unit_cell
2.4.51 cbf_set_reciprocal_cell
2.4.52 cbf_compute_cell_volume
2.4.53 cbf_compute_reciprocal_cell
----------------------------------------------------------------------
2.4.51 cbf_set_reciprocal_cell
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_reciprocal_cell (cbf_handle handle, double cell[6], double
cell_esd[6] );
DESCRIPTION
cbf_set_reciprocal_cell sets the reciprocal cell parameters to the
double values given in cell[0:2] for the reciprocal cell edge lengths
a*, b* and c* in AAngstroms-1, the double values given in cell[3:5] for
the reciprocal cell angles a*, b* and g* in degrees, the double values
given in cell_esd[0:2] for the estimated strandard deviations of the
reciprocal cell edge lengths a*, b* and c* in AAngstroms, and the double
values given in cell_esd[3:5] for the estimated standard deviations of
the reciprocal cell angles a*, b* and g* in degrees.
The values are placed in the first row of the "cell" category. If no
value has been given for "_cell.entry_id", it is set to the value of the
"diffrn.id" entry of the current data block.
cell or cell_esd may be NULL.
If cell is NULL, the reciprocal cell parameters are not set.
If cell_esd is NULL, the reciprocal cell parameter esds are not set.
If the "cell" category is not present, it is created. If any of the
necessary columns are not present, they are created.
ARGUMENTS
handle CBF handle.
cell Pointer to the array of 6 doubles for the reciprocal cell
parameters.
cell_esd Pointer to the array of 6 doubles for the reciprocal cell
parameter esds.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.4.48 cbf_get_unit_cell
2.4.49 cbf_set_unit_cell
2.4.50 cbf_get_reciprocal_cell
2.4.52 cbf_compute_cell_volume
2.4.53 cbf_compute_reciprocal_cell
----------------------------------------------------------------------
2.4.52 cbf_compute_cell_volume
PROTOTYPE
#include "cbf_simple.h"
int cbf_compute_cell_volume ( double cell[6], double *volume );
DESCRIPTION
cbf_compute_cell_volume sets *volume to point to the volume of the unit
cell computed from the double values in cell[0:2] for the cell edge
lengths a, b and c in AAngstroms and the double values given in
cell[3:5] for the cell angles a, b and g in degrees.
ARGUMENTS
cell Pointer to the array of 6 doubles giving the cell parameters.
volume Pointer to the doubles for cell volume.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.4.48 cbf_get_unit_cell
2.4.49 cbf_set_unit_cell
2.4.50 cbf_get_reciprocal_cell
2.4.51 cbf_set_reciprocal_cell
2.4.53 cbf_compute_reciprocal_cell
----------------------------------------------------------------------
2.4.53 cbf_compute_reciprocal_cell
PROTOTYPE
#include "cbf_simple.h"
int cbf_compute_reciprocal_cell ( double cell[6], double rcell[6] );
DESCRIPTION
cbf_compute_reciprocal_cell sets rcell to point to the array of
reciprocal cell parameters computed from the double values cell[0:2]
giving the cell edge lengths a, b and c in AAngstroms, and the double
values cell[3:5] giving the cell angles a, b and g in degrees. The
double values rcell[0:2] will be set to the reciprocal cell lengths a*,
b* and c* in AAngstroms-1 and the double values rcell[3:5] will be set
to the reciprocal cell angles a*, b* and g* in degrees.
ARGUMENTS
cell Pointer to the array of 6 doubles giving the cell parameters.
rcell Pointer to the destination array of 6 doubles giving the
reciprocal cell parameters.
volume Pointer to the doubles for cell volume.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.4.48 cbf_get_unit_cell
2.4.49 cbf_set_unit_cell
2.4.50 cbf_get_reciprocal_cell
2.4.51 cbf_set_reciprocal_cell
2.4.52 cbf_compute_cell_volume
----------------------------------------------------------------------
2.4.54 cbf_get_orientation_matrix, cbf_set_orientation_matrix
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_orientation_matrix (cbf_handle handle, double ub_matrix[9]);
int cbf_set_orientation_matrix (cbf_handle handle, double ub_matrix[9]);
DESCRIPTION
cbf_get_orientation_matrix sets ub_matrix to point to the array of
orientation matrix entries in the "diffrn" category in the order of
columns:
"UB[1][1]" "UB[1][2]" "UB[1][3]"
"UB[2][1]" "UB[2][2]" "UB[2][3]"
"UB[3][1]" "UB[3][2]" "UB[3][3]"
cbf_set_orientation_matrix sets the values in the "diffrn" category to
the values pointed to by ub_matrix.
ARGUMENTS
handle CBF handle.
ubmatric Source or destination array of 9 doubles giving the
orientation matrix parameters.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.55 cbf_get_bin_sizes, cbf_set_bin_sizes
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_bin_sizes(cbf_handle handle, unsigned int element_number,
double * slowbinsize, double * fastbinsize);
int cbf_set_bin_sizes(cbf_handle handle, unsigned int element_number,
double slowbinsize_in,double fastbinsize_in);
DESCRIPTION
cbf_get_bin_sizes sets slowbinsize to point to the value of the number
of pixels composing one array element in the dimension that changes at
the second-fastest rate and fastbinsize to point to the value of the
number of pixels composing one array element in the dimension that
changes at the fastest rate for the dectector element with the ordinal
element_number. cbf_set_bin_sizes sets the the pixel bin sizes in the
"array_intensities" category to the values of slowbinsize_in for the
number of pixels composing one array element in the dimension that
changes at the second-fastest rate and fastbinsize_in for the number of
pixels composing one array element in the dimension that changes at the
fastest rate for the dectector element with the ordinal element_number.
In order to allow for software binning involving fractions of pixels,
the bin sizes are doubles rather than ints.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
slowbinsize Pointer to the returned number of pixels composing
one array element in the dimension that changes at the
second-fastest rate.
fastbinsize Pointer to the returned number of pixels composing
one array element in the dimension that changes at the
fastest rate.
slowbinsize_in The number of pixels composing one array element in
the dimension that changes at the second-fastest rate.
fastbinsize_in The number of pixels composing one array element in
the dimension that changes at the fastest rate.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.5 F90 function interfaces
At the suggestion of W. Kabsch, Fortran 90/95 routines have been added
to CBFlib. As of this writing code has been written to allow the reading
of CBF_BYTE_OFFSET, CBF_PACKED and CBF_PACKED_V2 binary images. This
code has been gather into FCBlib (Fortran Crystallographic Binary
library) as lib/libfcb.
In general, most of the FCBlib functions return 0 for normal completion
and a non-zero value in case of an error. In a few cases, such as
FCB_ATOL_WCNT and FCB_NBLEN_ARRAY in order to conform to the conventions
for commonly used C-equivalent functions, the function return is the
value being computed.
For each function, an interface is given to be included in the
declarations of your Fortran 90/95 code. Some functions in FCBlIB are
not intended for external use and are subject to change:
FCB_UPDATE_JPA_POINTERS_I2, FCB_UPDATE_JPA_POINTERS_I4,
FCB_UPDATE_JPA_POINTERS_3D_I2, FCB_UPDATE_JPA_POINTERS_3D_I4 and
CNT2PIX. These names should not be used for user routines.
The functions involving reading of a CBF have been done strictly in
Fortran without the use of C code. This has required some compromises
and the use of direct access I/O. Rather than putting the buffer and its
control variables into COMMON these are passed as local arguments to
make the routines inherently 'threadsafe' in a parallel programming
environment. Note also, that a reading error could occur for the last
record if it does not fill a full block. The code is written to recover
from end-of-record and end-of-file errors, if possible. On many modern
system, no special action is required, but on some systems it may be
necessary to make use of the padding between the end of binary data and
the terminal MIME boundary marker in binary sections. To ensure maximum
portability of CBF files, a padding of 4095 bytes is recommended.
Existing files without padding can be converted to files with padding by
use of the new -p4 option for cif2cbf.
2.5.1 FCB_ATOL_WCNT
INTERFACE
INTEGER(8) FUNCTION FCB_ATOL_WCNT(ARRAY, N, CNT)
INTEGER(1),INTENT(IN):: ARRAY(N)
INTEGER, INTENT(IN):: N
INTEGER, INTENT(OUT):: CNT
END FUNCTION
END INTERFACE
FCB_ATOL_WCNT converts INTEGER(1) bytes in ARRAY of N bytes to an
INTEGER(8) value returned as the function value. The number of bytes of
ARRAY actually used before encountering a character not used to form the
number is returned in CNT.
The scan stops at the first byte in ARRAY that cannot be properly parsed
as part of the integer result.
ARGUMENTS
ARRAY The array of INTEGER(1) bytes to be scanned
N The INTEGER size of ARRAY
CNT The INTEGER size of the portion of ARRAY scanned.
RETURN VALUE
Returns the INTEGER(8) value derived from the characters ARRAY(1:CNT)
scanned.
----------------------------------------------------------------------
2.5.2 FCB_CI_STRNCMPARR
INTERFACE
INTEGER FUNCTION FCB_CI_STRNCMPARR(STRING>, ARRAY, N, LIMIT)
CHARACTER(LEN=*),INTENT(IN):: STRING>
INTEGER, INTENT(IN):: N, LIMIT
INTEGER(1), INTENT(IN):: ARRAY(N)
END FUNCTION
END INTERFACE
The function FCB_CI_STRNCMPARR compares up to LIMIT characters of
character string STRING and INTEGER(1) byte array ARRAY of dimension N
in a case-insensitive manner, returning 0 for a match.
ARGUMENTS
STRING A character string
ARRAY The array of INTEGER(1) bytes to be scanned
N The INTEGER size of ARRAY
N The INTEGER limit on the number of characters to consider in
the comparison
RETURN VALUE
Returns 0 if the string and array match, a non-zero value otherwise.
----------------------------------------------------------------------
2.5.3 FCB_EXIT_BINARY
INTERFACE
INTEGER FUNCTION FCB_EXIT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
PADDING )
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER(FCB_BYTES_IN_REC)
INTEGER(8),INTENT(IN) :: PADDING
END FUNCTION
END INTERFACE
The function FCB_EXIT_BINARY is used to skip from the end of a binary
section past any padding to the end of the text section that encloses
the binary section. The values of the arguments must be consistent with
those in the last call to FCB_NEXT_BINARY
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
LAST_CHAR The last character (as an INTEGER(1) byte) read.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
PADDING The INTEGER(8) number of bytes of padding after the
binary data and before the closing MIME boundary.
RETURN VALUE
Returns 0 if the function is successful. Returns whatever non-zero error
value is reported by FCB_READ_LINE if a necessary next line cannot be
read.
SEE ALSO
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.4 FCB_NBLEN_ARRAY
INTERFACE
INTEGER FUNCTION FCB_NBLEN_ARRAY(ARRAY, ARRAYLEN)
INTEGER, INTENT(IN):: ARRAYLEN
INTEGER(1), INTENT(IN):: ARRAY(ARRAYLEN)
END FUNCTION
END INTERFACE
The function FCB_NBLEN_ARRAY returns the trimmed length of the
INTEGER(1) byte array ARRAY of dimension ARRAYLEN after removal of
trailing ASCII blanks, horizontal tabs (Z'09'), newlines (Z'0A') and
carriage returns (Z'0D'). The resulting length may be zero.
The INTEGER trimmed length is returned as the function value.
ARGUMENTS
ARRAY The array of bytes for which the trimmed length is
required.
ARRAYLEN The dimension of the array of bytes to be scanned.
RETURN VALUE
Returns the trimmed length of the array ARRAY.
----------------------------------------------------------------------
2.5.5 FCB_NEXT_BINARY
INTERFACE
INTEGER FUNCTION FCB_NEXT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
ENCODING,SIZE,ID,DIGEST, &
COMPRESSION,BITS,VORZEICHEN,REELL,&
BYTEORDER,DIMOVER,DIM1,DIM2,DIM3, &
PADDING )
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER(FCB_BYTES_IN_REC)
INTEGER, INTENT(OUT) :: ENCODING
INTEGER, INTENT(OUT) :: SIZE !Binary size
INTEGER, INTENT(OUT) :: ID !Binary ID
CHARACTER(len=*),INTENT(OUT):: DIGEST !Message digest
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER, INTENT(OUT):: BITS,VORZEICHEN,REELL
CHARACTER(len=*),INTENT(OUT):: BYTEORDER
INTEGER(8), INTENT(OUT):: DIMOVER
INTEGER(8), INTENT(OUT):: DIM1
INTEGER(8), INTENT(OUT):: DIM2
INTEGER(8), INTENT(OUT):: DIM3
INTEGER(8), INTENT(OUT):: PADDING
END FUNCTION
END INTERFACE
The function FCB_NEXT_BINARY skips to the start of the next binary
section in the image file on unit TAPIN leaving the file positioned for
a subsequent read of the image data. The skip may prior to the text
field that contains the binary section. When the text filed is reached,
it will be scanned for a MIME boundary marker, and, if it is found the
subsequence MIME headers will be used to populate the arguments
ENCODING, SIZE, ID, DIGEST, COMPRESSION, BITS, VORZEICHEN,REELL,
BYTEORDER, DIMOVER, DIM1, DIM2,DIM3, PADDING.
The value returned in ENCODING is taken from the MIME header
Content-Transfer-Encoding as an INTEGER. It is returned as 0 if not
specified. The reported value is one of the integer values ENC_NONE
(Z'0001') for BINARY encoding, ENC_BASE64 (Z'0002') for BASE64 encoding,
ENC_BASE32K (Z'0004') for X-BASE32K encoding, ENC_QP (Z'0008') for
QUOTED-PRINTABLE encoding, ENC_BASE10 (Z'0010') for BASE10 encoding,
ENC_BASE16 (Z'0020') for BASE16 encoding or ENC_BASE8 (Z'0040') for
BASE8 encoding. At this time FCBlib only supports ENC_NONE BINARY
encoding.
The value returned in SIZE is taken from the MIME header X-Binary-Size
as an INTEGER. It is returned as 0 if not specified.
The value returned in ID is taken from the MIME header X-Binary-ID as an
INTEGER. It is returned as 0 if not specified.
The value returned in DIGEST is taken from the MIME header Content-MD5.
It is returned as a character string. If no digest is given, an empty
string is returned.
The value returned in COMPRESSION is taken from the MIME header
Content-Type in the conversions parameter. The reported value is one of
the INTEGER values CBF_CANONICAL (Z'0050'), CBF_PACKED (Z'0060'),
CBF_PACKED_V2 (Z'0090'), CBF_BYTE_OFFSET (Z'0070'), CBF_PREDICTOR
(Z'0080'), CBF_NONE (Z'0040'). Two flags may be combined with CBF_PACKED
or CBF_PACKED_V2: CBF_UNCORRELATED_SECTIONS (Z'0100') or CBF_FLAT_IMAGE
(Z'0200'). At this time FCBlib does not support CBF_PREDICTOR or
CBF_NONE compression.
The values returned in BITS, VORZEICHEN and REELL are the parameters of
the data types of the elements. These values are taken from the MIME
header X-Binary-Element-Type, which has values of the form "signed
BITS-bit integer", "unsigned BITS-bit integer", "signed BITS-bit real
IEEE" or "signed BITS-bit complex IEEE". If no value is given, REELL is
reported as -1. If the value in one of the integer types, REELL is
reported as 0. If the value is one of the real or complex types, REELL
is reported as 1. In the current release of FCBlib only the integer
types for BITS equal to 16 or 32 are supported.
The value returned in BYTEORDER is the byte order of the data in the
image file as reported in the MIME header. The value, if specified, will
be either the character string "LITTLE_ENDIAN" or the character string
"BIG_ENDIAN". If no byte order is specified, "LITTLE_ENDIAN" is
reported. This value is taken from the MIME header
X-Binary-Element-Byte-Order. As of this writing, CBFlib will not
generate "BIG_ENDIAN" byte-order files. However, both CBFlib and FCBlib
read "LITTLE_ENDIAN" byte-order files, even on big-endian machines.
The value returned in DIMOVER is the overall number of elements in the
image array, if specified, or zero, if not specified. This value is
taken from the MIME header X-Binary-Number-of-Elements. The values
returned in DIM1, DIM2 and DIM3 are the sizes of the fastest changing,
second fastest changing and third fastest changing dimensions of the
array, if specified, or zero, if not specified. These values are taken
from the MIME header X-Binary-Size-Fastest-Dimension,
X-Binary-Size-Second-Dimension and X-Binary-Size-Third-Dimension
respectively.
The value returned in PADDING is the size of the post-data padding, if
any, if specified or zero, if not specified. The value is given as a
count of octets. This value is taken from the MIME header
X-Binary-Size-Padding.
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
LAST_CHAR The last character (as an INTEGER(1) byte) read.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
ENCODING INTEGER type of encoding for the binary section as
reported in the MIME header.
ID INTEGER binary identifier as reported in the MIME
header.
SIZE INTEGER size of compressed binary section as
reported in the MIME header.
DIGEST The MD5 message digest as reported in the MIME
header.
COMPRESSION INTEGER compression method as reported in the MIME
header.
BITS INTEGER number of bits in each element as reported
in the MIME header.
VORZEICHEN INTEGER flag for signed or unsigned elements as
reported in the MIME header. Set to 1 if the elements
can be read as signed values, 0 otherwise.
REELL INTEGER flag for real elements as reported in the
MIME header. Set to 1 if the elements can be read as
REAL
BYTEORDER The byte order as reported in the MIME header.
DIM1 Pointer to the destination fastest dimension.
DIM2 Pointer to the destination second fastest
dimension.
DIM3 Pointer to the destination third fastest dimension.
PADDING Pointer to the destination padding size.
RETURN VALUE
Returns 0 if the function is successful. SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.6 FCB_OPEN_CIFIN
INTERFACE
INTEGER FUNCTION FCB_OPEN_CIFIN(FILNAM,TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER)
CHARACTER(len=*),INTENT(IN) :: FILNAM
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER(1), INTENT(OUT):: LAST_CHAR
INTEGER, INTENT(OUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1), INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER FCB_RECORD_SIZE
END FUNCTION
END INTERFACE
The function FCB_OPEN_CIFIN opens the CBF image file given by the file
name in the character string FILNAM on the logical unit TAPIN. The
calling routine must provide an INTEGER(1) byte buffer BUFFER of some
appropriate INTEGER size FCB_BYTES_IN_REC. The size must be chosen to
suit the machine, but in most cases, 4096 will work. The values returned
in LAST_CHAR, BYTE_IN_FILE, and REC_IN_FILE are for use in subsequent
FCBlib I/O routines.
The image file will be checked for the initial characters "###CBF: ". If
there is no match the error value CBF_FILEREAD is returned.
ARGUMENTS
FILNAM The character string name of the image file to be
opened.
TAPIN The INTEGER Fortran device unit number assigned to
image file.
LAST_CHAR The last character (as an INTEGER(1) byte) read.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
RETURN VALUE
Returns 0 if the function is successful. SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.7 FCB_PACKED: FCB_DECOMPRESS_PACKED_I2, FCB_DECOMPRESS_PACKED_I4,
FCB_DECOMPRESS_PACKED_3D_I2, FCB_DECOMPRESS_PACKED_3D_I4
INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_I2 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_I4 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_3D_I2 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_3D_I4 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
The functions FCB_DECOMPRESS_PACKED_I2, FCB_DECOMPRESS_PACKED_I4,
FCB_DECOMPRESS_PACKED_3D_I2 and FCB_DECOMPRESS_PACKED_3D_I4, decompress
images compress according the the CBF_PACKED or CBF_PACKED_V2
compression described in section 3.3.2 on J. P. Abrahams CCP4 packed
compression.
The relevant function should be called immediately after a call to
FCB_NEXT_BINARY, using the values returned by FCB_NEXT_BINARY to select
the appropriate version of the function.
ARGUMENTS
ARRAY The array to receive the image
NELEM The INTEGER(8) number of elements to be read
NELEM_READ The INTEGER(8) returned value of the number of
elements actually read
ELSIGN The INTEGER value of the flag for signed (1) OR
unsigned (0) data
COMPRESSION The compression of the image
DIM1 The INTEGER(8) value of the fastest dimension of
ARRAY
DIM2 The INTEGER(8) value of the second fastest
dimension
DIM3 The INTEGER(8) value of the third fastest dimension
TAPIN The INTEGER Fortran device unit number assigned to
image file.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
RETURN VALUE
Returns 0 if the function is successful.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.8 FCB_READ_BITS
INTERFACE
INTEGER FUNCTION FCB_READ_BITS(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
BITCOUNT,IINT,LINT)
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER, INTENT(INOUT):: BCOUNT
INTEGER(1),INTENT(INOUT):: BBYTE
INTEGER, INTENT(IN):: BITCOUNT
INTEGER, INTENT(IN):: LINT
INTEGER(4), INTENT(OUT):: IINT(LINT)
END FUNCTION
END INTERFACE
The function FCB_READ_BITS gets the integer value starting at
BYTE_IN_FILE from file TAPIN continuing through BITCOUNT bits, with sign
extension. BYTE_IN_FILE is left at the entry value and not incremented.
The resulting, sign-extended integer value is stored in the INTEGER(4)
array IINT of dimension LINT with the least significant portion in
IINT(1).
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
BCOUNT The INTEGER count of bits remaining unused from the
last call to FCB_READ_BITS.
BBYTE The INTEGER(1) byte containing the unused bits from
the last call to FCB_READ_BITS.
BITCOUNT The INTEGER count of the number of bits to be
extracted from the image file.
IINT The INTEGER(4) array into which to store the value
extracted from the image file.
LINT The INTEGER length of the array IINT.
RETURN VALUE
Returns 0 if the function is successful. Because of the use of direct
access I/O in blocks of size FCB_BYTES_IN_REC the precise location of
the end of file may not be detected.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.9 FCB_READ_BYTE
INTERFACE
INTEGER FUNCTION FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,IBYTE)
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER(1), INTENT(OUT):: IBYTE
END FUNCTION
END INTERFACE
The function FCB_READ_BYTE reads the byte at the position BYTE_IN_FILE
in the image file TAPIN. The first byte in the file is at BYTE_IN_FILE =
1. BYTE_IN_FILE should be set to the desired value before the call to
the function and is not incremented within the function.
The function attempts to suppress the error caused by a read of a short
last record, and in most systems cannot determine the exact location of
the end of the image file, returning zero bytes until the equivalent of
a full final record has been read.
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
IBYTE The INTEGER(1) byte found in the image file at the
byte position BYTE_IN_FILE.
RETURN VALUE
Returns 0 if the function is successful. Because of the use of direct
access I/O in blocks of size FCB_BYTES_IN_REC the precise location of
the end of file may not be detected.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.9 FCB_READ_BITS
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.10 FCB_READ_IMAGE_I2, FCB_READ_IMAGE_I4, FCB_READ_IMAGE_3D_I2,
FCB_READ_IMAGE_3D_I4
INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_I2(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, &
PADDING,TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_I4(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, &
PADDING,TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_3D_I2(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, &
PADDING,TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_3D_I4(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, &
PADDING,TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
The function FCB_READ_IMAGE_I2 reads a 16-bit twos complement INTEGER(2)
2D image. The function FCB_READ_IMAGE_I4 read a 32-bit twos complement
INTEGER(4) 2D image. The function FCB_READ_IMAGE_3D_I2 reads a 16-bit
twos complement INTEGER(2) 3D image. The function FCB_READ_IMAGE_3D_I4
reads a 32-bit twos complement INTEGER(4) 3D image. In each case the
image is compressed either by a BYTE_OFFSET algorithm by W. Kabsch based
on a proposal by A. Hammersley or by a PACKED algorithm by J. P.
Abrahams as used in CCP4, with modifications by P. Ellis and H. J.
Bernstein.
The relevant function automatically first calls FCB_NEXT_BINARY to skip
to the next binary section and then starts to read. An error return will
result if the parameters of this call are inconsistent with the values
in MIME header.
ARGUMENTS
ARRAY The array to receive the image
NELEM The INTEGER(8) number of elements to be read
NELEM_READ The INTEGER(8) returned value of the number of
elements actually read
ELSIGN The INTEGER value of the flag for signed (1) OR
unsigned (0) data
COMPRESSION The actual compression of the image
DIM1 The INTEGER(8) value of the fastest dimension of
ARRAY
DIM2 The INTEGER(8) value of the second fastest
dimension
DIM3 The INTEGER(8) value of the third fastest dimension
TAPIN The INTEGER Fortran device unit number assigned to
image file.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
RETURN VALUE
Returns 0 if the function is successful.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.7 FCB_DECOMPRESS: FCB_DECOMPRESS_PACKED_I2,
FCB_DECOMPRESS_PACKED_I4, FCB_DECOMPRESS_PACKED_3D_I2,
FCB_DECOMPRESS_PACKED_3D_I4
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.11 FCB_READ_LINE
INTERFACE
INTEGER FUNCTION FCB_READ_LINE(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC, &
BYTE_IN_FILE,REC_IN_FILE,BUFFER,LINE,N,LINELEN)
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC,N
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER, INTENT(OUT):: LINELEN
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER,(FCB_BYTES_IN_REC)
INTEGER(1), INTENT(OUT):: LINE(N)
END FUNCTION
END INTERFACE
The function FCB_READ_LINE reads successive bytes into the INTEGER(1)
byte array LINE of dimension N), stopping at N bytes or the first error
or the first CR (Z'0D') or LF (Z'0A'), whichever comes first. It
discards an LF after a CR. The variable LAST_CHAR is checked for the
last character from the previous line to make this determination.
The actual number of bytes read into the line, not including any
terminal CR or LF is stored in LINELEN.
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
LAST_CHAR The INTEGER(1) byte holding the ASCII value of the
last character read for each line read.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN.
LINE The INTEGER(1) array of length N to hold the line
to be read from TAPIN.
N The INTEGER dimension of LINE.
LINELEN The INTEGER number of characters read into LINE.
RETURN VALUE
Returns 0 if the function is successful.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.7 FCB_DECOMPRESS: FCB_DECOMPRESS_PACKED_I2,
FCB_DECOMPRESS_PACKED_I4, FCB_DECOMPRESS_PACKED_3D_I2,
FCB_DECOMPRESS_PACKED_3D_I4
2.5.9 FCB_READ_BYTE
2.5.12 FCB_READ_XDS_I2
INTERFACE
INTEGER FUNCTION FCB_READ_XDS_I2(FILNAM,TAPIN,NX,NY,IFRAME,JFRAME)
CHARACTER(len=*),INTENT(IN) :: FILNAM
INTEGER, INTENT(IN) :: TAPIN,NX,NY
INTEGER(2), INTENT(OUT):: IFRAME(NX*NY)
INTEGER(4), INTENT(OUT):: JFRAME(NX,NY)
END FUNCTION
END INTERFACE
The function FCB_READ_XDS_I2 read a 32-bit integer twos complement image
into a 16-bit INTEGER(2) XDS image using the CBF_BYTE_OFFSET, CBF_PACKED
or CBF_PACKED_V2 compressions for the 32-bit data. The BYTE_OFFSET
algorithm is a variant of the September 2006 version by W. Kabsch which
was based on a suggestion by A. Hammersley and which was further
modified by H. Bernstein.
The file named FILNAM is opened on the logical unit TAPIN and
FCB_NEXT_BINARY is used to skip to the next binary image. The binary
image is then decompressed to produce an XDS 16-bit integer image array
IFRAME which is NX by NY. The dimensions must agree with the dimensions
specified in MIME header.
The conversion from a 32-bit integer I32 to 16-bit XDS pixel I16 is done
as per W. Kabsch as follows: The value I32 is limited to the range -1023
=< I32 =< 1048576. If I32 is outside that range it is truncated to the
closer boundary. The generate I16, the 16-bit result, if I32 > 32767, it
is divided by 32 (producing a number between 1024 and 32768), and then
negated (producing a number between -1024 and -32768).
For CBF_BYTE_OFFSET this conversion can be done on the fly directly into
the target array IFRAME, but for the CBF_PACKED or CBF_PACKED_V2, the
full 32 bit precision is needed during the decompression, forcing the
use of an intermediate INTEGER(4) array JFRAME to hold the 32-bit image
in that case.
The image file is closed after reading one image.
ARGUMENTS
FILNAM The character string name of the image file to be opened.
TAPIN The INTEGER Fortran device unit number assigned to image
file.
NX The INTEGER fast dimension of the image array.
NY The INTEGER slow dimension of the image array.
IFRAME The INTEGER(2) XDS image array.
JFRAME The INTEGER(4) 32-bit image scratch array needed for
CBF_PACKED or CBF_PACKED_V2 images.
RETURN VALUE
Returns 0 if the function is successful, CBF_FORMAT (=1) if it cannot
handle this CBF format (not implemented), -1 if it cannot determine
endian architecture of this machine, -2: if it cannot open the image
file, -3: if it finds the wrong image format and -4 if it cannot read
the image.
----------------------------------------------------------------------
2.5.13 FCB_SKIP_WHITESPACE
INTERFACE
INTEGER FUNCTION FCB_SKIP_WHITESPACE(TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER,&
LINE,N,LINELEN,ICUR,FRESH_LINE)
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC,N
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE,LINELEN,ICUR, &
FRESH_LINE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC),LINE(N), &
LAST_CHAR
END INTERFACE
The function FCB_SKIP_WHITESPACE skips forward on the current INTEGER(1)
byte array LINE of size N with valid data in LINE(1:LINELEN) from the
current position ICUR moving over MIME header whitespace and comments,
reading new lines into LINE if needed. The flag FRESH_LINE indicates
that a fresh line should be read on entry.
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
LAST_CHAR The INTEGER(1) byte holding the ASCII value of the
last character read for each line read.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN.
LINE The INTEGER(1) array of length N to hold the line
to be read from TAPIN.
N The INTEGER dimension of LINE.
LINELEN The INTEGER number of characters read into LINE.
ICUR The INTEGER position within the line.
FRESH_LINE The INTEGER flag that a fresh line is needed.
RETURN VALUE
Returns 0 if the function is successful.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.7 FCB_DECOMPRESS: FCB_DECOMPRESS_PACKED_I2,
FCB_DECOMPRESS_PACKED_I4, FCB_DECOMPRESS_PACKED_3D_I2,
FCB_DECOMPRESS_PACKED_3D_I4
2.5.9 FCB_READ_BYTE
----------------------------------------------------------------------
3. File format
3.1 General description
With the exception of the binary sections, a CBF file is an mmCIF-format
ASCII file, so a CBF file with no binary sections is a CIF file. An
imgCIF file has any binary sections encoded as CIF-format ASCII strings
and is a CIF file whether or not it contains binary sections. In most
cases, CBFlib can also be used to access normal CIF files as well as CBF
and imgCIF files.
3.2 Format of the binary sections
Before getting to the binary data itself, there are some preliminaries
to allow a smooth transition from the conventions of CIF to those of raw
or encoded streams of "octets" (8-bit bytes). The binary data is given
as the essential part of a specially formatted semicolon-delimited CIF
multi-line text string. This text string is the value associated with
the tag "_array_data.data".
The specific format of the binary sections differs between an imgCIF and
a CBF file.
3.2.1 Format of imgCIF binary sections
Each binary section is encoded as a semicolon-delimited string. Within
the text string, the conventions developed for transmitting email
messages including binary attachments are followed. There is secondary
ASCII header information, formatted as Multipurpose Internet Mail
Extensions (MIME) headers (see RFCs 2045-49 by Freed, et al.). The
boundary marker for the beginning of all this is the special string
--CIF-BINARY-FORMAT-SECTION--
at the beginning of a line. The initial "--" says that this is a MIME
boundary. We cannot put "###" in front of it and conform to MIME
conventions. Immediately after the boundary marker are MIME headers,
describing some useful information we will need to process the binary
section. MIME headers can appear in different orders, and can be very
confusing (look at the raw contents of a email message with
attachments), but there is only one header which is has to be understood
to process an imgCIF: "Content-Transfer-Encoding". If the value given on
this header is "BINARY", this is a CBF and the data will be presented as
raw binary, containing a count (in the header described in 3.2.2 Format
of CBF binary sections) so that we'll know when to start looking for
more information.
If the value given for "Content-Transfer-Encoding" is one of the real
encodings: "BASE64", "QUOTED-PRINTABLE", "X-BASE8", "X-BASE10" or
"X-BASE16", the file is an imgCIF, and we'll need some other headers to
process the encoded binary data properly. It is a good practice to give
headers in all cases. The meanings of various encodings is given in the
CBF extensions dictionary, cif_img_1.5.4.dic, as one html file, or as
separate pages for each defintion.
For certain compressions (e.g. CBF_PACKED) MIME headers are essential to
determine the parameters of the compression. The full list of MIME
headers recognized by and generated by CBFlib is:
* Content-Type:
* Content-Transfer-Encoding:
* Content-MD5:
* X-Binary-Size:
* X-Binary-ID:
* X-Binary-Element-Type:
* X-Binary-Element-Byte-Order:
* X-Binary-Number-of-Elements:
* X-Binary-Size-Fastest-Dimension:
* X-Binary-Size-Second-Dimension:
* X-Binary-Size-Third-Dimension:
* X-Binary-Size-Padding:
* Content-Type:
The "Content-Type" header tells us what sort of data we
have (currently always "application/octet-stream" for a
miscellaneous stream of binary data) and, optionally, the
conversions that were applied to the original data. The default is
to compress the data with the "CBF-PACKED" algorithm. The
Content-Type may be any of the discrete types permitted in RFC 2045;
'application/octet-stream' is recommended. If an octet stream was
compressed, the compression should be specified by the parameter
'conversions="X-CBF_PACKED"' or the parameter
'conversions="X-CBF_PACKED_V2"' or the parameter
'conversions="X-CBF_CANONICAL"' or the parameter
'conversions="X-CBF_BYTE_OFFSET"'
If the parameter 'conversions="X-CBF_PACKED"' or
'conversions="X-CBF_PACKED_V2"' is given it may be further modified
with the parameters '"uncorrelated_sections"' or '"flat"'
If the '"uncorrelated_sections"' parameter is given, each section
will be compressed without using the prior section for averaging. If
the '"flat"' parameter is given, each the image will be treated as
one long row.
* Content-Transfer-Encoding:
The "Content-Transfer-Encoding" may be 'BASE64', 'Quoted-Printable',
'X-BASE8', 'X-BASE10', 'X-BASE16' or 'X-BASE32K', for an imgCIF or
'BINARY' for a CBF. The octal, decimal and hexadecimal transfer
encodings are provided for convenience in debugging and are not
recommended for archiving and data interchange.
In a CIF, one of the parameters 'charset=us-ascii', 'charset=utf-8'
or 'charset=utf-16' may be used on the Content-Transfer-Encoding to
specify the character set used for the external presentation of the
encoded data. If no charset parameter is given, the character set of
the enclosing CIF is assumed. In any case, if a BOM flag is detected
(FE FF for big-endian UTF-16, FF FE for little-endian UTF-16 or EF
BB BF for UTF-8) is detected, the indicated charset will be assumed
until the end of the encoded data or the detection of a different
BOM. The charset of the Content-Transfer-Encoding is not the
character set of the encoded data, only the character set of the
presentation of the encoded data and should be respecified for each
distinct STAR string.
In an imgCIF file, the encoded binary data begins after the empty
line terminating the header. In an imgCIF file, the encoded binary
data ends with the terminating boundary delimiter
'\n--CIF-BINARY-FORMAT-SECTION----' in the currently effective
charset or with the '\n; ' that terminates the STAR string.
In a CBF, the raw binary data begins after an empty line terminating
the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of the message
size or in the calculation of the message digest.
* Content-MD5:
An MD5 message digest may, optionally, be used. The 'RSA Data
Security, Inc. MD5 Message-Digest Algorithm' should be used. No
portion of the header is included in the calculation of the message
digest. The optional "Content-MD5" header provides a much more
sophisticated check on the integrity of the binary data than size
checks alone can provide.
* X-Binary-Size:
The "X-Binary-Size" header specifies the size of the equivalent
binary data in octets. This is the size after any compressions, but
before any ascii encodings. This is useful in making a simple check
for a missing portion of this file. The 8 bytes for the Compression
type (see below) are not counted in this field, so the value of
"X-Binary-Size" is 8 less than the quantity in bytes 12-19 of the
raw binary data ( 3.2.2 Format of CBF binary sections).
* X-Binary-ID:
The "X-Binary-ID" header should contain the same value as was given
for "_array_data.binary_id".
* X-Binary-Element-Type:
The "X-Binary-Element-Type" header specifies the type of binary data
in the octets, using the same descriptive phrases as in
_array_structure.encoding_type. The default value is 'unsigned
32-bit integer'.
* X-Binary-Element-Byte-Order:
The "X-Binary-Element-Byte-Order" can specify either '"BIG_ENDIAN"'
or '"LITTLE_ENDIAN"' byte order of the image data. CBFlib only
writes '"LITTLE_ENDIAN"', and in general can only process
LITTLE_ENDIAN even on machines that are BIG_ENDIAN.
* X-Binary-Number-of-Elements:
The "X-Binary-Number-of-Elements" specifies the number of elements
(not the number of octets) in the decompressed, decoded image.
* X-Binary-Size-Fastest-Dimension:
The optional "X-Binary-Size-Fastest-Dimension" specifies the number
of elements (not the number of octets) in one row of the fastest
changing dimension of the binary data array. This information must
be in the MIME header for proper operation of some of the
decompression algorithms.
* X-Binary-Size-Second-Dimension:
The optional "X-Binary-Size-Second-Dimension" specifies the number
of elements (not the number of octets) in one column of the
second-fastest changing dimension of the binary data array. This
information must be in the MIME header for proper operation of some
of the decompression algorithms.
* X-Binary-Size-Third-Dimension:
The optional "X-Binary-Size-Third-Dimension" specifies the number of
sections for the third-fastest changing dimension of the binary data
array.
* X-Binary-Size-Padding:
The optional "X-Binary-Size-Padding" specifies the size in octets of
an optional padding after the binary array data and before the
closing flags for a binary section. CBFlib always writes this
padding as zeros, but this information should be in the MIME header
for a binary section that uses padding, especially if non-zero
padding is used.
A blank line separator immediately precedes the start of the encoded
binary data. Blank spaces may be added prior to the preceding "line
separator" if desired (e.g. to force word or block alignment).
Because CBFLIB may jump forward in the file from the MIME header, the
length of encoded data cannot be greater than the value defined by
"X-Binary-Size" (except when "X-Binary-Size" is zero, which means that
the size is unknown), unless "X-Binary-Size-Padding" is specified to
allow for the padding. At exactly the byte following the full binary
section as defined by the length and padding values is the end of binary
section identifier. This consists of the line-termination sequence
followed by:
--CIF-BINARY-FORMAT-SECTION----
;
with each of these lines followed by a line-termination sequence. This
brings us back into a normal CIF environment. This identifier is, in a
sense, redundant because the binary data length value tells the a
program how many bytes to jump over to the end of the binary data. This
redundancy has been deliberately added for error checking, and for
possible file recovery in the case of a corrupted file and this
identifier must be present at the end of every block of binary data.
3.2.2 Format of CBF binary sections
In a CBF file, each binary section is encoded as a ;-delimited string,
starting with an arbitrary number of pure-ASCII characters.
Note: For historical reasons, CIFlib has the option of writing simple
header and footer sections: "START OF BINARY SECTION" at the start of a
binary section and "END OF BINARY SECTION" at the end of a binary
section, or writing MIME-type header and footer sections (3.2.1 Format
of imgCIF binary sections). If the simple header is used, the actual
ASCII text is ignored when the binary section is read. Use of the simple
binary header is deprecated.
The MIME header is recommended.
Between the ASCII header and the actual CBF binary data is a series of
bytes ("octets") to try to stop the listing of the header, bytes which
define the binary identifier which should match the "binary_id" defined
in the header, and bytes which define the length of the binary section.
Octet Hex Decimal Purpose
1 0C 12 (ctrl-L) End of Page
2 1A 26 (ctrl-Z) Stop listings in MS-DOS
3 04 04 (Ctrl-D) Stop listings in UNIX
4 D5 213 Binary section begins
5..5+n-1 Binary data (n octets)
NOTE: When a MIME header is used, only bytes 5 through 5+n-1 are
considered in computing the size and the message digest, and only these
bytes are encoded for the equivalent imgCIF file using the indicated
Content-Transfer-Encoding.
If no MIME header has been requested (a deprecated use), then bytes 5
through 28 are used for three 8-byte words to hold the binary_id, the
size and the compression type:
5..12 Binary Section Identifier
(See _array_data.binary_id)
64-bit, little endian
13..20 The size (n) of the
binary section in octets
(i.e. the offset from octet
29 to the first byte following
the data)
21..28 Compression type:
CBF_NONE 0x0040 (64)
CBF_CANONICAL 0x0050 (80)
CBF_PACKED 0x0060 (96)
CBF_BYTE_OFFSET 0x0070 (112)
CBF_PREDICTOR 0x0080 (128)
...
The binary data then follows in bytes 29 through 29+n-1.
The binary characters serve specific purposes:
o The Control-L (from-feed) will terminate printing of the current
page on most operating systems.
o The Control-Z will stop the listing of the file on MS-DOS type
operating systems.
o The Control-D will stop the listing of the file on Unix type
operating systems.
o The unsigned byte value 213 (decimal) is binary 11010101. (Octal
325, and hexadecimal D5). This has the eighth bit set so can be used
for error checking on 7-bit transmission. It is also asymmetric, but
with the first bit also set in the case that the bit order could be
reversed (which is not a known concern).
o (The carriage return, line-feed pair before the START_OF_BIN and
other lines can also be used to check that the file has not been
corrupted e.g. by being sent by ftp in ASCII mode.)
At present four compression schemes are implemented are defined:
CBF_NONE (for no compression), CBF_CANONICAL (for and entropy-coding
scheme based on the canonical-code algorithm described by Moffat, et
al. (International Journal of High Speed Electronics and Systems,
Vol 8, No 1 (1997) 179-231)), CBF_PACKED or CBF_PACKED_V2 for J. P.
Abrahams CCP4-style packing schemes and CBF_BYTE_OFFSET for a simple
byte_offset compression scheme.. Other compression schemes will be
added to this list in the future.
For historical reasons, CBFlib can read or write a binary string without
a MIME header. The structure of a binary string with simple headers is:
Byte ASCII Decimal Description
symbol value
1 ; 59 Initial ; delimiter
2 carriage-return 13
3 line-feed 10 The CBF new-line code is
carriage-return, line-feed
4 S 83
5 T 84
6 A 65
7 R 83
8 T 84
9 32
10 O 79
11 F 70
12 32
13 B 66
14 I 73
15 N 78
16 A 65
17 R 83
18 Y 89
19 32
20 S 83
21 E 69
22 C 67
23 T 84
24 I 73
25 O 79
26 N 78
27 carriage-return 13
28 line-feed 10
29 form-feed 12
30 substitute 26 Stop the listing of the file
in MS-DOS
31 end-of-transmission 4 Stop the listing of the file
in unix
32 213 First non-ASCII value
33 .. 40 Binary section identifier
(64-bit little-endien)
41 .. 48 Offset from byte 57 to the
first ASCII character
following the binary data
49 .. 56 Compression type
57 .. 57 + n-1 Binary data (nbytes)
57 + n carriage-return 13
58 + n line-feed 10
59 + n E 69
60 + n N 78
61 + n D 68
62 + n 32
63 + n O 79
64 + n F 70
65 + n 32
66 + n B 66
67 + n I 73
68 + n N 78
69 + n A 65
70 + n R 83
71 + n Y 89
72 + n 32
73 + n S 83
74 + n E 69
75 + n C 67
76 + n T 84
77 + n I 73
78 + n O 79
79 + n N 78
80 + n carriage-return 13
81 + n line-feed 10
82 + n ; 59 Final ; delimiter
3.3 Compression schemes
Two schemes for lossless compression of integer arrays (such as images)
have been implemented in this version of CBFlib:
1. An entropy-encoding scheme using canonical coding
2. A CCP4-style packing scheme.
Both encode the difference (or error) between the current element in the
array and the prior element. Parameters required for more sophisticated
predictors have been included in the compression functions and will be
used in a future version of the library.
3.3.1 Canonical-code compression
The canonical-code compression scheme encodes errors in two ways:
directly or indirectly. Errors are coded directly using a symbol
corresponding to the error value. Errors are coded indirectly using a
symbol for the number of bits in the (signed) error, followed by the
error iteslf.
At the start of the compression, CBFlib constructs a table containing a
set of symbols, one for each of the 2^n direct codes from -2^(n-1) ..
2^(n-1)-1, one for a stop code, and one for each of the maxbits -n
indirect codes, where n is chosen at compress time and maxbits is the
maximum number of bits in an error. CBFlib then assigns to each symbol a
bit-code, using a shorter bit code for the more common symbols and a
longer bit code for the less common symbols. The bit-code lengths are
calculated using a Huffman-type algorithm, and the actual bit-codes are
constructed using the canonical-code algorithm described by Moffat, et
al. (International Journal of High Speed Electronics and Systems, Vol 8,
No 1 (1997) 179-231).
The structure of the compressed data is:
Byte Value
1 .. 8 Number of elements (64-bit
little-endian number)
9 .. 16 Minimum element
17 .. 24 Maximum element
25 .. 32 (reserved for future use)
33 Number of bits directly coded, n
34 Maximum number of bits encoded, maxbits
35 .. 35+2^n-1 Number of bits in each direct code
35+2^n Number of bits in the stop code
35+2^n+1 .. 35+2^n+maxbits-n Number of bits in each indirect code
35+2^n+maxbits-n+1 .. Coded data
3.3.2 CCP4-style compression
Starting with CBFlib 0.7.7, CBFlib supports three variations on
CCP4-style compression: the "flat" version supported in versions of
CBFlib prior to release 0.7.7, as well as both version 1 and version 2
of J. P. Abrahams "pack_c" compression.
The CBF_PACKED and CBF_PACKED_V2 compression and decompression code
incorporated in CBFlib is derived in large part from the J. P. Abrahams
pack_c.c compression code in CCP4. This code is incorporated in CBFlib
under the GPL and the LGPL with both the permission Jan Pieter Abrahams,
the original author of pack_c.c (email from Jan Pieter Abrahams of 15
January 2007) and of the CCP4 project (email from Martyn Winn on 12
January 2007). The cooperation of J. P. Abrahams and of the CCP4 project
is gratefully acknowledged.
The basis for all three versions is a scheme to pack offsets
(differences from a base value) into a small-endian bit stream. The
stream is organized into blocks. Each block begins with a header of 6
bits in the flat packed version and version 1 of J. P. Abrahams
compression, and 7 bits in version 2 of J. P. Abrahams compression. The
header gives the number of offsets that follow and the number of bits in
each offset. Each offset is a signed, 2's complement integer.
The first 3 bits in the header gives the logarithm base 2 of the numer
of offsets that follow the header. For example, if a header has a zero
in bits, only one offset follows the header. If those same bits contain
the number n, the number of offsets in the block is 2n.
The following 3 bits (flat and version 1) or 4 bits (version 2) contains
a number giving an index into a table of bit-lengths for the offsets.
All offsets in a given block are of the same length.
Bits 3 .. 5 (flat and version 1) or bits 3 .. 6 (version 2) encode the
number of bits in each offset as follows:
Value in Number of bits Number of bits
bits 3 .. 5 in each V1 offset in each V2 offset
0 0 0
1 4 3
2 5 4
3 6 5
4 7 6
5 8 7
6 16 8
7 max 9
8 10
9 11
10 12
11 13
12 14
13 15
14 16
15 max
The value "max" is determined by the compression version and the element
size. If the compression used is "flat", then "max" is 65. If the
compression is version 1 or version 2 of the JPA compression, then "max"
is the number of bits in each element, i.e. 8, 16, 32 or 64 bits.
The major difference between the three variants of packed compression is
the choice of the base value from which the offset is measured. In all
cases the first offset is measured from zero, i.e. the first offset is
the value of the first pixel of the image. If "flat" is chosen or if the
dimensions of the data array are not given, then the remaining offset
are measure against the prior value, making it similar in approach to
the "byte offset" compression described in section 3.3.3 Byte offset
compression, but with a more efficient representation of the offsets.
In version 1 and version 2 of the J. P. Abrahams compression, the
offsets are measured against an average of earlier pixels. If there is
only one row only the prior pxiel is used, starting with the same
offsets for that row as for "flat". After the first row, three pixels
from the prior row are used in addition to using the immediately prior
pixel. If there are multiple sections, and the sections are marked as
correlated, after the first section, 4 pixels from the prior section are
included in the average. The CBFlib code differs from the pack_c code in
the handling of the beginnings and ends of rows and sections. The pack_c
code will use pixels from the other side of the image in doing the
averaging. The CBFlib code drops pixels from the other side of the image
from the pool. The details follow.
After dealing with the special case of the first pixel, The algorithm
uses an array of pointers, trail_char_data. The assignment of pixels to
the pool to be averaged begins with trail_char_data[0] points to the
pixel immediately prior to the next pixel to be processed, either in the
same row (fastest index) or, at the end of the prior row if the next
data element to be processed is at the end of a row. The location of the
pixel pointed to by trail_char_data[0] is used to compute the locations
of the other pixels in the pool. It will be dropped from the pool before
averaging if it is on the opposite side of the image. The pool will
consist of 1, 2, 4 or 8 pixels.
Assume ndim1, ndim2, ndim3 are the indices of the same pixel as
trail_char_data[0] points to. These indices are incremented to be the
indices of the next pixel to be processed before populating
trail_char_data.
On exit, trail_char_data[0 .. 7] will have been populated with pointers
to the pixels to be used in forming the average. Pixels that will not be
used will be set to NULL. Note that trail_char_data[0] may be set to
NULL.
If we mark the next element to be processed with a "*" and the entries
in trail_char_data with their array indices 0 .. 7, the possible
patterns of settings in the general case are:
current section:
- - - - 0 * - - - -
- - - - 3 2 1 - - -
- - - - - - - - - -
prior section:
- - - - - 4 - - - -
- - - - 7 6 5 - - -
- - - - - - - - - -
If there is no prior section (i.e. ndim3 is 0, or the
CBF_UNCORRELATED_SECTIONS flag is set to indicate discontinuous
sections), the values for trail_char_data[4 .. 7] will all be NULL. When
there is a prior section, trail_char_data[5..7] are pointers to the
pixels immediately below the elements pointed to by
trail_char_data[1..3], except trail_char_data[4] is one element further
along its row to be directly below the next element to be processed.
The first element of the first row of the first section is a special
case, with no averaging.
In the first row of the first section (ndim2 == 0, and ndim3 == 0),
after the first element (ndim1 > 0), only trail_char_data[0] is used
current section:
- - - - 0 * - - - -
For subsequent rows of the first section (ndim2 > 0, and ndim3 == 0),
for the first element (ndim1 == 0), two elements from the prior row are
used:
current section:
* - - - - - - - - -
2 1 - - - - - - - -
- - - - - - - - - -
while for element after the first element, but before the last element
of the row, a full set of 4 elements is used:
current section:
- - - - 0 * - - - -
- - - - 3 2 1 - - -
- - - - - - - - - -
For the last element of a row (ndim1 == dim1-1), two elements are used
current section:
- - - - - - - - 0 *
- - - - - - - - - 2
- - - - - - - - - -
For sections after the first section, provided the
CBF_UNCORRELATED_SECTIONS flag is not set in the compression, for each
non-NULL entry in trail_char_data [0..3] an entry is made in
trail_char_data [4..7], except for the first element of the first row of
a section. In that case an entry is made in trail_char_data[4].
The structure of the compressed data is:
Byte Value
1 .. 8 Number of elements (64-bit little-endian number)
9 .. 16 Minumum element (currently unused)
17 .. 24 Maximum element (currently unused)
25 .. 32 (reserved for future use)
33 .. Coded data
3.3.3 Byte_offset compression
Starting with CBFlib 0.7.7, CBFlib supports a simple and efficient
"byte_offset" algorithm originally proposed by Andy Hammerley and
modified by Wolgang Kabsch and Herbert Bernstein. The original proposal
was called "byte_offsets". We distinguish this variant by calling it
"byte_offset". The major differences are that the "byte_offsets"
algorithm started with explicit storage of the first element of the
array as a 4-byte signed two's integer, and checked for image edges to
changes the selection of prior pixel. The CBFlib "byte_offset"
alogorithm starts with an assumed zero before the first pixel and
represents the value of the first pixel as an offset of whatever number
of size is needed to hold the value, and for speed, treats the entire
image as a simple linear array, allowing use of the last pixel of one
row as the base against which to compute the offset for the first
element of the next row.
The algorithm is simple and easily implemented. This algorithm can never
achieve better than a factor of two compression relative to 16-bit raw
data or 4 relative to 32-bit raw data, but for most diffraction data the
compression will indeed be very close to these ideal values. It also has
the advantage that integer values up to 32 bits (or 31 bits and sign)
may be stored efficiently without the need for special over-load tables.
It is a fixed algorithm which does not need to calculate any image
statistics, so is fast.
The algorithm works because of the following property of almost all
diffraction data and much other image data: The value of one element
tends to be close to the value of the adjacent elements, and the vast
majority of the differences use little of the full dynamic range.
However, noise in experimental data means that run-length encoding is
not useful (unless the image is separated into different bit-planes). If
a variable length code is used to store the differences, with the number
of bits used being inversely proportional to the probability of
occurrence, then compression ratios of 2.5 to 3.0 may be achieved.
However, the optimum encoding becomes dependent of the exact properties
of the image, and in particular on the noise. Here a lower compression
ratio is achieved, but the resulting algorithm is much simpler and more
robust.
The "byte_offset" compression algorithm is the following:
1. Start with a base pixel value of 0.
2. Compute the difference delta between the next pixel value and the
base pixel value.
3. If -127 =< delta =< 127, output delta as one byte, make the current
pixel value the base pixel value and return to step 2.
4. Otherwise output -128 (80 hex).
5. We still have to output delta. If -32767 =< delta =< 32767, output
delta as a little_endian 16-bit quantity, make the current pixel
value the base pixel value and return to step 2.
6. Otherwise output -32768 (8000 hex, little_endian, i.e. 00 then 80)
7. We still have to output delta. If -2147483647 =< delta =<
2147483647, output delta as a little_endian 32 bit quantity, make
the current pixel value the base pixel value and return to step 2.
8. Otherwise output -2147483648 (80000000 hex, little_endian, i.e. 00,
then 00, then 00, then 80) and then output the pixel value as a
little-endian 64 bit quantity, make the current pixel value the base
pixel value and return to step 2.
The "byte_offset" decompression algorithm is the following:
1. Start with a base pixel value of 0.
2. Read the next byte as delta
3. If -127 =< delta =< 127, add delta to the base pixel value, make
that the new base pixel value, place it on the output array and
return to step 2.
4. If delta is 80 hex, read the next two bytes as a little_endian
16-bit number and make that delta.
5. If -32767 =< delta =< 32767, add delta to the base pixel value, make
that the new base pixel value, place it on the output array and
return to step 2.
6. If delta is 8000 hex, read the next 4 bytes as a little_endian
32-bit number and make that delta
7. If -2147483647 =< delta =< 2147483647, add delta to the base pixel
value, make that the new base pixel value, place it on the output
array and return to step 2.
8. If delta is 80000000 hex, read the next 8 bytes as a little_endian
64-bit number and make that delta, add delta to the base pixel
value, make that the new base pixel value, place it on the output
array and return to step 2.
Let us look at an example, of two 1000 x 1000 flat field images
presented as a mimimal imgCIF file. The first image uses 32-bit unsigned
integers and the second image uses 16-bit unsigned integers.
The imgCIF file begins with some identifying comments (magic numbers) to
track the version of the dictionary and library:
###CBF: VERSION 1.5
# CBF file written by CBFlib v0.7.7
This is followed by the necessary syntax to start a CIF data block and
by whatever tags and values are appropriate to describe the experiment.
The minimum is something like
data_testflat
eventually we come to the actual binary data, which begins the loop
header for the array_data category
loop_
_array_data.data
with any additional tags needed, and then the data itself, which starts
with the mini-header:
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_BYTE_OFFSET"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 1000002
X-Binary-ID: 1
X-Binary-Element-Type: "unsigned 32-bit integer"
X-Binary-Element-Byte-Order: LITTLE_ENDIAN
Content-MD5: +FqUJGxXhvCijXMFHC0kaA==
X-Binary-Number-of-Elements: 1000000
X-Binary-Size-Fastest-Dimension: 1000
X-Binary-Size-Second-Dimension: 1000
X-Binary-Size-Padding: 4095
followed by an empty line and then the sequence of characters:
^L^Z^D
followed immediately by the compressed data.
The binary data begins with the hex byte 80 to flag the need for a value
that will not fit in one byte. That is followed by the small_endian hex
value 3E8 saying that the first delta is 1000. Then 999,999 bytes of
zero follow, since this is a flat field, with all values equal to zero.
That gives us our entire 1000x1000 compressed flat field. However,
because we asked for 4095 bytes of padding, there is an additional 4095
bytes of zero that are not part of the compressed field. They are just
pad and can be ignored. Finally, after the pad, the CIF text field that
began with
;
--CIF-BINARY-FORMAT-SECTION--
is completed with
--CIF-BINARY-FORMAT-SECTION----
;
notice the extra --
The second flat field then follows, with a very similar mini-header:
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_BYTE_OFFSET"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 1000002
X-Binary-ID: 2
X-Binary-Element-Type: "unsigned 16-bit integer"
X-Binary-Element-Byte-Order: LITTLE_ENDIAN
Content-MD5: +FqUJGxXhvCijXMFHC0kaA==
X-Binary-Number-of-Elements: 1000000
X-Binary-Size-Fastest-Dimension: 1000
X-Binary-Size-Second-Dimension: 1000
X-Binary-Size-Padding: 4095
^L^Z^D
The only difference is that we have declared this array to be 16-bit and
have chosen a different binary id (2 instead of 1). Even the checksum is
the same.
4. Installation
CBFlib should be built on a disk with at least 200 megabytes of free
space. CBFlib.tar.gz is a "gzipped" tar of the code as it now stands.
Place the gzipped tar in the directory that is intended to contain a new
directory, named CBFlib_0.7.5 (the "top-level" directory) and uncompress
it with gunzip and unpack it with tar:
gunzip CBFlib.tar.gz
tar xvf CBFLIB.tar
As with prior releases, to run the test programs, you will also need
Paul Ellis's sample MAR345 image, example.mar2300, and Chris Nielsen's
sample ADSC Quantum 315 image, mb_LP_1_001.img as sample data. Both
these files will be extracted by the Makefile from
CBFlib_0.7.7_Data_Files. Do not download copies into the top level
directory.
After unpacking the archive, the top-level directory should contain a
makefile:
Makefile Makefile for unix
and the subdirectories:
src/ CBFLIB source files
include/ CBFLIB header files
m4/ CBFLIB m4 macro files (used to build .f90 files)
examples/ Example program source files
doc/ Documentation
lib/ Compiled CBFLIB library
bin/ Executable example programs
html_images/ JPEG images used in rendering the HTML files
For instructions on compiling and testing the library, go to the
top-level directory and type:
make
The CBFLIB source and header files are in the "src" and "include"
subdirectories. The FCBLIB source and m4 files are in the "src" and "m4"
subdirectories. The files are:
src/ include/ m4/ Description
cbf.c cbf.h CBFLIB API
functions
cbf_alloc.c cbf_alloc.h Memory allocation
functions
cbf_ascii.c cbf_ascii.h Function for
writing ASCII
values
cbf_binary.c cbf_binary.h Functions for
binary values
cbf_byte_offset.c cbf_byte_offset.h Byte-offset
compression
cbf_canonical.c cbf_canonical.h Canonical-code
compression
cbf_codes.c cbf_codes.h Encoding and
message digest
functions
cbf_compress.c cbf_compress.h General
compression
routines
cbf_context.c cbf_context.h Control of
temporary files
cbf_file.c cbf_file.h File in/out
functions
cbf_lex.c cbf_lex.h Lexical analyser
cbf_packed.c cbf_packed.h CCP4-style
packing compression
cbf_predictor.c cbf_predictor.h Predictor-Huffman
compression (not
implemented)
cbf_read_binary.c cbf_read_binary.h Read binary
headers
cbf_read_mime.c cbf_read_mime.h Read MIME-encoded
binary sections
cbf_simple.c cbf_simple.h Higher-level
CBFlib functions
cbf_string.c cbf_string.h Case-insensitive
string comparisons
cbf_stx.c cbf_stx.h Parser (generated
from cbf.stx.y)
cbf_tree.c cbf_tree.h CBF
tree-structure
functions
cbf_uncompressed.c cbf_uncompressed.h Uncompressed
binary sections
cbf_write.c cbf_write.h Functions for
writing
cbf_write_binary.c cbf_write_binary.h Write binary
sections
cbf.stx.y bison grammar to
define cbf_stx.c
(see WARNING)
md5c.c md5.h RSA message
digest software
from mpack
global.h
fcb_atol_wcnt.f90 Function to
convert a string to
an integer
fcb_ci_strncmparr.f90 Function to do a
case-insensitive
comparison of a
string to a byte
array
fcb_nblen_array.f90 Function to
determine the
non-blank length of
a byte array
fcb_read_byte.f90 Function to read
a single byte
fcb_read_line.f90 Function to read
a line into a byte
array
fcb_skip_whitespace.f90 Function to skip
whitespace and
comments in a MIME
header
fcb_exit_binary.m4 Function to skip
past the end of the
current binary text
field
fcb_next_binary.m4 Function to skip
to the next binary
fcb_open_cifin.m4 Function to open
a CBF file for
reading
fcb_packed.m4 Functions to read
a JPA CCP4
compressed image
fcb_read_bits.m4 Functions to read
nay number of bits
as an integer
fcb_read_image.m4 Functions to read
the next image in
I2, I4, 3D_I2 and
3D_I4 format
fcb_read_xds_i2.m4 Function to read
a single xds image.
fcblib_defines.m4 General m4 macro
file for FCBLIB
routines.
In the "examples" subdirectory, there are 2 additional files used by the
example programs (section 5) for reading MAR300, MAR345 or ADSC CCD
images:
img.c img.h Simple image library
and the example programs themselves:
makecbf.c Make a CBF file from an image
img2cif.c Make an imgCIF or CBF from an image
cif2cbf.c Copy a CIF/CBF to a CIF/CBF
convert_image.c Convert an image file to a cbf using a template file
cif2c.c Convert a template cbf file into a function to
produce the same template in an internal cbf data
structure
testcell.C Exercise the cell functions
as well as three template files: template_adscquantum4_2304x2304.cbf,
template_mar345_2300x2300.cbf, and
template_adscquantum315_3072x3072.cbf.
Two additional examples (test_fcb_read_image.f90 and
test_xds_binary.f90) are created from two files (test_fcb_read_image.m4
and test_xds_binary.m4) in the m4 directory.
The documentation files are in the "doc" subdirectory:
CBFlib.html This document (HTML)
CBFlib.txt This document (ASCII)
CBFlib_NOTICES.html Important NOTICES -- PLEASE READ
CBFlib_NOTICES.txt Important NOTICES -- PLEASE READ
gpl.txt GPL -- PLEASE READ
lgpl.txt LGPL -- PLEASE READ
cbf_definition_rev.txt Draft CBF/ImgCIF definition (ASCII)
cbf_definition_rev.html Draft CBF/ImgCIF definition (HTML)
cif_img.html CBF/ImgCIF extensions dictionary (HTML)
cif_img.dic CBF/ImgCIF extensions dictionary (ASCII)
ChangeLog,html Summary of change history (HTML)
ChangeLog Summary of change history (ASCII)
5. Example programs
The example programs makecbf.c, img2cif.c and convert_image.c read an
image file from a MAR300, MAR345 or ADSC CCD detector and then uses
CBFlib to convert it to CBF format (makecbf) or either imgCIF or CBF
format (img2cif). makecbf writes the CBF-format image to disk, reads it
in again, and then compares it to the original. img2cif just writes the
desired file. makecbf works only from stated files on disk, so that
random I/O can be used. img2cif includes code to process files from
stdin and to stdout. convert_image reads a template as well as the image
file and produces a complete CBF. The program convert_minicbf reads a
minimal CBF file with just and image and some lines of text specifying
the parameters of the data collection as done at SLS and combines the
result with a template to produce a full CBF. The program cif2cbf can be
used to convert among carious compression and encoding schemes. The
program sauter_test.C is a C++ test program contributed by Nick Sauter
to help in resolving a memory leak he found. The programs adscimg2cbf
and cbf2adscimg are a "jiffies" contributed by Chris Nielsen of ADSC to
convert ADSC images to imgCIF/CBF format and vice versa.
makecbf.c is a good example of how many of the CBFlib functions can be
used. To compile makecbf and the other example programs use the Makefile
in the top-level directory:
make all
This will place the programs in the bin directory.
makecbf
To run makecbf with the example image, type:
./bin/makecbf example.mar2300 test.cbf
The program img2cif has the following command line interface:
img2cif [-i input_image] \
[-o output_cif] \
[-c {p[acked]|c[annonical]|[n[one]}] \
[-m {h[eaders]|n[oheaders]}] \
[-d {d[igest]|n[odigest]}] \
[-e {b[ase64]|q[uoted-printable]| \
d[ecimal]|h[exadecimal]|o[ctal]|n[one]}] \
[-b {f[orward]|b[ackwards]}] \
[input_image] [output_cif]
the options are:
-i input_image (default: stdin)
the input_image file in MAR300, MAR345 or ADSC CCD detector
format is given. If no input_image file is specified or is
given as "-", an image is copied from stdin to a temporary file.
-o output_cif (default: stdout)
the output cif (if base64 or quoted-printable encoding is used)
or cbf (if no encoding is used). if no output_cif is specified
or is given as "-", the output is written to stdout
-c compression_scheme (packed, canonical or none, default packed)
-m [no]headers (default headers for cifs, noheaders for cbfs)
selects MIME (N. Freed, N. Borenstein, RFC 2045, November 1996)
headers within binary data value text fields.
-d [no]digest (default md5 digest [R. Rivest, RFC 1321, April
1992 using"RSA Data Security, Inc. MD5 Message-Digest
Algorithm"] when MIME headers are selected)
-e encoding (base64, quoted-printable, decimal, hexadecimal,
octal or none, default: base64) specifies one of the standard
MIME encodings (base64 or quoted-printable) or a non-standard
decimal, hexamdecimal or octal encoding for an ascii cif
or "none" for a binary cbf
-b direction (forward or backwards, default: backwards)
specifies the direction of mapping of bytes into words
for decimal, hexadecimal or octal output, marked by '>' for
forward or '<' for backwards as the second character of each
line of output, and in '#' comment lines.
cif2cbf
The test program cif2cbf uses many of the same command line options as
img2cif, but accepts either a CIF or a CBF as input instead of an image
file:
cif2cbf [-i input_cif] [-o output_cbf] \
[-u update_cif] \
[-c {p[acked]|c[annonical]|{b[yte_offset]}|\
{v[2packed}|{f[latpacked}[n[one]}] \
[-C highclipvalue] \
[-D ] \
[-I {0|2|4|8}] \
[-R {0|4|8}] \
[-L {0|4|8}] \
[-m {h[eaders]|noh[eaders]}] \
[-m {d[imensions]|nod[imensions}] \
[-d {d[igest]|n[odigest]|w[arndigest]}] \
[-B {read|liberal|noread}] [-B {write|nowrite}] \
[-S {read|noread}] [-S {write|nowrite}] \
[-T {read|noread}] [-T {write|nowrite}] \
[-e {b[ase64]|q[uoted-printable]|\
d[ecimal]|h[examdecimal|o[ctal]|n[one]}] \
[-b {f[orward]|b[ackwards]}\
[-p {1|2|4}\
[-v dictionary]* [-w] [-W]\
[input_cif] [output_cbf]
the options are:
-i input_cif (default: stdin)
the input file in CIF or CBF format. If input_cif is not
specified or is given as "-", it is copied from stdin to a
temporary file.
-o output_cbf (default: stdout)
the output cif (if base64 or quoted-printable encoding is used)
or cbf (if no encoding is used). if no output_cif is specified
or is given as "-", the output is written to stdout
if the output_cbf is /dev/null, no output is written.
-u update_cif (no default)
and optional second input file in CIF or CBF format containing
data blocks to be merged with data blocks from the primary
input CIF or CBF
The remaining options specify the characteristics of the
output cbf. Most of the characteristics of the input cif are
derived from context, except when modified by the -B, -S, -T, -v
and -w flags.
-b byte_order (forward or backwards, default forward (1234) on
little-endian machines, backwards (4321) on big-endian machines
-B [no]read or liberal (default noread)
read to enable reading of DDLm style brackets
liberal to accept whitespace for commas
-B [no]write (default write)
write to enable writing of DDLm style brackets
-c compression_scheme (packed, canonical, byte_offset,
v2packed, flatpacked or none,
default packed)
-C highclipvalue
specifies a double precision value to which to clip the data
-d [no]digest or warndigest (default md5 digest [R. Rivest,
RFC 1321, April 1992 using"RSA Data Security, Inc. MD5
Message-Digest Algorithm"] when MIME headers are selected)
-D test cbf_construct_detector
-e encoding (base64, k, quoted-printable or none, default base64)
specifies one of the standard MIME encodings for an ascii cif
or "none" for a binary cbf
-I 0 or integer element size
specifies integer conversion of the data, 0 to use the input
number of bytes, 2, 4 or 8 for short, long or long long
output integers
-L lowclipvalue
specifies a double precision value to cut off the data from
below
-m [no]headers (default headers)
selects MIME (N. Freed, N. Borenstein, RFC 2045, November 1996)
headers within binary data value text fields.
-m [nod]imensions (default dimensions)
selects detailed recovery of dimensions from the input CIF
for use in the MIME header of the output CIF
-p K_of_padding (0, 1, 2, 4) for no padding after binary data
1023, 2047 or 4095 bytes of padding after binary data
-R 0 or integer element size
specifies real conversion of the data, 0 to use the input
number of bytes, 4 or 8 for float or double output reals
-S [no]read or (default noread)
read to enable reading of whitespace and comments
-S [no]write (default write)
write to enable writing of whitespace and comments
-T [no]read or (default noread)
read to enable reading of DDLm style triple quotes
-T [no]write (default write)
write to enable writing of DDLm style triple quotes
-v dictionary specifies a dictionary to be used to validate
the input cif and to apply aliases to the output cif.
This option may be specified multiple times, with dictionaries
layered in the order given.
-w process wide (2048 character) lines
-W write wide (2048 character) lines
convert_image
The program convert_image requires two arguments: imagefile and cbffile.
Those are the primary input and output. The detector type is extracted
from the image file or from the command line, converted to lower case
and used to construct the name of a template cbf file to use for the
copy. The template file name is of the form template_name_columnsxrows.
The full set of options is:
convert_image [-i input_img] [-o output_cbf] [-p template_cbf]\
[-d detector name] -m [x|y|x=y] [-z distance] \
[-c category_alias=category_root]* \
[-t tag_alias=tag_root]* [-F] [-R] \
[input_img] [output_cbf]
the options are:
-i input_img (default: stdin)
the input file as an image in smv, mar300, or mar345 format.
If input_img is not specified or is given as "-", it is copied
from stdin to a temporary file.
-p template_cbf
the template for the final cbf to be produced. If template_cbf
is not specified the name is constructed from the first token
of the detector name and the image size as
template__x.cbf
-o output_cbf (default: stdout )
the output cbf combining the image and the template. If the
output_cbf is not specified or is given as "-", it is written
to stdout.
-d detectorname
a detector name to be used if none is provided in the image
header.
-F
when writing packed compression, treat the entire image as
one line with no averaging
-m [x|y|x=y] (default x=y, square arrays only)
mirror the array in the x-axis (y -> -y)
in the y-axis (x -> -x)
or in x=y ( x -> y, y-> x)
-r n
rotate the array n times 90 degrees counter clockwise
x -> y, y -> -x for each rotation, n = 1, 2 or 3
-R
if setting a beam center, set reference values of
axis settings as well as standard settings
-z distance
detector distance along Z-axis
-c category_alias=category_root
-t tag_alias=tagroot
map the given alias to the given root, so that instead
of outputting the alias, the root will be presented in the
output cbf instead. These options may be repeated as many
times as needed.
convert_minicbf
The program convert_minicbf requires two arguments: minicbf and cbffile.
Those are the primary input and output. The detector type is extracted
from the image file or from the command line, converted to lower case
and used to construct the name of a template cbf file to use for the
copy. The template file name is of the form template_name_columnsxrows.
The full set of options is:
convert_minicbf [-i input_cbf] [-o output_cbf] [-p template_cbf]\
[-q] [-C convention] \
[-d detector name] -m [x|y|x=y] [-z distance] \
[-c category_alias=category_root]* \
[-t tag_alias=tag_root]* [-F] [-R] \
[input_cbf] [output_cbf]
the options are:
-i input_cbf (default: stdin)
the input file as a CBF with at least an image.
-p template_cbf
the template for the final cbf to be produced. If template_cbf
is not specified the name is constructed from the first token
of the detector name and the image size as
template__x.cbf
-o output_cbf (default: stdout )
the output cbf combining the image and the template. If the
output_cbf is not specified or is given as "-", it is written
to stdout.
-q
exit quickly with just the miniheader expanded
after the data. No template is used.
-Q
exit quickly with just the miniheader unexpanded
before the data. No template is used.
-C convention
convert the comment form of miniheader into the
_array_data.header_convention convention
_array_data.header_contents
overriding any existing values
-d detectorname
a detector name to be used if none is provided in the image
header.
-F
when writing packed compression, treat the entire image as
one line with no averaging
-m [x|y|x=y] (default x=y, square arrays only)
mirror the array in the x-axis (y -> -y)
in the y-axis (x -> -x)
or in x=y ( x -> y, y-> x)
-r n
rotate the array n times 90 degrees counter clockwise
x -> y, y -> -x for each rotation, n = 1, 2 or 3
-R
if setting a beam center, set reference values of
axis settings as well as standard settings
-z distance
detector distance along Z-axis
-c category_alias=category_root
-t tag_alias=tagroot
map the given alias to the given root, so that instead
of outputting the alias, the root will be presented in the
output cbf instead. These options may be repeated as many
times as needed.
testreals, testflat and testflatpacked
The example programs testreals, testflat and testflatpacked exercise the
handling of reals, byte_offset compression and packed compression. Each
is run without any arguments. testreals will read real images from the
data file testrealin.cbf and write a file with real images in
testrealout.cbf, which should be identical to testrealin.cbf. testflat
and testflatpacked read 4 1000x1000 2D images and one 50x60x70 3D image
and produce an output file that should be identical to the input.
testflat reads testflatin.cbf and produces testflatout.cbf using
CBF_BYTE_OFFSET compression. testflatpacked reads testflatpackedin.cbf
and produces testflatpackedout.cbf. The images are:
* A 1000 x 1000 array of 32-bit integers forming a flat field with all
pixels set to 1000.
* A 1000 x 1000 array of 16-bit integers forming a flat field with all
pixels set to 1000.
* A 1000 x 1000 array of 32-bit integers forming a flat field with all
pixels set to 1000, except for -3 along the main diagonal and its
transpose.
* A 1000 x 1000 array of 16-bit integers forming a flat field with all
pixels set to 1000, except for -3 along the main diagonal and its
transpose.
* A 50 x 60 x 70 array of 32-bit integers in a flat field of 1000,
except for -3 along the main diagonal and the values i+j+k (counting
from zero) every 1000th pixel
test_fcb_read_image, test_xds_binary
The example programs test_fcb_read_image and test_xds_binary are
designed read the output of testflat and testflatpacked using the FCBlib
routines in lib/libfcb. test_xds_binary reads only the first image and
closes the file immediately. test_fcb_read_image reads all 5 images from
the input file. The name of the input file should be provided on stdin,
as in:
* echo testflatout.cbf | bin/test_xds_binary
* echo testflatpackedout.cbf | bin/test_xds_binary
* echo testflatout.cbf | bin/test_fcb_read_image
* echo testflatpackedout.cbf | bin/test_fcb_read_image
In order to compile these programs correctly for the G95 compiler it is
important to set the record size for reading to be no larger than the
padding after binary images. This in controlled in Makefile by the line
M4FLAGS = -Dfcb_bytes_in_rec=131072 which provides good performance for
gfortran. For g95, this line must be changed to M4FLAGS =
-Dfcb_bytes_in_rec=4096
sauter_test
The program sauter_test.C is a C++ test program contributed by Nick
Sauter to help in resolving a memory leak he found. The program is run
as bin/sauter_test and should run long enough to allow a check with top
to ensure that it has constant memory demands. In addition, starting
with release 0.7.8.1, the addition of -DCBFLIB_MEM_DEBUG to the compiler
flags will cause detailed reports on memory use to stderr to be
reported.
adscimg2cbf
The example program adscimg2cbf accepts any number of raw or compressed
ADSC images with .img, .img.gz, .img.bz2 or .img.Z extensions and
converts each of them to an imgCIF/CBF file with a .cbf extension.
adscimg2cbf [--flag[,modifier]] file1.img ... filen.img (creates file1.cbf ... filen.cbf)
Image files may also be compressed (.gz, .bz2, .Z)
Flags:
--cbf_byte_offset Use BYTE_OFFSET compression (DEFAULT)
--cbf_packed Use CCP4 packing (JPA) compression.
--cbf_packed_v2 Use CCP4 packing version 2 (JPA) compression.
--no_compression No compression.
The following two modifiers can be appended to the flags (syntax: --flag,modifier):
flat Flat (linear) images.
uncorrelated Uncorrelated sections.
adscimg2cbf
The example program cbf2adscimg accepts any number of cbfs of ADSC
images created by adscimg1cbf or convert_image and produces raw or
compressed adsc image files with .img, .img.gz or .img.bz2 extensions.
cbf2adscimg [--flag] file1.cbf ... filen.cbf (creates file1.img ... filen.img)
Image files may be compressed on output: (.gz, .bz2) by using the flags below.\n");
Flags:
--gz Output a .gz file (e.g., filen.img.gz).
--bz2 Output a .bz2 file (e.g., filen.img.bz2).
tiff2cbf
The test program tiff2cbf converts a tiff data file to a cbf data file.
The program converts the tiff data samples directly into a minicbf with
the tiff header stored at the value of _array_data.header_contents. This
conversion is supported for the sample formats SAMPLEFORMAT_UINT
(unsigned integer data), SAMPLEFORMAT_INT (unsigned integer data),
SAMPLEFORMAT_INT (signed integer data), SAMPLEFORMAT_IEEEFP (IEEE
floating point data), SAMPLEFORMAT_COMPLEXINT (complex signed int) and
SAMPLEFORMAT_COMPLEXIEEEFP (complex ieee floating). Conversions from
these formats to other CBF formats can be handled by cif2cbf. If you
wish to convert and xxx.tif written with IEEE floating point samples
into a CBF with integer values compressed by byte-offset compression for
use by XDS, creating an xxx_view.cbf with values clipped between 0 and
100, and an xxx_xds.cbf with unclipped values for processing:
tiff2cbf xxx.tif xxx.cbf
cif2cbf -I 4 -C 100. -L 0. -e n -c b -i xxx.cbf -o xxx_view.cbf
cif2cbf -I 4 -e n -c b -i xxx.cbf -o xxx_xds.cbf
----------------------------------------------------------------------
----------------------------------------------------------------------
Updated 29 March 2011. Contact: yaya at bernstein-plus-sons dot com
./CBFlib-0.9.2.2/doc/cif_img_1_2_4.html 0000644 0000765 0000765 00000676476 11603702115 015544 0 ustar yaya yaya
cif_img.dic v1.2.4
# #
# #
# Extensions Dictionary #
##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.2.4 #
# of 2001-07-14 #
# by Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook #
# #
# This dictionary was adapted from the imgCIF Workshop, held at BNL Oct 1997#
# and the Crystallographic Binary File Format Draft Proposal by Andy #
# Hammersley. The first DDL 2.1 Version was created by John Westbrook. #
# This version was drafted by Herbert J. Bernstein and incorporates comments #
# by I. David Brown, John Westbrook, Brian McMahon, Bob Sweet, Paul Ellis, #
# Harry Powell, Wilfred Li and others. #
##############################################################################
data_cif_img.dic
_dictionary.title cif_img.dic
_dictionary.version 1.2.3
_dictionary.datablock_id cif_img.dic
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.gain
# _array_intensities.gain_esd
# _array_intensities.linearity
# _array_intensities.offset
# _array_intensities.scaling
# _array_intensities.overload
# _array_intensities.undefined_value
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.encoding_type
# _array_structure.id
#
# category ARRAY_STRUCTURE_LIST
#
# _array_structure_list.axis_set_id
# _array_structure_list.array_id
# _array_structure_list.dimension
# _array_structure_list.direction
# _array_structure_list.index
# _array_structure_list.precedence
#
# category ARRAY_STRUCTURE_LIST_AXIS
#
# _array_structure_list_axis.axis_id
# _array_structure_list_axis.axis_set_id
# _array_structure_list_axis.angle
# _array_structure_list_axis.angle_increment
# _array_structure_list_axis.displacement_increment
# _array_structure_list_axis.angular_pitch
# _array_structure_list_axis.radial_pitch
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.type
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
#
# category DIFFRN_DATA_FRAME
#
# _diffrn_data_frame.array_id
# _diffrn_data_frame.binary_id
# _diffrn_data_frame.detector_element_id
# _diffrn_data_frame.id
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.id
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.axis_id
# _diffrn_detector_axis.detector_id
#
# category DIFFRN_DETECTOR_ELEMENT
#
# _diffrn_detector_element.center[1]
# _diffrn_detector_element.center[2]
# _diffrn_detector_element.id
# _diffrn_detector_element.detector_id
#
# category DIFFRN_MEASUREMENT
#
# _diffrn_measurement.diffrn_id
# _diffrn_measurement.details
# _diffrn_measurement.device
# _diffrn_measurement.device_details
# _diffrn_measurement.device_type
# _diffrn_measurement.id
# _diffrn_measurement.method
# _diffrn_measurement.number_of_axes
# _diffrn_measurement.specimen_support
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.axis_id
# _diffrn_measurement_axis.measurement_device
# _diffrn_measurement_axis.measurement_id
#
# category DIFFRN_RADIATION
#
# _diffrn_radiation.collimation
# _diffrn_radiation.diffrn_id
# _diffrn_radiation.div_x_source
# _diffrn_radiation.div_y_source
# _diffrn_radiation.div_x_y_source
# _diffrn_radiation.filter_edge'
# _diffrn_radiation.inhomogeneity
# _diffrn_radiation.monochromator
# _diffrn_radiation.polarisn_norm
# _diffrn_radiation.polarisn_ratio
# _diffrn_radiation.polarizn_source_norm
# _diffrn_radiation.polarizn_source_ratio
# _diffrn_radiation.probe
# _diffrn_radiation.type
# _diffrn_radiation.xray_symbol
# _diffrn_radiation.wavelength_id
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.date_end
# _diffrn_scan.date_start
# _diffrn_scan.integration_time
# _diffrn_scan.frame_id_start
# _diffrn_scan.frame_id_end
# _diffrn_scan.frames
#
# category DIFFRN_SCAN_AXIS
#
# _diffrn_scan_axis.axis_id
# _diffrn_scan_axis.angle_start
# _diffrn_scan_axis.angle_range
# _diffrn_scan_axis.angle_increment
# _diffrn_scan_axis.angle_rstrt_incr
# _diffrn_scan_axis.displacement_start
# _diffrn_scan_axis.displacement_range
# _diffrn_scan_axis.displacement_increment
# _diffrn_scan_axis.displacement_rstrt_incr
# _diffrn_scan_axis.scan_id
#
# category DIFFRN_SCAN_FRAME
#
# _diffrn_scan_frame.date
# _diffrn_scan_frame.frame_id
# _diffrn_scan_frame.frame_number
# _diffrn_scan_frame.integration_time
# _diffrn_scan_frame.scan_id
#
# category DIFFRN_SCAN_FRAME_AXIS
#
# _diffrn_scan_frame_axis.axis_id
# _diffrn_scan_frame_axis.angle
# _diffrn_scan_frame_axis.angle_increment
# _diffrn_scan_frame_axis.angle_rstrt_incr
# _diffrn_scan_frame_axis.displacement
# _diffrn_scan_frame_axis.displacement_increment
# _diffrn_scan_frame_axis.displacement_rstrt_incr
# _diffrn_scan_frame_axis.frame_id
#
# ***DEPRECATED*** category DIFFRN_FRAME_DATA
#
# _diffrn_frame_data.array_id
# _diffrn_frame_data.binary_id
# _diffrn_frame_data.detector_element_id
# _diffrn_frame_data.id
#
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
;
Data items in the ARRAY_DATA category are the containers for
the array data items described in category ARRAY_STRUCTURE.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and
presented as hexadecimal data. The first character "H" on the
data lines means hexadecimal. It could have been "O" for octal
or "D" for decimal. The second character on the line shows
the number of bytes in each word (in this case "4"), which then
requires 8 hexadecimal digits per word. The third character
gives the order of octets within a word, in this case "<"
for the ordering 4321 (i.e. "big-endian"). Alternatively the
character ">" could have been used for the ordering 1234
(i.e. "little-endian"). The block has a "message digest"
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id_array_data.binary_id_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 1
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-Id, these values should be equal.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
"--CIF-BINARY-FORMAT-SECTION--" (including the
required initial "--").
The Content-Type may be any of the discrete types permitted
in RFC 2045; "application/octet-stream" is recommended.
If an octet stream was compressed, the compression should
be specified by the parameter 'conversions="x-CBF_PACKED"'
or the parameter 'conversions="x-CBF_CANONICAL"'.
The Content-Transfer-Encoding may be "BASE64",
"Quoted-Printable", "X-BASE8", "X-BASE10", or
"X-BASE16" for an imgCIF or "BINARY" for a CBF. The
octal, decimal and hexadecimal transfer encodings are
for convenience in debugging, and are not recommended
for archiving and data interchange.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In a CBF, the
raw binary data begins after an empty line terminating
the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of
the message size, nor in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. An adjustment is made for
the deprecated binary formats in which 8 bytes of binary
header are used for the compression type. In that case,
the 8 bytes used for the compression type is subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is "unsigned 32-bit integer".
An MD5 message digest may, optionally, be used. The "RSA Data
Security, Inc. MD5 Message-Digest Algorithm" should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is "X-BASE8", "X-BASE10", or
"X-BASE16", the data is presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ("big-
endian") or 1234... (little-endian). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as "==" for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is "H", "O", or "D" for hexadecimal, octal or
decimal, n is the number of octets per word. and d is "<"
for ">" for the "...4321" and "1234..." octet orderings
respectively. The "==" padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hex, octal and decimal formats, only, comments
beginning with "#" are permitted to improve readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three, c1, c2, c3. The resulting 24 bits
are broken into four 6-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order 4 bits of the second octet ((c1 & 3)<<4 | (c2>>4)),
then the bottom 4 bits of the second octet followed by the
high order two bits of the last octet ((c2 & 15)<<2 | (c3>>6)),
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
With short groups of octets padded on the right with one "="
if c3 is missing, and with "==" if both c2 and c3 are missing.
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32..38,
42, 48..57, 59..60, 62, 64..126 and the octet is not a ";"
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
"wrapped" with a terminating "=" (i.e. the MIME conventions
for an implicit line terminator are never used).
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
;
Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.index
_item_description.description
;
This item is a pointer to _array_structure_list.index in the
ARRAY_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
;
The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
;
Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The actual detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
'_array_intensities.gain'. If raw, uncorrected values
are presented (e.g for calibration experiments), the
value of '_array_intensities.linearity' will be 'raw'
and '_array_intensities.gain' will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id_array_intensities.linearity_array_intensities.gain_array_intensities.overload_array_intensities.undefined_value
image_1 linear 1.2 655535 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
;
Detector "gain". The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
;
The estimated standard deviation in detector "gain".
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
;
The intensity linearity scaling used from raw intensity
to the stored element value:
'linear' is obvious
'offset' means that the value defined by
'_array_intensities.offset' should be added to each
element value.
'scaling' means that the value defined by
'_array_intensities.scaling' should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by '_array_intensities.scaling' is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
'logarithmic_scaled' means that the logarithm based 10 of
raw intensities multiplied by '_array_intensities.scaling'
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and calculating 10
to the power of this number.
'raw' means that the data is the raw is a set of raw values
straight from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
;
The value defined by '_array_intensities.offset' should
be added to each element value.
;
'scaling'
;
The value defined by '_array_intensities.scaling' should be
multiplied with each element value.
;
'scaling_offset'
;
The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
;
The square root of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
;
'logarithmic_scaled'
;
The logarithm based 10 of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
'_array_intensities.scaling' and calculating 10 to the
power of this number.
;
'raw'
;
The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
;
Offset value to add to array element values in the manner
described by item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.scaling
_item_description.description
;
Multiplicative scaling value to be applied to array data
in the manner described by item _array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
;
The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.undefined_value
_item_description.description
;
A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
;
Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data which may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
_category_key.name '_array_structure.id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
;
The order of bytes for integer values which require more
than 1-byte.
(IBM-PC's and compatibles, and Dec-Vaxes use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. Dec-Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
;
The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
;
The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
;
Type of data compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code code
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'none'
;
Data are stored in normal format as defined by
'_array_structure.encoding_type' and
'_array_structure.byte_order'.
;
'byte_offsets'
;
Using the compression scheme defined in CBF definition
Section 5.0.
;
'packed'
;
Using the 'packed' compression scheme, a CCP4-style packing
(CBFlib section 3.3.2)
;
'canonical'
;
Using the 'canonical' compression scheme (CBFlib section
3.3.1)
;
save_
save__array_structure.encoding_type
_item_description.description
;
Data encoding of a single element of array data.
In several cases, the IEEE format is referenced.
See "IEEE Standard for Binary Floating-Point Arithmetic",
ANSI/IEEE Std 754-1985, the Institute of Electrical and
Electronics Engineers, Inc., NY 1985.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure yes
'_array_data.array_id' array_data yes
'_array_structure_list.array_id' array_structure_list yes
'_array_intensities.array_id' array_intensities yes
'_diffrn_data_frame.array_id' diffrn_data_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
;
Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left-to-right (increasing) in
first dimension and bottom-to-top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differ
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the "poise" of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
;
The number of elements stored in the array structure in this
dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
;
Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
;
Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
;
Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
;
Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
;
Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
;
Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axis, one for the angular
direction, one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
'_array_structure_list_axis.axis_set_id'
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
;
The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id .
This item is a pointer to _array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
save_
save__array_structure_list_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of '_array_structure_list.axis_set_id'. If the index is
specified as 'increasing' this will be the center of the
pixel with index value 1. If the index is specified as
'decreasing' this will be the center of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
;
The pixel-center-to-pixel-center increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified in that case.
See '_array_structure_list_axis.angular_pitch'.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
;
The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of '_array_structure_list.axis_set_id'. If the index is
specified as 'increasing' this will be the center of the
pixel with index value 1. If the index is specified as
'decreasing' this will be the center of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
;
The pixel-center-to-pixel-center increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
;
The pixel-center-to-pixel-center distance for a one step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans,
or for uncoupled angular scans at a constant radius
(cylindrical scan) and should not be specified for cases
in which the angle between pixels, rather than the distance
between pixels is uniform.
See '_array_structure_list_axis.angle_increment'.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
;
The radial distance from one "cylinder" of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of '_array_structure_list_axis.displacement_increment'.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
########
# AXIS #
########
save_AXIS
_category.description
;
Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection. The location of each
axis is specified by two vectors: the axis itself, given as a unit
vector, and an offset to the base of the unit vector. These vectors
are referenced to a right-handed laboratory coordinate system with
its origin in the sample or specimen:
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
These axes are based on the goniometer, not on the orientation of the
detector, gravity, etc. The vectors necessary to specify all other
axes are given by sets of three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to, but significantly
different from the choice in MOSFLM (Andrew G.W. Leslie, Harry Powell,
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH,UK
http://www.dl.ac.uk/CCP/CCP4/dist/x-windows/Mosflm/). In MOSFLM,
X is along the X-ray beam (our Z axis) and Z is along the rotation axis.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam center.
The location of the beam center on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected mm from the (0,0) corner
of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, we need to specify the
location of the beam center on the detector in terms of the origin of the
detector, which is, of course, not coincident with the center of the
sample.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows the axis specification of the axes of a kappa
geometry goniometer (See "X-Ray Structure Determination, A Practical
Guide", 2nd ed. by G. H. Stout, L. H. Jensen, Wiley Interscience,
1989, 453 pp, p 134.).
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X-axis. The next innermost axis, kappa,
is at a 50 degree angle to the X-axis, pointed away from the source.
The innermost axis, phi, aligns with the X-axis when omega and
phi are at their zero-points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
x' = (T-omega) (T-kappa) (T-phi) x
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
This example show the axis specification of the axes of a
detector, source and gravity. We have juggled the order as a
reminder that the ordering of presentation of tokens is not
significant. We have taken the center of rotation of the detector
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.type specifies the next outermost
axis upon which this axis depends.
This item is a pointer to axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.type specifies the type of equipment
using the axis: goniometer, detector, gravity, source
or general
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so that the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: rotation, translation (or general when the type is
not relevant, as for gravity)
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
;
Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases, but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element is
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id
;
;
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0.00
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
;
This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.id
_item_description.description
;
The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Need new example here.
;
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detectors used to measure
the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
;
The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of _diffrn_detector.diffrn_id
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
;
The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id
The word "positioner" is a general term used in instrumentation
design for devices that are used to change the positions of
portions of apparatus by linear translation, rotation, or
combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
;
Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
;
This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named '_diffrn_detector_axis.id'
which is now a deprecated name. The old name is
provided as an alias, but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
;
Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, the more detailed information provided
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
are preferable to simply providing the centre.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square. in the pattern
1 2
*
3 4
Note that the beam center is slightly off of each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4.
;
;
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id_diffrn_detector_element.center[1]_diffrn_detector_element.center[2]
d1 d1_ccd_1 201.5 -1.5
d1 d1_ccd_2 -1.8 -1.5
d1 d1_ccd_3 201.6 201.4
d1 d1_ccd_4 -1.7 201.5
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.center[1]
_item_description.description
;
The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
;
The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.id
_item_description.description
;
The value of _diffrn_detector_element.id must uniquely identify
each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
;
This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the diffraction
data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model x'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; Need new example here
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support and
orient the specimen.
If the value of _diffrn_measurement.device is not given, it is
implicitly equal to the value of _diffrn_measurement.diffrn_id
Either '_diffrn_measurement.device' or '_diffrn_measurement.id'
may be used to link to other categories. If the experimental
setup admits multiple devices, then '_diffrn_measurement.id'
is used to provide a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to measure
the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'homemade'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
;
The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of _diffrn_measurement.diffrn_id
Either '_diffrn_measurement.device' or '_diffrn_measurement.id'
may be used to link to other categories. If the experimental
setup admits multiple devices, then '_diffrn_measurement.id'
is used to provide a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
;
The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
;
Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
;
This data item is a pointer to _diffrn_measurement.device in
the DIFFRN_MEASUREMENT category.
;
_item.name '_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
;
This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named '_diffrn_measurement_axis.id'
which is now a deprecated name. The old name is
provided as an alias, but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0.00
_item.mandatory_code implicit
save_
####################
# DIFFRN_RADIATION #
####################
save_DIFFRN_RADIATION
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used in measuring diffraction intensities,
its collimation and monochromatisation before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
_category_key.name '_diffrn_radiation.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the esd of the directions of photons in the X-Z plane
around the mean source beam direction.
Note that some synchrotrons specify this value in milliradians,
in which case a conversion would be needed. To go from a
value in milliradians to a value in degrees, multiply by 0.180
and divide by Pi.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the esd of the directions of photons in the Y-Z plane
around the mean source beam direction.
Note that some synchrotrons specify this value in milliradians,
in which case a conversion would be needed. To go from a
value in milliradians to a value in degrees, multiply by 0.180
and divide by Pi.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation degrees**2 between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
directin of each photons in X-Z plane times the deviations
of the direction of the same photon in the Y-Z plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons specify this value in
milliradians**2, in which case a conversion would be needed.
To go from a value in milliradians**2 to a value in
degrees**2, multiply by 0.180**2 and divide by Pi**2.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a mono-
chromator crystal is used the material and the indices of the
Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarisation and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarisation ratio of the diffraction beam incident on the
crystal. It is the ratio of the perpendicularly polarised to the
parallel polarised component of the radiation. The perpendicular
component forms an angle of _diffrn_radiation.polarisn_norm to
the normal to the diffraction plane of the sample (i.e. the
plane containing the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
normal to the polarization plane and the laboratory Y axis as
defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monchromater.
This differs from the value of '_diffrn_radiation.polarisn_norm'
in that '_diffrn_radiation.polarisn_norm' refers to polarization
relative to the diffraction plane rather than to the laboratory
axis system.
In the case of an unpolarized beam, or a beam with true circular
polarization, in which no single plane of polarization can be
determined, the plane should be taken as the X-Z plane, and the
angle as 0.
See '_diffrn_radiation.polarizn_source_ratio'.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity (amplitude squared)
of the electric vector in the plane of polarization and In is
the intensity (amplitude squared) of the electric vector
in plane of the normal to the plane of polarization.
Thus, if we had complete polarization in the plane of
polarization, the value of
'_diffrn_radiation.polarizn_source_ratio' would
be 1, and an unpolarized beam would have a value of 0.
If the X-axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of "MONOCHROMATOR" in the Denzo glossary, and values of near
1 should be expected for a bending magnet source. However,
if the X-axis were, for some reason to be, say, perpendicular
to the polarization plane (not a common choice), then the
Denzo value would be the negative of
'_diffrn_radiation.polarizn_source_ratio'.
See http://www.hkl-xray.com for information on Denzo, and
Z. Otwinowski and W. Minor, " Processing of X-ray Diffraction
Data Collected in Oscillation Mode ", Methods in Enzymology,
Volume 276: Macromolecular Crystallography, part A, p.307-326,
1997,C.W. Carter, Jr. & R. M. Sweet, Eds., Academic Press.
This differs both in the choice of ratio and choice of
orientation from '_diffrn_radiation.polarisn_ratio', which,
unlike '_diffrn_radiation.polarizn_source_ratio', is unbounded.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly encouraged
that this field be specified so that the probe radiation
can be simply determined.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'x-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for probe radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to _diffrn_radiation_wavelength.id
in the DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.mandatory_code yes
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
;
This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
;
_category.id diffrn_refln
_category.mandatory_code no
_category_key.name '_diffrn_refln.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
;
This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
;
Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
_category_key.name '_diffrn_scan.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. We have specified three rotation axes and one translation axis
at non-zero values, with one axis stepping. There is no reason why
more axes could not have been specified to step. We have specified
range information, but note that it is redundant from the number of
frames and the increment, so we could drop the data item
_diffrn_scan_axis.angle_range .
We have specified both the sweep data and the data for a single frame.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
'_diffrn_scan.integration_time' and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
'_diffrn_scan_frame.integration_time' and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustements are made to
scan times and non-linear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.angle_increment_diffrn_scan_frame_axis.displacement_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
;
Example 2 - a more extensive example, R. M. Sweet, P. Ellis, H. Bernstein.
We place a detector 240 mm along the Z axis from the goniometer.
This presents us with a choice -- either we define the axes of
the detector at the origin, and then put a Z setting of -240 in
for the actual use, or we define the axes with the necessary Z-offset.
In this case we use the setting, and leave the offset as zero.
We call this axis DETECTOR_Z.
The axis for positioning the detector in the Y-direction depends
on the detector Z-axis. We call this axis, DETECTOR_Y.
The axis for positioning the dector in the X-direction depends
on the detector Y-axis (and therefore on the detector Z-axis).
We call this axis DETECTOR_X.
This detector may be rotated around the Y-axis. This rotation axis
depends on the three translation axies. We call it DETECTOR_PITCH.
We define a coordinate system on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm x 0.150mm, the center of the first pixel is at (0.075,
0.075) in this coordinate system.
;
;
###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.displacement_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
;
Example 3 - Example 2 revised for a spiral scan, R. M. Sweet,
P. Ellis, H. Bernstein.
We place a detector 240 mm along the Z axis from the goniometer,
as in Example 2, above, but in this example, the image plate is
scanned in a spiral pattern outside edge in.
The axis for positioning the detector in the Y-direction depends
on the detector Z-axis. We call this axis, DETECTOR_Y.
The axis for positioning the dector in the X-direction depends
on the detector Y-axis (and therefore on the detector Z-axis).
We call this axis DETECTOR_X.
This detector may be rotated around the Y-axis. This rotation axis
depends on the three translation axies. We call it DETECTOR_PITCH.
We define a coordinate system on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. Let us call rotation axis ELEMENT_ROT, and the
radial axis ELEMENT_RAD. We assume 150 um radial pitch and 75 um
'constant velocity' angular pitch.
We index first on the rotation axis and make the radial axis
dependent on
it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
;
###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.angle_array_structure_list_axis.displacement_array_structure_list_axis.angular_pitch_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
;
The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
;
The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
;
Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
'_diffrn_scan_frame.integration_time', even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
;
The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frame_id_end
_item_description.description
;
The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frames
_item_description.description
;
The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
;
The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
'_diffrn_scan.id'.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
'_diffrn_scan.id'.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.angle_start
_item_description.description
;
The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
;
The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
;
The increment for each step for the specified axis
in degrees. In general, this will agree with
'_diffrn_scan_frame_axis.angle_increment'. The
sum of the values of '_diffrn_scan_frame_axis.angle' and
'_diffrn_scan_frame_axis.angle_increment' is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
'_diffrn_scan_axis.angle_increment' will be
representative
of the ensemble of values of
'_diffrn_scan_frame_axis.angle_increment' (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
;
The increment after each step for the specified axis
in degrees. In general, this will agree with
'_diffrn_scan_frame_axis.angle_increment'. The
sum of the values of '_diffrn_scan_frame_axis.angle'
and '_diffrn_scan_frame_axis.angle_increment'
and '_diffrn_scan_frame_axis.angle_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame, and
should equal '_diffrn_scan_frame_axis.angle' for that
next frame. If the individual frame values
vary, then the value of
'_diffrn_scan_axis.angle_rstrt_incr' will be
representative
of the ensemble of values of
'_diffrn_scan_frame_axis.angle_rstrt_inc' (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
;
The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
;
The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
;
The increment for each step for the specified axis
in millimetres. In general, this will agree with
'_diffrn_scan_frame_axis.displacement_increment'.
The sum of the values of
'_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
'_diffrn_scan_axis.displacement_increment' will be
representative
of the ensemble of values of
'_diffrn_scan_frame_axis.displacement_increment' (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
;
The increment for each step for the specified axis
in millimetres. In general, this will agree with
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
The sum of the values of
'_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' and
'_diffrn_scan_frame_axis.displacement_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame, and
should equal '_diffrn_scan_frame_axis.displacement'
for that next frame. If the individual frame values
vary, then the value of
'_diffrn_scan_axis.displacement_rstrt_incr' will be
representative
of the ensemble of values of
'_diffrn_scan_frame_axis.displacement_rstrt_incr' (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
;
Data items in the DIFFRN_SCAN_FRAME category describe
the relationship of particular frames to scans.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
;
The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
save__diffrn_scan_frame.frame_number
_item_description.description
;
The value of this data item is the number of the frame within
the scan, starting with 1. It is not necessarily the same as
the value of _diffrn_scan_frame.frame_id, but may
be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
;
The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of '_diffrn_scan.integration_time'.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the settings
of axes for particular frames. Unspecified axes are assumed to be at
their zero points. If, for any given frame, non-zero values apply
for any of the data items in this category, those values should be
given explicitly in this category and not simply inferred from values
in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
;
The increment for this frame for angular setting of
the specified axis in degrees. The sum of the values
of '_diffrn_scan_frame_axis.angle' and
'_diffrn_scan_frame_axis.angle_increment' is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
;
The increment after this frame for angular setting of
the specified axis in degrees. The sum of the values
of '_diffrn_scan_frame_axis.angle' and
'_diffrn_scan_frame_axis.angle_increment' and
'_diffrn_scan_frame_axis.angle_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame, and should equal
'_diffrn_scan_frame_axis.angle' for that next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
;
The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
;
The increment for this frame for displacement setting of
the specified axis in millimetres. The sum of the values
of '_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
;
The increment for this frame for displacement setting of
the specified axis in millimetres. The sum of the values
of '_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' and
'_diffrn_scan_frame_axis.displacement_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame, and should equal
'_diffrn_scan_frame_axis.displacement' for that next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id .
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
######################### DEPRECATED CATEGORY ##############################
#####################
# DIFFRN_FRAME_DATA #
#####################
save_DIFFRN_FRAME_DATA
_category.description
;
Data items in the DIFFRN_FRAME_DATA category record
the details about each frame of data.
The items in this category are now in the
DIFFRN_DATA_FRAME category.
The items in the DIFFRN_FRAME_DATA category
are now deprecated. The items from this category
are provided as aliases in the 1.0.0 dictionary,
but should not be used for new work.
The items from the old category are provided
in this dictionary for completeness,
but should not be used or cited. To avoid
confusion, the example has been removed,
and the redundant parent child-links to other
categories removed.
;
_category.id diffrn_frame_data
_category.mandatory_code no
loop_
_category_key.name '_diffrn_frame_data.id'
'_diffrn_frame_data.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
THE DIFFRN_DATA_FRAME category is deprecated and should not be used.
;
;
# EXAMPLE REMOVED #
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_frame_data.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.array_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.binary_id'
_item.category_id diffrn_frame_data
_item.mandatory_code implicit
_item_type.code int
save_
save__diffrn_frame_data.detector_element_id
_item_description.description
;
This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.detector_element_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.id
_item_description.description
;
The value of _diffrn_frame_data.id must uniquely identify
each complete frame of data.
DEPRECATED -- DO NOT USE
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_frame_data.id' diffrn_frame_data yes
_item_type.code code
save_
################ END DEPRECATED SECTION ###########
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive)
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items (case insensitive)
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]\
(T[0-2][0-9]:[0-5][0-9]:[0-5][0-9](.[0-9]+)([+-][0-5][0-9]:[0-5][0-9]))
;
;
Standard format for CIF date and time strings (see
http://www.iucr.orgiucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character "T" followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
decimal fraction on the seconds of time.
Time is local time if no time-zone offset is given.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2))'
'millimetres' 'millimetres (metres * 10^( -3))'
'nanometres' 'nanometres (metres * 10^( -9))'
'angstroms' 'angstroms (metres * 10^(-10))'
'picometres' 'picometres (metres * 10^(-12))'
'femtometres' 'femtometres (metres * 10^(-15))'
#
'reciprocal_metres' 'reciprocal metres (metres^(-1))'
'reciprocal_centimetres' 'reciprocal centimetres ((metres * 10^( -2))^(-1))'
'reciprocal_millimetres' 'reciprocal millimetres ((metres * 10^( -3))^(-1))'
'reciprocal_nanometres' 'reciprocal nanometres ((metres * 10^( -9))^(-1))'
'reciprocal_angstroms' 'reciprocal angstroms ((metres * 10^(-10))^(-1))'
'reciprocal_picometres' 'reciprocal picometres ((metres * 10^(-12))^(-1))'
'reciprocal_metres' 'reciprocal metres (metres * 10^-1)'
'reciprocal_centimetres' 'reciprocal centimetres (metres * 10^( -2)^-1)'
'reciprocal_millimetres' 'reciprocal millimetres (metres * 10^( -3)^-1)'
'reciprocal_nanometres' 'reciprocal nanometres (metres * 10^( -9)^-1)'
'reciprocal_angstroms' 'reciprocal angstroms (metres * 10^(-10)^-1)'
'reciprocal_picometres' 'reciprocal picometres (metres * 10^(-12)^-1)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9))^2'
'angstroms_squared' 'angstroms squared (metres * 10^(-10))^2'
'8pi2_angstroms_squared' '8pi^2 * angstroms squared (metres * 10^(-10))^2'
'picometres_squared' 'picometres squared (metres * 10^(-12))^2'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9))^3'
'angstroms_cubed' 'angstroms cubed (metres * 10^(-10))^3'
'picometres_cubed' 'picometres cubed (metres * 10^(-12))^3'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^( -9))^(-3))
;
'electrons_per_angstroms_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^(-10))^(-3));
;
'electrons_per_picometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^(-12))^(-3));
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.2.4 2003-07-14
;
Changes as per I. David Brown.
+ Enhance descriptions in DIFFRN_SCAN_AXIS to make them less
dependent on the descriptions in DIFFRN_SCAN_FRAME_AXIS.
+ Provide a copy of the deprecated DIFFRN_FRAME_DATA
category for completeness.
(HJB)
;
1.2.3 2003-07-03
;
Cleanup to conform to ITVG.
+ Correct sign error in ..._cubed units.
+ Correct '_diffrn_radiation.polarisn_norm' range.
(HJB)
;
1.2.2 2003-03-10
;
Correction of typos in various DIFFRN_SCAN_AXIS descriptions.
(HJB)
;
1.2.1 2003-02-22
;
Correction of ATOM_ for ARRAY_ typos in various descriptions.
(HJB)
;
1.2 2003-02-07
;
Corrections to encodings (remove extraneous hyphens) remove
extraneous underscore in _array_structure.encoding_type
enumeration. Correct typos in items units list.
(HJB)
;
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li
;
1.1.1 2001-02-16
;
Several typo corrections by JW
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to '_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source', '_diffrn_radiation.polarizn_source_norm',
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add _diffrn_measurement.device to category key
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to allow
for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes (JW)
+ Correct spelling of diffrn_measurement_axis in _axis.id
+ Correct ordering of uses of _item.mandatory_code and _item_default.value
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown (HJB)
+ Added further comments on '\n' and '\t'
+ Updated ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Changed all spelling 'meter' to 'metre' throughout.
+ Added missing enumerations to _array_structure.compression_type
and made 'none' the default.
+ Removed parent-child relationship between _array_structure_list.index
and _array_structure_list.precedence .
+ Improve alphabetization.
+ Fix _array_intensities_gain.esd related function.
+ Improved comments in AXIS.
+ Fixed DIFFRN_FRAME_DATA example.
+ Removed erroneous DIFFRN_MEASUREMENT example.
+ Added _diffrn_measurement_axis.id to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for _diffrn_scan.id definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header (HJB)
+ Restored _diffrn_detector.diffrn_id to DIFFRN_DETECTOR KEY.
+ Added AXIS category.
+ Brought complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
in from cif_mm.dic for clarity.
+ changed _array_structure.encoding_type from type code to uline and
added X-Binary-Element-Type to MIME header.
+ added detector beam center _diffrn_detector_element.center[1] and
_diffrn_detector_element.center[2]
+ corrected item name of _diffrn_refln.frame_id
+ replace reference to _array_intensities.undefined by
_array_intensities.undefined_value
+ replace references to _array_intensity.scaling with
_array_intensities.scaling
+ added DIFFRN_SCAN... categories
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft (HJB)
+ Reflowed comment lines over 80 characters and corrected typos.
+ Updated examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF (HJB)
+ Added binary type, which is a text field containing a variant on
MIME encoded data.
+ Changed type of _array_data.data to binary and specified internal
structure of raw binary data.
+ Added _array_data.binary_id, and made
_diffrn_frame_data.binary_id and _array_intensities.binary_id
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft (JW):
+ Added category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes were made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA was renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE was renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for _diffrn_frame_data.array_id was changed from
array_structure_list.array_id to array_structure.id. Item
_diffrn_detector.array_id was deleted.
+ Added data item _diffrn_frame_data.binary_id to identify data groups
within a binary section. The formal identification of the binary section
is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version was adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley (AH).
Modifications to the CBF draft (JW):
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories have been
generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category ARRAY_DATA .
This departs from the CBF notion of data existing in some special comment.
In this description, data is handled as an ordinary data item encapsulated
in a character data type. Although handling binary data this manner
deviates from CIF conventions, it does not violate any DDL 2.1 rules.
DDL 2.1 regular expressions can be used to define the binary
representation which will permit some level of data validation. In
this version, the placeholder type code "any" has been used.
This translates to a regular expression which will match any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary. It
may be possible to use the DDL 2.1 ITEM_STRUCTURE and ITEM_STRUCTURE_LIST
categories to provide the information that is carried in by the
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By moving the array
structure to the DDL level it would be possible to define an array
type as well as a regular expression defining the data format.
+ Multiple array sections can be properly handled within a single datablock.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.5.3 #
# of 2007-07-08 #
# ################################################################### #
# # *** WARNING *** THIS IS A DRAFT FOR DISCUSSSION *** WARNING *** # #
# # SUBJECT TO CHANGE WITHOUT NOTICE # #
# # SEND COMMENTS TO imgcif-l@iucr.org CITING THE VERSION # #
# ################################################################### #
# This draft edited by H. J. Bernstein #
# #
# by Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook #
# #
# This dictionary was adapted from format discussed at the imgCIF Workshop, #
# held at BNL Oct 1997 and the Crystallographic Binary File Format Draft #
# Proposal by Andrew Hammersley. The first DDL 2.1 Version was created by #
# John Westbrook. This version was drafted by Herbert J. Bernstein and #
# incorporates comments by I. David Brown, John Westbrook, Brian McMahon, #
# Bob Sweet, Paul Ellis, Harry Powell, Wilfred Li, Gotzon Madariaga, #
# Frances C. Bernstein, Chris Nielsen, Nicola Ashcroft and others. #
##############################################################################
data_cif_img.dic
_dictionary.title cif_img.dic
_dictionary.version 1.5.3
_dictionary.datablock_id cif_img.dic
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
# SUB_CATEGORY
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
# _array_data.header_contents
# _array_data.header_convention
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.gain
# _array_intensities.gain_esd
# _array_intensities.linearity
# _array_intensities.offset
# _array_intensities.scaling
# _array_intensities.overload
# _array_intensities.undefined_value
# _array_intensities.pixel_fast_bin_size
# _array_intensities.pixel_slow_bin_size
# _array_intensities.pixel_binning_method
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.compression_type_flag
# _array_structure.encoding_type
# _array_structure.id
#
# category ARRAY_STRUCTURE_LIST
#
# _array_structure_list.axis_set_id
# _array_structure_list.array_id
# _array_structure_list.dimension
# _array_structure_list.direction
# _array_structure_list.index
# _array_structure_list.precedence
#
# category ARRAY_STRUCTURE_LIST_AXIS
#
# _array_structure_list_axis.axis_id
# _array_structure_list_axis.axis_set_id
# _array_structure_list_axis.angle
# _array_structure_list_axis.angle_increment
# _array_structure_list_axis.displacement
# _array_structure_list_axis.fract_displacement
# _array_structure_list_axis.displacement_increment
# _array_structure_list_axis.fract_displacement_increment
# _array_structure_list_axis.angular_pitch
# _array_structure_list_axis.radial_pitch
# _array_structure_list_axis.reference_angle
# _array_structure_list_axis.reference_displacement
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.type
# _axis.system
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
#
# category DIFFRN_DATA_FRAME
#
# _diffrn_data_frame.array_id
# _diffrn_data_frame.binary_id
# _diffrn_data_frame.center_fast
# _diffrn_data_frame.center_slow
# _diffrn_data_frame.center_units
# _diffrn_data_frame.detector_element_id
# _diffrn_data_frame.id
# _diffrn_data_frame.details
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.id
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.axis_id
# _diffrn_detector_axis.detector_id
#
# category DIFFRN_DETECTOR_ELEMENT
#
# _diffrn_detector_element.id
# _diffrn_detector_element.detector_id
# _diffrn_detector_element.reference_center_fast
# _diffrn_detector_element.reference_center_slow
# _diffrn_detector_element.reference_center_units
#
# category DIFFRN_MEASUREMENT
#
# _diffrn_measurement.diffrn_id
# _diffrn_measurement.details
# _diffrn_measurement.device
# _diffrn_measurement.device_details
# _diffrn_measurement.device_type
# _diffrn_measurement.id
# _diffrn_measurement.method
# _diffrn_measurement.number_of_axes
# _diffrn_measurement.sample_detector_distance
# _diffrn_measurement.sample_detector_voffset
# _diffrn_measurement.specimen_support
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.axis_id
# _diffrn_measurement_axis.measurement_device
# _diffrn_measurement_axis.measurement_id
#
# category DIFFRN_RADIATION
#
# _diffrn_radiation.collimation
# _diffrn_radiation.diffrn_id
# _diffrn_radiation.div_x_source
# _diffrn_radiation.div_y_source
# _diffrn_radiation.div_x_y_source
# _diffrn_radiation.filter_edge'
# _diffrn_radiation.inhomogeneity
# _diffrn_radiation.monochromator
# _diffrn_radiation.polarisn_norm
# _diffrn_radiation.polarisn_ratio
# _diffrn_radiation.polarizn_source_norm
# _diffrn_radiation.polarizn_source_ratio
# _diffrn_radiation.probe
# _diffrn_radiation.type
# _diffrn_radiation.xray_symbol
# _diffrn_radiation.wavelength_id
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.date_end
# _diffrn_scan.date_start
# _diffrn_scan.integration_time
# _diffrn_scan.frame_id_start
# _diffrn_scan.frame_id_end
# _diffrn_scan.frames
#
# category DIFFRN_SCAN_AXIS
#
# _diffrn_scan_axis.axis_id
# _diffrn_scan_axis.angle_start
# _diffrn_scan_axis.angle_range
# _diffrn_scan_axis.angle_increment
# _diffrn_scan_axis.angle_rstrt_incr
# _diffrn_scan_axis.displacement_start
# _diffrn_scan_axis.displacement_range
# _diffrn_scan_axis.displacement_increment
# _diffrn_scan_axis.displacement_rstrt_incr
# _diffrn_scan_axis.reference_angle
# _diffrn_scan_axis.reference_displacement
# _diffrn_scan_axis.scan_id
#
# category DIFFRN_SCAN_FRAME
#
# _diffrn_scan_frame.date
# _diffrn_scan_frame.frame_id
# _diffrn_scan_frame.frame_number
# _diffrn_scan_frame.integration_time
# _diffrn_scan_frame.scan_id
#
# category DIFFRN_SCAN_FRAME_AXIS
#
# _diffrn_scan_frame_axis.axis_id
# _diffrn_scan_frame_axis.angle
# _diffrn_scan_frame_axis.angle_increment
# _diffrn_scan_frame_axis.angle_rstrt_incr
# _diffrn_scan_frame_axis.displacement
# _diffrn_scan_frame_axis.displacement_increment
# _diffrn_scan_frame_axis.displacement_rstrt_incr
# _diffrn_scan_frame_axis.reference_angle
# _diffrn_scan_frame_axis.reference_displacement
# _diffrn_scan_frame_axis.frame_id
#
# categor MAP
#
# _map.details
# _map.diffrn_id
# _map.entry_id
# _map.id
#
# categor MAP_SEGMENT
#
# _map_segment.array_id
# _map_segment.binary_id
# _map_segment.mask_array_id
# _map_segment.mask_binary_id
# _map_segment.id
# _map_segment.map_id
# _map_segment.details
#
# ***DEPRECATED*** data items
#
# _diffrn_detector_axis.id
# _diffrn_detector_element.center[1]
# _diffrn_detector_element.center[2]
# _diffrn_measurement_axis.id
#
# ***DEPRECATED*** category DIFFRN_FRAME_DATA
#
# _diffrn_frame_data.array_id
# _diffrn_frame_data.binary_id
# _diffrn_frame_data.detector_element_id
# _diffrn_frame_data.id
# _diffrn_frame_data.details
#
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
##################
## SUB_CATEGORY ##
##################
loop_
_sub_category.id
_sub_category.description
'matrix'
; The collection of elements of a matrix.
;
'vector'
; The collection of elements of a vector.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
; Data items in the ARRAY_DATA category are the containers for
the array data items described in the category ARRAY_STRUCTURE.
It is recognized that the data in this category needs to be used in
two distinct ways. During a data collection the lack of ancillary
data and timing constraints in processing data may dictate the
need to make a 'miniCBF' nothing more than an essential minimum
of information to record the results of the data collection. In that
case it is proper to use the ARRAY_DATA category as a
container for just a single image and a compacted, beam-line
dependent list of data collection parameter values. In such
a case, only the tags '_array_data.header_convention',
'_array_data.header_contents' and '_array_data.data' need be
populated.
For full processing and archiving, most of the tags in this
dictionary will need to be populated.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and is
presented as hexadecimal data. The first character 'H' on the
data lines means hexadecimal. It could have been 'O' for octal
or 'D' for decimal. The second character on the line shows
the number of bytes in each word (in this case '4'), which then
requires eight hexadecimal digits per word. The third character
gives the order of octets within a word, in this case '<'
for the ordering 4321 (i.e. 'big-endian'). Alternatively, the
character '>' could have been used for the ordering 1234
(i.e. 'little-endian'). The block has a 'message digest'
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id_array_data.binary_id_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 2
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
This example shows a single image in a miniCBF, provided by
E. Eikenberry. The entire CBF consists of one data block
containing one category and three tags. The CBFlib
program convert_miniCBF and a suitable template file
can be used to convert this miniCBF to a full imgCIF
file.
;
;
###CBF: VERSION 1.5
# CBF file written by CBFlib v0.7.8
data_insulin_pilatus6m
_array_data.header_convention SLS_1.0
_array_data.header_contents
;
# Detector: PILATUS 6M SN: 60-0001
# 2007/Jun/17 15:12:36.928
# Pixel_size 172e-6 m x 172e-6 m
# Silicon sensor, thickness 0.000320 m
# Exposure_time 0.995000 s
# Exposure_period 1.000000 s
# Tau = 194.0e-09 s
# Count_cutoff 1048575 counts
# Threshold_setting 5000 eV
# Wavelength 1.2398 A
# Energy_range (0, 0) eV
# Detector_distance 0.15500 m
# Detector_Voffset -0.01003 m
# Beam_xy (1231.00, 1277.00) pixels
# Flux 22487563295 ph/s
# Filter_transmission 0.0008
# Start_angle 13.0000 deg.
# Angle_increment 1.0000 deg.
# Detector_2theta 0.0000 deg.
# Polarization 0.990
# Alpha 0.0000 deg.
# Kappa 0.0000 deg.
# Phi 0.0000 deg.
# Chi 0.0000 deg.
# Oscillation_axis X, CW
# N_oscillations 1
;
_array_data.data
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_BYTE_OFFSET"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 6247567
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
X-Binary-Element-Byte-Order: LITTLE_ENDIAN
Content-MD5: 8wO6i2+899lf5iO8QPdgrw==
X-Binary-Number-of-Elements: 6224001
X-Binary-Size-Fastest-Dimension: 2463
X-Binary-Size-Second-Dimension: 2527
X-Binary-Size-Padding: 4095
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
If not given, it defaults to 1.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code implicit
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id, should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-ID, the value of _array_data.binary_id
should be equal to the value given for X-Binary-ID.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
'\n--CIF-BINARY-FORMAT-SECTION--' (including the
required initial '\n--').
The Content-Type may be any of the discrete types permitted
in RFC 2045; 'application/octet-stream' is recommended
for diffraction images in the ARRAY_DATA category.
Note: When appropriate in other categories, e.g. for
photographs of crystals, more precise types, such as
'image/jpeg', 'image/tiff', 'image/png', etc. should be used.
If an octet stream was compressed, the compression should
be specified by the parameter
'conversions="X-CBF_PACKED"'
or the parameter
'conversions="X-CBF_CANONICAL"'
or the parameter
'conversions="X-CBF_BYTE_OFFSET"'
If the parameter
'conversions="X-CBF_PACKED"'
is given it may be further modified with the parameters
'"uncorrelated_sections"'
or
'"flat"'
If the '"uncorrelated_sections"' parameter is
given, each section will be compressed without using
the prior section for averaging.
If the '"flat"' parameter is given, each the
image will be treated as one long row.
The Content-Transfer-Encoding may be 'BASE64',
'Quoted-Printable', 'X-BASE8', 'X-BASE10',
'X-BASE16' or 'X-BASE32K', for an imgCIF or 'BINARY'
for a CBF. The octal, decimal and hexadecimal transfer
encodings are provided for convenience in debugging and
are not recommended for archiving and data interchange.
In a CIF, one of the parameters 'charset=us-ascii',
'charset=utf-8' or 'charset=utf-16' may be used on the
Content-Transfer-Encoding to specify the character set
used for the external presentation of the encoded data.
If no charset parameter is given, the character set of
the enclosing CIF is assumed. In any case, if a BOM
flag is detected (FE FF for big-endian UTF-16, FF FE for
little-endian UTF-16 or EF BB BF for UTF-8) is detected,
the indicated charset will be assumed until the end of the
encoded data or the detection of a different BOM. The
charset of the Content-Transfer-Encoding is not the character
set of the encoded data, only the character set of the
presentation of the encoded data and should be respecified
for each distinct STAR string.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In an imgCIF file,
the encoded binary data ends with the terminating boundary
delimiter '\n--CIF-BINARY-FORMAT-SECTION----'
in the currently effective charset or with the '\n; '
that terminates the STAR string.
In a CBF, the raw binary data begins after an empty line
terminating the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of
the message size or in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. An adjustment is made for
the deprecated binary formats in which eight bytes of binary
header are used for the compression type. In this case,
the eight bytes used for the compression type are subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is 'unsigned 32-bit integer'.
An MD5 message digest may, optionally, be used. The 'RSA Data
Security, Inc. MD5 Message-Digest Algorithm' should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is 'X-BASE8', 'X-BASE10' or
'X-BASE16', the data are presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ('big-
endian') or 1234... ('little-endian'). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as '==' for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is 'H', 'O' or 'D' for hexadecimal, octal or
decimal, n is the number of octets per word and d is '<'
or '>' for the '...4321' and '1234...' octet orderings,
respectively. The '==' padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hexadecimal, octal and decimal formats only,
comments beginning with '#' are permitted to improve
readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three: c1, c2, c3. The resulting 24 bits
are broken into four six-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order four bits of the second octet [(c1 & 3)<<4 | (c2>>4)],
then the bottom four bits of the second octet followed by the
high-order two bits of the last octet [(c2 & 15)<<2 | (c3>>6)],
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
With short groups of octets padded on the right with one '='
if c3 is missing, and with '==' if both c2 and c3 are missing.
X-BASE32K encoding is similar to BASE64 encoding, except that
sets of 15 octets are encoded as sets of 8 16-bit unicode
characters, by breaking the 120 bits into 8 15-bit quantities.
256 is added to each 15 bit quantity to bring it into a
printable uncode range. When encoding, zero padding is used
to fill out the last 15 bit quantity. If 8 or more bits of
padding are used, a single equals sign (hexadecimal 003D) is
appended. Embedded whitespace and newlines are introduced
to produce lines of no more than 80 characters each. On
decoding, all printable ascii characters and ascii whitespace
characters are ignored except for any trailing equals signs.
The number of trailing equals signs indicated the number of
trailing octets to be trimmed from the end of the decoded data.
(see Georgi Darakev, Vassil Litchev, Kostadin Z. Mitev, Herbert
J. Bernstein, 'Efficient Support of Binary Data in the XML
Implementation of the NeXus File Format',absract W0165,
ACA Summer Meeting, Honolulu, HI, July 2006).
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32...38,
42, 48...57, 59, 60, 62, 64...126 and the octet is not a ';'
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
'wrapped' with a terminating '=' (i.e. the MIME conventions
for an implicit line terminator are never used).
The "X-Binary-Element-Byte-Order" can specify either
'"BIG_ENDIAN"' or '"LITTLE_ENDIAN"' byte order of the imaage
data. Only LITTLE_ENDIAN is recommended. Processors
may treat BIG_ENDIAN as a warning of data that can
only be processed by special software.
The "X-Binary-Number-of-Elements" specifies the number of
elements (not the number of octets) in the decompressed, decoded
image.
The optional "X-Binary-Size-Fastest-Dimension" specifies the
number of elements (not the number of octets) in one row of the
fastest changing dimension of the binary data array. This
information must be in the MIME header for proper operation of
some of the decompression algorithms.
The optional "X-Binary-Size-Second-Dimension" specifies the
number of elements (not the number of octets) in one column of
the second-fastest changing dimension of the binary data array.
This information must be in the MIME header for proper operation
of some of the decompression algorithms.
The optional "X-Binary-Size-Third-Dimension" specifies the number
of sections for the third-fastest changing dimension of the
binary data array.
The optional "X-Binary-Size-Padding" specifies the size in
octets of an optional padding after the binary array data and
before the closing flags for a binary section.
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
save__array_data.header_contents
_item_description.description
; This item is an text field for use in minimal CBF files to carry
essential header information to be kept with image data
in _array_data.data when the tags that normally carry the
structured metadata for the image have not been populated.
Normally this data item should not appear when the full set
of tags have been populated and _diffrn_data_frame.details
appears.
;
_item.name '_array_data.header_contents'
_item.category_id array_data
_item.mandatory_code no
_item_type.code text
save_
save__array_data.header_convention
_item_description.description
; This item is an identifier for the convention followed in
constructing the contents of _array_data.header_contents
The permitted values are of the of an image creator identifier
followed by an underscore and a version string. To avoid
confusion about conventions, all creator identifiers
should be registered with the IUCr and the conventions
for all identifiers and versions should be posted on
the MEDSBIO.org web site.
;
_item.name '_array_data.header_convention'
_item.category_id array_data
_item.mandatory_code no
_item_type.code code
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
; Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code implicit
_item_type.code code
save_
save__array_element_size.index
_item_description.description
; This item is a pointer to _array_structure_list.index in
the ARRAY_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
; The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
; Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
_array_intensities.gain. If raw, uncorrected values
are presented (e.g. for calibration experiments), the
value of _array_intensities.linearity will be 'raw'
and _array_intensities.gain will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id_array_intensities.linearity_array_intensities.gain_array_intensities.overload_array_intensities.undefined_value_array_intensities.pixel_fast_bin_size_array_intensities.pixel_slow_bin_size_array_intensities.pixel_binning_method
image_1 linear 1.2 655535 0 2 2 hardware
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
; Detector 'gain'. The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
; The estimated standard deviation in detector 'gain'.
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
; The intensity linearity scaling method used to convert
from the raw intensity to the stored element value:
'linear' is linear.
'offset' means that the value defined by
_array_intensities.offset should be added to each
element value.
'scaling' means that the value defined by
_array_intensities.scaling should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by _array_intensities.scaling is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
'logarithmic_scaled' means that the logarithm base 10 of
raw intensities multiplied by _array_intensities.scaling
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and calculating 10
to the power of this number.
'raw' means that the data are a set of raw values straight
from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
; The value defined by _array_intensities.offset should
be added to each element value.
;
'scaling'
; The value defined by _array_intensities.scaling should be
multiplied with each element value.
;
'scaling_offset'
; The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
; The square root of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
;
'logarithmic_scaled'
; The logarithm base 10 of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
_array_intensities.scaling and calculating 10 to the
power of this number.
;
'raw'
; The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data-fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
; Offset value to add to array element values in the manner
described by the item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
; The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.pixel_fast_bin_size
_item_description.description
; The value of _array_intensities.pixel_fast_bin_size specifies
the number of pixels that compose one element in the direction
of the most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_fast_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_slow_bin_size
_item_description.description
; The value of _array_intensities.pixel_slow_bin_size specifies
the number of pixels that compose one element in the direction
of the second most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_slow_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_binning_method
_item_description.description
; The value of _array_intensities.pixel_binning_method specifies
the method used to derive array elements from multiple pixels.
;
_item.name '_array_intensities.pixel_binning_method'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'hardware'
; The element intensities were derived from the raw data of one
or more pixels by used of hardware in the detector, e.g. by use
of shift registers in a CCD to combine pixels into super-pixels.
;
'software'
; The element intensities were derived from the raw data of more
than one pixel by use of software.
;
'combined'
; The element intensities were derived from the raw data of more
than one pixel by use of both hardware and software, as when
hardware binning is used in one direction and software in the
other.
;
'none'
; In the both directions, the data has not been binned. The
number of pixels is equal to the number of elements.
When the value of _array_intensities.pixel_binning_method is
'none' the values of _array_intensities.pixel_fast_bin_size
and _array_intensities.pixel_slow_bin_size both must be 1.
;
'unspecified'
; The method used to derive element intensities is not specified.
;
_item_default.value 'unspecified'
save_
save__array_intensities.scaling
_item_description.description
; Multiplicative scaling value to be applied to array data
in the manner described by item
_array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.undefined_value
_item_description.description
; A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
; Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data that may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
_category_key.name '_array_structure.id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
; The order of bytes for integer values which require more
than 1 byte.
(IBM-PC's and compatibles and DEC VAXs use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. DEC Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
; The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
; The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
; Type of data-compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'byte_offset'
; Using the 'byte_offset' compression scheme as per A. Hammersley
and the CBFlib manual, section 3.3.3
;
'canonical'
; Using the 'canonical' compression scheme (International Tables
for Crystallography Volume G, Section 5.6.3.1) and CBFlib
manual section 3.3.1
;
'none'
; Data are stored in normal format as defined by
_array_structure.encoding_type and
_array_structure.byte_order.
;
'packed'
; Using the 'packed' compression scheme, a CCP4-style packing
as per J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
'packed_v2'
; Using the 'packed' compression scheme, version 2, as per
J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
save_
save__array_structure.compression_type_flag
_item_description.description
; Flags modifying the type of data-compression method used to
compress the arraydata.
;
_item.name '_array_structure.compression_type_flag'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'uncorrelated_sections'
; When applying packed or packed_v2 compression on an array with
uncorrelated sections, do not average in points from the prior
section.
;
'flat'
; When applying packed or packed_v2 compression on an array with
treat the entire image as a single line set the maximum number
of bits for an offset to 65 bits.
The flag is included for compatibility with software prior to
CBFlib_0.7.7, and should not be used for new data sets.
;
save_
save__array_structure.encoding_type
_item_description.description
; Data encoding of a single element of array data.
The type 'unsigned 1-bit integer' is used for
packed Booleans arrays for masks. Each element
of the array corresponds to a single bit
packed in unsigned 8-bit data.
In several cases, the IEEE format is referenced.
See IEEE Standard 754-1985 (IEEE, 1985).
Ref: IEEE (1985). IEEE Standard for Binary Floating-Point
Arithmetic. ANSI/IEEE Std 754-1985. New York: Institute of
Electrical and Electronics Engineers.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 1-bit integer'
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
This item has been made implicit and given a default value of 1
as a convenience in writing miniCBF files. Normally an
explicit name with useful content should be used.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure implicit
'_array_data.array_id' array_data implicit
'_array_structure_list.array_id' array_structure_list implicit
'_array_intensities.array_id' array_intensities implicit
'_diffrn_data_frame.array_id' diffrn_data_frame implicit
_item_default.value 1
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
; Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left to right (increasing) in the
first dimension and bottom to top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differs
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the 'poise' of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
; The number of elements stored in the array structure in this
dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
; Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
; Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
; Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
; Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
; Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
; Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets of axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axes: one for the angular
direction and one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes in the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
; The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to
_array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list_axis.angle
_item_description.description
; The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified for this case.
See _array_structure_list_axis.angular_pitch.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement
_item_description.description
; The setting of the specified axis as a decimal fraction of
the axis unit vector for the first data point of the array
index with the corresponding value of
_array_structure_list.axis_set_id.
If the index is specified as 'increasing', this will be the
centre of the pixel with index value 1. If the index is
specified as 'decreasing', this will be the centre of the
pixel with maximum index value.
;
_item.name '_array_structure_list_axis.fract_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis as a decimal fraction of the
axis unit vector.
;
_item.name
'_array_structure_list_axis.fract_displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
; The pixel-centre-to-pixel-centre distance for a one-step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans
or for uncoupled angular scans at a constant radius
(cylindrical scans) and should not be specified for cases
in which the angle between pixels (rather than the distance
between pixels) is uniform.
See _array_structure_list_axis.angle_increment.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
; The radial distance from one 'cylinder' of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of _array_structure_list_axis.displacement_increment.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.reference_angle
_item_description.description
; The value of _array_structure_list_axis.reference_angle
specifies the setting of the angle of this axis used for
determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the
value of _array_structure_list.angle.
;
_item.name '_array_structure_list_axis.reference_angle'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.reference_displacement
_item_description.description
; The value of _array_structure_list_axis.reference_displacement
specifies the setting of the displacement of this axis used
for determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the value
of _array_structure_list.displacement.
;
_item.name '_array_structure_list_axis.reference_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
########
# AXIS #
########
save_AXIS
_category.description
; Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection or the axes defining the
coordinate system of an image.
The location of each axis is specified by two vectors: the axis
itself, given by a unit vector in the direction of the axis, and
an offset to the base of the unit vector.
The vectors defining an axis are referenced to an appropriate
coordinate system. The axis vector, itself, is a dimensionless
unit vector. Where meaningful, the offset vector is given in
millimetres. In coordinate systems not measured in metres,
the offset is not specified and is taken as zero.
The available coordinate systems are:
The imgCIF standard laboratory coordinate system
The direct lattice (fractional atomic coordinates)
The orthogonal Cartesian coordinate system (real space)
The reciprocal lattice
An abstract orthogonal Cartesian coordinate frame
For consistency in this discussion, we call the three coordinate
system axes X, Y and Z. This is appropriate for the imgCIF
standard laboratory coordinate system, and last two Cartesian
coordinate systems, but for the direct lattice, X corresponds
to a, Y to b and Z to c, while for the reciprocal lattice,
X corresponds to a*, Y to b* and Z to c*.
For purposes of visualization, all the coordinate systems are
taken as right-handed, i.e., using the convention that the extended
thumb of a right hand could point along the first (X) axis, the
straightened pointer finger could point along the second (Y) axis
and the middle finger folded inward could point along the third (Z)
axis.
THE IMGCIF STANDARD LABORATORY COORDINATE SYSTEM
The imgCIF standard laboratory coordinate system is a right-handed
orthogonal coordinate similar to the MOSFLM coordinate system,
but imgCIF puts Z along the X-ray beam, rather than putting X along the
X-ray beam as in MOSFLM.
The vectors for the imgCIF standard laboratory coordinate system
form a right-handed Cartesian coordinate system with its origin
in the sample or specimen. The origin of the axis system should,
if possible, be defined in terms of mechanically stable axes to be
be both in the sample and in the beam. If the sample goniometer or other
sample positioner has two axes the intersection of which defines a
unique point at which the sample should be mounted to be bathed
by the beam, that will be the origin of the axis system. If no such
point is defined, then the midpoint of the line of intersection
between the sample and the center of the beam will define the origin.
For this definition the sample positioning system will be set at
its initial reference position for the experiment.
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer or
sample positioning system if the sample positioning system has an axis that
intersects the origin and which form an angle of more than 22.5 degrees
with the beam axis.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
If the conditions for the X-axis can be met, the coordinate system
will be based on the goniometer or other sample positioning system
and the beam and not on the orientation of the detector, gravity etc.
The vectors necessary to specify all other axes are given by sets of
three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right-handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to but significantly
different from the choice in MOSFLM (Leslie & Powell, 2004). In MOSFLM,
X is along the X-ray beam (the CBF/imgCIF Z axis) and Z is along the
rotation axis.
In some experimental techniques, there is no goniometer or the principal
axis of the goniometer is at a small acute angle with respect to
the source axis. In such cases, other reference axes are needed
to define a useful coordinate system. The order of priority in
defining directions in such cases is to use the detector, then
gravity, then north.
If the X-axis cannot be defined as above, then the
direction (not the origin) of the X-axis should be parallel to the axis
of the primary detector element corresponding to the most rapidly
varying dimension of that detector element's data array, with its
positive sense corresponding to increasing values of the index for
that dimension. If the detector is such that such a direction cannot
be defined (as with a point detector) or that direction forms an
angle of less than 22.5 degrees with respect to the source axis, then
the X-axis should be chosen so that if the Y-axis is chosen
in the direction of gravity, and the Z-axis is chosen to be along
the source axis, a right-handed orthogonal coordinate system is chosen.
In the case of a vertical source axis, as a last resort, the
X-axis should be chosen to point North.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam centre.
The location of the beam centre on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected millimetres from
the (0,0) corner of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, it is necessary to
specify the location of the beam centre on the detector in terms
of the origin of the detector, which is, of course, not coincident
with the centre of the sample.
The unit cell, reciprocal cell and crystallographic orthogonal
Cartesian coordinate system are defined by the CELL and the matrices
in the ATOM_SITES category.
THE DIRECT LATTICE (FRACTIONAL COORDINATES)
The direct lattice coordinate system is a system of fractional
coordinates aligned to the crystal, rather than to the laboratory.
This is a natural coordinate system for maps and atomic coordinates.
It is the simplest coordinate system in which to apply symmetry.
The axes are determined by the cell edges, and are not necessarily
othogonal. This coordinate system is not uniquely defined and
depends on the cell parameters in the CELL category and the
settings chosen to index the crystal.
Molecules in a crystal studied by X-ray diffracraction are organized
into a repeating regular array of unit cells. Each unit cell is defined
by three vectors, a, b and c. To quote from Drenth,
"The choice of the unit cell is not unique and therefore, guidelines
have been established for selecting the standard basis vectors and
the origin. They are based on symmetry and metric considerations:
"(1) The axial system should be right handed.
(2) The basis vectors should coincide as much as possible with
directions of highest symmetry."
(3) The cell taken should be the smallest one that satisfies
condition (2)
(4) Of all the lattice vectors, none is shorter than a.
(5) Of those not directed along a, none is shorter than b.
(6) Of those not lying in the ab plane, none is shorter than c.
(7) The three angles between the basis vectors a, b and c are
either all acute (<90°) or all obtuse (≥90°)."
These rules do not produce a unique result that is stable under
the assumption of experimental errors, and the the resulting cell
may not be primitive.
In this coordinate system, the vector (.5, .5, .5) is in the middle
of the given unit cell.
Grid coordinates are an important variation on fractional coordinates
used when working with maps. In imgCIF, the conversion from
fractional to grid coordinates is implicit in the array indexing
specified by _array_structure_list.dimension. Note that this
implicit grid-coordinate scheme is 1-based, not zero-based, i.e.
the origin of the cell for axes along the cell edges with no
specified _array_structure_list_axis.displacement will have
grid coordinates of (1,1,1), i.e. array indices of (1,1,1).
THE ORTHOGONAL CARTESIAN COORDINATE SYSTEM (REAL SPACE)
The orthogonal Cartesian coordinate system is a transformation of
the direct lattice to the actual physical coordinates of atoms in
space. It is similar to the laboratory coordinate system, but
is anchored to and moves with the crystal, rather than being
schored to the laboratory. The transformation from fractional
to orthogonal cartesian coordinates is given by the
_atom_sites.Cartn_transf_matrix[i][j] and
_atom_sites.Cartn_transf_vector[i]
tags. A common choice for the matrix of the transformation is
given in the 1992 PDB format document
| a b cos(γ) c cos(β) |
| 0 b sin(γ) c (cos(α) - cos(β)cos(γ))/sin(γ) |
| 0 0 V/(a b sin(γ)) |
This is a convenient coordinate system in which to do fitting
of models to maps and in which to understand the chemistry of
a molecule.
THE RECIPROCAL LATTICE
The reciprocal lattice coordinate system is used for diffraction
intensitities. It is based on the reciprocal cell, the dual of the cell,
in which reciprocal cell edges are derived from direct cell faces:
a* = bc sin(α)/V b* = ac sin(β)/V c* = ab sin(γ)/V
cos(α*) = (cos(β) cos(γ) - cos(α))/(sin(β) sin(γ))
cos(β*) = (cos(γ) cos(γ) - cos(β) )/(sin(α) sin(γ))
cos(γ*) = (cos(α) cos(β) - cos(γ))/(sin(α) sin(β))
V = abc √(1 - cos(α)2 - cos(β)2 - cos(γ)2
+ 2 cos(α) cos(β) cos(γ) )
In this form the dimensions of the reciprocal lattice are in reciprocal
Ångstroms (&A-1). A dimensionless form can be obtained by
multiplying by the wavelength. Reflections are commonly indexed against
this coordinate system as (h, k, l) triples.
References:
Drenth, J., "Introduction to basic crystallography." chapter
2.1 in Rossmann, M. G. and Arnold, E. "Crystallography of
biological macromolecules", Volume F of the IUCr's "International
tables for crystallography", Kluwer, Dordrecht 2001, pp 44 -- 63
Leslie, A. G. W. and Powell, H. (2004). MOSFLM v6.11.
MRC Laboratory of Molecular Biology, Hills Road, Cambridge, England.
http://www.CCP4.ac.uk/dist/X-windows/Mosflm/.
Stout, G. H. and Jensen, L. H., "X-ray structure determination",
2nd ed., Wiley, New York, 1989, 453 pp.
__, "PROTEIN DATA BANK ATOMIC COORDINATE AND BIBLIOGRAPHIC ENTRY
FORMAT DESCRIPTION," Brookhaven National Laboratory, February 1992.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
This example shows the axis specification of the axes of a kappa-
geometry goniometer [see Stout, G. H. & Jensen, L. H. (1989). X-ray
structure determination. A practical
guide, 2nd ed. p. 134. New York: Wiley Interscience].
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X axis. The next innermost axis, kappa,
is at a 50 degree angle to the X axis, pointed away from the source.
The innermost axis, phi, aligns with the X axis when omega and
phi are at their zero points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
X' = (T-omega) (T-kappa) (T-phi) X
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 -
This example shows the axis specification of the axes of a
detector, source and gravity. The order has been changed as a
reminder that the ordering of presentation of tokens is not
significant. The centre of rotation of the detector has been taken
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 3 -
This example show the axis specification of the axes for a map,
using fractional coordinates. Each cell edge has been divided
into a grid of 50 divisions in the ARRAY_STRUCTURE_LIST_AXIS
category. The map is using only the first octant of the grid
in the ARRAY_STRUCTURE_LIST category.
The fastest changing axis is the gris along A, then along B,
and the slowest is along C.
The map sampling is being done in the middle of each grid
division
;
;
loop_
_axis.id_axis.system_axis.vector[1]_axis.vector[2]_axis.vector[3]
CELL_A_AXIS fractional 1 0 0
CELL_B_AXIS fractional 0 1 0
CELL_C_AXIS fractional 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing CELL_A_AXIS
MAP 1 25 2 increasing CELL_B_AXIS
MAP 1 25 3 increasing CELL_C_AXIS
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.fract_displacement
_array_structure_list_axis.fract_displacement_increment
CELL_A_AXIS 0.01 0.02
CELL_B_AXIS 0.01 0.02
CELL_C_AXIS 0.01 0.02
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 4 -
This example show the axis specification of the axes for a map,
this time as orthogonal Angstroms, using the same coordinate system
as for the atomic coordinates. The map is sampling every 1.5
Angstroms (1.5e-7 millimeters) in a map segment 37.5 Angstroms on
a side.
;
;
loop_
_axis.id_axis.system_axis.vector[1]_axis.vector[2]_axis.vector[3]
X orthogonal 1 0 0
Y orthogonal 0 1 0
Z orthogonal 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing X
MAP 2 25 2 increasing Y
MAP 3 25 3 increasing Z
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
X 7.5e-8 1.5e-7
Y 7.5e-8 1.5e-7
Z 7.5e-8 1.5e-7
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.depends_on specifies the next outermost
axis upon which this axis depends.
This item is a pointer to _axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.equipment specifies the type of
equipment using the axis: 'goniometer', 'detector',
'gravity', 'source' or 'general'.
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.system
_item_description.description
; The value of _axis.system specifies the coordinate
system used to define the axis: 'laboratory', 'direct', 'orthogonal',
'reciprocal' or 'abstract'.
;
_item.name '_axis.system'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value laboratory
loop_
_item_enumeration.value
_item_enumeration.detail
laboratory
; the axis is referenced to the imgCIF standard laboratory Cartesian
coordinate system
;
direct
; the axis is referenced to the direct lattice
;
orthogonal
; the axis is referenced to the cell Cartesian orthogonal coordinates
;
reciprocal
; the axis is referenced to the reciprocal lattice
;
abstract
; the axis is referenced to abstract Cartesian cooridinate system
;
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: 'rotation' or 'translation' (or 'general' when
the type is not relevant, as for gravity).
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
; Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element are
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id.
;
;
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.center_fast
_item_description.description
; The value of _diffrn_data_frame.center_fast is
the fast index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_data_frame.center_units' along the fast
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement the current setting of detector
positioner given frame are used.
It is important to note that for measurements in millimetres,
the sense of the axis is used, rather than the sign of the
pixel-to-pixel increments.
;
_item.name '_diffrn_data_frame.center_fast'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_data_frame.center_slow
_item_description.description
; The value of _diffrn_data_frame.center_slow is
the slow index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_data_frame.center_units' along the slow
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement the current setting of detector
positioner given frame are used.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
;
_item.name '_diffrn_data_frame.center_slow'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_data_frame.center_units
_item_description.description
; The value of _diffrn_data_frame.center_units
specifies the units in which the values of
'_diffrn_data_frame.center_fast' and
'_diffrn_data_frame.center_slow'
are presented. The default is 'mm' for millimetres. The
alternatives are 'pixels' and 'bins'. In all cases the
center distances are measured from the center of the
first pixel, i.e. in a 2x2 binning, the measuring origin
is offset from the centers of the bins by one half pixel
towards the first pixel.
If 'bins' is specified, the data in
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size', and
'_array_intensities.pixel_binning_method'
is used to define the binning scheme.
;
_item.name '_diffrn_data_frame.center_units'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code code
loop_
_ item_enumeration.value
_ item_enumeration.detail
mm 'millimetres'
pixels 'detector pixels'
bins 'detector bins'
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.id
_item_description.description
; The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
save_
save__diffrn_data_frame.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
This is an appropriate location in which to record
information from vendor headers as presented in those
headers, but it should never be used as a substitute
for providing the fully parsed information within
the appropriate imgCIF/CBF categories.
Normally, when a conversion from a miniCBF has been done
the data from '_array_data.header_convention'
should be transferred to this data item and
'_array_data.header_convention'
should be removed.
;
_item.name '_diffrn_data_frame.details'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_frame_data.details'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.4
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
;
HEADER_BYTES = 512;
DIM = 2;
BYTE_ORDER = big_endian;
TYPE = unsigned_short;
SIZE1 = 3072;
SIZE2 = 3072;
PIXEL_SIZE = 0.102588;
BIN = 2x2;
DETECTOR_SN = 901;
TIME = 29.945155;
DISTANCE = 200.000000;
PHI = 85.000000;
OSC_START = 85.000000;
OSC_RANGE = 1.000000;
WAVELENGTH = 0.979381;
BEAM_CENTER_X = 157.500000;
BEAM_CENTER_Y = 157.500000;
PIXEL SIZE = 0.102588;
OSCILLATION RANGE = 1;
EXPOSURE TIME = 29.9452;
TWO THETA = 0;
BEAM CENTRE = 157.5 157.5;
;
; Example of header information extracted from an ADSC Quantum
315 detector header by CBFlib_0.7.6. Image provided by Chris
Nielsen of ADSC from a data collection at SSRL beamline 1-5.
;
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'slow mode'
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detector(s) used to
measure the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
; The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of
_diffrn_detector.diffrn_id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
; The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id.
The word 'positioner' is a general term used in
instrumentation design for devices that are used to change
the positions of portions of apparatus by linear
translation, rotation or combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
; Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named _diffrn_detector_axis.id
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
; Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, giving more detailed information
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
is preferable to simply providing the centre of the
detector element.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square, in the pattern
1 2
*
3 4
Note that the beam centre is slightly displaced from each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4. For each element, the detector
face coordiate system, is assumed to have the fast axis
running from left to right and the slow axis running from
top to bottom with the origin at the top left corner.
;
;
loop_
_diffrn_detector_element.detector_id_diffrn_detector_element.id_diffrn_detector_element.reference_center_fast_diffrn_detector_element.reference_center_slow_diffrn_detector_element.reference_center_units
d1 d1_ccd_1 201.5 201.5 mm
d1 d1_ccd_2 -1.8 201.5 mm
d1 d1_ccd_3 201.6 -1.4 mm
d1 d1_ccd_4 -1.7 -1.5 mm
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.id
_item_description.description
; The value of _diffrn_detector_element.id must uniquely
identify each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
; This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_element.reference_center_fast
_item_description.description
; The value of _diffrn_detector_element.reference_center_fast is
the fast index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_detector_element.reference_center_units' along the fast
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value given whould be
representive of the beam center as determined from the ensemble
of settings.
It is important to note that for measurements in millimetres,
the sense of the axis is used, rather than the sign of the
pixel-to-pixel increments.
;
_item.name '_diffrn_detector_element.reference_center_fast'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_detector_element.reference_center_slow
_item_description.description
; The value of _diffrn_detector_element.reference_center_slow is
the slow index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_detector_element.reference_center_units' along the slow
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value givien whould be
representive of the beam center as determined from the ensemble
of settings.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
;
_item.name '_diffrn_detector_element.reference_center_slow'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_detector_element.reference_center_units
_item_description.description
; The value of _diffrn_detector_element.reference_center_units
specifies the units in which the values of
'_diffrn_detector_element.reference_center_fast' and
'_diffrn_detector_element.reference_center_slow'
are presented. The default is 'mm' for millimetres. The
alternatives are 'pixels' and 'bins'. In all cases the
center distances are measured from the center of the
first pixel, i.e. in a 2x2 binning, the measuring origin
is offset from the centers of the bins by one half pixel
towards the first pixel.
If 'bins' is specified, the data in
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size', and
'_array_intensities.pixel_binning_method'
is used to define the binning scheme.
;
_item.name '_diffrn_detector_element.reference_center_units'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code code
loop_
_ item_enumeration.value
_ item_enumeration.detail
mm 'millimetres'
pixels 'detector pixels'
bins 'detector bins'
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the
diffraction data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model X'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector
angle 22.5 degrees
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support
and orient the specimen.
If the value of _diffrn_measurement.device is not given,
it is implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to
measure the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'home-made'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity
measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
; The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during the collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
; The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id.
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
# _diffrn_measurement.sample_detector_distance
# _diffrn_measurement.sample_detector_voffset
save__diffrn_measurement.sample_detector_distance
_item_description.description
; The value of _diffrn_measurement.sample_detector_distance gives the
unsigned distance in millimetres from the sample to the
detector along the beam.
;
_item.name '_diffrn_measurement.sample_detector_distance'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
_item_type.code float
_item_units.code mm
save_
save__diffrn_measurement.sample_detector_voffset
_item_description.description
; The value of _diffrn_measurement.sample_detector_voffset gives the
signed distance in millimetres in the vertical
direction (positive for up) from the center of
the beam to the center of the detector.
;
_item.name '_diffrn_measurement.sample_detector_voffset'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . .
. .
_item_type.code float
_item_units.code mm
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
; Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
; This data item is a pointer to _diffrn_measurement.device
in the DIFFRN_MEASUREMENT category.
;
_item.name
'_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_type.code text
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named _diffrn_measurement_axis.id,
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
####################
# DIFFRN_RADIATION #
####################
save_DIFFRN_RADIATION
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used for measuring diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
_category_key.name '_diffrn_radiation.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions of
photons in the XZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions
of photons in the YZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation degrees^2^ between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
direction of each photon in XZ plane times the deviations
of the direction of the same photon in the YZ plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons, this value is specified in
milliradians^2^, in which case a conversion would be needed.
To go from a value in milliradians^2^ to a value in
degrees^2^, multiply by 0.180^2^ and divide by \p^2^.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in \%Angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a
monochromator crystal is used, the material and the
indices of the Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarization ratio of the diffraction beam incident on the
crystal. This is the ratio of the perpendicularly polarized to
the parallel polarized component of the radiation. The
perpendicular component forms an angle of
_diffrn_radiation.polarisn_norm to the normal to the
diffraction plane of the sample (i.e. the plane containing
the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between
the normal to the polarization plane and the laboratory Y
axis as defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monochromater.
This differs from the value of
_diffrn_radiation.polarisn_norm
in that _diffrn_radiation.polarisn_norm refers to
polarization relative to the diffraction plane rather than
to the laboratory axis system.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane should be taken
as the XZ plane and the angle as 0.
See _diffrn_radiation.polarizn_source_ratio.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared)
of the electric vector in the plane of the normal to the
plane of polarization.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane is to be taken
as the XZ plane and the normal is parallel to the Y axis.
Thus, if there was complete polarization in the plane of
polarization, the value of
_diffrn_radiation.polarizn_source_ratio would be 1, and
for an unpolarized beam
_diffrn_radiation.polarizn_source_ratio would have a
value of 0.
If the X axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of 'MONOCHROMATOR' in the Denzo glossary, and values of near
1 should be expected for a bending-magnet source. However,
if the X axis were perpendicular to the polarization plane
(not a common choice), then the Denzo value would be the
negative of _diffrn_radiation.polarizn_source_ratio.
See http://www.hkl-xray.com for information on Denzo and
Otwinowski & Minor (1997).
This differs both in the choice of ratio and choice of
orientation from _diffrn_radiation.polarisn_ratio, which,
unlike _diffrn_radiation.polarizn_source_ratio, is
unbounded.
Reference: Otwinowski, Z. & Minor, W. (1997). 'Processing of
X-ray diffraction data collected in oscillation mode.' Methods
Enzymol. 276, 307-326.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly
recommended that this be given so that the
probe radiation is clearly specified.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'X-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for the probe
radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to
_diffrn_radiation_wavelength.id in the
DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.category_id diffrn_radiation
_item.mandatory_code yes
_item_type.code code
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
; This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
;
_category.id diffrn_refln
_category.mandatory_code no
_category_key.name '_diffrn_refln.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
; This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
; Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
_category_key.name '_diffrn_scan.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. In this example, three rotation axes and one translation axis
at nonzero values are specified, with one axis stepping. There is no
reason why more axes could not have been specified to step. Range
information has been specified, but note that it can be calculated from
the number of frames and the increment, so the data item
_diffrn_scan_axis.angle_range could be dropped.
Both the sweep data and the data for a single frame are specified.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
_diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
_diffrn_scan_frame.integration_time and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustments are made to
scan times and nonlinear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.angle_increment_diffrn_scan_frame_axis.displacement_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
; Example 2 - a more extensive example (R. M. Sweet, P. J. Ellis &
H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the goniometer.
This leads to a choice: either the axes of
the detector are defined at the origin, and then a Z setting of -240
is entered, or the axes are defined with the necessary Z offset.
In this case, the setting is used and the offset is left as zero.
This axis is called DETECTOR_Z.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm X 0.150mm, the centre of the first pixel is at (0.075,
0.075) in this coordinate system.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.displacement_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
; Example 3 - Example 2 revised for a spiral scan (R. M. Sweet,
P. J. Ellis & H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the
goniometer, as in Example 2 above, but in this example the
image plate is scanned in a spiral pattern from the outside edge in.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. The rotation axis is called ELEMENT_ROT and the
radial axis is called ELEMENT_RAD. A 150 micrometre radial pitch
and a 75 micrometre 'constant velocity' angular pitch are assumed.
Indexing is carried out first on the rotation axis and the radial axis
is made to be dependent on it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.angle_array_structure_list_axis.displacement_array_structure_list_axis.angular_pitch_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
; The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
; The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
; Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
_diffrn_scan_frame.integration_time, even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
; The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frame_id_end
_item_description.description
; The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frames
_item_description.description
; The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
; Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
; The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.angle_start
_item_description.description
; The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
; The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
; The increment for each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_increment. The
sum of the values of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
; The increment after each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_rstrt_incr. The
sum of the values of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment
and _diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.angle for this
next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
; The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
; The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_increment.
The sum of the values of
_diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_rstrt_incr.
The sum of the values of
_diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.displacement
for this next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_angle.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_angle will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_angle (e.g.
the mean).
If not specified, the value defaults to zero.
;
_item.name '_diffrn_scan_axis.reference_angle'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_displacement.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_displacement will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_displacement (e.g.
the mean).
If not specified, the value defaults to to the value of
_diffrn_scan_axis.displacement.
;
_item.name '_diffrn_scan_axis.reference_displacement'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
; Data items in the DIFFRN_SCAN_FRAME category describe
the relationships of particular frames to scans.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
; The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame.frame_number
_item_description.description
; The value of this data item is the number of the frame
within the scan, starting with 1. It is not necessarily
the same as the value of _diffrn_scan_frame.frame_id,
but it may be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
; The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of _diffrn_scan.integration_time.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
; Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the
settings of axes for particular frames. Unspecified axes are
assumed to be at their zero points. If, for any given frame,
nonzero values apply for any of the data items in this category,
those values should be given explicitly in this category and not
simply inferred from values in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
; The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
; The increment for this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
; The increment after this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment and
_diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.angle for this next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.displacement for this next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be zero.
;
_item.name '_diffrn_scan_frame_axis.reference_angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be equal to
_diffrn_scan_frame_axis.displacement.
;
_item.name '_diffrn_scan_frame_axis.reference_displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
#######
# MAP #
#######
save_MAP
_category.description
; Data items in the MAP category record
the details of a maps. Maps record values of parameters,
such as density, that are functions of position within
a cell or are functions of orthogonal coordinates in
three space.
A map may is composed of one or more map segments
specified in the MAP_SEGMENT category.
Examples are given in the MAP_SEGMENT category.
;
_category.id map
_category.mandatory_code no
loop_
_category_key.name '_map.id'
'_map.diffrn_id'
'_map.entry_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.details
_item_description.description
; The value of _map.details should give a
description of special aspects of each map.
;
_item.name '_map.details'
_item.category_id map
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.diffrn_id
_item_description.description
; This item is a pointer to _diffrn.id in the
DIFFRN category.
;
_item.name '_map.diffrn_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.entry_id
_item_description.description
; This item is a pointer to _entry.id in the
ENTRY category.
;
_item.name '_map.entry_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.id
_item_description.description
; The value of _map.id must uniquely identify
each map for the given diffrn.id or entry.id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map.id' map yes
'_map_segment.id' map_segment yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_segment.id' '_map.id'
save_
###########################
# MAP_SEGMENT #
###########################
save_MAP_SEGMENT
_category.description
; Data items in the MAP_SEGMENT category record
the details about each segment (section or brick) of a map.
;
_category.id map_segment
_category.mandatory_code no
loop_
_category_key.name '_map_segment.id'
'_map_segment.map_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map, each consisting of one
segment, both using the same array structure
and mask.
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
loop_
_map_segment.map_id
_map_segment.id
_map_segment.array_id
_map_segment.binary_id
_map_segment.mask_array_id
_map_segment.mask_binary_id
rho_calc rho_calc map_structure 1 mask_structure 1
rho_obs rho_obs map_structure 2 mask_structure 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map_segment.array_id
_item_description.description
; The value of _map_segment.array_id identifies the array structure
into which the map is organized.
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.array_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code code
save_
save__map_segment.binary_id
_item_description.description
; The value of _map_segment.binary_id distinguishes the particular
set of data organized according to _map_segment.array_id in
which the data values of the map are stored.
This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.mask_array_id
_item_description.description
; The value of _map_segment.mask_array_id, if given, the array
structure into which the mask for the map is organized. If no
value is given, then all elements of the map are valid. If a
value is given, then only elements of the map for which the
corresponding element of the mask is non-zero are valid. The
value of _map_segment.mask_array_id differs from the value of
_map_segment.array_id in order to permit the mask to be given
as, say, unsigned 8-bit integers, while the map is given as
a data type with more range. However, the two array structures
must be aligned, using the same axes in the same order with the
same displacements and increments
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.mask_array_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code code
save_
save__map_segment.mask_binary_id
_item_description.description
; The value of _map_segment.mask_binary_id identifies the
particular set of data organized according to
_map_segment.mask_array_id specifying the mask for the map.
This item is a pointer to _array_data.mask_binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.mask_binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.id
_item_description.description
; The value of _map_segment.id must uniquely
identify each segment of a map.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map_segment.id'
map_segment
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_data_frame.map_segment_id'
'_map_segment.id'
save_
save__map_segment.map_id
_item_description.description
; This item is a pointer to _map.id
in the MAP category.
;
_item.name '_map_segment.map_id'
_item.category_id map_segment
_item.mandatory_code yes
_item_type.code code
save_
save__map_segment.details
_item_description.description
; The value of _map_segment.details should give a
description of special aspects of each segment of a map.
;
_item.name '_map_segment.details'
_item.category_id map_segment
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
; Example to be provided
;
;
;
save_
######################## DEPRECATED DATA ITEMS ########################
save__diffrn_detector_axis.id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_detector_axis.id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_element.center[1]
_item_description.description
; The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
Because of ambiguity about the setting used to determine this center,
use of this data item is deprecated. The data item
_diffrn_data_frame.center_fast
which is referenced to the detector coordinate system and not
directly to the laboratory coordinate system should be used instead.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
; The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
Because of ambiguity about the setting used to determine this center,
use of this data item is deprecated. The data item
_diffrn_data_frame.center_slow
which is referenced to the detector coordinate system and not
directly to the laboratory coordinate system should be used instead.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_measurement_axis.id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_measurement_axis.id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
######################### DEPRECATED CATEGORY #########################
#####################
# DIFFRN_FRAME_DATA #
#####################
save_DIFFRN_FRAME_DATA
_category.description
; Data items in the DIFFRN_FRAME_DATA category record
the details about each frame of data.
The items in this category are now in the
DIFFRN_DATA_FRAME category.
The items in the DIFFRN_FRAME_DATA category
are now deprecated. The items from this category
are provided as aliases in the 1.0 dictionary
or, in the case of _diffrn_frame_data.details,
in the 1.4 dictionary. THESE ITEMS SHOULD NOT
BE USED FOR NEW WORK.
The items from the old category are provided
in this dictionary for completeness
but should not be used or cited. To avoid
confusion, the example has been removed
and the redundant parent-child links to other
categories have been removed.
;
_category.id diffrn_frame_data
_category.mandatory_code no
loop_
_category_key.name '_diffrn_frame_data.id'
'_diffrn_frame_data.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
THE DIFFRN_FRAME_DATA category is deprecated and should not be used.
;
;
# EXAMPLE REMOVED #
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_frame_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.array_id'
_item.category_id diffrn_frame_data
_item.mandatory_code implicit
_item_type.code code
save_
save__diffrn_frame_data.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.binary_id'
_item.category_id diffrn_frame_data
_item.mandatory_code implicit
_item_type.code int
save_
save__diffrn_frame_data.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.detector_element_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.id
_item_description.description
; The value of _diffrn_frame_data.id must uniquely identify
each complete frame of data.
DEPRECATED -- DO NOT USE
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_frame_data.id' diffrn_frame_data yes
_item_type.code code
save_
save__diffrn_frame_data.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.details'
_item.category_id diffrn_frame_data
_item.mandatory_code no
_item_type.code text
save_
################ END DEPRECATED SECTION ###########
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive) ...
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items (case insensitive)...
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
point numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9]?[0-9]\
((T[0-2][0-9](:[0-5][0-9](:[0-5][0-9](.[0-9]+)?)?)?)?\
([+-][0-5][0-9]:[0-5][0-9]))?
;
;
Standard format for CIF date and time strings (see
http://www.iucr.org/iucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character 'T' followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
decimal fraction on the seconds of time.
Time is local time if no time-zone offset is given.
Note that this type extends the mmCIF yyyy-mm-dd type
but does not conform to the mmCIF yyyy-mm-dd:hh:mm
type that uses a ':' in place if the 'T' specified
by the IUCr standard. For reading, both forms should
be accepted, but for writing, only the IUCr form should
be used.
For maximal compatibility, the special time zone
indicator 'Z' (for 'zulu') should be accepted on
reading in place of '+00:00' for GMT.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2)^)'
'millimetres' 'millimetres (metres * 10^( -3)^)'
'nanometres' 'nanometres (metres * 10^( -9)^)'
'angstroms' '\%Angstroms (metres * 10^(-10)^)'
'picometres' 'picometres (metres * 10^(-12)^)'
'femtometres' 'femtometres (metres * 10^(-15)^)'
#
'reciprocal_metres' 'reciprocal metres (metres^(-1)^)'
'reciprocal_centimetres'
'reciprocal centimetres ((metres * 10^( -2)^)^(-1)^)'
'reciprocal_millimetres'
'reciprocal millimetres ((metres * 10^( -3)^)^(-1)^)'
'reciprocal_nanometres'
'reciprocal nanometres ((metres * 10^( -9)^)^(-1)^)'
'reciprocal_angstroms'
'reciprocal \%Angstroms ((metres * 10^(-10)^)^(-1)^)'
'reciprocal_picometres'
'reciprocal picometres ((metres * 10^(-12)^)^(-1)^)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9)^)^2^'
'angstroms_squared' '\%Angstroms squared (metres * 10^(-10)^)^2^'
'8pi2_angstroms_squared'
'8\p^2^ * \%Angstroms squared (metres * 10^(-10)^)^2^'
'picometres_squared' 'picometres squared (metres * 10^(-12)^)^2^'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9)^)^3^'
'angstroms_cubed' '\%Angstroms cubed (metres * 10^(-10)^)^3^'
'picometres_cubed' 'picometres cubed (metres * 10^(-12)^)^3^'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^( -9)^)^(-3)^)
;
'electrons_per_angstroms_cubed'
; electrons per \%Angstroms cubed (electrons/(metres * 10^(-10)^)^(-3)^)
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (electrons/(metres * 10^(-12)^)^(-3)^)
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'pixels_per_element' '(image) pixels per (array) element'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.5.3 2007-07-08
; Changes to support SLS miniCBF and suggestions
from the 24 May 07 BNL imgCIF workshop (HJB)
+ Added new data items
'_array_data.header_contents',
'_array_data.header_convention',
'_diffrn_data_frame.center_fast',
'_diffrn_data_frame.center_slow',
'_diffrn_data_frame.center_units',
'_diffrn_measurement.sample_detector_distance',
'_diffrn_measurement.sample_detector_voffset
+ Deprecated data items
'_diffrn_detector_element.center[1]',
'_diffrn_detector_element.center[2]'
+ Added comments and example on miniCBF
+ Changed all array_id data items to implicit
;
1.5.2 2007-05-06
; Further clarifications of the coordinate system. (HJB)
;
1.5.1 2007-04-26
; Improve defintion of X-axis to cover the case of no goniometer
and clean up more line folds (HJB)
;
1.5 2007-07-25
; This is a cummulative list of the changes proposed since the
imgCIF workshop in Hawaii in July 2006. It is the result
of contributions by H. J. Bernstein, A. Hammersley,
J. Wright and W. Kabsch.
2007-02-19 Consolidated changes (edited by HJB)
+ Added new data items
'_array_structure.compression_type_flag',
'_array_structure_list_axis.fract_displacement',
'_array_structure_list_axis.displacement_increment',
'_array_structure_list_axis.reference_angle',
'_array_structure_list_axis.reference_displacement',
'_axis.system',
'_diffrn_detector_element.reference_center_fast',
'_diffrn_detector_element.reference_center_slow',
'_diffrn_scan_axis.reference_angle',
'_diffrn_scan_axis.reference_displacement',
'_map.details', '_map.diffrn_id',
'_map.entry_id', '_map.id',
'_map_segment.array_id', '_map_segment.binary_id',
'_map_segment.mask_array_id', '_map_segment.mask_binary_id',
'_map_segment.id', '_map_segment.map_id',
'_map_segment.details.
+ Change type of
'_array_structure.byte_order' and
'_array_structure.compression_type'
to ucode to make these values case-insensitive
+ Add values 'packed_v2' and 'byte_offset' to enumeration of values for
'_array_structure.compression_type'
+ Add to defintions for the binary data type to handle new compression types, maps,
and a variety of new axis types.
2007-07-25 Cleanup of typos for formal release (HJB)
+ Corrected text fields for reference_ tag descriptions that
were off by one column
+ Fix typos in comments listing fract_ tags
+ Changed name of release from 1.5_DRAFT to 1.5
+ Fix unclosed text fields in various map definitions
;
1.4 2006-07-04
; This is a change to reintegrate all changes made in the course of
publication of ITVG, by the RCSB from April 2005 through
August 2008 and changes for the 2006 imgCIF workshop in
Hawaii.
2006-07-04 Consolidated changes for the 2006 imgCIF workshop (edited by HJB)
+ Correct type of '_array_structure_list.direction' from 'int' to 'code'.
+ Added new data items suggested by CN
'_diffrn_data_frame.details'
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size and
'_array_intensities.pixel_binning_method
+ Added deprecated item for completeness
'_diffrn_frame_data.details'
+ Added entry for missing item in contents list
'_array_structure_list_axis.displacement'
+ Added new MIME type X-BASE32K based on work by VL, KM, GD, HJB
+ Correct description of MIME boundary delimiter to start in
column 1.
+ General cleanup of text fields to conform to changes for ITVG
by removing empty lines at start and finish of text field.
+ Amend example for ARRAY_INTENSITIES to include binning.
+ Add local copy of type specification (as 'code') for all children
of '_diffrn.id'.
+ For consistency, change all references to 'pi' to '\p' and all
references to 'Angstroms' to '\%Angstroms'.
+ Clean up all powers to use IUCr convention of '^power^', as in
'10^3^' for '10**3'.
+ Update 'yyyy-mm-dd' type regex to allow truncation from the right
and improve comments to explain handling of related mmCIF
'yyyy-mm-dd:hh:mm' type, and use of 'Z' for GMT time zone.
2005-03-08 and
2004-08-08 fixed cases where _item_units.code used
instead of _item_type.code (JDW)
2004-04-15 fixed item ordering in
_diffrn_measurement_axis.measurement_id
added sub_category 'vector' (JDW)
;
1.3.2 2005-06-25
; 2005-06-25 ITEM_TYPE_LIST: code, ucode, line, uline regexps updated
to those of current mmCIF; float modified by allowing integers
terminated by a point as valid. The 'time' part of
yyyy-mm-dd types made optional in the regexp. (BM)
2005-06-17 Minor corrections as for proofs for IT G Chapter 4.6
(NJA)
2005-02-21 Minor corrections to spelling and punctuation
(NJA)
2005-01-08 Changes as per Nicola Ashcroft.
+ Updated example 1 for DIFFRN_MEASUREMENT to agree with mmCIF.
+ Spelled out "micrometres" for "um" and "millimetres" for "mm".
+ Removed phrase "which may be stored" from ARRAY_STRUCTURE
description.
+ Removed unused 'byte-offsets' compressions and updated
cites to ITVG for '_array_structure.compression_type'.
(HJB)
;
1.3.1 2003-08-13
;
Changes as per Frances C. Bernstein.
+ Identify initials.
+ Adopt British spelling for centre in text.
+ Set \p and \%Angstrom and powers.
+ Clean up commas and unclear wordings.
+ Clean up tenses in history.
Changes as per Gotzon Madariaga.
+ Fix the ARRAY_DATA example to align '_array_data.binary_id'
and X-Binary-ID.
+ Add a range to '_array_intensities.gain_esd'.
+ In the example of DIFFRN_DETECTOR_ELEMENT,
'_diffrn_detector_element.id' and
'_diffrn_detector_element.detector_id' interchanged.
+ Fix typos for direction, detector and axes.
+ Clarify description of polarisation.
+ Clarify axes in '_diffrn_detector_element.center[1]'
'_diffrn_detector_element.center[2]'.
+ Add local item types for items that are pointers.
(HJB)
;
1.3.0 2003-07-24
;
Changes as per Brian McMahon.
+ Consistently quote tags embedded in text.
+ Clean up introductory comments.
+ Adjust line lengths to fit in 80 character window.
+ Fix several descriptions in AXIS category which
referred to '_axis.type' instead of the current item.
+ Fix erroneous use of deprecated item
'_diffrn_detector_axis.id' in examples for
DIFFRN_SCAN_AXIS.
+ Add deprecated items '_diffrn_detector_axis.id'
and '_diffrn_measurement_axis.id'.
(HJB)
;
1.2.4 2003-07-14
;
Changes as per I. David Brown.
+ Enhance descriptions in DIFFRN_SCAN_AXIS to make them less
dependent on the descriptions in DIFFRN_SCAN_FRAME_AXIS.
+ Provide a copy of the deprecated DIFFRN_FRAME_DATA
category for completeness.
(HJB)
;
1.2.3 2003-07-03
;
Cleanup to conform to ITVG.
+ Correct sign error in ..._cubed units.
+ Correct '_diffrn_radiation.polarisn_norm' range.
(HJB)
;
1.2.2 2003-03-10
;
Correction of typos in various DIFFRN_SCAN_AXIS descriptions.
(HJB)
;
1.2.1 2003-02-22
;
Correction of ATOM_ for ARRAY_ typos in various descriptions.
(HJB)
;
1.2 2003-02-07
;
Corrections to encodings (remove extraneous hyphens) remove
extraneous underscore in '_array_structure.encoding_type'
enumeration. Correct typos in items units list. (HJB)
;
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB.
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li.
;
1.1.1 2001-02-16
;
Several typo corrections by JW.
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS. (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME.
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to
'_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source',
'_diffrn_radiation.polarizn_source_norm',
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add '_diffrn_measurement.device' to category key.
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to
allow for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up. (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes. (JW)
+ Correct spelling of diffrn_measurement_axis in '_axis.id'
+ Correct ordering of uses of '_item.mandatory_code' and
'_item_default.value'.
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown. (HJB)
+ Add further comments on '\n' and '\t'.
+ Update ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Change 'meter' to 'metre' throughout.
+ Add missing enumerations to '_array_structure.compression_type'
and make 'none' the default.
+ Remove parent-child relationship between
'_array_structure_list.index' and '_array_structure_list.precedence'.
+ Improve alphabetization.
+ Fix '_array_intensities_gain.esd' related function.
+ Improve comments in AXIS.
+ Fix DIFFRN_FRAME_DATA example.
+ Remove erroneous DIFFRN_MEASUREMENT example.
+ Add '_diffrn_measurement_axis.id' to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data. (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors. (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for '_diffrn_scan.id' definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header. (HJB)
+ Restore '_diffrn_detector.diffrn_id' to DIFFRN_DETECTOR KEY.
+ Add AXIS category.
+ Bring in complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
from cif_mm.dic for clarity.
+ Change '_array_structure.encoding_type' from type code to uline and
added X-Binary-Element-Type to MIME header.
+ Add detector beam centre '_diffrn_detector_element.center[1]' and
'_diffrn_detector_element.center[2]'.
+ Correct item name of '_diffrn_refln.frame_id'.
+ Replace reference to '_array_intensities.undefined' by
'_array_intensities.undefined_value'.
+ Replace references to '_array_intensity.scaling' with
'_array_intensities.scaling'.
+ Add DIFFRN_SCAN... categories.
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft. (HJB)
+ Reflow comment lines over 80 characters and corrected typos.
+ Update examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF. (HJB)
+ Add binary type, which is a text field containing a variant on
MIME encoded data.
+ Change type of '_array_data.data' to binary and specify internal
structure of raw binary data.
+ Add '_array_data.binary_id', and make
'_diffrn_frame_data.binary_id' and '_array_intensities.binary_id'
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft. (JW)
+ Add category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes are made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA is renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE is renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for '_diffrn_frame_data.array_id' is changed from
'_array_structure_list.array_id' to '_array_structure.id'. Item
'_diffrn_detector.array_id' is deleted.
+ Add data item '_diffrn_frame_data.binary_id' to identify data
groups within a binary section. The formal identification of the
binary section is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version is adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley
(AH).
Modifications to the CBF draft. (JW)
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories
have been generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category
ARRAY_DATA. This departs from the CBF notion of data existing
in some special comment. In this description, data are handled as an
ordinary data item encapsulated in a character data type. Although
data this manner deviates from CIF conventions, it does not violate
any DDL 2.1 rules. DDL 2.1 regular expressions can be used to define
the binary representation which will permit some level of data
validation. In this version, the placeholder type code "any" has
been used. This translates to a regular expression which will match
any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary.
It may be possible to use the DDL 2.1 ITEM_STRUCTURE and
ITEM_STRUCTURE_LIST categories to provide the information that is
carried in by the ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By
moving the array structure to the DDL level it would be possible to
define an array type as well as a regular expression defining the
data format.
+ Multiple array sections can be properly handled within a single
datablock.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
by
Andy Hammersley
European Synchrotron Radiation Facility, BP 200, Grenoble, 38043, CEDEX, France
hammersley@esrf.fr
This document and the CBF definitions are still subject to change. This document
is a draft proposal for discussion.
This is a version of the CBF draft proposal, revised to include a coordinated
pure ASCII ImgCIF definition, based on
the Draft CBF Definition by Andy Hammersley,
the work done at the
Brookhaven imgCIF workshop, and
the work on "CBFLIB: An ANSI-C API for Crystallographic Binary File" by Paul Ellis,
ellis@SSRL.SLAC.STANFORD.EDU. For the binary CBF
format, a "binary-string" approach, as proposed by Paul Ellis, is used, while
for the ASCII imgCIF format, binary information is encoded using
a variant on MIME (Multipurpose Internet Mail
Extensions) format, which makes
the CBF and ImgCIF formats very similar.
This is just a proposal. My apologies in advance, especially to Andy, John and especially
to Paul for whatever I may have muddled here. Please be careful about basing any code on
this until and unless there has been a general agreement.
Notices
Please read the NOTICES, which
are part of this package, before making use of this software.
Most of this document is adapted from Andy's, so we follow his
convention by "...[separating] the definition from comments on discussion items by using
round brackets to refer to notes kept separate from the main text
e.g. (1) refers to point 1 in the notes section.". We have integrated
all comments to date into this document without special annotation.
A Draft Proposal
for
A Combined
Crystallographic Binary File (CBF)
and
Image-supporting Crystallographic Information File (ImgCIF)
Format
ABSTRACT
This document describes a proposal for a combined Crystallographic Binary File (CBF)
and Image-supporting Crystallographic Information File (ImgCIF) format;
a simple self-describing binary format for efficient transport and
archiving of experimental data for the crystallographic community, and well as
for the presentation of other image data, such as PICT, GIF and JPEG, within
publication CIFs. With minor differences, both the binary CBF format and
the ASCII ImgCIF have a similar, CIF-like structure. All the information
other than actual binary data is presented as ASCII strings in both formats.
The formats differ only in the handling of line termination and the
actual presentation of the binary data of an image. The CBF format, presents
binary information as a raw string of octets, while the ImgCIF format
presents the binary information as ASCII-encoded lines. The format of the binary file, and the new CIF data-items are defined. In this document we
concentrate on the representation of images per se. The
CBF/imgCIF dictionary
includes additional data items related to crystallographic
data acquisition. Those additional data items are not discussed here.
Note:
All numbers are decimal unless otherwise stated.
The terms octet and byte refer to a group of eight bits.
1.0 INTRODUCTION
The Crystallographic Binary File (CBF) format is a complementary format
to the Crystallographic Information File (CIF)
[1], supporting efficient
storage of large quantities of experimental data in a self-describing
binary format (1). The Image-supporting
Crystallographic Information File (ImgCIF) format is a proposed
extension to CIF to assist in ASCII debugging and archiving
of CBF files and to allow for convenient and standardized inclusion
of images, such as maps, diagrams and molecular drawing into
publication CIFs. It is our expectation that, for large images,
the raw binary CBF format
will be used both with in laboratories and for interchange among
collaborating groups. For smaller chunks of binary data, either format
should be be suitable, with the ASCII ImgCIF format being more
appropriate for interchange and archiving.
The initial aim is to support efficient storage of raw experimental data
from area-detectors (images) with no loss of information compared to
existing formats. The format should be both efficient in terms of
writing and reading speeds, and in terms of stored file sizes, and
should be simple enough to be easily coded, or ported to new computer
systems.
Flexibility and extensibility are required, and later the storage of
other forms of data may be added without affecting the present definitions.
The aims are achieved by a simple file format, consisting of
lines of ASCII information defining information about the binary
data as CIF tag-value pairs and tables, and either raw octets of
binary data in delimited sections, or ASCII-based presentations
of the same binary information in similarly delimited sections.
The present version of the format only tries to deal with simple Cartesian
data. This is essentially the "raw" data from detectors
that is typically stored in commercial formats or individual formats
internal to particular institutes, but could be other forms
of data. It is hoped that CBF can replace individual laboratory or
institute formats for "home" built detector systems, be used as a
inter-program data exchange format, and may be offered as an output
choice by a number of commercial detector manufacturers specialising in
X-ray and other detector systems.
This format does not imply any particular demands on processing software
nor on the manner in which such software should work. Definitions of units,
coordinate systems, etc. may quite different. The clear precise
definitions within CIF, and hence CBF, help, when necessary, to
convert from one system to another. Whilst no strict demands are made,
it is clearly to be hoped that software will make as much use as is
reasonable of information relevant to the processing which is stored
within the file. It is expected that processing software will give
clear and informative error messages when they encounter problems within
CBF's or do not support necessary mechanisms for inputting a file.
1.1 CBF and "imgCIF"
CBF and "imgCIF" are two aspects of the same format. Since CIF's
are pure ASCII text files, a separate binary format is needed to be
defined to allow the combination of pseudo-ASCII sections and
binary data sections. The binary file format is the Crystallographic
Binary File (CBF). The ASCII sections are very close to the CIF
standard, but must use operating system independent "line separators".
In describing the ASCII sections, we use the notation
"\r\n" (for the pair of characters carriage return, line-feed)
for a line terminator would allow the ASCII sections to viewed with standard system
utilities on a very wide range of operating systems. However,
an API to read
the binary format must accept any of the following three alternative
line terminators as the end of an ascii line: "\r",
"\n" or "\r\n". An API to write CBF should
write "\r\n" as the line terminator, if at all possible.
imgCIF is also the name of the CIF dictionary which contains the terms
specific to describing the binary data (the orginal, designed by John Westbrook, without the
modifications in this proposal is avaliable from
http://ndbserver.rutgers.edu/NDB/mmcif. Thus a CBF
or ImgCIF files uses data names
from the imgCIF dictionary and other CIF dictionaries.
2.0 A SIMPLE EXAMPLE
Before fully describing the format we start by showing a simple, but
important and complete usage of the format; that of storing a single
detector image in a file together with a small amount of useful
auxiliary information. It is intened to be a useful example for people
who like working from examples, as opposed to full definitions. It
should also serve as an introduction or overview of the format defintion.
This example uses CIF DDL2 based dictionary items.
The example is an image of 768 by 512 pixels stored as 16 bit unsigned
integers, in little endian byte order. (This is the native byte ordering
on a PC.) The pixel sizes are 100.5 by 99.5 microns. Comment lines starting
with a hash sign (#) are used to explain the contents of the header.
Only the ASCII part of the file is shown, but comments are used to
describe the start of the binary section.
First the file is shown with the minimum of comments that a typical
outputting program might add. Then it is repeated, but with "over-
commenting" to explain the format.
Here is how a file might appear if listed on a PC or on a Unix system
using "more":
Here the file is shown again, but this time with many comment
lines added to explain the format:
###CBF: VERSION 0.6
# This line starting with a "#" is a CIF and CBF comment line,
# but the first line with the three "#"s is a CBF identifier.
# (a "magic number") The text "###_CBF: VERSION" identifies
# the file as a CBF and must be present as the very first line of
# every CBF file. Following "VERSION" is the version number of
# the file, which is the corresponding version of the CBF/imgCIF
# extensions dictionary and supporting documentation. A version
# 0.6 CIF should be readable by any program which fully supports
# the version 1.0 CBF definitions.
# Comment lines and white space (blanks and new lines) may appear
# anywhere outside the binary sections.
# In a CIF, the descriptive tags and values may be presented in
# any convenient order, e.g. the data could come first, and the
# parameters necessary to interpret the data could come later.
# This order-independent convention holds for an imgCIF file, but
# for a CBF, all the tags and values describing binary data (i.e.
# all the tags other than those in the ARRAY_DATA category) should
# be presented before the binary data, in the form of a header.
# This does not mean that there cannot be more useful information
# after the binary data. There could be another full header and
# more blocks of binary data. All we are saying is that, in
# the interest of efficiency in processing a CBF, the parameters
# that relate to a particular block of binary data must appear
# earlier in the CBF than the block itself.
# The header begins with "data_", which is the CIF token to
# identify a data block. Within a data block, any given tag may
# be presented only once, either directly with an immediately
# following value, or as one of the column headings for the rows
# of a table. If you will need to resuse the same tag, you will
# have to start a new data block.
# Data block for image 1
data_image_1
# We've chosen to call this data block 'image_1', but this was an
# arbitary choice. Within a data block a data item may only be used
# once.
_entry.id 'image_1'
# Sample details
_chemical.entry_id 'image_1'
_chemical.name_common 'Protein X'
# The apostrophes enclose the string which contains a space.
# A double quote (") could have been used, just as well.
# There is also a third way to quote string, with the string
# "\n;", i.e. with a semicolon at the beginning of a line
# which allows multi-lined strings to be presented. We'll
# use that form of text quotation for the binary data.
# Experimental details
_exptl_crystal.id 'CX-1A'
_exptl_crystal.colour 'pale yellow'
_diffrn.id DS1
_diffrn.crystal_id 'CX-1A'
_diffrn_measurement.diffrn_id DS1
_diffrn_measurement.method Oscillation
_diffrn_measurement.sample_detector_distance 0.15
_diffrn_radiation_wavelength.id L1
_diffrn_radiation_wavelength.wavelength 0.7653
_diffrn_radiation_wavelength.wt 1.0
_diffrn_radiation.diffrn_id DS1
_diffrn_radiation.wavelength_id L1
_diffrn_source.diffrn_id DS1
_diffrn_source.source synchrotron
_diffrn_source.type 'ESRF BM-14'
_diffrn_detector.diffrn_id DS1
_diffrn_detector.id ESRFCCD1
_diffrn_detector.detector CCD
_diffrn_detector.type 'ESRF Be XRII/CCD'
_diffrn_detector_element.id 1
_diffrn_detector_element.detector_id ESRFCCD1
_diffrn_frame_data.id F1
_diffrn_frame_data.detector_element_id 1
_diffrn_frame_data.array_id 'image_1'
_diffrn_frame_data.binary_id 1
# Many more data items can be defined, but the above gives the idea
# of a useful minimum set (but not minimum in the sense of
# compulsory, the above data items are optional in a CIF or CBF).
# Define image storage mechanism
#
# Notice that we did not include a binary ID here. The idea of
# the ARRAY_STRUCTURE category is to present parameters which
# could be common to multiple blocks of binary data, which would
# all have the same array ID, but would have distinct binary ID's
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
# On the other hand, we do provide a binary ID for ARRAY_INTENSITIES,
# since there might be different paremeters for each binary block.
# We could have left it out here, since there is only one block and
# the default binary ID happens to be 1
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.undefined_value
_array_intensities.overload_value
image_1 1 linear 0 65535
# Define dimensionality and element rastering
# Here the size of the image and the ordering (rastering) of the data
# elements is defined. The CIF "loop_" structure is used to
# define different dimensions. (It can be used for defining multiple
# images.)
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
image_1 1 768 1 increasing
image_1 2 512 2 decreasing
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
image_1 1 100.5e-6
image_1 2 99.5e-6
# The "array_id" identifies data items belong to the same array.
# Here we have chosen the name "image_1", but another name could
# have been used, so long as it's used consistently. The "index"
# component refers to the dimension being defined, and the
# "dimension" component defines the number of elements in that
# dimension. The "precedence" component defines which precedence
# of rastering of the data. In this case the first dimension is the faster
# changing dimension. The "direction" component tells us the
# direction in which the data rasters within a dimension. Here the
# data rasters faster from minimum elements towards the maximum
# element ("increasing") in the first dimension, and more
# slowly from the maximum element towards the minimum element in
# the second dimension. (This is the default rastering order.)
# The storage of the binary data is now fully defined.
# Further data items could be defined, but we are ready to
# present the data. That is done with the ARRAY_DATA category.
# The start of this category marks the end of the header
# (Well, almost the end, there is a bit more header information
# below).
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
image_1 1
# The binary data itself will come just a little further down,
# as the essential part of the value of _array_data.data, which
# begins as semicolon-quoted text. The line immediately after
# the line with the semicolon is a MIME boundary marker. As for
# all MIME boundary markers, it begins with "--". The next
# few lines are MIME headers, describing some useful information
# we will need to process the binary section. MIME headers can
# appear in different orders, and can be very confusing (look
# at the raw contents of a email message with attachments), but
# there is only a few headers which is have to be understood to
# process a CBF:
#
# The "Content-Type" header may be any of discrete types
# permitted in RFC 2045; "application/octet-stream" is
# recommended. If an octet stream was compressed, the
# compression should be specified by the parameter
# 'conversions="x-CBF_PACKED"' or by specifying
# one of the other compression types.
#
# The "Content-Transfer-Encoding" header should be 'BINARY'
# for a CBF. We'll consider the other values used for imgCIF
# below.
#
# The "X-Binary-Size" header specifies the size of the
# binary data in octets. If compression was used, this size
# is the size after compression, including any book-keeping
# fields, but not the 8 bytes for the compression type.
#
# The "X-Binary-Element-Type" header specifies the
# type of binary data in the octets, using the same
# descriptive phrases as in _array_structure.encoding_type.
# The default value is "unsigned 32-bit integer".
#
# The MIME header items are followed by an empty line and then by
# a special sequence marked here as 'START_OF_BIN', consisting of
# Control-L, Control-Z, Control-D to stop printing on most systems,
# and then a single binary flag character of hexadecimal value D5
# (213 decimal). The binary data follows immediately after this
# flag character.
#
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 374578
X-Binary-ID: 1
X-Binary-Element-Type: "unsigned 16-bit integer"
Content-MD5: jGmkxkrpnizOetd9T/Np4NufAmA==
START_OF_BIN
*************'9*****`********* ...
[This is where the raw binary data would be -- we can't print it here]
--CIF-BINARY-FORMAT-SECTION----
;
# After the last octet (i.e. byte) of the binary data, there is a
# special trailer "\n--CIF-BINARY-FORMAT-SECTION----\n;"
# which repeats the initial bounday marker with an extra "--"
# at the end (a MIME convention for the last boundary marker), and
# then the closing semicolon quote for a text section. This
# is essential in an imgCIF, and we include it in a CBF for
# consistency.
OVERVIEW OF THE FORMAT
This section describes the major "components" of the CBF format.
CBF is a binary file, containing self-describing array data e.g. one
or more images, and auxiliary data e.g. describing the experiment.
Except for the handling of line terminators, the way binary data
is presented, and more liberal rules in ordinger information, an
ASCII imgCIF file is the same as a CBF binary file.
A CBF consists of pseudo-ASCII text header sections, which are "lines" of
no more than 80 ASCII characters separated by "line separators" which are the pair of
ASCII characters carriage return and line-feed (ASCII 13, ASCII 10),
followed by zero, one, or more binary sections presented as "binary
strings". This structure may be repeated.
An imgCIF consists of ASCII lines of no more than 80 characters using the
the normal line termination conventions of the current system (e.g.
ASCII 10 in UNIX) with MIME-encoded binary strings at any
appropriate point in the file.
The very start of the file has an identification item (magic number)
(2). This item
also describes the CBF version or level. The identifier is:
###CBF: VERSION
which must always be present so that a program can easily identify
whether or not a file is a CBF, by simply inputting the first 15
characters. (The space is a blank (ASCII 32) and not a tab. All
identifier characters are uppercase only.)
The first hash means that this line within a CIF would be a comment
line, but the three hashes mean that this is a line describing the
binary file layout for CBF. (All CBF internal identifiers start with
the three hashes, and all other must immediately follow a "line
separator".) No whitespace may precede the first hash sign.
Following the file identifier is the version number of the file. e.g.
the full line might appear as:
###CBF: VERSION 0.6
The version number must be separated from the file identifier
characters by whitespace e.g. a blank (ASCII 32).
The version number is defined as a major version number and minor
version number separated by the decimal point. A change in the major
version may well mean that a program for the previous version cannot
input the new version as some major change has occurred to CBF
(3). A
change in the minor version may also mean incompatibility, if the CBF
has been written using some new feature. e.g. a new form of linearity
scaling may be specified and this would be considered a minor version
change. A file containing the new feature would not be readable by a
program supporting only an older version of the format.
Note:
Until we reach major version 1 (the first official release), the
rules are a little more relaxed. While there will be some effort at
upwards compatability, in order to ensure a reasonable agreed specification
without too many strange artifacts, changes between minor versions
may, unfortunately, introduce incompatabilities which require
program changes to still read CBFs compliant with an earlier draft,
e.g. the change in the "magic number" and from binary sections to
binary strings in going to version 0.3, and a removal of the
redundant parts of the binary header in going to version 0.6.
Naturally, such changes should be sufficiently well documented to allow
for conversions.>>>
Header Information:
The start of an header section is delimited by the
usual CIF "data_" token. Optionally, the formerly specified
header identifier,
###_START_OF_HEADER
may be used before the "data_" taken, followed by the carriage return, line-feed pair,
as an aid in debugging, but it is no longer required. (Naturally, another carriage return,
line-feed pair should immediately precedes this and all other CBF identifiers, with
the exception of the CBF file identifier which is at the very start of the
file.)
A header section, including the identification items which delimit
it, uses only ASCII characters, and is divided into "lines". The "line
separator" symbols, "\r\n" (carriage return, line-feed) are the same regardless
of the operating system on which the file is written. (This is an
importance difference with CIF, but must be so, as the file contains
binary data, so cannot be translated from one O.S. to another, which is
the case for ASCII text files.) While a properly functioning CBF API
should write the full "\r\n" line separator, it should recognize
any of three sequences "\r", "\n", "\r\n" as valid
line separators, so that hand-edited headers will not be rejected.
The header section within the delimiting identification items
obeys all CIF rules [1] with the
exception of the line separators.
e.g.
"Lines" are a maximum of 80 characters long. (For CBF it is probably
best to allow for this maximum to be larger.)
The tokens "data_" and "loop_" have special meaning to CIF, and
should not be used except in their indicated places. The tokens
"save_", "stop_" and "global_" also have special meaning to CIF's
parent language, STAR, and also should not be used.
All data names (tags) start with an underscore character.
The hash symbol (#) (outside a character string) means that all text
up to the line separator is a comment.
Whitespace outside of character strings is not significant.
Data names are case insensitive.
The data item follows the data name separator, and may be of one of
two types: character string (char) or number (numb). (The type is
specified for each data name.)
Character strings may be delimited with single of double quotes, or blocks of
text may be delimited by semi-colons occurring as the first character on
a line.
The "loop_" mechanism allows a data name to have multiple values.
Immediately following the "loop_", one or more data names are listed without
their values, as column headings. Then one or more rows of values
are given.
Any CIF data name may occur within the header section.
A single header section may contain one or more data blocks (CIF
terminology).
The end of the header information is marked by
coming to the tags from the "ARRAY_DATA" category. The formerly
specifier special
identifier:
###_END_OF_HEADER
followed by carriage return, line-feed, may be used as well as an aid to
debugging, but it is not required.
The header information must contain sufficient data names to fully
describe the binary data section(s) which follow(s).
Binary Information:
Note: Under CBFlib "binary sections" have been replaced by "binary strings"
values within a data name/value pair. The structure of the proposed
"binary string" is similar to the former binary sections, but there are
significant differences.
Before getting to the binary data, itself, there are some preliminaries
to allow a smooth transition from the conventions of CIF to those of
raw streams of "octets" (8-bit bytes). The binary data is
given as the essential part of a specially formatted semicolon-delimited
CIF multi-line text string. This text string is the value associated with the
tag "_array_data.data".
Within that text string, the conventions developed for
transmitting email messages including binary attachments are followed.
There is secondary ASCII header information, formatted as Multipurpose
Internet Mail Extensions (MIME) headers (see RFCs 2045-49 by
Freed, et. al). The bounday marker for the beginning of all this
is the special string
--CIF-BINARY-FORMAT-SECTION--
at the beginning of a line. The initial "--" says that
this is a MIME boundary. We cannot put "###" in front
of it and conform to MIME conventions. Immediately after the boundary
marker are MIME headers, describing some useful information
we will need to process the binary section. MIME headers can
appear in different orders, and can be very confusing (look
at the raw contents of a email message with attachments), but there
is only a few headers with a narrow range of values which is have
to be understood to process a CBF (as opposed of an imgCIF, for which the
headers can be more varied):
The "Content-Type" header may be any of discrete types
permitted in RFC 2045; "application/octet-stream" is
recommended. If an octet stream was compressed, the
compression should be specified by the parameter
'conversions="x-CBF_PACKED"' or by specifying
one of the other compression types.
The "Content-Transfer-Encoding" header should be 'BINARY'
for a CBF. We'll consider the other values used for imgCIF
below.
The "X-Binary-Size" header specifies the size of the
binary data in octets. If compression was used, this size
is the size after compression, including any book-keeping
fields, but not the 8 bytes for the compression type.
The "X-Binary-Element-Type" header specifies the
type of binary data in the octets, using the same
descriptive phrases as in _array_structure.encoding_type.
The default value is "unsigned 32-bit integer".
The MIME header items are followed by an empty line and then by
a special sequence marked here as 'START_OF_BIN', consisting of
Control-L, Control-Z, Control-D to stop printing on most systems,
and then a single binary flag character of hexadecimal value D5
(213 decimal). The binary data follows immediately after this
flag character.
In general, if the value given for "Content-Transfer-Encoding" is one of the
real encodings: "BASE64", "QUOTED-PRINTABLE", "X-BASE8",
"X-BASE10" or "X-BASE16", this file is an imgCIF.
For either a CBF or an imgCIF the optional "Content-MD5" header provides a much more
sophisticated check on the integrity of the binary data.
In a CBF, the raw binary data begins after an empty line terminating
the MIME headers and after the START_OF_BIN identifier.
"START_OF_BIN" contains bytes to separate the "ASCII" lines
from the binary data, bytes to try to stop the listing of the header,
bytes which define the binary identifier which should match the
"binary_id" defined in the header, and bytes which define the
length of the binary section.
Octet
Hex
Decimal
Purpose
1
0C
12
(ctrl-L) End the current page
2
1A
26
(ctrl-Z) Stop listings in MS-DOS
3
04
04
(Ctrl-D) Stop listings in UNIX
4
D5
213
Binary section begins
5..5+n-1
Binary data (n octets)
Only bytes 5..5+n-1 are encoded for an imgCIF file
using the indicated Content-Transfer-Encoding.
Note: Earlier versions of the specification included three 8-byte words
of information in binary which replicated information now available in
the MIME header:
5..12
Binary Section Identifier
(See _array_data.binary_id)
64-bit, little endian
13..20
the size (n) of the
binary section in octets
(i.e. the offset from octet
29 to the first byte following
the data)
21..28
Compression type:
CBF_NONE
0x0040 (64)
CBF_CANONICAL
0x0050 (80)
CBF_PACKED
0x0060 (96)
...
&NBSP;
followed by binary data. These three 8-byte words are no longer included when
a MIME header is provided. In addition, in still earlier versions, the size
given in the second 8-byte word was n+8, rather than n.
The binary characters serve specific purposes:
The Control-L will terminate the current page in listings
on most operating systems.
The Control-Z will stop the listing of the file on MS-DOS
type operating systems.
The Control-D will stop the listing of the file on Unix
type operating systems.
The unsigned byte value 213 (decimal) is binary 11010101.
(Octal 325, and hexadecimal D5).
This has the eighth bit set so can be used for error checking
on 7-bit transmission. It is also asymmetric, but with the first
bit also set in the case that the bit order could be reversed
(which is not a known concern).
(The carriage return, line-feed pair before the START_OF_BIN
and other lines can also be used to check that the file has not
been corrupted e.g. by being sent by ftp in ASCII mode.)
The "line separator" immediately precedes the "start of binary
identifier", but blank spaces may be added prior to the preceding
"line separator" if desired (e.g. to force word or block alignment).
The binary data does not have to completely fill the bytes defined
by the byte length value, but clearly cannot be greater than this
value (except when the value zero has been stored, which means that
the size is unknown, and no other headers follow). The values of
any unused bytes are undefined.
At exactly the byte following the full binary section as defined by
the length value is the end of binary section identifier. This consists
of the carriage return / line feed pair followed by:
--CIF-BINARY-FORMAT-SECTION--
;
with each of these lines followed by the carriage return / line feed pair.
This brings us back into a normal CIF environment
The first "line separator" separates the binary data from the
pseudo-ASCII line.
This identifier is in a sense redundant since the binary data
length value tells the a program how many bytes to jump over to
the end of the binary data. However, this redundancy has been
deliberately added for error checking, and for possible file
recovery in the case of a corrupted file.
This identifier must be present at the end of every block of
binary data.
Whitespace may be used within the pseudo-ASCII sections prior to the
"start of binary section" identifier to align the start binary data
sections to word or block boundaries. Similar use may be made of unused
bytes in binary sections. However, no blank lines should be introduced
among the MIME headers, since that would terminate processing of those
headers and start the scan for binary data.
However, in general no guarantee is made of block nor word alignment
in a CBF of unknown origin.
The end of the file need not be not explicitly indicated, but
including a comment of the form:
###_END_OF_CBF
(including the carriage return, line-feed pair) can help in debugging.
All binary data described in a single data block should follow the
header section prior to another data block, or the end of the
file, so allow for the most efficient processing of CBF files.
However, since binary strings can be parsed anywhere within the
context of a CBF or imgCIf file, it is recommended that processing
software from CBF accept such strings in any order and it is mandatory
that processing software for imgCIF accept such string in any order.
The binary identifier values used within a given data block section, and
hence the binary data must be unique for any
given array_id, and, it would be best to make them truly unique.
A different data block may reuse binary identifier values.
(This allows concatenation of files without re-numbering the
binary identifiers, and provides a certain level of localization
of data within the file, to avoid programs having to search
potentially huge files for missing binary sections.)
The recommended file extension for a CBF is: cbf
This allows users to recognise file types easily, and gives programs a
chance to "know" the file type without having to prompt the user.
Although they should check for at least the file identifier to
ensure that the file type is indeed a CBF.
The recommended file extensions for imgCIF are: icf or cif (use of "cif" subject to IUCr approval).
CBF format files are binary files and when ftp is used to transfer
files between different computer systems "binary" or "image" mode
transfer should be selected.
imgCIF files are ASCII files and when ftp is used to transfer
files between different computer systems "ascii"
transfer should be selected.
3.1 SIMPLE EXAMPLE OF THE ORDERING OF IDENTIFIERS
Here only the ASCII part of the file structuring identifiers is shown.
The CIF data items are not shown, apart from the "data_" identifier
which indicates the beginning of a data block.
This shows the structuring of a simple example e.g. one header section
followed by one binary section. Such as could be used to store a
single image.
###CBF: VERSION 0.3
data_
### ... various CIF tags and values here
loop_
array_data.id
array_data.binary_id
array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BINARY
X-Binary-ID: 1
Content-MD5: jGmkxiOetd9T/Np4NufAmA==
START_OF_BIN
*************'9*****`********* ...
[This is where the raw binary data would be -- we can't print it here]
--CIF-BINARY-FORMAT-SECTION----
;
###_END_OF_CBF
3.2 MORE COMPLICATED EXAMPLE OF THE ORDERING OF IDENTIFIERS
Here only the ASCII part of the file structuring identifiers is shown.
The CIF data items are not shown, apart from the "data_" identifier
which indicates the beginning of a data block.
This shows the a possible structuring of a more complicated example.
Two header sections, the first contains two data blocks and defines
three binary sections. CIF comment lines, starting with a hash (#) are
used to example the structure.
###CBF: VERSION 0.6
# CBF file written by cbflib v0.6
# A comment cannot appear before the file identifier, but can appear
# anywhere else, except within the binary sections.
# Here the first data block starts
data_
### ... various CIF tags and values here
### but none that define array data items
# The "data_" identifier finishes the first data block and starts the
# second
data_
### ... various CIF tags and values here
### including ones that define array data items
loop_
array_data.array_id
array_data.binary_id
array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 3745758
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
START_OF_BIN
<D5>^P<B8>P^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ ...
[This is where the raw binary data would be -- we can't print it here]
--CIF-BINARY-FORMAT-SECTION----
;
# Following the "end of binary" identifier the file is pseudo-ASCII
# again, so comments are valid up to the next "start of binary"
# identifier. Note that we have bumped the binary ID.
image_1 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 3745758
X-Binary-ID: 2
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: xR5kxiOetd9T/Nr5vMfAmA==
START_OF_BIN
<D5>^P<B8>P^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@ ...
[This is where the raw binary data would be -- we can't print it here]
--CIF-BINARY-FORMAT-SECTION----
;
# Third binary section, note that we have a new array id.
image_2 3
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BINARY
X-Binary-ID: 3
Content-MD5: yS5kxiOetd9T/NrqTLfAmA==
START_OF_BIN
*************'9*****`********* ...
[This is where the raw binary data would be -- we can't print it here]
--CIF-BINARY-FORMAT-SECTION----
;
# Second Header section
data_
### ... various CIF tags and values here
### including ones that define array data items
# Since we only have one block left, we won't use a loop
array_data.id image
array_data.binary_id 1
array_data.data
# Note that I can put a comment here
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BINARY
X-Binary-ID: 1
Content-MD5: fooxiOetd9T/serNufAmA==
START_OF_BIN
*************'9*****`********* ...
[This is where the raw binary data would be -- we can't print it here]
--CIF-BINARY-FORMAT-SECTION----
;
###_END_OF_CBF
DATA NAME CATEGORIES
John Westbrook has proposed a number of data name categories as part of
his DDL2 based "imgCIF" dictionary. This category list may be expanded
to cover a structuring of the often multiple data-sets which might be used
in a structurial investigation. Here we only consider the categories
concerned with storing an image (or other N-dimensional topographically
regular cartesian grid).
The _array_* categories cover all data names concerned with
the storage of images or regular array data.
Data names from any of the existing categories may be relevant as
auxiliary information in the header section, but data names from the
_diffrn_ category, are likely to be the most relevant, and a
number of new data names in this category are necessary.
The "array" Class of Binary Data
The "array" class is used to store regular arrays of data values, such
as 1-D histograms, area-detector data, series of area-detector data, and
volume data. Normally such data is regularly spaced in space or time,
however spatial distorted data could nevertheless be stored in such a format.
There is only one data "value" stored per lattice position, although that
value may be of type complex.
The "array" class is defined by data names from the ARRAY_STRUCTURE
and ARRAY_STRUCTURE_LIST categories.
Here is a short summary of the data names and their purposes.
_array_structure.id: Alpha numeric identifier for
the array structure
_array_structure.compression_type: Type of data compression used
_array_structure.byte_order: Order of bytes for multi-byte
integer or reals
_array_structure.encoding_type: Native data type used to
store elements.
e.g. "unsigned_16_bit_integer" is used if the stored image was 16 bit
unsigned integer values, regardless of any compression scheme used.
"Array" Dimensions and Element Rastering and Orientation
The array dimension sizes, i.e. the number of elements in each dimension
are defined by _array_structure_list.dimension.
Which takes an integer value. This is used in a loop together with
the _array_structure_list.index
item to define the different dimensions for one or more arrays.
Fundamental to treating a long line of data values as a 2-D image or
an N-dimensional volume or hyper-volume is the knowledge of the manner
in which the values need to be wrapped. For the raster orientation to
be meaningful we define the sense of the view:
For a detector image the sense of the view is defined as that looking
from the crystal towards the detector.
(For the present we consider only an equatorial plane geometry, with
2-theta = 0; the detector as being vertically mounted.)
The rastering is defined by the three data names
_array_structure_list.index, _array_structure_list.precedence, and
_array_structure_list.direction data names.
index refers to the dimension index i.e. In an image 1 refers to the
X-direction (horizontal), 2 refers to the Y-direction (vertical).
precedence refers to the order in which the data in wrapped.
direction refers the direction of the rastering for that index.
We define a preferred rastering orientation,
which is the default if the keyword is not defined. This is with the
start in the upper-left-hand corner and the fastest changing direction
for the rastering horizontally, and the slower change from top to bottom.
(Note: With off-line scanners the rastering type depending on which way
round the imaging plate or film is entered into the scanner. Care may
need to be taken to make this consistent.)
"Array_Structure" Examples
To define an image array of 1300 times 1200 elements, with the raster
faster in the first dimension, from left to right, and slower in the
second dimension from top to bottom, the following header section
might be used:
To define two arrays, the first a volume of 100 times 100 times 50
elements, fastest changing in the first dimension, from left to right,
changing from bottom to top in the second dimension, and slowest
changing in the third dimension from front to back; the second an image
of 1024 times 1280 pixels, with the second dimension changing fastest
from top to bottom, and the first dimension changing slower from left
to right; the following header section might be used:
Existing data storage formats use a wide variety of methods for storing
physical intensities as element values. The simplest is a linear
relationship, but square root and logarithm scaling methods have
attractions and are used. Additionally some formats use a lower dynamic
range to store the vast majority of element values, and use some other
mechanism to store the elements which over-flow this limited dynamic
range. The problem of limited dynamic range storage is solved by the data
compression methods byte_offsets and predictor_huffman
(see next Section), but the possibility of defining non-linear scaling
must also be provided.
The _array_intensities.linearity data item specifies how the
intensity scaling is defined. Apart from linear scaling, which is
specified by the value linear, two other methods are available
to specify the scaling.
One is to refer to the detector system, and then knowledge of the
manufacturers method will either be known or not by a program. This has
the advantage that any system can be easily accommodated, but requires
external knowledge of the scaling system.
The recommended alternative is to define a number of standard intensity
linearity scaling methods, with additional data items when needed. A
number of standard methods are defined by _array_intensities.linearity
values: offset, scaling_offset, sqrt_scaled, and
logarithmic_scaled.
The "offset" methods require the data item _array_intensities.offset
to be defined, and the "scaling" methods require the data item
_array_intensities.scaling to be defined.
The above scaling methods allow the element values to be converted to a
linear scale, but do not necessarily relate the linear intensities to
physical units. When appropriate the data item _array_intensities.gain
can be defined. Dividing the linearized intensities by the value of
_array_intensities.gain should produce counts.
Two special optional data flag values may be defined which both refer to
the values of the "raw" stored intensities in the file (after
decompression if necessary), and not to the linearized scaled values.
_array_intensities.undefined_value specifies a value which
indicates that
the element value is not known. This may be due to data missing e.g. a
circular image stored in a square array, or where the data values are
flagged as missing e.g. behind a beam-stop.
_array_intensities.overload_value indicates the intensity value
at which and above, values are considered unreliable. This is usually due to
saturation.
"Array_intensities" Example
To define the characteristics of image_1 as linear with a gain
of 1.2, and an undefined value of 0, and a saturated (overloaded)
value of 65535, the following header section might be used:
One of the primary aims of imgCIF / CBF is to allow efficient storage, and
efficient reading and writing of data, so data compression is of great
interest. Despite the extra CPU over-heads it can very often be faster
to compress data prior to storage, as much smaller amounts of data need
to be written to disk, and disk I/O is relatively slow. However, optimum
data compression can result in complicated algorithms, and be highly
data specific.
In CBFlib version 0.1, Paul Ellis has coded two lossless compression
algorithms: canonical and packed.
Canonical-code compression
The canonical-code compression scheme encodes errors in two ways: directly or indirectly.
Errors are coded directly using a symbol corresponding to the error value. Errors
are coded indirectly using a symbol for the number of bits in the (signed) error,
followed by the error iteslf.
At the start of the compression, CBFLIB constructs a table containing a set of symbols,
one for each of the 2^n
direct codes from -(2^(n-1)) .. 2^(n-1)
-1, one for a stop code, and one for each of the maxbits
-n
indirect codes, where n
is chosen at compress time and maxbits
is the maximum number of bits in an error. CBFLIB then assigns to each symbol a
bit-code, using a shorter bit code for the more common symbols and a longer bit code
for the less common symbols. The bit-code lengths are calculated using a Huffman-type
algorithm, and the actual bit-codes are constructed using the canonical-code algorithm
described by Moffat, et al. (International Journal of High
Speed Electronics and Systems, Vol 8, No 1 (1997) 179-231).
The structure of the compressed data is:
Byte
Value
1 .. 8
Number of elements (64-bit little-endian number)
9 .. 16
Minimum element
17 .. 24
Maximum element
25 .. 32
Repeat length (currently unused)
33
Number of bits directly coded, n
34
Maximum number of bits encoded, maxbits
35 .. 35+2^n-1
Number of bits in each direct code
35+2^n
Number of bits in the stop code
35+2^n+1 .. 35+2^n+maxbits-n
Number of bits in each indirect code
35+2^n+maxbits-n+1 ..
Coded data
CCP4-style compression
The CCP4-style compression writes the errors in blocks . Each block begins with a
6-bit code. The number of errors in the block is 2^n,
where n
is the value in bits 0 .. 2.
Bits 3 .. 5 encode the number of bits in each error:
Value in bits 3 .. 5
Number of bits in each error
0
0
1
4
2
5
3
6
4
7
5
8
6
16
7
65
The structure of the compressed data is:
Byte
Value
1 .. 8
Number of elements (64-bit little-endian number)
9 .. 16
Minumum element (currently unused)
17 .. 24
Maximum element (currently unused)
25 .. 32
Repeat length (used, starting with version 0.2)
33 ..
Coded data
Additional Compression Schemes
In addition, Andy Hammersley has proposed two types of lossless data compression algorithms
for CBF version 1.0. In later versions other types including lossy algorithms
may be added.
The first algorithm is referred to as byte_offsets and has been
chosen for the following characteristics: it is very simple,
may be easily implemented, and can easily lead to faster reading and
writing to hard disk as the arithmetic complication is very small.
This algorithm can never achieve better than a factor of two compression
relative to 16-bit raw data, but for most diffraction data the
compression will indeed be very close to a factor 2.
The second algorithm is referred to as predictor_huffman and has
been chosen as it can achieve close to optimum compression on typical
diffraction patterns, with a relatively fast algorithm, whilst avoiding
patent problems and licensing fees. This will typically provide a
compression ratio between 2.5 and 3 on well exposed diffraction images,
and will achieve greater ratios on more weakly exposed data e.g.
4 - 5 on "thin phi-slicing" images. Normally, this would be a two
pass algorithm; 1st pass to define symbol probabilities; second pass
to entropy encode the data symbols. However, the Huffman algorithm
makes it possible to use a fixed table of symbol codes, so faster single
pass compression may be implemented with a small loss in compression
ratio. With very fast cpus this approach may provide faster hard disk
reading and writing than the "byte_offsets" algorithm owing to the
smaller amounts of data to be stored.
There are practical disadvantages to data compression: the value of
a particular element cannot be obtained without calculating the values of
all previous elements, and there is no simple relationship between element
position and stored bytes. If generally the whole array is required this
disadvantage does not apply. These disadvantages can be reduced by
compressing separately different regions of the arrays, which is an
approach available in TIFF, but this adds to the complexity reading and
writing images.
For simple predictor algorithms such as the byte_offsets
algorithm a simple alternative is an optional data item, which defines a
look-up table of element addresses, values, and byte positions within
the compressed data, and it is suggested that this approach is followed.
THE "BYTE_OFFSETS" ALGORITHM
The byte_offsets algorithm will typically
result in close to a factor of two reduction in data storage size
relative to typical 2-byte diffraction images. It should give similar
gains in disk I/O and network transfer. It also has the advantage that
integer values up to 32 bits (31 bits unsigned) may be stored efficiently
without the need for special over-load tables. It is a fixed algorithm
which does not need to calculate any image statistics, so is fast.
The algorithm works because of the following property of almost all
diffraction data and much other image data: The value of one element
tends to be close to the value of the adjacent elements, and the vast
majority of the differences use little of the full dynamic range.
However, noise in experimental data means that run-length encoding is
not useful (unless the image is separated into different bit-planes). If
a variable length code is used to store the differences, with the number
of bits used being inversely proportional to the probability of
occurrence, then compression ratios of 2.5 to 3.0 may be achieved.
However, the optimum encoding becomes dependent of the exact properties
of the image, and in particular on the noise. Here a lower compression
ratio is achieved, but the resulting algorithm is much simpler and more
robust.
The byte_offsets algorithm is the following:
The first element of the array is stored as a 4-byte signed
two's integer regardless of the raw array element type. The byte
order for this and all subsequent multi-byte integers is
little_endian regardless of the native computer architecture
i.e. the first byte is the least significant, and the last byte the
most. This value is the first reference value ("previous element") for
calculating pixel to pixel differences.
For all elements, including the first element, the value of the
previous element is subtracted to produce the difference. For the first
element on a line the value to subtract is the value of the first element
of the previous line. For the first element of a subsequent image (or
plane) the value to subtract is the value of the first element of the
previous image (or plane).
If the difference is less than +-127, then one byte is used to store
the difference as a signed two's complement integer, otherwise the byte
is set to -128 (80 in hex) and if the difference is less than
+-32767, then the next two bytes are used to store the difference as a
signed two byte two's complement integer, otherwise -32768 (8000 in hex,
which will be output as 00 80 in little-endian format) is written into
the two bytes and the following 4-bytes store the difference as a full
signed 32-bit two's complement integer.
The array element order follows the normal ordering as defined by
the _array_structure_list entries index, precedence
and direction.
It may be noted that one element value may require up to 7 bytes for
storage, however for almost all 16-bit experimental data the vast
majority of element values will be within +-127 units of the previous
element and so only require 1 byte for storage and a compression factor of
close to 2 is achieved.
This page was produced on 23 April 2001
by Herbert J. Bernstein (email:
yaya@bernstein-plus-sons.com),
based on the 14 November 1998 and 8 July 1998 versions and the
page produced by Andy Hammersley (E-mail: hammersley@esrf.fr).
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
./CBFlib-0.9.2.2/doc/cif_img_1.5.2_6May07.dic 0000644 0000765 0000765 00000712270 11603702115 016220 0 ustar yaya yaya ##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.5.2 #
# of 2007-05-07 #
# ################################################################### #
# # *** WARNING *** THIS IS A DRAFT FOR DISCUSSSION *** WARNING *** # #
# # SUBJECT TO CHANGE WITHOUT NOTICE # #
# # VERSIONS WILL BE POSTED AS cif_img_1.5_DDMMMYY_draft.html # #
# # SEND COMMENTS TO imgcif-l@iucr.org CITING THE VERSION # #
# ################################################################### #
# This draft edited by H. J. Bernstein #
# #
# by Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook #
# #
# This dictionary was adapted from format discussed at the imgCIF Workshop, #
# held at BNL Oct 1997 and the Crystallographic Binary File Format Draft #
# Proposal by Andrew Hammersley. The first DDL 2.1 Version was created by #
# John Westbrook. This version was drafted by Herbert J. Bernstein and #
# incorporates comments by I. David Brown, John Westbrook, Brian McMahon, #
# Bob Sweet, Paul Ellis, Harry Powell, Wilfred Li, Gotzon Madariaga, #
# Frances C. Bernstein, Chris Nielsen, Nicola Ashcroft and others. #
##############################################################################
data_cif_img.dic
_dictionary.title cif_img.dic
_dictionary.version 1.5.2
_dictionary.datablock_id cif_img.dic
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
# SUB_CATEGORY
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.gain
# _array_intensities.gain_esd
# _array_intensities.linearity
# _array_intensities.offset
# _array_intensities.scaling
# _array_intensities.overload
# _array_intensities.undefined_value
# _array_intensities.pixel_fast_bin_size
# _array_intensities.pixel_slow_bin_size
# _array_intensities.pixel_binning_method
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.compression_type_flag
# _array_structure.encoding_type
# _array_structure.id
#
# category ARRAY_STRUCTURE_LIST
#
# _array_structure_list.axis_set_id
# _array_structure_list.array_id
# _array_structure_list.dimension
# _array_structure_list.direction
# _array_structure_list.index
# _array_structure_list.precedence
#
# category ARRAY_STRUCTURE_LIST_AXIS
#
# _array_structure_list_axis.axis_id
# _array_structure_list_axis.axis_set_id
# _array_structure_list_axis.angle
# _array_structure_list_axis.angle_increment
# _array_structure_list_axis.displacement
# _array_structure_list_axis.fract_displacement
# _array_structure_list_axis.displacement_increment
# _array_structure_list_axis.fract_displacement_increment
# _array_structure_list_axis.angular_pitch
# _array_structure_list_axis.radial_pitch
# _array_structure_list_axis.reference_angle
# _array_structure_list_axis.reference_displacement
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.type
# _axis.system
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
#
# category DIFFRN_DATA_FRAME
#
# _diffrn_data_frame.array_id
# _diffrn_data_frame.binary_id
# _diffrn_data_frame.detector_element_id
# _diffrn_data_frame.id
# _diffrn_data_frame.details
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.id
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.axis_id
# _diffrn_detector_axis.detector_id
#
# category DIFFRN_DETECTOR_ELEMENT
#
# _diffrn_detector_element.center[1]
# _diffrn_detector_element.center[2]
# _diffrn_detector_element.id
# _diffrn_detector_element.detector_id
# _diffrn_detector_element.reference_center_fast
# _diffrn_detector_element.reference_center_slow
#
# category DIFFRN_MEASUREMENT
#
# _diffrn_measurement.diffrn_id
# _diffrn_measurement.details
# _diffrn_measurement.device
# _diffrn_measurement.device_details
# _diffrn_measurement.device_type
# _diffrn_measurement.id
# _diffrn_measurement.method
# _diffrn_measurement.number_of_axes
# _diffrn_measurement.specimen_support
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.axis_id
# _diffrn_measurement_axis.measurement_device
# _diffrn_measurement_axis.measurement_id
#
# category DIFFRN_RADIATION
#
# _diffrn_radiation.collimation
# _diffrn_radiation.diffrn_id
# _diffrn_radiation.div_x_source
# _diffrn_radiation.div_y_source
# _diffrn_radiation.div_x_y_source
# _diffrn_radiation.filter_edge'
# _diffrn_radiation.inhomogeneity
# _diffrn_radiation.monochromator
# _diffrn_radiation.polarisn_norm
# _diffrn_radiation.polarisn_ratio
# _diffrn_radiation.polarizn_source_norm
# _diffrn_radiation.polarizn_source_ratio
# _diffrn_radiation.probe
# _diffrn_radiation.type
# _diffrn_radiation.xray_symbol
# _diffrn_radiation.wavelength_id
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.date_end
# _diffrn_scan.date_start
# _diffrn_scan.integration_time
# _diffrn_scan.frame_id_start
# _diffrn_scan.frame_id_end
# _diffrn_scan.frames
#
# category DIFFRN_SCAN_AXIS
#
# _diffrn_scan_axis.axis_id
# _diffrn_scan_axis.angle_start
# _diffrn_scan_axis.angle_range
# _diffrn_scan_axis.angle_increment
# _diffrn_scan_axis.angle_rstrt_incr
# _diffrn_scan_axis.displacement_start
# _diffrn_scan_axis.displacement_range
# _diffrn_scan_axis.displacement_increment
# _diffrn_scan_axis.displacement_rstrt_incr
# _diffrn_scan_axis.reference_angle
# _diffrn_scan_axis.reference_displacement
# _diffrn_scan_axis.scan_id
#
# category DIFFRN_SCAN_FRAME
#
# _diffrn_scan_frame.date
# _diffrn_scan_frame.frame_id
# _diffrn_scan_frame.frame_number
# _diffrn_scan_frame.integration_time
# _diffrn_scan_frame.scan_id
#
# category DIFFRN_SCAN_FRAME_AXIS
#
# _diffrn_scan_frame_axis.axis_id
# _diffrn_scan_frame_axis.angle
# _diffrn_scan_frame_axis.angle_increment
# _diffrn_scan_frame_axis.angle_rstrt_incr
# _diffrn_scan_frame_axis.displacement
# _diffrn_scan_frame_axis.displacement_increment
# _diffrn_scan_frame_axis.displacement_rstrt_incr
# _diffrn_scan_frame_axis.reference_angle
# _diffrn_scan_frame_axis.reference_displacement
# _diffrn_scan_frame_axis.frame_id
#
# categor MAP
#
# _map.details
# _map.diffrn_id
# _map.entry_id
# _map.id
#
# categor MAP_SEGMENT
#
# _map_segment.array_id
# _map_segment.binary_id
# _map_segment.mask_array_id
# _map_segment.mask_binary_id
# _map_segment.id
# _map_segment.map_id
# _map_segment.details
#
# ***DEPRECATED*** data items
#
# _diffrn_detector_axis.id
# _diffrn_measurement_axis.id
#
# ***DEPRECATED*** category DIFFRN_FRAME_DATA
#
# _diffrn_frame_data.array_id
# _diffrn_frame_data.binary_id
# _diffrn_frame_data.detector_element_id
# _diffrn_frame_data.id
# _diffrn_frame_data.details
#
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
##################
## SUB_CATEGORY ##
##################
loop_
_sub_category.id
_sub_category.description
'matrix'
; The collection of elements of a matrix.
;
'vector'
; The collection of elements of a vector.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
; Data items in the ARRAY_DATA category are the containers for
the array data items described in the category ARRAY_STRUCTURE.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and is
presented as hexadecimal data. The first character 'H' on the
data lines means hexadecimal. It could have been 'O' for octal
or 'D' for decimal. The second character on the line shows
the number of bytes in each word (in this case '4'), which then
requires eight hexadecimal digits per word. The third character
gives the order of octets within a word, in this case '<'
for the ordering 4321 (i.e. 'big-endian'). Alternatively, the
character '>' could have been used for the ordering 1234
(i.e. 'little-endian'). The block has a 'message digest'
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 2
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id, should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-ID, the value of _array_data.binary_id
should be equal to the value given for X-Binary-ID.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
'\n--CIF-BINARY-FORMAT-SECTION--' (including the
required initial '\n--').
The Content-Type may be any of the discrete types permitted
in RFC 2045; 'application/octet-stream' is recommended.
If an octet stream was compressed, the compression should
be specified by the parameter
'conversions="X-CBF_PACKED"'
or the parameter
'conversions="X-CBF_CANONICAL"'
or the parameter
'conversions="X-CBF_BYTE_OFFSET"'
If the parameter
'conversions="X-CBF_PACKED"'
is given it may be further modified with the parameters
'"uncorrelated_sections"'
or
'"flat"'
If the '"uncorrelated_sections"' parameter is
given, each section will be compressed without using
the prior section for averaging.
If the '"flat"' parameter is given, each the
image will be treated as one long row.
The Content-Transfer-Encoding may be 'BASE64',
'Quoted-Printable', 'X-BASE8', 'X-BASE10',
'X-BASE16' or 'X-BASE32K', for an imgCIF or 'BINARY'
for a CBF. The octal, decimal and hexadecimal transfer
encodings are provided for convenience in debugging and
are not recommended for archiving and data interchange.
In a CIF, one of the parameters 'charset=us-ascii',
'charset=utf-8' or 'charset=utf-16' may be used on the
Content-Transfer-Encoding to specify the character set
used for the external presentation of the encoded data.
If no charset parameter is given, the character set of
the enclosing CIF is assumed. In any case, if a BOM
flag is detected (FE FF for big-endian UTF-16, FF FE for
little-endian UTF-16 or EF BB BF for UTF-8) is detected,
the indicated charset will be assumed until the end of the
encoded data or the detection of a different BOM. The
charset of the Content-Transfer-Encoding is not the character
set of the encoded data, only the character set of the
presentation of the encoded data and should be respecified
for each distinct STAR string.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In an imgCIF file,
the encoded binary data ends with the terminating boundary
delimiter '\n--CIF-BINARY-FORMAT-SECTION----'
in the currently effective charset or with the '\n; '
that terminates the STAR string.
In a CBF, the raw binary data begins after an empty line
terminating the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of
the message size or in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. An adjustment is made for
the deprecated binary formats in which eight bytes of binary
header are used for the compression type. In this case,
the eight bytes used for the compression type are subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is 'unsigned 32-bit integer'.
An MD5 message digest may, optionally, be used. The 'RSA Data
Security, Inc. MD5 Message-Digest Algorithm' should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is 'X-BASE8', 'X-BASE10' or
'X-BASE16', the data are presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ('big-
endian') or 1234... ('little-endian'). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as '==' for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is 'H', 'O' or 'D' for hexadecimal, octal or
decimal, n is the number of octets per word and d is '<'
or '>' for the '...4321' and '1234...' octet orderings,
respectively. The '==' padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hexadecimal, octal and decimal formats only,
comments beginning with '#' are permitted to improve
readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three: c1, c2, c3. The resulting 24 bits
are broken into four six-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order four bits of the second octet [(c1 & 3)<<4 | (c2>>4)],
then the bottom four bits of the second octet followed by the
high-order two bits of the last octet [(c2 & 15)<<2 | (c3>>6)],
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
With short groups of octets padded on the right with one '='
if c3 is missing, and with '==' if both c2 and c3 are missing.
X-BASE32K encoding is similar to BASE64 encoding, except that
sets of 15 octets are encoded as sets of 8 16-bit unicode
characters, by breaking the 120 bits into 8 15-bit quantities.
256 is added to each 15 bit quantity to bring it into a
printable uncode range. When encoding, zero padding is used
to fill out the last 15 bit quantity. If 8 or more bits of
padding are used, a single equals sign (hexadecimal 003D) is
appended. Embedded whitespace and newlines are introduced
to produce lines of no more than 80 characters each. On
decoding, all printable ascii characters and ascii whitespace
characters are ignored except for any trailing equals signs.
The number of trailing equals signs indicated the number of
trailing octets to be trimmed from the end of the decoded data.
(see Georgi Darakev, Vassil Litchev, Kostadin Z. Mitev, Herbert
J. Bernstein, 'Efficient Support of Binary Data in the XML
Implementation of the NeXus File Format',absract W0165,
ACA Summer Meeting, Honolulu, HI, July 2006).
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32...38,
42, 48...57, 59, 60, 62, 64...126 and the octet is not a ';'
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
'wrapped' with a terminating '=' (i.e. the MIME conventions
for an implicit line terminator are never used).
The "X-Binary-Element-Byte-Order" can specify either
'"BIG_ENDIAN"' or '"LITTLE_ENDIAN"' byte order of the imaage
data. Only LITTLE_ENDIAN is recommended. Processors
may treat BIG_ENDIAN as a warning of data that can
only be processed by special software.
The "X-Binary-Number-of-Elements" specifies the number of
elements (not the number of octets) in the decompressed, decoded
image.
The optional "X-Binary-Size-Fastest-Dimension" specifies the
number of elements (not the number of octets) in one row of the
fastest changing dimension of the binary data array. This
information must be in the MIME header for proper operation of
some of the decompression algorithms.
The optional "X-Binary-Size-Second-Dimension" specifies the
number of elements (not the number of octets) in one column of
the second-fastest changing dimension of the binary data array.
This information must be in the MIME header for proper operation
of some of the decompression algorithms.
The optional "X-Binary-Size-Third-Dimension" specifies the number
of sections for the third-fastest changing dimension of the
binary data array.
The optional "X-Binary-Size-Padding" specifies the size in
octets of an optional padding after the binary array data and
before the closing flags for a binary section.
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
; Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.index
_item_description.description
; This item is a pointer to _array_structure_list.index in
the ARRAY_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
; The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
; Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
_array_intensities.gain. If raw, uncorrected values
are presented (e.g. for calibration experiments), the
value of _array_intensities.linearity will be 'raw'
and _array_intensities.gain will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.overload
_array_intensities.undefined_value
_array_intensities.pixel_fast_bin_size
_array_intensities.pixel_slow_bin_size
_array_intensities.pixel_binning_method
image_1 linear 1.2 655535 0 2 2 hardware
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
; Detector 'gain'. The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
; The estimated standard deviation in detector 'gain'.
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
; The intensity linearity scaling method used to convert
from the raw intensity to the stored element value:
'linear' is linear.
'offset' means that the value defined by
_array_intensities.offset should be added to each
element value.
'scaling' means that the value defined by
_array_intensities.scaling should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by _array_intensities.scaling is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
'logarithmic_scaled' means that the logarithm base 10 of
raw intensities multiplied by _array_intensities.scaling
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and calculating 10
to the power of this number.
'raw' means that the data are a set of raw values straight
from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
; The value defined by _array_intensities.offset should
be added to each element value.
;
'scaling'
; The value defined by _array_intensities.scaling should be
multiplied with each element value.
;
'scaling_offset'
; The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
; The square root of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
;
'logarithmic_scaled'
; The logarithm base 10 of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
_array_intensities.scaling and calculating 10 to the
power of this number.
;
'raw'
; The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data-fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
; Offset value to add to array element values in the manner
described by the item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
; The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.pixel_fast_bin_size
_item_description.description
; The value of _array_intensities.pixel_fast_bin_size specifies
the number of pixels that compose one element in the direction
of the most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_fast_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_slow_bin_size
_item_description.description
; The value of _array_intensities.pixel_slow_bin_size specifies
the number of pixels that compose one element in the direction
of the second most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_slow_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_binning_method
_item_description.description
; The value of _array_intensities.pixel_binning_method specifies
the method used to derive array elements from multiple pixels.
;
_item.name '_array_intensities.pixel_binning_method'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'hardware'
; The element intensities were derived from the raw data of one
or more pixels by used of hardware in the detector, e.g. by use
of shift registers in a CCD to combine pixels into super-pixels.
;
'software'
; The element intensities were derived from the raw data of more
than one pixel by use of software.
;
'combined'
; The element intensities were derived from the raw data of more
than one pixel by use of both hardware and software, as when
hardware binning is used in one direction and software in the
other.
;
'none'
; In the both directions, the data has not been binned. The
number of pixels is equal to the number of elements.
When the value of _array_intensities.pixel_binning_method is
'none' the values of _array_intensities.pixel_fast_bin_size
and _array_intensities.pixel_slow_bin_size both must be 1.
;
'unspecified'
; The method used to derive element intensities is not specified.
;
_item_default.value 'unspecified'
save_
save__array_intensities.scaling
_item_description.description
; Multiplicative scaling value to be applied to array data
in the manner described by item
_array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.undefined_value
_item_description.description
; A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
; Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data that may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
_category_key.name '_array_structure.id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
; The order of bytes for integer values which require more
than 1 byte.
(IBM-PC's and compatibles and DEC VAXs use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. DEC Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
; The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
; The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
; Type of data-compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'byte_offset'
; Using the 'byte_offset' compression scheme as per A. Hammersley
and the CBFlib manual, section 3.3.3
;
'canonical'
; Using the 'canonical' compression scheme (International Tables
for Crystallography Volume G, Section 5.6.3.1) and CBFlib
manual section 3.3.1
;
'none'
; Data are stored in normal format as defined by
_array_structure.encoding_type and
_array_structure.byte_order.
;
'packed'
; Using the 'packed' compression scheme, a CCP4-style packing
as per J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
'packed_v2'
; Using the 'packed' compression scheme, version 2, as per
J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
save_
save__array_structure.compression_type_flag
_item_description.description
; Flags modifying the type of data-compression method used to
compress the arraydata.
;
_item.name '_array_structure.compression_type_flag'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'uncorrelated_sections'
; When applying packed or packed_v2 compression on an array with
uncorrelated sections, do not average in points from the prior
section.
;
'flat'
; When applying packed or packed_v2 compression on an array with
treat the entire image as a single line set the maximum number
of bits for an offset to 65 bits.
The flag is included for compatibility with software prior to
CBFlib_0.7.7, and should not be used for new data sets.
;
save_
save__array_structure.encoding_type
_item_description.description
; Data encoding of a single element of array data.
In several cases, the IEEE format is referenced.
See IEEE Standard 754-1985 (IEEE, 1985).
Ref: IEEE (1985). IEEE Standard for Binary Floating-Point
Arithmetic. ANSI/IEEE Std 754-1985. New York: Institute of
Electrical and Electronics Engineers.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure yes
'_array_data.array_id' array_data yes
'_array_structure_list.array_id' array_structure_list yes
'_array_intensities.array_id' array_intensities yes
'_diffrn_data_frame.array_id' diffrn_data_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
; Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left to right (increasing) in the
first dimension and bottom to top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differs
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the 'poise' of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
; The number of elements stored in the array structure in this
dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
; Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
; Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
; Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
; Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
; Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
; Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets of axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axes: one for the angular
direction and one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes in the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
; The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to
_array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list_axis.angle
_item_description.description
; The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified for this case.
See _array_structure_list_axis.angular_pitch.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement
_item_description.description
; The setting of the specified axis as a decimal fraction of
the axis unit vector for the first data point of the array
index with the corresponding value of
_array_structure_list.axis_set_id.
If the index is specified as 'increasing', this will be the
centre of the pixel with index value 1. If the index is
specified as 'decreasing', this will be the centre of the
pixel with maximum index value.
;
_item.name '_array_structure_list_axis.fract_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis as a decimal fraction of the
axis unit vector.
;
_item.name
'_array_structure_list_axis.fract_displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
; The pixel-centre-to-pixel-centre distance for a one-step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans
or for uncoupled angular scans at a constant radius
(cylindrical scans) and should not be specified for cases
in which the angle between pixels (rather than the distance
between pixels) is uniform.
See _array_structure_list_axis.angle_increment.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
; The radial distance from one 'cylinder' of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of _array_structure_list_axis.displacement_increment.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.reference_angle
_item_description.description
; The value of _array_structure_list_axis.reference_angle
specifies the setting of the angle of this axis used for
determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the
value of _array_structure_list.angle.
;
_item.name '_array_structure_list_axis.reference_angle'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.reference_displacement
_item_description.description
; The value of _array_structure_list_axis.reference_displacement
specifies the setting of the displacement of this axis used
for determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the value
of _array_structure_list.displacement.
;
_item.name '_array_structure_list_axis.reference_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
########
# AXIS #
########
save_AXIS
_category.description
; Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection or the axes defining the
coordinate system of an image.
The location of each axis is specified by two vectors: the axis
itself, given by a unit vector in the direction of the axis, and
an offset to the base of the unit vector.
The vectors defining an axis are referenced to an appropriate
coordinate system. The axis vector, itself, is a dimensionless
unit vector. Where meaningful, the offset vector is given in
millimetres. In coordinate systems not measured in metres,
the offset is not specified and is taken as zero.
The available coordinate systems are:
The imgCIF standard laboratory coordinate system
The direct lattice (fractional atomic coordinates)
The orthogonal Cartesian coordinate system (real space)
The reciprocal lattice
An abstract orthogonal Cartesian coordinate frame
For consistency in this discussion, we call the three coordinate
system axes X, Y and Z. This is appropriate for the imgCIF
standard laboratory coordinate system, and last two Cartesian
coordinate systems, but for the direct lattice, X corresponds
to a, Y to b and Z to c, while for the reciprocal lattice,
X corresponds to a*, Y to b* and Z to c*.
For purposes of visualization, all the coordinate systems are
taken as right-handed, i.e., using the convention that the extended
thumb of a right hand could point along the first (X) axis, the
straightened pointer finger could point along the second (Y) axis
and the middle finger folded inward could point along the third (Z)
axis.
THE IMGCIF STANDARD LABORATORY COORDINATE SYSTEM
The imgCIF standard laboratory coordinate system is a right-handed
orthogonal coordinate similar to the MOSFLM coordinate system,
but imgCIF puts Z along the X-ray beam, rather than putting X along the
X-ray beam as in MOSFLM.
The vectors for the imgCIF standard laboratory coordinate system
form a right-handed Cartesian coordinate system with its origin
in the sample or specimen. The origin of the axis system should,
if possible, be defined in terms of mechanically stable axes to be
in the sample and in the beam. If the sample goniometer or other
sample positioner has two axes the intersection which defines a
unique point at which the sample should be mounted to be bathed
by the beam, that will be the origin of the axis system. If no such
point is defined, then the midpoint of the line of intersection
between the sample and the center of the beam will define the origin.
For this definition the sample positioning system will be set at
its initial reference position for the experiment.
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer or
sample positioning system if the sample positioning system has an axis that
intersects the origin and which form an angle of more than 22.5 degrees
with the beam axis.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
If the conditions for the X-axis can be met, the coordinate system
will be based on the goniometer or other sample positioning system
and the beam and not on the orientation of the detector, gravity etc.
The vectors necessary to specify all other axes are given by sets of
three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right-handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to but significantly
different from the choice in MOSFLM (Leslie & Powell, 2004). In MOSFLM,
X is along the X-ray beam (the CBF/imgCIF Z axis) and Z is along the
rotation axis.
In some experimental techniques, there is no goniometer or the principal
axis of the goniometer is at a small acute angle with respect to
the source axis. In such cases, other reference axes are needed
to define a useful coordinate system. The order of priority in
defining directions in such cases is to use the detector, then
gravity, then north.
If the X-axis cannot be defined as above, then the
direction (not the origin) of the X-axis should be parallel to the axis
of the primary detector element corresponding to the most rapidly
varying dimension of that detector element's data array, with its
positive sense corresponding to increasing values of the index for
that dimension. If the detector is such that such a direction cannot
be defined (as with a point detector) or that direction forms an
angle of less than 22.5 degrees with respect to the source axis, then
the X-axis should be chosen so that if the Y-axis is chosen
in the direction of gravity, and the Z-axis is chosen to be along
the source axis, a right-handed orthogonal coordinate system is chosen.
In the case of a vertical source axis, as a last resort, the
X-axis should be chosen to point North.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam centre.
The location of the beam centre on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected millimetres from
the (0,0) corner of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, it is necessary to
specify the location of the beam centre on the detector in terms
of the origin of the detector, which is, of course, not coincident
with the centre of the sample.
The unit cell, reciprocal cell and crystallographic orthogonal
Cartesian coordinate system are defined by the CELL and the matrices
in the ATOM_SITES category.
THE DIRECT LATTICE (FRACTIONAL COORDINATES)
The direct lattice coordinate system is a system of fractional
coordinates aligned to the crystal, rather than to the laboratory.
This is a natural coordinate system for maps and atomic coordinates.
It is the simplest coordinate system in which to apply symmetry.
The axes are determined by the cell edges, and are not necessarily
othogonal. This coordinate system is not uniquely defined and
depends on the cell parameters in the CELL category and the
settings chosen to index the crystal.
Molecules in a crystal studied by X-ray diffracraction are organized
into a repeating regular array of unit cells. Each unit cell is defined
by three vectors, a, b and c. To quote from Drenth,
"The choice of the unit cell is not unique and therefore, guidelines
have been established for selecting the standard basis vectors and
the origin. They are based on symmetry and metric considerations:
"(1) The axial system should be right handed.
(2) The basis vectors should coincide as much as possible with
directions of highest symmetry."
(3) The cell taken should be the smallest one that satisfies
condition (2)
(4) Of all the lattice vectors, none is shorter than a.
(5) Of those not directed along a, none is shorter than b.
(6) Of those not lying in the ab plane, none is shorter than c.
(7) The three angles between the basis vectors a, b and c are
either all acute (<90 degrees) or all obtuse (>=90 degrees)."
These rules do not produce a unique result that is stable under
the assumption of experimental errors, and the the resulting cell
may not be primitive.
In this coordinate system, the vector (.5, .5, .5) is in the middle
of the given unit cell.
Grid coordinates are an important variation on fractional coordinates
used when working with maps. In imgCIF, the conversion from
fractional to grid coordinates is implicit in the array indexing
specified by _array_structure_list.dimension. Note that this
implicit grid-coordinate scheme is 1-based, not zero-based, i.e.
the origin of the cell for axes along the cell edges with no
specified _array_structure_list_axis.displacement will have
grid coordinates of (1,1,1), i.e. array indices of (1,1,1).
THE ORTHOGONAL CARTESIAN COORDINATE SYSTEM (REAL SPACE)
The orthogonal Cartesian coordinate system is a transformation of
the direct lattice to the actual physical coordinates of atoms in
space. It is similar to the laboratory coordinate system, but
is anchored to and moves with the crystal, rather than being
schored to the laboratory. The transformation from fractional
to orthogonal cartesian coordinates is given by the
_atom_sites.Cartn_transf_matrix[i][j] and
_atom_sites.Cartn_transf_vector[i]
tags. A common choice for the matrix of the transformation is
given in the 1992 PDB format document
| a b cos(g) c cos(b) |
| 0 b sin(g) c (cos(a) - cos(b)cos(g))/sin(g) |
| 0 0 V/(a b sin(g)) |
This is a convenient coordinate system in which to do fitting
of models to maps and in which to understand the chemistry of
a molecule.
THE RECIPROCAL LATTICE
The reciprocal lattice coordinate system is used for diffraction
intensitities. It is based on the reciprocal cell, the dual of the cell,
in which reciprocal cell edges are derived from direct cell faces:
a* = bc sin(a)/V b* = ac sin(b)/V c* = ab sin(g)/V
cos(a*) = (cos(b) cos(g) - cos(a))/(sin(b) sin(g))
cos(b*) = (cos(g) cos(g) - cos(b) )/(sin(a) sin(g))
cos(g*) = (cos(a) cos(b) - cos(g))/(sin(a) sin(b))
V = abc SQRT (1 - cos(a)2 - cos(b)2 - cos(g)2
+ 2 cos(a) cos(b) cos(g) )
In this form the dimensions of the reciprocal lattice are in reciprocal
\%Angstroms (\%A^-1). A dimensionless form can be obtained by
multiplying by the wavelength. Reflections are commonly indexed against
this coordinate system as (h, k, l) triples.
References:
Drenth, J., "Introduction to basic crystallography." chapter
2.1 in Rossmann, M. G. and Arnold, E. "Crystallography of
biological macromolecules", Volume F of the IUCr's "International
tables for crystallography", Kluwer, Dordrecht 2001, pp 44 -- 63
Leslie, A. G. W. and Powell, H. (2004). MOSFLM v6.11.
MRC Laboratory of Molecular Biology, Hills Road, Cambridge, England.
http://www.CCP4.ac.uk/dist/X-windows/Mosflm/.
Stout, G. H. and Jensen, L. H., "X-ray structure determination",
2nd ed., Wiley, New York, 1989, 453 pp.
__, "PROTEIN DATA BANK ATOMIC COORDINATE AND BIBLIOGRAPHIC ENTRY
FORMAT DESCRIPTION," Brookhaven National Laboratory, February 1992.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
This example shows the axis specification of the axes of a kappa-
geometry goniometer [see Stout, G. H. & Jensen, L. H. (1989). X-ray
structure determination. A practical
guide, 2nd ed. p. 134. New York: Wiley Interscience].
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X axis. The next innermost axis, kappa,
is at a 50 degree angle to the X axis, pointed away from the source.
The innermost axis, phi, aligns with the X axis when omega and
phi are at their zero points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
X' = (T-omega) (T-kappa) (T-phi) X
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 -
This example shows the axis specification of the axes of a
detector, source and gravity. The order has been changed as a
reminder that the ordering of presentation of tokens is not
significant. The centre of rotation of the detector has been taken
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 3 -
This example show the axis specification of the axes for a map,
using fractional coordinates. Each cell edge has been divided
into a grid of 50 divisions in the ARRAY_STRUCTURE_LIST_AXIS
category. The map is using only the first octant of the grid
in the ARRAY_STRUCTURE_LIST category.
The fastest changing axis is the gris along A, then along B,
and the slowest is along C.
The map sampling is being done in the middle of each grid
division
;
;
loop_
_axis.id
_axis.system
_axis.vector[1] _axis.vector[2] _axis.vector[3]
CELL_A_AXIS fractional 1 0 0
CELL_B_AXIS fractional 0 1 0
CELL_C_AXIS fractional 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing CELL_A_AXIS
MAP 1 25 2 increasing CELL_B_AXIS
MAP 1 25 3 increasing CELL_C_AXIS
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.fract_displacement
_array_structure_list_axis.fract_displacement_increment
CELL_A_AXIS 0.01 0.02
CELL_B_AXIS 0.01 0.02
CELL_C_AXIS 0.01 0.02
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 4 -
This example show the axis specification of the axes for a map,
this time as orthogonal Angstroms, using the same coordinate system
as for the atomic coordinates. The map is sampling every 1.5
Angstroms (1.5e-7 millimeters) in a map segment 37.5 Angstroms on
a side.
;
;
loop_
_axis.id
_axis.system
_axis.vector[1] _axis.vector[2] _axis.vector[3]
X orthogonal 1 0 0
Y orthogonal 0 1 0
Z orthogonal 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing X
MAP 2 25 2 increasing Y
MAP 3 25 3 increasing Z
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
X 7.5e-8 1.5e-7
Y 7.5e-8 1.5e-7
Z 7.5e-8 1.5e-7
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.depends_on specifies the next outermost
axis upon which this axis depends.
This item is a pointer to _axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.equipment specifies the type of
equipment using the axis: 'goniometer', 'detector',
'gravity', 'source' or 'general'.
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.system
_item_description.description
; The value of _axis.system specifies the coordinate
system used to define the axis: 'laboratory', 'direct', 'orthogonal',
'reciprocal' or 'abstract'.
;
_item.name '_axis.system'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value laboratory
loop_
_item_enumeration.value
_item_enumeration.detail
laboratory
; the axis is referenced to the imgCIF standard laboratory Cartesian
coordinate system
;
direct
; the axis is referenced to the direct lattice
;
orthogonal
; the axis is referenced to the cell Cartesian orthogonal coordinates
;
reciprocal
; the axis is referenced to the reciprocal lattice
;
abstract
; the axis is referenced to abstract Cartesian cooridinate system
;
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: 'rotation' or 'translation' (or 'general' when
the type is not relevant, as for gravity).
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
; Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element are
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id.
;
;
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.id
_item_description.description
; The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
save_
save__diffrn_data_frame.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
This is an appropriate location in which to record
information from vendor headers as presented in those
headers, but it should never be used as a substitute
for providing the fully parsed information within
the appropriate imgCIF/CBF categories.
;
_item.name '_diffrn_data_frame.details'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_frame_data.details'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.4
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
;
HEADER_BYTES = 512;
DIM = 2;
BYTE_ORDER = big_endian;
TYPE = unsigned_short;
SIZE1 = 3072;
SIZE2 = 3072;
PIXEL_SIZE = 0.102588;
BIN = 2x2;
DETECTOR_SN = 901;
TIME = 29.945155;
DISTANCE = 200.000000;
PHI = 85.000000;
OSC_START = 85.000000;
OSC_RANGE = 1.000000;
WAVELENGTH = 0.979381;
BEAM_CENTER_X = 157.500000;
BEAM_CENTER_Y = 157.500000;
PIXEL SIZE = 0.102588;
OSCILLATION RANGE = 1;
EXPOSURE TIME = 29.9452;
TWO THETA = 0;
BEAM CENTRE = 157.5 157.5;
;
; Example of header information extracted from an ADSC Quantum
315 detector header by CBFlib_0.7.6. Image provided by Chris
Nielsen of ADSC from a data collection at SSRL beamline 1-5.
;
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'slow mode'
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detector(s) used to
measure the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
; The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of
_diffrn_detector.diffrn_id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
; The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id.
The word 'positioner' is a general term used in
instrumentation design for devices that are used to change
the positions of portions of apparatus by linear
translation, rotation or combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
; Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named _diffrn_detector_axis.id
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
; Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, giving more detailed information
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
is preferable to simply providing the centre of the
detector element.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square, in the pattern
1 2
*
3 4
Note that the beam centre is slightly displaced from each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4.
;
;
loop_
_diffrn_detector_element.detector_id
_diffrn_detector_element.id
_diffrn_detector_element.center[1]
_diffrn_detector_element.center[2]
d1 d1_ccd_1 201.5 -1.5
d1 d1_ccd_2 -1.8 -1.5
d1 d1_ccd_3 201.6 201.4
d1 d1_ccd_4 -1.7 201.5
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.center[1]
_item_description.description
; The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
; The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.id
_item_description.description
; The value of _diffrn_detector_element.id must uniquely
identify each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
; This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_element.reference_center_fast
_item_description.description
; The value of _diffrn_detector_element.reference_center_fast is
the fast index axis beam center position relative to the detector
element face in millimetres along that from the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value given whould be
representive of the beam center as determined from the ensemble
of settings.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
;
_item.name '_diffrn_detector_element.reference_center_fast'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.reference_center_slow
_item_description.description
; The value of _diffrn_detector_element.reference_center_slow is
the slow index axis beam center position relative to the detector
element face in millimetres along that from the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value givien whould be
representive of the beam center as determined from the ensemble
of settings.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
;
_item.name '_diffrn_detector_element.reference_center_slow'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
_item_units.code millimetres
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the
diffraction data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model X'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector
angle 22.5 degrees
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support
and orient the specimen.
If the value of _diffrn_measurement.device is not given,
it is implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to
measure the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'home-made'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity
measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
; The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during the collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
; The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id.
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
; Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
; This data item is a pointer to _diffrn_measurement.device
in the DIFFRN_MEASUREMENT category.
;
_item.name
'_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_type.code text
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named _diffrn_measurement_axis.id,
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
####################
# DIFFRN_RADIATION #
####################
save_DIFFRN_RADIATION
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used for measuring diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
_category_key.name '_diffrn_radiation.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions of
photons in the XZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions
of photons in the YZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation degrees^2^ between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
direction of each photon in XZ plane times the deviations
of the direction of the same photon in the YZ plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons, this value is specified in
milliradians^2^, in which case a conversion would be needed.
To go from a value in milliradians^2^ to a value in
degrees^2^, multiply by 0.180^2^ and divide by \p^2^.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in \%Angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a
monochromator crystal is used, the material and the
indices of the Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarization ratio of the diffraction beam incident on the
crystal. This is the ratio of the perpendicularly polarized to
the parallel polarized component of the radiation. The
perpendicular component forms an angle of
_diffrn_radiation.polarisn_norm to the normal to the
diffraction plane of the sample (i.e. the plane containing
the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between
the normal to the polarization plane and the laboratory Y
axis as defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monochromater.
This differs from the value of
_diffrn_radiation.polarisn_norm
in that _diffrn_radiation.polarisn_norm refers to
polarization relative to the diffraction plane rather than
to the laboratory axis system.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane should be taken
as the XZ plane and the angle as 0.
See _diffrn_radiation.polarizn_source_ratio.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared)
of the electric vector in the plane of the normal to the
plane of polarization.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane is to be taken
as the XZ plane and the normal is parallel to the Y axis.
Thus, if there was complete polarization in the plane of
polarization, the value of
_diffrn_radiation.polarizn_source_ratio would be 1, and
for an unpolarized beam
_diffrn_radiation.polarizn_source_ratio would have a
value of 0.
If the X axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of 'MONOCHROMATOR' in the Denzo glossary, and values of near
1 should be expected for a bending-magnet source. However,
if the X axis were perpendicular to the polarization plane
(not a common choice), then the Denzo value would be the
negative of _diffrn_radiation.polarizn_source_ratio.
See http://www.hkl-xray.com for information on Denzo and
Otwinowski & Minor (1997).
This differs both in the choice of ratio and choice of
orientation from _diffrn_radiation.polarisn_ratio, which,
unlike _diffrn_radiation.polarizn_source_ratio, is
unbounded.
Reference: Otwinowski, Z. & Minor, W. (1997). 'Processing of
X-ray diffraction data collected in oscillation mode.' Methods
Enzymol. 276, 307-326.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly
recommended that this be given so that the
probe radiation is clearly specified.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'X-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for the probe
radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to
_diffrn_radiation_wavelength.id in the
DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.category_id diffrn_radiation
_item.mandatory_code yes
_item_type.code code
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
; This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
;
_category.id diffrn_refln
_category.mandatory_code no
_category_key.name '_diffrn_refln.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
; This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
; Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
_category_key.name '_diffrn_scan.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. In this example, three rotation axes and one translation axis
at nonzero values are specified, with one axis stepping. There is no
reason why more axes could not have been specified to step. Range
information has been specified, but note that it can be calculated from
the number of frames and the increment, so the data item
_diffrn_scan_axis.angle_range could be dropped.
Both the sweep data and the data for a single frame are specified.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
_diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
_diffrn_scan_frame.integration_time and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustments are made to
scan times and nonlinear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.angle_increment
_diffrn_scan_frame_axis.displacement
_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
; Example 2 - a more extensive example (R. M. Sweet, P. J. Ellis &
H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the goniometer.
This leads to a choice: either the axes of
the detector are defined at the origin, and then a Z setting of -240
is entered, or the axes are defined with the necessary Z offset.
In this case, the setting is used and the offset is left as zero.
This axis is called DETECTOR_Z.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm X 0.150mm, the centre of the first pixel is at (0.075,
0.075) in this coordinate system.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
; Example 3 - Example 2 revised for a spiral scan (R. M. Sweet,
P. J. Ellis & H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the
goniometer, as in Example 2 above, but in this example the
image plate is scanned in a spiral pattern from the outside edge in.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. The rotation axis is called ELEMENT_ROT and the
radial axis is called ELEMENT_RAD. A 150 micrometre radial pitch
and a 75 micrometre 'constant velocity' angular pitch are assumed.
Indexing is carried out first on the rotation axis and the radial axis
is made to be dependent on it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.angle
_array_structure_list_axis.displacement
_array_structure_list_axis.angular_pitch
_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
; The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
; The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
; Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
_diffrn_scan_frame.integration_time, even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
; The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frame_id_end
_item_description.description
; The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frames
_item_description.description
; The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
; Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
; The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.angle_start
_item_description.description
; The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
; The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
; The increment for each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_increment. The
sum of the values of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
; The increment after each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_rstrt_incr. The
sum of the values of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment
and _diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.angle for this
next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
; The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
; The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_increment.
The sum of the values of
_diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_rstrt_incr.
The sum of the values of
_diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.displacement
for this next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_angle.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_angle will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_angle (e.g.
the mean).
If not specified, the value defaults to zero.
;
_item.name '_diffrn_scan_axis.reference_angle'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_displacement.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_displacement will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_displacement (e.g.
the mean).
If not specified, the value defaults to to the value of
_diffrn_scan_axis.displacement.
;
_item.name '_diffrn_scan_axis.reference_displacement'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
; Data items in the DIFFRN_SCAN_FRAME category describe
the relationships of particular frames to scans.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
; The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame.frame_number
_item_description.description
; The value of this data item is the number of the frame
within the scan, starting with 1. It is not necessarily
the same as the value of _diffrn_scan_frame.frame_id,
but it may be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
; The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of _diffrn_scan.integration_time.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
; Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the
settings of axes for particular frames. Unspecified axes are
assumed to be at their zero points. If, for any given frame,
nonzero values apply for any of the data items in this category,
those values should be given explicitly in this category and not
simply inferred from values in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
; The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
; The increment for this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
; The increment after this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment and
_diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.angle for this next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.displacement for this next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be zero.
;
_item.name '_diffrn_scan_frame_axis.reference_angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be equal to
_diffrn_scan_frame_axis.displacement.
;
_item.name '_diffrn_scan_frame_axis.reference_displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
#######
# MAP #
#######
save_MAP
_category.description
; Data items in the MAP category record
the details of a maps. Maps record values of parameters,
such as density, that are functions of position within
a cell or are functions of orthogonal coordinates in
three space.
A map may is composed of one or more map segments
specified in the MAP_SEGMENT category.
Examples are given in the MAP_SEGMENT category.
;
_category.id map
_category.mandatory_code no
loop_
_category_key.name '_map.id'
'_map.diffrn_id'
'_map.entry_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id
_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.details
_item_description.description
; The value of _map.details should give a
description of special aspects of each map.
;
_item.name '_map.details'
_item.category_id map
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id
_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.diffrn_id
_item_description.description
; This item is a pointer to _diffrn.id in the
DIFFRN category.
;
_item.name '_map.diffrn_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.entry_id
_item_description.description
; This item is a pointer to _entry.id in the
ENTRY category.
;
_item.name '_map.entry_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.id
_item_description.description
; The value of _map.id must uniquely identify
each map for the given diffrn.id or entry.id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map.id' map yes
'_map_segment.id' map_segment yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_segment.id' '_map.id'
save_
###########################
# MAP_SEGMENT #
###########################
save_MAP_SEGMENT
_category.description
; Data items in the MAP_SEGMENT category record
the details about each segment (section or brick) of a map.
;
_category.id map_segment
_category.mandatory_code no
loop_
_category_key.name '_map_segment.id'
'_map_segment.map_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map, each consisting of one
segment, both using the same array structure
and mask.
;
;
loop_
_map.id
_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
loop_
_map_segment.map_id
_map_segment.id
_map_segment.array_id
_map_segment.binary_id
_map_segment.mask_array_id
_map_segment.mask_binary_id
rho_calc rho_calc map_structure 1 mask_structure 1
rho_obs rho_obs map_structure 2 mask_structure 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map_segment.array_id
_item_description.description
; The value of _map_segment.array_id identifies the array structure
into which the map is organized.
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.array_id'
_item.category_id map_segment
_item.mandatory_code yes
_item_type.code code
save_
save__map_segment.binary_id
_item_description.description
; The value of _map_segment.binary_id distinguishes the particular
set of data organized according to _map_segment.array_id in
which the data values of the map are stored.
This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.mask_array_id
_item_description.description
; The value of _map_segment.mask_array_id, if given, the array
structure into which the mask for the map is organized. If no
value is given, then all elements of the map are valid. If a
value is given, then only elements of the map for which the
corresponding element of the mask is non-zero are valid. The
value of _map_segment.mask_array_id differs from the value of
_map_segment.array_id in order to permit the mask to be given
as, say, unsigned 8-bit integers, while the map is given as
a data type with more range. However, the two array structures
must be aligned, using the same axes in the same order with the
same displacements and increments
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.mask_array_id'
_item.category_id map_segment
_item.mandatory_code no
_item_type.code code
save_
save__map_segment.mask_binary_id
_item_description.description
; The value of _map_segment.mask_binary_id identifies the
particular set of data organized according to
_map_segment.mask_array_id specifying the mask for the map.
This item is a pointer to _array_data.mask_binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.mask_binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.id
_item_description.description
; The value of _map_segment.id must uniquely
identify each segment of a map.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map_segment.id'
map_segment
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_data_frame.map_segment_id'
'_map_segment.id'
save_
save__map_segment.map_id
_item_description.description
; This item is a pointer to _map.id
in the MAP category.
;
_item.name '_map_segment.map_id'
_item.category_id map_segment
_item.mandatory_code yes
_item_type.code code
save_
save__map_segment.details
_item_description.description
; The value of _map_segment.details should give a
description of special aspects of each segment of a map.
;
_item.name '_map_segment.details'
_item.category_id map_segment
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
; Example to be provided
;
;
;
save_
######################## DEPRECATED DATA ITEMS ########################
save__diffrn_detector_axis.id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_detector_axis.id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_measurement_axis.id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
######################### DEPRECATED CATEGORY #########################
#####################
# DIFFRN_FRAME_DATA #
#####################
save_DIFFRN_FRAME_DATA
_category.description
; Data items in the DIFFRN_FRAME_DATA category record
the details about each frame of data.
The items in this category are now in the
DIFFRN_DATA_FRAME category.
The items in the DIFFRN_FRAME_DATA category
are now deprecated. The items from this category
are provided as aliases in the 1.0 dictionary
or, in the case of _diffrn_frame_data.details,
in the 1.4 dictionary. THESE ITEMS SHOULD NOT
BE USED FOR NEW WORK.
The items from the old category are provided
in this dictionary for completeness
but should not be used or cited. To avoid
confusion, the example has been removed
and the redundant parent-child links to other
categories have been removed.
;
_category.id diffrn_frame_data
_category.mandatory_code no
loop_
_category_key.name '_diffrn_frame_data.id'
'_diffrn_frame_data.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
THE DIFFRN_FRAME_DATA category is deprecated and should not be used.
;
;
# EXAMPLE REMOVED #
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_frame_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.array_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.binary_id'
_item.category_id diffrn_frame_data
_item.mandatory_code implicit
_item_type.code int
save_
save__diffrn_frame_data.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.detector_element_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.id
_item_description.description
; The value of _diffrn_frame_data.id must uniquely identify
each complete frame of data.
DEPRECATED -- DO NOT USE
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_frame_data.id' diffrn_frame_data yes
_item_type.code code
save_
save__diffrn_frame_data.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.details'
_item.category_id diffrn_frame_data
_item.mandatory_code no
_item_type.code text
save_
################ END DEPRECATED SECTION ###########
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive) ...
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items (case insensitive)...
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
point numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9]?[0-9]\
((T[0-2][0-9](:[0-5][0-9](:[0-5][0-9](.[0-9]+)?)?)?)?\
([+-][0-5][0-9]:[0-5][0-9]))?
;
;
Standard format for CIF date and time strings (see
http://www.iucr.org/iucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character 'T' followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
decimal fraction on the seconds of time.
Time is local time if no time-zone offset is given.
Note that this type extends the mmCIF yyyy-mm-dd type
but does not conform to the mmCIF yyyy-mm-dd:hh:mm
type that uses a ':' in place if the 'T' specified
by the IUCr standard. For reading, both forms should
be accepted, but for writing, only the IUCr form should
be used.
For maximal compatibility, the special time zone
indicator 'Z' (for 'zulu') should be accepted on
reading in place of '+00:00' for GMT.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2)^)'
'millimetres' 'millimetres (metres * 10^( -3)^)'
'nanometres' 'nanometres (metres * 10^( -9)^)'
'angstroms' '\%Angstroms (metres * 10^(-10)^)'
'picometres' 'picometres (metres * 10^(-12)^)'
'femtometres' 'femtometres (metres * 10^(-15)^)'
#
'reciprocal_metres' 'reciprocal metres (metres^(-1)^)'
'reciprocal_centimetres'
'reciprocal centimetres ((metres * 10^( -2)^)^(-1)^)'
'reciprocal_millimetres'
'reciprocal millimetres ((metres * 10^( -3)^)^(-1)^)'
'reciprocal_nanometres'
'reciprocal nanometres ((metres * 10^( -9)^)^(-1)^)'
'reciprocal_angstroms'
'reciprocal \%Angstroms ((metres * 10^(-10)^)^(-1)^)'
'reciprocal_picometres'
'reciprocal picometres ((metres * 10^(-12)^)^(-1)^)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9)^)^2^'
'angstroms_squared' '\%Angstroms squared (metres * 10^(-10)^)^2^'
'8pi2_angstroms_squared'
'8\p^2^ * \%Angstroms squared (metres * 10^(-10)^)^2^'
'picometres_squared' 'picometres squared (metres * 10^(-12)^)^2^'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9)^)^3^'
'angstroms_cubed' '\%Angstroms cubed (metres * 10^(-10)^)^3^'
'picometres_cubed' 'picometres cubed (metres * 10^(-12)^)^3^'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^( -9)^)^(-3)^)
;
'electrons_per_angstroms_cubed'
; electrons per \%Angstroms cubed (electrons/(metres * 10^(-10)^)^(-3)^)
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (electrons/(metres * 10^(-12)^)^(-3)^)
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'pixels_per_element' '(image) pixels per (array) element'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.5.2 2007-05-06
; Further clarifications of the coordinate system. (HJB)
;
1.5.1 2007-04-26
; Improve defintion of X-axis to cover the case of no goniometer
and clean up more line folds (HJB)
;
1.5 2007-07-25
; This is a cummulative list of the changes proposed since the
imgCIF workshop in Hawaii in July 2006. It is the result
of contributions by H. J. Bernstein, A. Hammersley,
J. Wright and W. Kabsch.
2007-02-19 Consolidated changes (edited by HJB)
+ Added new data items
'_array_structure.compression_type_flag',
'_array_structure_list_axis.fract_displacement',
'_array_structure_list_axis.displacement_increment',
'_array_structure_list_axis.reference_angle',
'_array_structure_list_axis.reference_displacement',
'_axis.system',
'_diffrn_detector_element.reference_center_fast',
'_diffrn_detector_element.reference_center_slow',
'_diffrn_scan_axis.reference_angle',
'_diffrn_scan_axis.reference_displacement',
'_map.details', '_map.diffrn_id',
'_map.entry_id', '_map.id',
'_map_segment.array_id', '_map_segment.binary_id',
'_map_segment.mask_array_id', '_map_segment.mask_binary_id',
'_map_segment.id', '_map_segment.map_id',
'_map_segment.details.
+ Change type of
'_array_structure.byte_order' and
'_array_structure.compression_type'
to ucode to make these values case-insensitive
+ Add values 'packed_v2' and 'byte_offset' to enumeration of values for
'_array_structure.compression_type'
+ Add to defintions for the binary data type to handle new compression types, maps,
and a variety of new axis types.
2007-07-25 Cleanup of typos for formal release (HJB)
+ Corrected text fields for reference_ tag descriptions that
were off by one column
+ Fix typos in comments listing fract_ tags
+ Changed name of release from 1.5_DRAFT to 1.5
+ Fix unclosed text fields in various map definitions
;
1.4 2006-07-04
; This is a change to reintegrate all changes made in the course of
publication of ITVG, by the RCSB from April 2005 through
August 2008 and changes for the 2006 imgCIF workshop in
Hawaii.
2006-07-04 Consolidated changes for the 2006 imgCIF workshop (edited by HJB)
+ Correct type of '_array_structure_list.direction' from 'int' to 'code'.
+ Added new data items suggested by CN
'_diffrn_data_frame.details'
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size and
'_array_intensities.pixel_binning_method
+ Added deprecated item for completeness
'_diffrn_frame_data.details'
+ Added entry for missing item in contents list
'_array_structure_list_axis.displacement'
+ Added new MIME type X-BASE32K based on work by VL, KM, GD, HJB
+ Correct description of MIME boundary delimiter to start in
column 1.
+ General cleanup of text fields to conform to changes for ITVG
by removing empty lines at start and finish of text field.
+ Amend example for ARRAY_INTENSITIES to include binning.
+ Add local copy of type specification (as 'code') for all children
of '_diffrn.id'.
+ For consistency, change all references to 'pi' to '\p' and all
references to 'Angstroms' to '\%Angstroms'.
+ Clean up all powers to use IUCr convention of '^power^', as in
'10^3^' for '10**3'.
+ Update 'yyyy-mm-dd' type regex to allow truncation from the right
and improve comments to explain handling of related mmCIF
'yyyy-mm-dd:hh:mm' type, and use of 'Z' for GMT time zone.
2005-03-08 and
2004-08-08 fixed cases where _item_units.code used
instead of _item_type.code (JDW)
2004-04-15 fixed item ordering in
_diffrn_measurement_axis.measurement_id
added sub_category 'vector' (JDW)
;
1.3.2 2005-06-25
; 2005-06-25 ITEM_TYPE_LIST: code, ucode, line, uline regexps updated
to those of current mmCIF; float modified by allowing integers
terminated by a point as valid. The 'time' part of
yyyy-mm-dd types made optional in the regexp. (BM)
2005-06-17 Minor corrections as for proofs for IT G Chapter 4.6
(NJA)
2005-02-21 Minor corrections to spelling and punctuation
(NJA)
2005-01-08 Changes as per Nicola Ashcroft.
+ Updated example 1 for DIFFRN_MEASUREMENT to agree with mmCIF.
+ Spelled out "micrometres" for "um" and "millimetres" for "mm".
+ Removed phrase "which may be stored" from ARRAY_STRUCTURE
description.
+ Removed unused 'byte-offsets' compressions and updated
cites to ITVG for '_array_structure.compression_type'.
(HJB)
;
1.3.1 2003-08-13
;
Changes as per Frances C. Bernstein.
+ Identify initials.
+ Adopt British spelling for centre in text.
+ Set \p and \%Angstrom and powers.
+ Clean up commas and unclear wordings.
+ Clean up tenses in history.
Changes as per Gotzon Madariaga.
+ Fix the ARRAY_DATA example to align '_array_data.binary_id'
and X-Binary-ID.
+ Add a range to '_array_intensities.gain_esd'.
+ In the example of DIFFRN_DETECTOR_ELEMENT,
'_diffrn_detector_element.id' and
'_diffrn_detector_element.detector_id' interchanged.
+ Fix typos for direction, detector and axes.
+ Clarify description of polarisation.
+ Clarify axes in '_diffrn_detector_element.center[1]'
'_diffrn_detector_element.center[2]'.
+ Add local item types for items that are pointers.
(HJB)
;
1.3.0 2003-07-24
;
Changes as per Brian McMahon.
+ Consistently quote tags embedded in text.
+ Clean up introductory comments.
+ Adjust line lengths to fit in 80 character window.
+ Fix several descriptions in AXIS category which
referred to '_axis.type' instead of the current item.
+ Fix erroneous use of deprecated item
'_diffrn_detector_axis.id' in examples for
DIFFRN_SCAN_AXIS.
+ Add deprecated items '_diffrn_detector_axis.id'
and '_diffrn_measurement_axis.id'.
(HJB)
;
1.2.4 2003-07-14
;
Changes as per I. David Brown.
+ Enhance descriptions in DIFFRN_SCAN_AXIS to make them less
dependent on the descriptions in DIFFRN_SCAN_FRAME_AXIS.
+ Provide a copy of the deprecated DIFFRN_FRAME_DATA
category for completeness.
(HJB)
;
1.2.3 2003-07-03
;
Cleanup to conform to ITVG.
+ Correct sign error in ..._cubed units.
+ Correct '_diffrn_radiation.polarisn_norm' range.
(HJB)
;
1.2.2 2003-03-10
;
Correction of typos in various DIFFRN_SCAN_AXIS descriptions.
(HJB)
;
1.2.1 2003-02-22
;
Correction of ATOM_ for ARRAY_ typos in various descriptions.
(HJB)
;
1.2 2003-02-07
;
Corrections to encodings (remove extraneous hyphens) remove
extraneous underscore in '_array_structure.encoding_type'
enumeration. Correct typos in items units list. (HJB)
;
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB.
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li.
;
1.1.1 2001-02-16
;
Several typo corrections by JW.
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS. (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME.
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to
'_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source',
'_diffrn_radiation.polarizn_source_norm',
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add '_diffrn_measurement.device' to category key.
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to
allow for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up. (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes. (JW)
+ Correct spelling of diffrn_measurement_axis in '_axis.id'
+ Correct ordering of uses of '_item.mandatory_code' and
'_item_default.value'.
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown. (HJB)
+ Add further comments on '\n' and '\t'.
+ Update ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Change 'meter' to 'metre' throughout.
+ Add missing enumerations to '_array_structure.compression_type'
and make 'none' the default.
+ Remove parent-child relationship between
'_array_structure_list.index' and '_array_structure_list.precedence'.
+ Improve alphabetization.
+ Fix '_array_intensities_gain.esd' related function.
+ Improve comments in AXIS.
+ Fix DIFFRN_FRAME_DATA example.
+ Remove erroneous DIFFRN_MEASUREMENT example.
+ Add '_diffrn_measurement_axis.id' to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data. (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors. (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for '_diffrn_scan.id' definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header. (HJB)
+ Restore '_diffrn_detector.diffrn_id' to DIFFRN_DETECTOR KEY.
+ Add AXIS category.
+ Bring in complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
from cif_mm.dic for clarity.
+ Change '_array_structure.encoding_type' from type code to uline and
added X-Binary-Element-Type to MIME header.
+ Add detector beam centre '_diffrn_detector_element.center[1]' and
'_diffrn_detector_element.center[2]'.
+ Correct item name of '_diffrn_refln.frame_id'.
+ Replace reference to '_array_intensities.undefined' by
'_array_intensities.undefined_value'.
+ Replace references to '_array_intensity.scaling' with
'_array_intensities.scaling'.
+ Add DIFFRN_SCAN... categories.
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft. (HJB)
+ Reflow comment lines over 80 characters and corrected typos.
+ Update examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF. (HJB)
+ Add binary type, which is a text field containing a variant on
MIME encoded data.
+ Change type of '_array_data.data' to binary and specify internal
structure of raw binary data.
+ Add '_array_data.binary_id', and make
'_diffrn_frame_data.binary_id' and '_array_intensities.binary_id'
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft. (JW)
+ Add category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes are made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA is renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE is renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for '_diffrn_frame_data.array_id' is changed from
'_array_structure_list.array_id' to '_array_structure.id'. Item
'_diffrn_detector.array_id' is deleted.
+ Add data item '_diffrn_frame_data.binary_id' to identify data
groups within a binary section. The formal identification of the
binary section is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version is adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley
(AH).
Modifications to the CBF draft. (JW)
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories
have been generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category
ARRAY_DATA. This departs from the CBF notion of data existing
in some special comment. In this description, data are handled as an
ordinary data item encapsulated in a character data type. Although
data this manner deviates from CIF conventions, it does not violate
any DDL 2.1 rules. DDL 2.1 regular expressions can be used to define
the binary representation which will permit some level of data
validation. In this version, the placeholder type code "any" has
been used. This translates to a regular expression which will match
any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary.
It may be possible to use the DDL 2.1 ITEM_STRUCTURE and
ITEM_STRUCTURE_LIST categories to provide the information that is
carried in by the ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By
moving the array structure to the DDL level it would be possible to
define an array type as well as a regular expression defining the
data format.
+ Multiple array sections can be properly handled within a single
datablock.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
./CBFlib-0.9.2.2/doc/cif_core.dic 0000644 0000765 0000765 00001575772 11603702115 014625 0 ustar yaya yaya ##############################################################################
# #
# CIF CORE DEFINITIONS #
# -------------------- #
# #
# This dictionary contains the names and definitions of the Core data items #
# recognised by the International Union of Crystallography for the exchange #
# of data between laboratories and submissions to journals and databases. #
# #
# The STAR/DDL dictionary is available as the file "ddl_core.dic" #
# located at URL ftp://ftp.iucr.org/pub/ddldic.c95 #
# #
# Copyright 2004 International Union of Crystallography #
##############################################################################
data_on_this_dictionary
_dictionary_name cif_core.dic
_dictionary_version 2.3.1
_dictionary_update 2005-06-27
_dictionary_history
;
1991-05-27 Created from CIF Dictionary text. SRH
1991-05-30 Validated with CYCLOPS & CIF ms. SRH
1991-06-03 Adjustments to some definitions. SRH
1991-06-06 Adjustments a la B. McMahon. SRH
1991-06-18 Additions & some redefinitions. SRH
1991-07-04 Corrected 90:0 in *_detect_slit_. SRH
1991-09-20 Additions & some redefinitions. SRH
1991-09-20 Final published version. IUCr
1991-11-12 Add _diffrn_ambient_environment. SRH
1991-11-12 Allow 'c' for _atom_site_calc_flag. SRH
1993-02-23 Apply global_ and 'unknown' -> '?' SRH
1993-03-05 Changes resulting from MM dictionary. SRH
1993-05-20 Changes arising from new DDL commands. SRH
1993-08-05 Additional finetuning pre-Beijing. SRH
1993-12-22 Introductory sections added to categories. BMcM
1993-12-22 Additional categories from mm work: audit_author,
citation, atom_sites_fract_tran_matrix. BMcM
1994-03-01 Add 'undef' to _refine_ls_hydrogen_treatment. BMcM
1994-03-01 Add '_publ_section_exptl_prep' and '*_refinement'. BMcM
1994-03-01 Add 'atom_site_aniso_ratio'. BMcM
1994-04-15 Comments from IDB on draft version for circulation. BMcM
1994-04-15 Added _publ_section_exptl_solution. BMcM
1994-07-14 Added B. H. Toby's suggested _diffrn_radiation_xray_symbol
and _diffrn_radiation_xray_target. BMcM
1994-08-05 Revised definition for _diffrn_reflns_number (S.R. Hall). BMcM
1994-08-05 Added _atom_type_scat_length_neutron (B.H. Toby). BMcM
1994-10-13 Reworded _diffrn_standards_ a la S.R. Hall. BMcM
1994-10-13 Added _diffrn_radiation_probe for non-X-ray experiments. BMcM
1995-01-17 Rewording of definition of _chemical_melting_point. BMcM
1995-02-24 Changed text references to e.s.d to 'standard uncertainty'. BMcM
1995-07-08 Added _chemical_formula_iupac. BMcM
1995-07-09 Finally added _symmetry_equiv_pos_id. BMcM
1995-07-09 _units_extension, _units_conversion and _units_description
superseded by _units and _units_detail. Suffixed datanames
retained as separate entries. BMcM
1995-10-23 Added _refine_ls_R_Fsqd_factor and _refine_ls_R_I_factor BMcM
1996-03-25 Correlated with mmCIF release 0.8 BMcM
1996-05-16 Added some extra datanames for use by Acta:
_publ_section_synopsis, _publ_section_title_footnote,
_publ_author_footnote, _journal_paper_category, and various
_journal_index_ categories BMcM
1996-05-20 Added geom_hbond category BMcM
1996-06-10 Datanames with suffixes to indicate units moved to a new
compatibility dictionary cif_compat.dic BMcM
1996-06-10 Embarrassing _units_ stuff removed from geom_hbond BMcM
1996-06-10 _list_mandatory and _list_reference added to _publ_author_
datanames (where _list was given as "both") BMcM
1996-06-10 Added audit_conform category BMcM
1996-06-11 Added audit_link category BMcM
1996-06-11 Reworded _exptl_crystal_F_000 definition BMcM
1996-06-11 Added _atom_site_U_equiv_geom BMcM
1996-06-11 Added publ_body category BMcM
1996-06-27 Added examples for most of the remaining category overviews
BMcM
1996-06-27 Added _journal_language BMcM
1996-06-28 Added area-detector definitions from mmCIF dictionary:
_diffrn_measurement_device_details, *_specific and *_type;
_diffrn_radiation_detector_details, *_specific, *_type;
_diffrn_radiation_source_details, *_power, *_specific,
*_target, *_type; reflns_shell category BMcM
Added _refine_ls_d_res_high and *_low and changed wording of
definitions for R factors to include these. BMcM
Added 'h' and 'f' flags to _refln_observed_status. BMcM
1996-07-05 Some typos fixed and examples modified as suggested by
P.Strickland and I.D.Brown. BMcM
1996-07-27 BMcM:
Added example for _diffrn_orient_refln_[] from G. Madariaga
U~ij~ changed to U^ij^ a la Nomenclature Commission
Definition of _diffrn_ambient_environment changed to omit vacuum
as a possible default environment
Changed definitions of *_site_symmetry_* items to I.D.Brown's
suggested wording.
Compressed various journal indexing categories into one
Changed upper enumeration values for _refln_symmetry_epsilon
and _refln_symmetry_multiplicity to 48.
Added references to deprecated use of B values.
Modified descriptions of phone, fax number conventions
_publ_manuscript_incl_ entries reworded for greater
clarity and given individual data blocks
Added _list_reference to _symmetry_equiv_pos_id and changed
_list value to 'both' for *_as_xyz to allow the P1 case
Added _atom_site_B_equiv_geom for completeness
Modified definitions of _atom_sites_[Cartn,fract]_tran_vector_
Added _units stuff to _chemical_formula_weight_* and
_exptl_crystal_density_ items
Added *_theta, *_omega to _diffrn_orient_refln_angle_
Added 'q' to enumeration list for _diffrn_refln_scan_mode
Reworded definition in _diffrn_scale_group_[]
Permitted esd for _refln_phase_meas (necessitates splitting
_refln_phase_ datablock in two)
Added _type_conditions esd for _reflns_scale_meas_
1996-07-28 BMcM:
Added example for refln_scale_[] and second example for
_refln_[] from Xtal test data set.
Changed references to category names to CAPITALS.
Merged CELL and CELL_MEASUREMENT categories.
Added _units deg to all angle quantities.
Renamed _citation_journal_coden_CAS as
_citation_journal_abstract_id_CAS
Removed _diffrn_measurement_device_details, *_specific,
*_type, _diffrn_radiation_detector_details, *_specific,
*_type, _diffrn_radiation_source_power, *_specific,
*_target, *_type, pending full analysis of requirements
for describing diffraction apparatus.
Reworded _exptl_crystal_F_000 definition again
1996-08-03 Reworded _refine_ls_number_reflns definition a la S.R.Hall BMcM
1996-09-10 BMcM:
Clarified _diffrn_attenuator_scale definition with help from SRH
In _refln_symmetry_multiplicity, changed 'structure-factor
value' to 'structure-factor magnitudes'
Slight modification to _diffrn_reflns_number to exclude all
systematic absences, not just those due to centring
Removed footnote markers from example of
_publ_section_title_footnote
Added new example to SYMMETRY_EQUIV category to explain the
use of _symmetry_equiv_pos_id
Reworking of DIFFRN_RADIATION and DIFFRN_MEASUREMENT
categories and introduction of DIFFRN_DETECTOR and
DIFFRN_SOURCE a la I.D.Brown
1996-09-11 Corrected category assignment for _diffrn_standards_ items BMcM
1996-09-12 BMcM:
Added _cell_id and _cell_measurement_refln_id
Changed the term "id" to "identifier" in definitions
Renamed _citation_journal_abstract_id_CAS as
_citation_abstract_id_CAS
Added _audit_block_code and changed definition of
_audit_link_block_code to refer to it
1996-09-18 BMcM:
Fine tuning of IDB's new DIFFRN categories: in DIFFRN_DETECTOR
changed *_type to *_device and added *_device_type. Moved
_diffrn_radiation_detector back to DIFFRN_RADIATION category
with expanded definition. Reworded definitions of
_diffrn_measurement_device and *_device_type. In
DIFFRN_RADIATION changed enumeration range for
*_polarisn_norm to -180:180 and added 'as viewed from the
specimen' to the definition; also added 'Cu K-L~2,3~' to
examples for *_type. Reworded definitions for
_diffrn_refln_index and _diffrn_source_target, and changed
_type of _diffrn_source_power to "numb".
Introduced _diffrn_detector_dtime in the DIFFRN_DETECTOR
category and restored _diffrn_radiation_detector_dtime to
DIFFRN_RADIATION
1996-09-25 BMcM:
Reworded definitions of _atom_site_disorder_assembly and *_group
1996-10-02 BMcM:
Changed _symmetry_equiv_pos_id to _symmetry_equiv_pos_site_id
in recognition of the technical meaning of 'position' in
International Tables
Addition of the names of the relevant units to definitions of
_atom_type_scat_length_neutron, _exptl_crystal_size_,
_geom_hbond_distance_, _refine_ls_d_res_high and *_low,
_reflns_shell_d_res_high and *_low; and cosmetic expansion
of units listed in the definitions for _diffrn_source_current,
*_power and *_voltage
Addition of '_related_function conversion' to
_atom_site_B_equiv_geom and *_U_equiv_geom and
_atom_site_B_iso_or_equiv and *_U_iso_or_equiv
Examples for CELL_MEASUREMENT_REFLN and DIFFRN_REFLN from
Gotzon Madariaga
Renamed _atom_site_U_equiv_geom as _atom_site_U_equiv_geom_mean
and likewise for *_B_* to increase the consistency of
abbreviations, as suggested by I.D. Brown
Added disorder example to the ATOM_SITE category description
1996-10-15 BMcM:
Modified description of example for DIFFRN_REFLN
Changed _enumeration_range of _atom_site_attached_hydrogens
from 0:4 to 0:8 (cf CSD entry with refcode DUTMAG01) (PRE)
Added '_enumeration_default cif' to _publ_body_format
Changed underscores to spaces in the example for the Hall
spacegroup symbol in data_symmetry_[]
Deleted extraneous '_' in data_(_)citation_abstract_id_CAS
1996-10-27 BMcM: Changed psiscan to psi-scan at request of SRH
1996-11-05 BMcM:
Changed _citation_book_coden_ISBN to _citation_book_id_ISBN,
_citation_journal_coden_ASTM to _citation_journal_id_ASTM,
_citation_journal_coden_CSD to _citation_journal_id_CSD,
_citation_journal_coden_ISSN to _citation_journal_id_ISSN,
and _citation_Medline_AN to _citation_database_id_Medline.
Also modified description of CODEN in _citation_journal_id_ASTM
and _database_journal_ASTM (suggested by PMDF)
The phrase 'diffraction data' modified to 'intensities' in
several places, some other cosmetic commas and enforcement
of consistent lower-case units names (PMDF)
Clarification of the definition for
_diffrn_radiation_polarisn_norm (PMDF)
Added 'constr' to _refine_ls_hydrogen_treatment (SRH)
Corrected misassignment of category of
_diffrn_radiation_detector_dtime (H.J.Bernstein)
1996-11-06 BMcM:
Added "_list yes" to items in the REFLNS_SHELL category (IDB)
Added "measured" to definition of _reflns_shell_number_unique_all
Changed enumeration range for _diffrn_standards_decay_% to
":100" and added statement about negative values (PMDF/SRH)
1996-11-08 BMcM:
_diffrn_radiation_detector, _diffrn_radiation_detector_dtime and
_diffrn_radiation_source removed (these will be transferred to
cif_compat.dic for compatibility with files conforming to the
original dictionary)
_diffrn_radiation_wavelength_* items moved to new category
1996-11-12 BMcM:
Deleted _cell_id and _cell_measurement_refln_id, and
clarified the intent of the CELL category in _cell_[] (PMDF)
Some small rewordings of various _diffrn_* items due to
B.H.Toby
1996-11-14 BMcM:
Imposed consistency on the nomenclature of diffraction device
data names: _diffrn_detector_device_type -> *_detector_type,
_diffrn_measurement_device_details -> *_measurement_details,
*_measurement_device_type -> *_measurement_type; introduction
of _diffrn_source_device and parallel definitions. Existing
*_measurement_details example moved to *_special_details (PMDF)
1996-11-21 BMcM:
Reintroduced _diffrn_measurement_device_details, further tidying
of data names thus: _diffrn_measurement_type -> *_device_type;
_diffrn_detector_device and _diffrn_source_device both drop
"_device" (PMDF)
Added _journal_data_validation_number and
_publ_requested_category to enable handling of CIF-access
submissions by Acta Cryst. C
1996-11-23 A few typos fixed. BMcM
1996-11-24 BMcM:
Added 'gaussian', 'multi-scan' and 'numerical' to enumeration
list for _exptl_absorpt_correction_type (SRH)
Added 'mixed' to enumeration list for
_refine_ls_hydrogen_treatment (SRH)
1996-11-25 A few typos fixed (BMcM)
1996-11-27 BMcM:
Removed looped _related_item from _publ_contact_author and
reintroduced _diffrn_radiation_detector, *_dtime and
_diffrn_radiation_source (see 1996-11-08) with
"_related_function replace" as a preparation for
using this mechanism further in version 2.1.
1996-11-27 Release version 2.0. IUCr
1997-01-20 BMcM:
Some small changes thanks to PMDF. Double space after period
at end of sentence changed to single space throughout;
_citation_database_id_Medline _diffrn_detector_type moved
to correct alphabetic sequence; space introduced between
sentences in definition of _citation_journal_id_CSD; some
other minor grammatical changes
1997-10-30 BMcM: (changes to align with Acta C Notes for Authors)
Obsoleted *_obs_* entries in REFLNS and REFINE_LS categories
and replaced with *_gt_*; obsoleted _refine_ls_shift/esd_
by _refine_ls_shift/su_; obsoleted
_atom_site_thermal_displace_type by *_adp_type
1997-11-05 BMcM: (changes to align with Acta C Notes for Authors)
Added _diffrn_detector_area_resol_mean,
_diffrn_measured_fraction_theta_max and *_full,
_diffrn_reflns_theta_full
1997-11-05 BMcM: Added _reflns_number_Friedel; changed various *_obs
items in examples to *_gt equivalents and likewise for
other obsoleted items
1997-11-24 BMcM: Slightly changed wording of _reflns_number_Friedel and
_reflns_threshold_expression at suggestion of I.D.Brown.
Modified definition of _refine_ls_abs_structure_Flack and
changed the text of the example in category REFINE at
the request of H.D.Flack.
1997-12-08 BMcM: Removed the phrase "(enantiomorph or polarity)" from
_refine_ls_abs_structure_Flack and *_Rogers because
"absolute structure" is a phrase uniquely defined (H.D.Flack)
1997-12-08 BMcM: Several instances of \s changed to u
1997-12-08 BMcM: Modified definitions of _reflns_number_total and
*_Friedel (after H.D.Flack) to clarify the distinction between
crystal-class and Laue-symmetry independent reflection sets
1997-12-08 BMcM: Added _chemical_absolute_configuration and
_chemical_optical_rotation (H.D.Flack)
1998-08-04 BMcM: Moved _diffrn_pressure_history and _diffrn_thermal_history
from draft msCIF dictionary to core as
_exptl_crystal_pressure_history and
_exptl_crystal_thermal_history (G. Madariaga/I.D.Brown)
Moved _diffrn_symmetry_description and REFINE_LS_CLASS
from draft msCIF dictionary to core (G. Madariaga/I.D.Brown)
1998-08-04 BMcM: Minor rewordings of _refine_ls_R_Fsqd_factor,
_refine_ls_R_I_factor, various definitions referring to
F_calc in electrons, and _reflns_shell_number_unique_*
(I.D.Brown)
1998-08-04 BMcM: added _reflns_Friedel_coverage (H.D.Flack/S.R.Hall)
1998-08-04 BMcM: changed formula for F(000) (from
F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^ to
F(000) = [ (sum f~r~)^2^ + (sum f~i~)^2^ ]^1/2^ ) (H.D.Flack)
1998-08-04 BMcM: added 'syn' and 'unk' as enumerations to
_chemical_absolute_configuration (H.D.Flack/A.Linden)
1998-09-02 BMcM: added _exptl_crystal_size_length and modified slightly
the definition of _exptl_crystal_size_ (W.Clegg/I.D.Brown)
Added _diffrn_attenuator_material (I.D.Brown)
Added sentence explaining the physical meaning of the
_enumeration_range to _refine_ls_abs_structure_Flack
(H.D.Flack)
Some rewording in _chemical_absolute_configuration implying
that for absolute configuration determination the measurement
and reporting of the optical rotation in solution are
considered mandatory. (H.D.Flack)
Some rewording in _reflns_number_total and *_gt to clarify
the inclusion of Friedel reflections; addition of
_reflns_Friedel_coverage; deletion of _reflns_number_Friedel
(H.D.Flack/S.R.Hall)
Further minor rewording to _reflns_shell_number_unique_all,
*_gt, *_obs (H.D.Flack)
1998-09-10 BMcM: transferred _diffrn_reflns_number_of_classes and the
categories DIFFRN_REFLNS_CLASS, REFLNS_CLASS and
REFLNS_SHELL_CLASS from the draft msCIF dictionary; added
_diffrn_refln_class_code and _refln_class_code to link
individual reflections to their related categories.
1998-12-08 BMcM: implemented H.D. Flack's reworking of DIFFRN_REFLNS_CLASS,
REFLNS_CLASS, REFLNS_SHELL_CLASS and REFINE_LS_CLASS, deleting
the latter two; removed _diffrn_reflns_number_of_classes.
1998-12-15 BMcM: completed the above reworking; fixed embarrassing typo for
_related_function
1999-01-16 BMcM: coreDMG review of version 2.1beta5. Numerous small changes
from I.D.Brown, the most significant being:
_atom_site_occupancy definition clarifies how to impose an
experimental uncertainty on the _enumeration_range;
_atom_site_U_iso_or_equiv enumeration range set to infinity;
_atom_type_analytical_mass_% enumeration range set as 0:100;
expanded definitions of _diffrn_radiation_probe and *_type to
clarify the distinction between these two items;
added reference to _exptl_crystal_size to the definition of
_exptl_crystal_description, and modified the definition of
_exptl_crystal_face_diffr_ ;
new data item _refln_d_spacing;
clarified the role of _reflns_special_details in specifying
whether Friedel pairs have been averaged;
Numerous small changes from H.D.Flack, most significantly:
removed enumeration range from _diffrn_refln_counts_ because
*_net can go negative;
fixed various typos in equations for wR and S;
removed reference to Friedel reflections from
_refln_symmetry_multiplicity
1999-01-24 BMcM: further revision to wording of _refln_symmetry_multiplicity
following discussions by HDF and IDB
Numerous small changes from G.Madariaga, most significantly:
a instead of A for real-space cell lengths
(_atom_site_B_iso_or_equiv and _atom_site_U_iso_or_equiv);
_related_function alternate for _atom_site_Cartn_ & _fract_;
"or scattering lengths" added to _atom_type_scat_source;
deleted incorrect _list_reference in DIFFRN_RADIATION;
added rtf to enumeration in _publ_body_format;
added enumeration range to _refine_ls_abs_structure_Rogers
1999-02-04 BMcM: fixed some long lines
1999-02-06 BMcM: data names using sigma as an indicator of experimental
standard uncertainty replaced by equivalents using the
preferred 'u' notation (HDF):
_diffrn_refln_intensity_sigma
_diffrn_reflns_av_sigmaI/netI
_diffrn_reflns_class_av_sgI/I
_diffrn_standards_scale_sigma
_reflns_shell_meanI_over_sigI_all
_reflns_shell_meanI_over_sigI_gt
(_reflns_shell_meanI_over_sigI_obs already replaced by *_gt)
addition of '_related function alternate' to new data
items corresponding to old items with
'_related_function replace' (SRH)
Example for _citation_journal_id_CSD changed to 0070 to
reflect current practice at PDB (F.C.Bernstein)
Added _atom_type_scat_dispersion_source (GM)
1999-03-24 Some minor cosmetic modifications (BMcM)
1999-03-24 Release version 2.1. IUCr
2001-01-09 BMcM: simplified entry for _chemical_absolute_configuration
(H.D.Flack)
Added _geom_bond_valence and the new categories
VALENCE_PARAM and VALENCE_REF (I.D.Brown)
2001-01-11 BMcM: Categories EI, EO, EM added to _publ_requested_category
2001-01-11 Release version 2.2. IUCr
2003-09-28 BMcM: incorporated changes approved by COMCIFS following
discussions of the core Dictionary Management Group:
_atom_site_fract_ nonsense enumeration default value removed
_atom_site_refinement_flags deprecated in favour of new
*_flags_posn, *_adp and *_occupancy items
_atom_sites_special_details added
_cell_reciprocal_angle_ and *_length_ added
'_type_conditions esd' added to _chemical_melting_point
_chemical_melting_point_gt and *_lt added
Added several new items describing chemical properties to
the CHEMICAL category: _chemical_properties_biological and
*_physical, _chemical_temperature_decomposition_* and
*_sublimation_*, at the request of CCDC
_citation_database_id_CSD added at request of CCDC
Several additional tags storing deposition numbers of
database entries and record revision history at
request of CCDC: _database_code_depnum_ccdc_fiz,
*_journal, *_archive and _database_CSD_history
Added _diffrn_ambient_pressure_gt,lt and *_temperature_gt,lt
Added _diffrn_source_take-off_angle
Added _diffrn_standards_decay_%_lt
_diffrn_reflns_measured_fraction_resolution_full and *_max
introduced as replacements for
_diffrn_measured_fraction_theta_full and *_max, moved
to a more appropriate category and defined in terms
of resolution rather than angle which depends on the
radiation used.
Likewise for _diffrn_reflns_resolution_full and *_max as
replacements for _diffrn_reflns_theta_full and *_max
More specific parsable tags for crystal colour introduced as
_exptl_crystal_colour_primary, *_modifier and *_lustre
Added _exptl_crystal_density_meas_gt,lt and *_meas_temp_gt,lt
Added _exptl_crystal_recrystallization_method
Added _publ_contact_author_id_iucr and _publ_author_id_iucr
to allow unique author identification by IUCr database
reference identifier
More datanames for recording imprecise quantities:
_refine_ls_shift/su_max_lt and _refine_ls_shift/su_mean_lt
Added the categories SPACE_GROUP and SPACE_GROUP_SYMOP
as imports from the symmetry dictionary cif_sym.dic
Added _related_function 'replace' to a number of items in
the old SYMMETRY category pointing to the preferred
items from the new SPACE_GROUP category
2003-08-19 BMcM: formal approval for COMCIFS for the additions and
contingent changes discussed on the coreDMG discussion
list from June 2002
2003-09-29 BMcM: second round of changes from coreDMG discussions:
Added _enumeration_range to new _chemical_temperature_* items;
Expanded definition of _space_group_symop_operation_xyz to
make explicit the need for inclusion of centring
translations (HDF/IDB)
Removed _diffrn_reflns_measured_fraction_resolution_full and
*_max for reconsideration following suggestion by
Curt Haltiwanger that terms are needed that do not
refer to resolution or theta
Likewise removed _diffrn_standards_decay_%_lt for further
consideration, and added _type_conditions esd to
_diffrn_standards_decay_% as a measurable quantity
(CH/HDF)
Modified _example_detail for _space_group_symop_operation_xyz
to use a full and unambiguous wording in accordance
with International Tables A (CH/IDB/HDF)
2003-09-29 Removed "_type_conditions esd" from the remaining *_gt and
*_lt items at the suggestion of Gotzon Madariaga:
since these are ceiling/floor values a measurable
uncertainty is pointless (BMcM)
2003-10-01 Fixed some typos following checking by IDB (BMcM)
2003-10-03 BMcM: Final editorial pass. Added _related_function alternate
to _exptl_crystal_colour. Also added this flag to the
new items which replace existing ones:
_atom_site_refinement_flags_* and the _space_group_ items
2003-10-04 Release version 2.3. IUCr
2004-06-06 BMcM: minor editorial changes for International Tables Volume G.
Text of _atom_sites_*_tran_* definitions changed to
ATOM_SITE from STOM_SITES.
Some realignment of examples to fit column width.
2004-09-11 BMcM: corrected related item error in
_atom_site_refinement_flags_posn, *_adp and *_occupancy
2004-11-26 NJA: updated reference to IT Vol A from 1987 to 2002
2004-12-22 NJA: minor corrections to hyphenation, spelling and punctuation
atom_site definition: ', and so on' removed
_atom_site_aniso_B_: 1/4 in formula replaced by (1/4)
_atom_site_aniso_label: '...atom coordinate list' changed
to '...atom in the atom coordinate list'
_atom_site_B_iso_or_equiv: 'anisotropic temperature factor
parameters' changed to 'anisotropic displacement
components'
_atom_site_label: 'Each label may have...' changed to
'Different labels may have...'
_atom_site_type_symbol: '...atom specie(s)...' changed to
'atom species (singular or plural)...'
_atom_type_scat_Cromer_Mann_: reference to Volume C
updated to 2004
_atom_type_symbol: 'atom specie(s)' changed to
'atom species (singular or plural)'
_audit_conform_dict_location: 'where the conformant
dictionary resides' changed to 'for the dictionary
to which the current data block conforms'
_audit_conform_dict_version: 'conformant dictionary'
changed to 'dictionary to which the current data
block conforms'
2004-12-23 NJA: minor corrections to hyphenation, spelling and punctuation
_audit_contact_author_fax,_audit_contact_author_phone:
edited slightly
_cell_angle_: 'in degrees of the reported structure'
changed to 'of the reported structure in degrees'
_cell_measurement_pressure: 'pressure used to synthesize
the sample' changed to 'pressure at which the sample
was synthesized'
_cell_measurement_theta_: 'angles in degrees of reflections
used to measure the unit cell' changed to 'angles
of reflections used to measure the unit cell in degrees'
_cell_reciprocal_angle_: 'angles in degrees defining
the reciprocal cell' changed to 'angles defining
the reciprocal cell in degrees'
_chemical_[]: 'compounds' changed to 'compound'
_chemical_optical_rotation: 'c is the value of CONC in g'
changed to 'c is the value of CONC as defined above'.
_chemical_properties_physical, _biological: 'free
description' changed to 'free-text description'
_chemical_conn_atom_display_: 'if absent...staff.' deleted
_citation_[]: 'literature cited relevant' changed to
'literature cited as being relevant'
_citation_*: 'book chapters' changed to 'books or
book chapters'
_citation_country: 'both journal articles and' deleted
_citation_database_id_CSD: 'containing' changed to
'that contains'
_citation_language: 'citation appears' changed to
'cited article is written'
_diffrn_crystal_treatment: 'intensity measurement' changed
to 'the intensity measurements'
_diffrn_special_details: 'diffraction measurement' changed
to 'intensity-measurement'
_diffrn_attenuator_scale: 'This scale must be multiplied
by the measured intensity to convert it...' changed
to 'The measured intensity must be multiplied by
this scale to convert it...'
_diffrn_orient_matrix_[]: 'used in data measurement'
changed to 'used in the measurement of the
diffraction intensities'
_diffrn_orient_refln_angle_: 'in degrees of a reflection...
matrix' changed to 'of a reflection...matrix in degrees'
_diffrn_radiation_probe,_diffrn_radiation_type:
definitions reworded slightly
_diffrn_refln_angle_: 'in degrees of a reflection' changed
to 'of a reflection in degrees'
_diffrn_refln_elapsed_time: 'diffraction measurement'
changed to 'the diffraction experiment'
_diffrn_refln_scale_group_code: 'applying' changed to
'applicable'
_diffrn_refln_scan_mode: 'with a diffractometer' changed to
'for measurements using a diffractometer'
_diffrn_refln_scan_rate: 'to measure the intensity in
degrees per minute' changed to 'in degrees per minute
to measure the intensity'
_diffrn_refln_standard_code: 'identifying' changed to
'indicating'; 'intensity' changed to 'reflection'
_diffrn_reflns_class_d_res_high,_low: defintions rephrased.
_diffrn_source_details: 'used' deleted.
_diffrn_source_target: 'for generation of' changed to
'to generate'
_diffrn_standards_decay_%: 'at the start of the measurement
process and at the finish' changed to 'from the start of
the measurement process to the end'
_diffrn_standards_number: 'used in the diffraction
measurements' changed to 'used during the measurement of
the diffraction intensities'
_exptl_absorpt_correction_type: 'no more detailed
information is' changed to 'more detailed information
is not'.
_exptl_crystal_[]: 'and so on' deleted
_exptl_crystal_face_perp_dist: 'millimetres of the face'
changed to 'millimetres from the face'
_geom_[], _geom_angle_[], _geom_bond_[], _geom_contact_[],
_geom_hbond_[], _geom_torsion_[]: 'contents of the' deleted
_geom_contact_[], _geom_torsion_[]: year for reference for
example 1 corrected from 1991 to 1992
_geom_hbond_angle_DHA: 'Site at *_D' changed to 'Site at *_H'
_publ_contact_author_fax: definition rephrased slightly
_publ_requested_category: Cif-access codes marked as '(no
longer in use)'
2005-01-05 NJA: minor corrections to hyphenation, spelling and punctuation
_refine_ls_*: 'least squares' changed to 'least-squares
refinement'
_refine_ls_restrained_S_all: `Y(calc) = the observed
coefficients` changed to `Y(calc) = the calculated
coefficients`
_refine_ls_restrained_S_gt: `Y(calc) = the observed
coefficients` changed to `Y(calc) = the calculated
coefficients`
_refine_ls_restrained_S_obs: `Y(calc) = the observed
coefficients` changed to `Y(calc) = the calculated
coefficients`
_refine_ls_shift/esd_*: 'divided by' changed to 'to'
_refine_ls_shift/su_*: 'divided by' changed to 'to'
_refine_ls_class_d_res_*: edited slightly
_refine_ls_d_res_*: edited slightly
_refln_intensity_*: edited slightly
_refln_symmetry_multiplicity: reference to Volume A updated
to (2002), Chapter 10.1
_reflns_d_resolution_*: edited slightly
_reflns_class_d_res_*: edited slightly
_reflns_shell_d_res_*: edited slightly
_space_group_name_Hall: erratum added to reference to Hall
(1981); reference to Volume B updated to 2001.
_space_group_name_H-M_alt: reference to Volume A updated
to (2002)
_symmetry_Int_Tables_number: reference to Volume A updated
to (2002)
_symmetry_space_group_name_Hall: erratum added to reference
to Hall (1981)
_symmetry_space_group_name_H-M: reference to Volume A
updated to (2002)
_symmetry_equiv_pos_as_xyz: reference to Volume A updated
to (2002)
2005-01-11 NJA: more minor corrections to hyphenation, spelling and
punctuation
2005-01-21 NJA: _reflns_shell_Rmerge_I_obs: related item changed from
_reflns_shell_Rmerge_I_obs to _reflns_shell_Rmerge_I_gt
2005-06-21 NJA: corrections to proofs of Intl Tables G Chapter 4.1 included.
New data name _publ_author_email added.
2005-06-27 BMcM: Removed _list_mandatory yes from _atom_site_aniso_label
in response to cif-developers list discussion
;
###############
## ATOM_SITE ##
###############
data_atom_site_[]
_name '_atom_site_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_calc_flag
_atom_site_calc_attached_atom
O1 .4154(4) .5699(1) .3026(0) .060(1) Uani ? ?
C2 .5630(5) .5087(2) .3246(1) .060(2) Uani ? ?
C3 .5350(5) .4920(2) .3997(1) .048(1) Uani ? ?
N4 .3570(3) .5558(1) .4167(0) .039(1) Uani ? ?
C5 .3000(5) .6122(2) .3581(1) .045(1) Uani ? ?
O21 .6958(5) .4738(2) .2874(1) .090(2) Uani ? ?
C31 .4869(6) .3929(2) .4143(2) .059(2) Uani ? ?
# - - - - data truncated for brevity - - - -
H321C .04(1) .318(3) .320(2) .14000 Uiso ? ?
H322A .25(1) .272(4) .475(3) .19000 Uiso ? ?
H322B .34976 .22118 .40954 .19000 Uiso calc C322
H322C .08(1) .234(4) .397(3) .19000 Uiso ? ?
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_site_aniso_label
_atom_site_aniso_B_11
_atom_site_aniso_B_22
_atom_site_aniso_B_33
_atom_site_aniso_B_12
_atom_site_aniso_B_13
_atom_site_aniso_B_23
_atom_site_aniso_type_symbol
O1 .071(1) .076(1) .0342(9) .008(1) .0051(9) -.0030(9) O
C2 .060(2) .072(2) .047(1) .002(2) .013(1) -.009(1) C
C3 .038(1) .060(2) .044(1) .007(1) .001(1) -.005(1) C
N4 .037(1) .048(1) .0325(9) .0025(9) .0011(9) -.0011(9) N
C5 .043(1) .060(1) .032(1) .001(1) -.001(1) .001(1) C
# - - - - data truncated for brevity - - - -
O21 .094(2) .109(2) .068(1) .023(2) .038(1) -.010(1) O
C51 .048(2) .059(2) .049(1) .002(1) -.000(1) .007(1) C
C511 .048(2) .071(2) .097(3) -.008(2) -.003(2) .010(2) C
C512 .078(2) .083(2) .075(2) .009(2) -.005(2) .033(2) C
C513 .074(2) .055(2) .075(2) .004(2) .001(2) -.010(2) C
# - - - - data truncated for brevity - - - -
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_site_label
_atom_site_chemical_conn_number
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
S1 1 0.74799(9) -0.12482(11) 0.27574(9) 0.0742(3)
S2 2 1.08535(10) 0.16131(9) 0.34061(9) 0.0741(3)
N1 3 1.0650(2) -0.1390(2) 0.2918(2) 0.0500(5)
C1 4 0.9619(3) -0.0522(3) 0.3009(2) 0.0509(6)
# - - - - data truncated for brevity - - - -
;
;
Example 3 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_site_label # *_assembly 'M' is a disordered methyl
_atom_site_occupancy # with configurations 'A' and 'B':
_atom_site_disorder_assembly #
_atom_site_disorder_group # H11B H11A H13B
# . | .
C1 1 . . # . | .
H11A .5 M A # . | .
H12A .5 M A # C1 --------C2---
H13A .5 M A # / . \
H11B .5 M B # / . \
H12B .5 M B # / . \
H13B .5 M B # H12A H12B H13A
;
;
Example 4 - hypothetical example to illustrate the description of a
disordered methyl group.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the ATOM_SITE category record details about
the atom sites in a crystal structure, such as the positional
coordinates, atomic displacement parameters, and magnetic moments
and directions.
;
data_atom_site_adp_type
_name '_atom_site_adp_type'
_category atom_site
_type char
_related_item '_atom_site_thermal_displace_type'
_related_function alternate
_list yes
_list_reference '_atom_site_label'
loop_ _enumeration
_enumeration_detail Uani 'anisotropic Uij'
Uiso 'isotropic U'
Uovl 'overall U'
Umpe 'multipole expansion U'
Bani 'anisotropic Bij'
Biso 'isotropic B'
Bovl 'overall B'
_definition
; A standard code used to describe the type of atomic displacement
parameters used for the site.
;
data_atom_site_aniso_B_
loop_ _name '_atom_site_aniso_B_11'
'_atom_site_aniso_B_12'
'_atom_site_aniso_B_13'
'_atom_site_aniso_B_22'
'_atom_site_aniso_B_23'
'_atom_site_aniso_B_33'
_category atom_site
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_aniso_label'
_related_item '_atom_site_aniso_U_'
_related_function conversion
_units A^2^
_units_detail 'angstroms squared'
_definition
; These are the standard anisotropic atomic displacement
components in angstroms squared which appear in the
structure-factor term
T = exp{-(1/4) sum~i~ [ sum~j~ (B^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are
entered by row.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
data_atom_site_aniso_label
_name '_atom_site_aniso_label'
_category atom_site
_type char
_list yes
_list_link_parent '_atom_site_label'
_definition
; Anisotropic atomic displacement parameters are usually looped in
a separate list. If this is the case, this code must match the
_atom_site_label of the associated atom in the atom coordinate
list and conform with the same rules described in
_atom_site_label.
;
data_atom_site_aniso_ratio
_name '_atom_site_aniso_ratio'
_category atom_site
_type numb
_list yes
_list_reference '_atom_site_aniso_label'
_enumeration_range 1.0:
_definition
; Ratio of the maximum to minimum principal axes of
displacement (thermal) ellipsoids.
;
data_atom_site_aniso_type_symbol
_name '_atom_site_aniso_type_symbol'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_aniso_label'
_list_link_parent '_atom_site_type_symbol'
_definition
; This _atom_type_symbol code links the anisotropic atom
parameters to the atom-type data associated with this site and
must match one of the _atom_type_symbol codes in this list.
;
data_atom_site_aniso_U_
loop_ _name '_atom_site_aniso_U_11'
'_atom_site_aniso_U_12'
'_atom_site_aniso_U_13'
'_atom_site_aniso_U_22'
'_atom_site_aniso_U_23'
'_atom_site_aniso_U_33'
_category atom_site
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_aniso_label'
_related_item '_atom_site_aniso_B_'
_related_function conversion
_units A^2^
_units_detail 'angstroms squared'
_definition
; These are the standard anisotropic atomic displacement
components in angstroms squared which appear in the
structure-factor term
T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
h = the Miller indices
a* = the reciprocal-space cell lengths
The unique elements of the real symmetric matrix are
entered by row.
;
data_atom_site_attached_hydrogens
_name '_atom_site_attached_hydrogens'
_category atom_site
_type numb
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0:8
_enumeration_default 0
loop_ _example
_example_detail 2 'water oxygen'
1 'hydroxyl oxygen'
4 'ammonium nitrogen'
_definition
; The number of hydrogen atoms attached to the atom at this site
excluding any hydrogen atoms for which coordinates (measured or
calculated) are given.
;
data_atom_site_B_equiv_geom_mean
_name '_atom_site_B_equiv_geom_mean'
_category atom_site
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
loop_ _related_item
_related_function '_atom_site_B_iso_or_equiv' alternate
'_atom_site_U_equiv_geom_mean' conversion
_units A^2^
_units_detail 'angstroms squared'
_definition
; Equivalent isotropic atomic displacement parameter, B(equiv),
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
B(equiv) = (B~i~ B~j~ B~k~)^1/3^
B~n~ = the principal components of the orthogonalized B^ij^
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
data_atom_site_B_iso_or_equiv
_name '_atom_site_B_iso_or_equiv'
_category atom_site
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
loop_ _related_item
_related_function '_atom_site_B_equiv_geom_mean' alternate
'_atom_site_U_iso_or_equiv' conversion
_units A^2^
_units_detail 'angstroms squared'
_definition
; Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, B(equiv), in angstroms squared,
calculated from anisotropic displacement components.
B(equiv) = (1/3) sum~i~[sum~j~(B^ij^ a*~i~ a*~j~ a~i~ a~j~)]
a = the real-space cell lengths
a* = the reciprocal-space cell lengths
B^ij^ = 8 pi^2^ U^ij^
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
775-776.
The IUCr Commission on Nomenclature recommends against the use
of B for reporting atomic displacement parameters. U, being
directly proportional to B, is preferred.
;
data_atom_site_calc_attached_atom
_name '_atom_site_calc_attached_atom'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_enumeration_default '.'
_definition
; The _atom_site_label of the atom site to which the 'geometry-
calculated' atom site is attached.
;
data_atom_site_calc_flag
_name '_atom_site_calc_flag'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_ _enumeration
_enumeration_detail d 'determined from diffraction measurements'
calc 'calculated from molecular geometry'
c 'abbreviation for "calc"'
dum 'dummy site with meaningless coordinates'
_enumeration_default d
_definition
; A standard code to signal whether the site coordinates have been
determined from the intensities or calculated from the geometry
of surrounding sites, or have been assigned dummy coordinates.
The abbreviation 'c' may be used in place of 'calc'.
;
data_atom_site_Cartn_
loop_ _name '_atom_site_Cartn_x'
'_atom_site_Cartn_y'
'_atom_site_Cartn_z'
_category atom_site
_type numb
_type_conditions esd
_related_item '_atom_site_fract_'
_related_function alternate
_list yes
_list_reference '_atom_site_label'
_units A
_units_detail 'angstroms'
_definition
; The atom-site coordinates in angstroms specified according to a
set of orthogonal Cartesian axes related to the cell axes as
specified by the _atom_sites_Cartn_transform_axes description.
;
data_atom_site_chemical_conn_number
_name '_atom_site_chemical_conn_number'
_category atom_site
_type numb
_list yes
_list_link_parent '_chemical_conn_atom_number'
_list_reference '_atom_site_label'
_enumeration_range 1:
_definition
; This number links an atom site to the chemical connectivity list.
It must match a number specified by _chemical_conn_atom_number.
;
data_atom_site_constraints
_name '_atom_site_constraints'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_enumeration_default '.'
_example 'pop=1.0-pop(Zn3)'
_definition
; A description of the constraints applied to parameters at this
site during refinement. See also _atom_site_refinement_flags
and _refine_ls_number_constraints.
;
data_atom_site_description
_name '_atom_site_description'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_example 'Ag/Si disordered'
_definition
; A description of special aspects of this site. See also
_atom_site_refinement_flags.
;
data_atom_site_disorder_assembly
_name '_atom_site_disorder_assembly'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_ _example
_example_detail A 'disordered methyl assembly with groups 1 and 2'
B 'disordered sites related by a mirror'
S 'disordered sites independent of symmetry'
_definition
; A code which identifies a cluster of atoms that show long-range
positional disorder but are locally ordered. Within each such
cluster of atoms, _atom_site_disorder_group is used to identify
the sites that are simultaneously occupied. This field is only
needed if there is more than one cluster of disordered atoms
showing independent local order.
;
data_atom_site_disorder_group
_name '_atom_site_disorder_group'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_ _example
_example_detail 1 'unique disordered site in group 1'
2 'unique disordered site in group 2'
-1 'symmetry-independent disordered site'
_definition
; A code which identifies a group of positionally disordered atom
sites that are locally simultaneously occupied. Atoms that are
positionally disordered over two or more sites (e.g. the hydrogen
atoms of a methyl group that exists in two orientations) can
be assigned to two or more groups. Sites belonging to the same
group are simultaneously occupied, but those belonging to
different groups are not. A minus prefix (e.g. "-1") is used to
indicate sites disordered about a special position.
;
data_atom_site_fract_
loop_ _name '_atom_site_fract_x'
'_atom_site_fract_y'
'_atom_site_fract_z'
_category atom_site
_type numb
_type_conditions esd
_related_item '_atom_site_Cartn_'
_related_function alternate
_list yes
_list_reference '_atom_site_label'
_definition
; Atom-site coordinates as fractions of the _cell_length_ values.
;
data_atom_site_label
_name '_atom_site_label'
_category atom_site
_type char
_list yes
_list_mandatory yes
loop_ _list_link_child '_atom_site_aniso_label'
'_geom_angle_atom_site_label_1'
'_geom_angle_atom_site_label_2'
'_geom_angle_atom_site_label_3'
'_geom_bond_atom_site_label_1'
'_geom_bond_atom_site_label_2'
'_geom_contact_atom_site_label_1'
'_geom_contact_atom_site_label_2'
'_geom_hbond_atom_site_label_D'
'_geom_hbond_atom_site_label_H'
'_geom_hbond_atom_site_label_A'
'_geom_torsion_atom_site_label_1'
'_geom_torsion_atom_site_label_2'
'_geom_torsion_atom_site_label_3'
'_geom_torsion_atom_site_label_4'
loop_ _example C12 Ca3g28 Fe3+17 H*251
boron2a C_a_phe_83_a_0 Zn_Zn_301_A_0
_definition
; The _atom_site_label is a unique identifier for a particular site
in the crystal. This code is made up of a sequence of up to seven
components, _atom_site_label_component_0 to *_6, which may be
specified as separate data items. Component 0 usually matches one
of the specified _atom_type_symbol codes. This is not mandatory
if an _atom_site_type_symbol item is included in the atom-site
list. The _atom_site_type_symbol always takes precedence over
an _atom_site_label in the identification of the atom type. The
label components 1 to 6 are optional, and normally only
components 0 and 1 are used. Note that components 0 and 1 are
concatenated, while all other components, if specified, are
separated by an underscore. Underscores are
only used if higher-order components exist. If an intermediate
component is not used, it may be omitted provided the underscore
separators are inserted. For example, the label 'C233__ggg' is
acceptable and represents the components C, 233, '' and ggg.
Different labels may have a different number of components.
;
data_atom_site_label_component_
loop_ _name '_atom_site_label_component_0'
'_atom_site_label_component_1'
'_atom_site_label_component_2'
'_atom_site_label_component_3'
'_atom_site_label_component_4'
'_atom_site_label_component_5'
'_atom_site_label_component_6'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_definition
; Component 0 is normally a code which matches identically with
one of the _atom_type_symbol codes. If this is the case, then the
rules governing the _atom_type_symbol code apply. If, however,
the data item _atom_site_type_symbol is also specified in the
atom-site list, component 0 need not match this symbol or adhere
to any of the _atom_type_symbol rules.
Component 1 is referred to as the "atom number". When component 0
is the atom-type code, it is used to number the sites with the
same atom type. This component code must start with at least one
digit which is not followed by a + or - sign (to distinguish it
from the component 0 rules).
Components 2 to 6 contain the identifier, residue, sequence,
asymmetry identifier and alternate codes, respectively. These
codes may be composed of any characters except an underscore.
;
data_atom_site_occupancy
_name '_atom_site_occupancy'
_category atom_site
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:1.0
_enumeration_default 1.0
_definition
; The fraction of the atom type present at this site.
The sum of the occupancies of all the atom types at this site
may not significantly exceed 1.0 unless it is a dummy site. The
value must lie in the 99.97% Gaussian confidence interval
-3u =< x =< 1 + 3u. The _enumeration_range of 0.0:1.0 is thus
correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
;
data_atom_site_refinement_flags
_name '_atom_site_refinement_flags'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
loop_
_related_item
_related_function
'_atom_site_refinement_flags_posn' replace
'_atom_site_refinement_flags_adp' replace
'_atom_site_refinement_flags_occupancy' replace
loop_ _enumeration
_enumeration_detail . 'no refinement constraints'
S 'special-position constraint on site'
G 'rigid-group refinement of site'
R 'riding-atom site attached to non-riding atom'
D 'distance or angle restraint on site'
T 'thermal displacement constraints'
U 'Uiso or Uij restraint (rigid bond)'
P 'partial occupancy constraint'
_definition
; A concatenated series of single-letter codes which indicate the
refinement restraints or constraints applied to this site. This
item should not be used. It has been replaced by
_atom_site_refinement_flags_posn, *_adp and *_occupancy. It is
retained in this dictionary only to provide compatibility with
legacy CIFs.
;
data_atom_site_refinement_flags_adp
_name '_atom_site_refinement_flags_adp'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_related_item '_atom_site_refinement_flags'
_related_function alternate
loop_ _enumeration
_enumeration_detail
. 'no constraints on atomic displacement parameters'
T 'special-position constraints on atomic displacement parameters'
U 'Uiso or Uij restraint (rigid bond)'
TU 'both constraints applied'
_definition
; A code which indicates the refinement restraints or constraints
applied to the atomic displacement parameters of this site.
;
data_atom_site_refinement_flags_occupancy
_name '_atom_site_refinement_flags_occupancy'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_related_item '_atom_site_refinement_flags'
_related_function alternate
loop_ _enumeration
_enumeration_detail . 'no constraints on site-occupancy parameters'
P 'site-occupancy constraint'
_definition
; A code which indicates that refinement restraints or
constraints were applied to the occupancy of this site.
;
data_atom_site_refinement_flags_posn
_name '_atom_site_refinement_flags_posn'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_related_item '_atom_site_refinement_flags'
_related_function alternate
loop_ _enumeration
_enumeration_detail
. 'no constraints on positional coordinates'
D 'distance or angle restraint on positional coordinates'
G 'rigid-group refinement of positional coordinates'
R 'riding-atom site attached to non-riding atom'
S 'special-position constraint on positional coordinates'
DG 'combination of the above constraints'
DR 'combination of the above constraints'
DS 'combination of the above constraints'
GR 'combination of the above constraints'
GS 'combination of the above constraints'
RS 'combination of the above constraints'
DGR 'combination of the above constraints'
DGS 'combination of the above constraints'
DRS 'combination of the above constraints'
GRS 'combination of the above constraints'
DGRS 'combination of the above constraints'
_definition
; A code which indicates the refinement restraints or constraints
applied to the positional coordinates of this site.
;
data_atom_site_restraints
_name '_atom_site_restraints'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_example 'restrained to planar ring'
_definition
; A description of restraints applied to specific parameters at
this site during refinement. See also _atom_site_refinement_flags
and _refine_ls_number_restraints.
;
data_atom_site_symmetry_multiplicity
_name '_atom_site_symmetry_multiplicity'
_category atom_site
_type numb
_list yes
_list_reference '_atom_site_label'
_enumeration_range 1:192
_definition
; The multiplicity of a site due to the space-group symmetry as
given in International Tables for Crystallography Vol. A (2002).
;
data_atom_site_thermal_displace_type
_name '_atom_site_thermal_displace_type'
_category atom_site
_type char
_related_item '_atom_site_adp_type'
_related_function replace
_list yes
_list_reference '_atom_site_label'
loop_ _enumeration
_enumeration_detail Uani 'anisotropic Uij'
Uiso 'isotropic U'
Uovl 'overall U'
Umpe 'multipole expansion U'
Bani 'anisotropic Bij'
Biso 'isotropic B'
Bovl 'overall B'
_definition
; A standard code used to describe the type of atomic displacement
parameters used for the site.
;
data_atom_site_type_symbol
_name '_atom_site_type_symbol'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_list_link_parent '_atom_type_symbol'
_list_link_child '_atom_site_aniso_type_symbol'
loop_ _example Cu Cu2+ dummy Fe3+Ni2+
S- H* H(SDS)
_definition
; A code to identify the atom species (singular or plural)
occupying this site.
This code must match a corresponding _atom_type_symbol. The
specification of this code is optional if component 0 of the
_atom_site_label is used for this purpose. See _atom_type_symbol.
;
data_atom_site_U_equiv_geom_mean
_name '_atom_site_U_equiv_geom_mean'
_category atom_site
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
loop_ _related_item
_related_function '_atom_site_U_iso_or_equiv' alternate
'_atom_site_B_equiv_geom_mean' conversion
_units A^2^
_units_detail 'angstroms squared'
_definition
; Equivalent isotropic atomic displacement parameter, U(equiv),
in angstroms squared, calculated as the geometric mean of
the anisotropic atomic displacement parameters.
U(equiv) = (U~i~ U~j~ U~k~)^1/3^
U~n~ = the principal components of the orthogonalized U^ij^
;
data_atom_site_U_iso_or_equiv
_name '_atom_site_U_iso_or_equiv'
_category atom_site
_type numb
_type_conditions esd
_list yes
_list_reference '_atom_site_label'
_enumeration_range 0.0:
loop_ _related_item
_related_function '_atom_site_U_equiv_geom_mean' alternate
'_atom_site_B_iso_or_equiv' conversion
_units A^2^
_units_detail 'angstroms squared'
_definition
; Isotropic atomic displacement parameter, or equivalent isotropic
atomic displacement parameter, U(equiv), in angstroms squared,
calculated from anisotropic atomic displacement parameters.
U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
a = the real-space cell lengths
a* = the reciprocal-space cell lengths
Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44,
775-776.
;
data_atom_site_Wyckoff_symbol
_name '_atom_site_Wyckoff_symbol'
_category atom_site
_type char
_list yes
_list_reference '_atom_site_label'
_definition
; The Wyckoff symbol (letter) as listed in the space-group tables
of International Tables for Crystallography Vol. A (2002).
;
################
## ATOM_SITES ##
################
data_atom_sites_[]
_name '_atom_sites_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_atom_sites_Cartn_transform_axes
'c along z, astar along x, b along y'
_atom_sites_Cartn_tran_matrix_11 58.39
_atom_sites_Cartn_tran_matrix_12 0.00
_atom_sites_Cartn_tran_matrix_13 0.00
_atom_sites_Cartn_tran_matrix_21 0.00
_atom_sites_Cartn_tran_matrix_22 86.70
_atom_sites_Cartn_tran_matrix_23 0.00
_atom_sites_Cartn_tran_matrix_31 0.00
_atom_sites_Cartn_tran_matrix_32 0.00
_atom_sites_Cartn_tran_matrix_33 46.27
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the ATOM_SITES category record details about
the crystallographic cell and cell transformations, which are
common to all atom sites.
;
data_atom_sites_Cartn_tran_matrix_
loop_ _name '_atom_sites_Cartn_tran_matrix_11'
'_atom_sites_Cartn_tran_matrix_12'
'_atom_sites_Cartn_tran_matrix_13'
'_atom_sites_Cartn_tran_matrix_21'
'_atom_sites_Cartn_tran_matrix_22'
'_atom_sites_Cartn_tran_matrix_23'
'_atom_sites_Cartn_tran_matrix_31'
'_atom_sites_Cartn_tran_matrix_32'
'_atom_sites_Cartn_tran_matrix_33'
_category atom_sites
_type numb
_definition
; Matrix elements used to transform fractional coordinates in
the ATOM_SITE category to Cartesian coordinates. The axial
alignments of this transformation are described in
_atom_sites_Cartn_transform_axes. The 3 x 1 translation is
defined in _atom_sites_Cartn_tran_vector_.
x' |11 12 13| x | 1 |
( y' ) Cartesian = |21 22 23| ( y ) fractional + | 2 |
z' |31 32 33| z | 3 |
;
data_atom_sites_Cartn_transform_axes
_name '_atom_sites_Cartn_transform_axes'
_category atom_sites
_type char
_example 'a parallel to x; b in the plane of y and z'
_definition
; A description of the relative alignment of the crystal cell
axes to the Cartesian orthogonal axes as applied in the
transformation matrix _atom_sites_Cartn_tran_matrix_.
;
data_atom_sites_Cartn_tran_vector_
loop_ _name '_atom_sites_Cartn_tran_vector_1'
'_atom_sites_Cartn_tran_vector_2'
'_atom_sites_Cartn_tran_vector_3'
_category atom_sites
_type numb
_definition
; Elements of a 3 x 1 translation vector used in the
transformation of fractional coordinates in the
ATOM_SITE category to Cartesian coordinates. The axial
alignments of this transformation are described in
_atom_sites_Cartn_transform_axes.
x' |11 12 13| x | 1 |
( y' ) Cartesian = |21 22 23| ( y ) fractional + | 2 |
z' |31 32 33| z | 3 |
;
data_atom_sites_fract_tran_matrix_
loop_ _name '_atom_sites_fract_tran_matrix_11'
'_atom_sites_fract_tran_matrix_12'
'_atom_sites_fract_tran_matrix_13'
'_atom_sites_fract_tran_matrix_21'
'_atom_sites_fract_tran_matrix_22'
'_atom_sites_fract_tran_matrix_23'
'_atom_sites_fract_tran_matrix_31'
'_atom_sites_fract_tran_matrix_32'
'_atom_sites_fract_tran_matrix_33'
_category atom_sites
_type numb
_definition
; Matrix elements used to transform Cartesian coordinates in
the ATOM_SITE category to fractional coordinates. The axial
alignments of this transformation are described in
_atom_sites_Cartn_transform_axes. The 3 x 1 translation is
defined in _atom_sites_fract_tran_vector_.
x' |11 12 13| x | 1 |
( y' ) fractional = |21 22 23| ( y ) Cartesian + | 2 |
z' |31 32 33| z | 3 |
;
data_atom_sites_fract_tran_vector_
loop_ _name '_atom_sites_fract_tran_vector_1'
'_atom_sites_fract_tran_vector_2'
'_atom_sites_fract_tran_vector_3'
_category atom_sites
_type numb
_definition
; Elements of a 3 x 1 translation vector used in the
transformation of Cartesian coordinates in the
ATOM_SITE category to fractional coordinates. The axial
alignments of this transformation are described in
_atom_sites_Cartn_transform_axes.
x' |11 12 13| x | 1 |
( y' ) fractional = |21 22 23| ( y ) Cartesian + | 2 |
z' |31 32 33| z | 3 |
;
data_atom_sites_solution_
loop_ _name '_atom_sites_solution_primary'
'_atom_sites_solution_secondary'
'_atom_sites_solution_hydrogens'
_category atom_sites
_type char
loop_ _enumeration
_enumeration_detail difmap 'difference Fourier map'
vecmap 'real-space vector search'
heavy 'heavy-atom method'
direct 'structure-invariant direct methods'
geom 'inferred from neighbouring sites'
disper 'anomalous-dispersion techniques'
isomor 'isomorphous structure methods'
_definition
; Codes which identify the methods used to locate the initial
atom sites. The *_primary code identifies how the first
atom sites were determined; the *_secondary code identifies
how the remaining non-hydrogen sites were located; and the
*_hydrogens code identifies how the hydrogen sites were located.
;
data_atom_sites_special_details
_name '_atom_sites_special_details'
_category atom_sites
_type char
_definition
; Additional information about the atomic coordinates not coded
elsewhere in the CIF.
;
###############
## ATOM_TYPE ##
###############
data_atom_type_[]
_name '_atom_type_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_atom_type_symbol
_atom_type_oxidation_number
_atom_type_number_in_cell
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C 0 72 .017 .009 International_Tables_Vol_IV_Table_2.2B
H 0 100 0 0 International_Tables_Vol_IV_Table_2.2B
O 0 12 .047 .032 International_Tables_Vol_IV_Table_2.2B
N 0 4 .029 .018 International_Tables_Vol_IV_Table_2.2B
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the ATOM_TYPE category record details about
properties of the atoms that occupy the atom sites, such as the
atomic scattering factors.
;
data_atom_type_analytical_mass_%
_name '_atom_type_analytical_mass_%'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_range 0.0:100.0
_definition
; Mass percentage of this atom type derived from chemical analysis.
;
data_atom_type_description
_name '_atom_type_description'
_category atom_type
_type char
_list yes
_list_reference '_atom_type_symbol'
loop_ _example deuterium 0.34Fe+0.66Ni
_definition
; A description of the atom(s) designated by this atom type. In
most cases, this will be the element name and oxidation state of
a single atom species. For disordered or nonstoichiometric
structures it will describe a combination of atom species.
;
data_atom_type_number_in_cell
_name '_atom_type_number_in_cell'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_range 0:
_definition
; Total number of atoms of this atom type in the unit cell.
;
data_atom_type_oxidation_number
_name '_atom_type_oxidation_number'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_range -8:8
_enumeration_default 0
_definition
; Formal oxidation state of this atom type in the structure.
;
data_atom_type_radius_
loop_ _name '_atom_type_radius_bond'
'_atom_type_radius_contact'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_range 0.0:5.0
_units A
_units_detail 'angstroms'
_definition
; The effective intra- and intermolecular bonding radii in
angstroms of this atom type.
;
data_atom_type_scat_Cromer_Mann_
loop_ _name '_atom_type_scat_Cromer_Mann_a1'
'_atom_type_scat_Cromer_Mann_a2'
'_atom_type_scat_Cromer_Mann_a3'
'_atom_type_scat_Cromer_Mann_a4'
'_atom_type_scat_Cromer_Mann_b1'
'_atom_type_scat_Cromer_Mann_b2'
'_atom_type_scat_Cromer_Mann_b3'
'_atom_type_scat_Cromer_Mann_b4'
'_atom_type_scat_Cromer_Mann_c'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_definition
; The Cromer-Mann scattering-factor coefficients used to calculate
the scattering factors for this atom type.
Ref: International Tables for X-ray Crystallography (1974).
Vol. IV, Table 2.2B
or International Tables for Crystallography (2004). Vol. C,
Tables 6.1.1.4 and 6.1.1.5
;
data_atom_type_scat_dispersion_
loop_ _name '_atom_type_scat_dispersion_imag'
'_atom_type_scat_dispersion_real'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_default 0.0
_definition
; The imaginary and real components of the anomalous-dispersion
scattering factor, f'' and f', in electrons for this atom type
and the radiation given in _diffrn_radiation_wavelength.
;
data_atom_type_scat_dispersion_source
_name '_atom_type_scat_dispersion_source'
_category atom_type
_type char
_list yes
_list_reference '_atom_type_symbol'
_example 'International Tables Vol. IV Table 2.3.1'
_definition
; Reference to source of real and imaginary dispersion
corrections for scattering factors used for this atom type.
;
data_atom_type_scat_length_neutron
_name '_atom_type_scat_length_neutron'
_category atom_type
_type numb
_list yes
_list_reference '_atom_type_symbol'
_enumeration_default 0.0
_units fm
_units_detail 'femtometres'
_definition
; The bound coherent scattering length in femtometres for the
atom type at the isotopic composition used for the diffraction
experiment.
;
data_atom_type_scat_source
_name '_atom_type_scat_source'
_category atom_type
_type char
_list yes
_list_reference '_atom_type_symbol'
_example 'International Tables Vol. IV Table 2.4.6B'
_definition
; Reference to source of scattering factors or scattering lengths
used for this atom type.
;
data_atom_type_scat_versus_stol_list
_name '_atom_type_scat_versus_stol_list'
_category atom_type
_type char
_list yes
_list_reference '_atom_type_symbol'
_definition
; A table of scattering factors as a function of sin theta over
lambda. This table should be well commented to indicate the
items present. Regularly formatted lists are strongly
recommended.
;
data_atom_type_symbol
_name '_atom_type_symbol'
_category atom_type
_type char
_list yes
_list_mandatory yes
_list_link_child '_atom_site_type_symbol'
loop_ _example C Cu2+ H(SDS) dummy FeNi
_definition
; The code used to identify the atom species (singular or plural)
representing this atom type. Normally this code is the element
symbol. The code may be composed of any character except an
underscore with the additional proviso that digits designate an
oxidation state and must be followed by a + or - character.
;
###########
## AUDIT ##
###########
data_audit_[]
_name '_audit_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_audit_block_code TOZ_1991-03-20
_audit_creation_date 1991-03-20
_audit_creation_method from_xtal_archive_file_using_CIFIO
_audit_update_record
; 1991-04-09 text and data added by Tony Willis.
1991-04-15 rec'd by co-editor as manuscript HL0007.
1991-04-17 adjustments based on first referee report.
1991-04-18 adjustments based on second referee report.
;
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the AUDIT category record details about the
creation and subsequent updating of the data block.
;
data_audit_block_code
_name '_audit_block_code'
_category audit
_type char
_example TOZ_1991-03-20
_definition
; A code intended to identify uniquely the current data block.
;
data_audit_creation_date
_name '_audit_creation_date'
_category audit
_type char
_example 1990-07-12
_definition
; The date that the data block was created. The date format
is yyyy-mm-dd.
;
data_audit_creation_method
_name '_audit_creation_method'
_category audit
_type char
_example 'spawned by the program QBEE'
_definition
; A description of how data were entered into the data block.
;
data_audit_update_record
_name '_audit_update_record'
_category audit
_type char
_example '1990-07-15 Updated by the Co-editor'
_definition
; A record of any changes to the data block. The update format
is a date (yyyy-mm-dd) followed by a description of the
changes. The latest update entry is added to the bottom of
this record.
;
##################
## AUDIT_AUTHOR ##
##################
data_audit_author_[]
_name '_audit_author_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_audit_author_name
_audit_author_address
'Fitzgerald, Paula M. D.'
; Department of Biophysical Chemistry
Merck Research Laboratories
PO Box 2000, Ry80M203
Rahway
New Jersey 07065
USA
;
'Van Middlesworth, J. F.'
; Department of Biophysical Chemistry
Merck Research Laboratories
PO Box 2000, Ry80M203
Rahway
New Jersey 07065
USA
;
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the AUDIT_AUTHOR category record details about
the author(s) of the data block.
;
data_audit_author_address
_name '_audit_author_address'
_category audit_author
_type char
_list yes
_list_reference '_audit_author_name'
_example
; Department
Institute
Street
City and postcode
COUNTRY
;
_definition
; The address of an author of this data block. If there are
multiple authors, _audit_author_address is looped with
_audit_author_name.
;
data_audit_author_name
_name '_audit_author_name'
_category audit_author
_type char
_list yes
_list_mandatory yes
loop_ _example 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A.'
'M\"uller, H.A.'
'Ross II, C.R.'
_definition
; The name of an author of this data block. If there are multiple
authors, _audit_author_name is looped with _audit_author_address.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
###################
## AUDIT_CONFORM ##
###################
data_audit_conform_[]
_name '_audit_conform_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_audit_conform_dict_name cif_core.dic
_audit_conform_dict_version 2.3.1
_audit_conform_dict_location
ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic
;
;
Example 1 - any file conforming to the current CIF core dictionary.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the AUDIT_CONFORM category describe the
dictionary versions against which the data names appearing in
the current data block are conformant.
;
data_audit_conform_dict_location
_name '_audit_conform_dict_location'
_category audit_conform
_type char
_list both
_list_reference '_audit_conform_dict_name'
_definition
; A file name or uniform resource locator (URL) for the
dictionary to which the current data block conforms.
;
data_audit_conform_dict_name
_name '_audit_conform_dict_name'
_category audit_conform
_type char
_list both
_list_mandatory yes
_definition
; The string identifying the highest-level dictionary defining
data names used in this file.
;
data_audit_conform_dict_version
_name '_audit_conform_dict_version'
_category audit_conform
_type char
_list both
_list_reference '_audit_conform_dict_name'
_definition
; The version number of the dictionary to which the
current data block conforms.
;
##########################
## AUDIT_CONTACT_AUTHOR ##
##########################
data_audit_contact_author_[]
_name '_audit_contact_author_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_audit_contact_author_name
_audit_contact_author_address
_audit_contact_author_email
_audit_contact_author_fax
_audit_contact_author_phone
'Fitzgerald, Paula M. D.'
; Department of Biophysical Chemistry
Merck Research Laboratories
PO Box 2000, Ry80M203
Rahway
New Jersey 07065
USA
;
'paula_fitzgerald@merck.com'
'1(908)5945510'
'1(908)5945510'
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the AUDIT_CONTACT_AUTHOR category record details
about the name and address of the author to be contacted
concerning the contents of this data block.
;
data_audit_contact_author_address
_name '_audit_contact_author_address'
_category audit_contact_author
_type char
_example
; Department
Institute
Street
City and postcode
COUNTRY
;
_definition
; The mailing address of the author of the data block to whom
correspondence should be addressed.
;
data_audit_contact_author_email
_name '_audit_contact_author_email'
_category audit_contact_author
_type char
loop_ _example name@host.domain.country
bm@iucr.org
_definition
; The electronic mail address of the author of the data block
to whom correspondence should be addressed, in a form
recognizable to international networks. The format of e-mail
addresses is given in Section 3.4, Address Specification, of
Internet Message Format, RFC 2822, P. Resnick (Editor),
Network Standards Group, April 2001.
;
data_audit_contact_author_fax
_name '_audit_contact_author_fax'
_category audit_contact_author
_type char
loop_
_example '12(34)9477334'
'12()349477334'
_definition
; The facsimile telephone number of the author of the data
block to whom correspondence should be addressed.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number with no spaces.
;
data_audit_contact_author_name
_name '_audit_contact_author_name'
_category audit_contact_author
_type char
loop_ _example 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A.'
'M\"uller, H.A.'
'Ross II, C.R.'
_definition
; The name of the author of the data block to whom correspondence
should be addressed.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
data_audit_contact_author_phone
_name '_audit_contact_author_phone'
_category audit_contact_author
_type char
loop_
_example '12(34)9477330'
'12()349477330'
'12(34)9477330x5543'
_definition
; The telephone number of the author of the data block to whom
correspondence should be addressed.
The recommended style starts with the international dialing
prefix, followed by the area code in parentheses, followed by the
local number and any extension number prefixed by 'x',
with no spaces.
;
################
## AUDIT_LINK ##
################
data_audit_link_[]
_name '_audit_link_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_audit_link_block_code
_audit_link_block_description
. 'discursive text of paper with two structures'
morA_(1) 'structure 1 of 2'
morA_(2) 'structure 2 of 2'
;
;
Example 1 - multiple structure paper, as illustrated
in A Guide to CIF for Authors (1995). IUCr: Chester.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_audit_link_block_code
_audit_link_block_description
. 'publication details'
KSE_COM 'experimental data common to ref./mod. structures'
KSE_REF 'reference structure'
KSE_MOD 'modulated structure'
;
;
Example 2 - example file for the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the AUDIT_LINK category record details about the
relationships between data blocks in the current CIF.
;
data_audit_link_block_code
_name '_audit_link_block_code'
_category audit_link
_type char
_list yes
_list_mandatory yes
_definition
; The value of _audit_block_code associated with a data block
in the current file related to the current data block. The
special value '.' may be used to refer to the current data
block for completeness.
;
data_audit_link_block_description
_name '_audit_link_block_description'
_category audit_link
_type char
_list yes
_list_reference '_audit_link_block_code'
_definition
; A textual description of the relationship of the referenced
data block to the current one.
;
##########
## CELL ##
##########
data_cell_[]
_name '_cell_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_cell_length_a 5.959(1)
_cell_length_b 14.956(1)
_cell_length_c 19.737(3)
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 1759.0(3)
_cell_measurement_temperature 293
_cell_measurement_reflns_used 25
_cell_measurement_theta_min 25
_cell_measurement_theta_max 31
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the CELL category record details about the
crystallographic cell parameters and their measurement.
;
data_cell_angle_
loop_ _name '_cell_angle_alpha'
'_cell_angle_beta'
'_cell_angle_gamma'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:180.0
_enumeration_default 90.0
_units deg
_units_detail 'degrees'
_definition
; Unit-cell angles of the reported structure in degrees.
The values of _refln_index_h, *_k, *_l must correspond to the
cell defined by these values and _cell_length_a, *_b and *_c.
The values of _diffrn_refln_index_h, *_k, *_l may not correspond
to these values if a cell transformation took place following
the measurement of the diffraction intensities. See also
_diffrn_reflns_transf_matrix_.
;
data_cell_formula_units_Z
_name '_cell_formula_units_Z'
_category cell
_type numb
_enumeration_range 1:
_definition
; The number of the formula units in the unit cell as specified
by _chemical_formula_structural, _chemical_formula_moiety or
_chemical_formula_sum.
;
data_cell_length_
loop_ _name '_cell_length_a'
'_cell_length_b'
'_cell_length_c'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; Unit-cell lengths in angstroms corresponding to the structure
reported. The values of _refln_index_h, *_k, *_l must
correspond to the cell defined by these values and _cell_angle_
values. The values of _diffrn_refln_index_h, *_k, *_l may not
correspond to these values if a cell transformation took place
following the measurement of the diffraction intensities. See
also _diffrn_reflns_transf_matrix_.
;
data_cell_measurement_pressure
_name '_cell_measurement_pressure'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units kPa
_units_detail 'kilopascals'
_definition
; The pressure in kilopascals at which the unit-cell parameters
were measured (not the pressure at which the sample was
synthesized).
;
data_cell_measurement_radiation
_name '_cell_measurement_radiation'
_category cell
_type char
loop_ _example 'neutron' 'Cu K\a' 'synchrotron'
_definition
; Description of the radiation used to measure the unit-cell data.
See also _cell_measurement_wavelength.
;
data_cell_measurement_reflns_used
_name '_cell_measurement_reflns_used'
_category cell
_type numb
_definition
; The total number of reflections used to determine the unit cell.
These reflections may be specified as _cell_measurement_refln_
data items.
;
data_cell_measurement_temperature
_name '_cell_measurement_temperature'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units K
_units_detail kelvin
_definition
; The temperature in kelvins at which the unit-cell parameters
were measured (not the temperature of synthesis).
;
data_cell_measurement_theta_
loop_ _name '_cell_measurement_theta_max'
'_cell_measurement_theta_min'
_category cell
_type numb
_enumeration_range 0.0:90.0
_units deg
_units_detail 'degrees'
_definition
; The maximum and minimum theta angles of reflections
used to measure the unit cell in degrees.
;
data_cell_measurement_wavelength
_name '_cell_measurement_wavelength'
_category cell
_type numb
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The wavelength in angstroms of the radiation used to measure
the unit cell. If this is not specified, the wavelength is
assumed to be the same as that given in
_diffrn_radiation_wavelength.
;
data_cell_reciprocal_angle_
loop_ _name '_cell_reciprocal_angle_alpha'
'_cell_reciprocal_angle_beta'
'_cell_reciprocal_angle_gamma'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:180.0
_enumeration_default 90.0
_units deg
_units_detail 'degrees'
_definition
; The angles defining the reciprocal cell in degrees. These
are related to those in the real cell by:
cos(recip-alpha)
= [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)]
cos(recip-beta)
= [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)]
cos(recip-gamma)
= [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)]
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
data_cell_reciprocal_length_
loop_ _name '_cell_reciprocal_length_a'
'_cell_reciprocal_length_b'
'_cell_reciprocal_length_c'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units A^-1^
_units_detail 'reciprocal angstroms'
_definition
; The reciprocal-cell lengths in inverse angstroms. These are
related to the real cell by:
recip-a = b*c*sin(alpha)/V
recip-b = c*a*sin(beta)/V
recip-c = a*b*sin(gamma)/V
where V is the cell volume.
Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360.
New York: John Wiley & Sons Inc.
;
data_cell_special_details
_name '_cell_special_details'
_category cell
_type char
loop_ _example 'pseudo-orthorhombic'
'standard setting from 45 deg rotation around c'
_definition
; A description of special aspects of the cell choice, noting
possible alternative settings.
;
data_cell_volume
_name '_cell_volume'
_category cell
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units A^3^
_units_detail 'cubic angstroms'
_definition
; Cell volume V in angstroms cubed.
V = a b c [1 - cos^2^(alpha) - cos^2^(beta) - cos^2^(gamma)
+ 2 cos(alpha) cos(beta) cos(gamma) ] ^1/2^
a = _cell_length_a
b = _cell_length_b
c = _cell_length_c
alpha = _cell_angle_alpha
beta = _cell_angle_beta
gamma = _cell_angle_gamma
;
############################
## CELL_MEASUREMENT_REFLN ##
############################
data_cell_measurement_refln_[]
_name '_cell_measurement_refln_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_cell_measurement_refln_index_h
_cell_measurement_refln_index_k
_cell_measurement_refln_index_l
_cell_measurement_refln_theta
-2 4 1 8.67
0 3 2 9.45
3 0 2 9.46
-3 4 1 8.93
-2 1 -2 7.53
10 0 0 23.77
0 10 0 23.78
-5 4 1 11.14
# - - - - data truncated for brevity - - - -
;
;
Example 1 - extracted from the CAD-4 listing for Rb~2~S~2~O~6~ at room
temperature (unpublished).
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the CELL_MEASUREMENT_REFLN category record
details about the reflections used in the determination of the
crystallographic cell parameters.
The _cell_measurement_refln_ data items would in general be used
only for diffractometer measurements.
;
data_cell_measurement_refln_index_
loop_ _name '_cell_measurement_refln_index_h'
'_cell_measurement_refln_index_k'
'_cell_measurement_refln_index_l'
_category cell_measurement_refln
_type numb
_list yes
_list_mandatory yes
_definition
; Miller indices of a reflection used for measurement of
the unit cell.
;
data_cell_measurement_refln_theta
_name '_cell_measurement_refln_theta'
_category cell_measurement_refln
_type numb
_list yes
_list_reference '_cell_measurement_refln_index_'
_enumeration_range 0.0:90.0
_units deg
_units_detail 'degrees'
_definition
; Theta angle in degrees for the reflection used for
measurement of the unit cell with the indices
_cell_measurement_refln_index_.
;
##############
## CHEMICAL ##
##############
data_chemical_[]
_name '_chemical_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_chemical_name_systematic
trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)
;
;
Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan
[Acta Cryst. (1996), C52, 765-767].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the CHEMICAL category record details about the
composition and chemical properties of the compound. The
formula data items must agree with those that specify the
density, unit-cell and Z values.
;
data_chemical_absolute_configuration
_name '_chemical_absolute_configuration'
_category chemical
_type char
loop_ _enumeration
_enumeration_detail rm
; absolute configuration established by
the structure determination of a
compound containing a chiral reference
molecule of known absolute
configuration
;
ad
; absolute configuration established by
anomalous-dispersion effects in
diffraction measurements on the
crystal
;
rmad
; absolute configuration established by
the structure determination of a
compound containing a chiral reference
molecule of known absolute
configuration and confirmed by
anomalous-dispersion effects in
diffraction measurements on the
crystal
;
syn
; absolute configuration has not been
established by anomalous-dispersion
effects in diffraction measurements on
the crystal. The enantiomer has been
assigned by reference to an unchanging
chiral centre in the synthetic
procedure
;
unk
; absolute configuration is unknown,
there being no firm chemical evidence
for its assignment to hand and it
having not been established by
anomalous-dispersion effects in
diffraction measurements on the
crystal. An arbitrary choice of
enantiomer has been made
;
. 'inapplicable'
_definition
; Necessary conditions for the assignment of
_chemical_absolute_configuration are given by H. D. Flack and
G. Bernardinelli (1999, 2000).
Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55,
908-915. (http://www.iucr.org/paper?sh0129)
Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst.
33, 1143-1148. (http://www.iucr.org/paper?ks0021)
;
data_chemical_compound_source
_name '_chemical_compound_source'
_category chemical
_type char
loop_ _example 'From Norilsk (USSR)'
'Extracted from the bark of Cinchona Naturalis'
_definition
; Description of the source of the compound under study, or of the
parent molecule if a simple derivative is studied. This includes
the place of discovery for minerals or the actual source of a
natural product.
;
data_chemical_melting_point
_name '_chemical_melting_point'
_category chemical
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units K
_units_detail kelvin
_definition
; The temperature in kelvins at which the crystalline solid changes
to a liquid.
;
data_chemical_melting_point_
loop_ _name '_chemical_melting_point_gt'
'_chemical_melting_point_lt'
_category chemical
_type numb
_related_item '_chemical_melting_point'
_related_function alternate
_enumeration_range 0.0:
_units K
_units_detail kelvin
_definition
; A temperature in kelvins below which (*_lt) or above
which (*_gt) the melting point (the temperature at which the
crystalline solid changes to a liquid) lies. These items allow a
range of temperatures to be given.
_chemical_melting_point should always be used in preference
to these items whenever possible.
;
data_chemical_name_common
_name '_chemical_name_common'
_category chemical
_type char
_example '1-bromoestradiol'
_definition
; Trivial name by which the compound is commonly known.
;
data_chemical_name_mineral
_name '_chemical_name_mineral'
_category chemical
_type char
_example chalcopyrite
_definition
; Mineral name accepted by the International Mineralogical
Association. Use only for natural minerals. See also
_chemical_compound_source.
;
data_chemical_name_structure_type
_name '_chemical_name_structure_type'
_category chemical
_type char
loop_ _example perovskite sphalerite A15
_definition
; Commonly used structure-type name. Usually only applied to
minerals or inorganic compounds.
;
data_chemical_name_systematic
_name '_chemical_name_systematic'
_category chemical
_type char
_example '1-bromoestra-1,3,5(10)-triene-3,17\b-diol'
_definition
; IUPAC or Chemical Abstracts full name of the compound.
;
data_chemical_optical_rotation
_name '_chemical_optical_rotation'
_category chemical
_type char
_example '[\a]^25^~D~ = +108 (c = 3.42, CHCl~3~)'
_definition
; The optical rotation in solution of the compound is
specified in the following format:
'[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)'
where:
TEMP is the temperature of the measurement in degrees
Celsius,
WAVE is an indication of the wavelength of the light
used for the measurement,
CONC is the concentration of the solution given as the
mass of the substance in g per 100 ml of solution,
SORT is the signed value (preceded by a + or a - sign)
of 100.\a/(l.c), where \a is the signed optical
rotation in degrees measured in a cell of length l in
dm and c is the value of CONC as defined above, and
SOLV is the chemical formula of the solvent.
;
data_chemical_properties_biological
_name '_chemical_properties_biological'
_category chemical
_type char
loop_ _example
; diverse biological activities including use as a
laxative and strong antibacterial activity against
S. aureus and weak activity against
cyclooxygenase-1 (COX-1)
;
; antibiotic activity against Bacillus subtilis
(ATCC 6051) but no significant activity against
Candida albicans (ATCC 14053), Aspergillus flavus
(NRRL 6541) and Fusarium verticillioides (NRRL
25457)
;
; weakly potent lipoxygenase nonredox inhibitor
;
; no influenza A virus sialidase inhibitory and
plaque reduction activities
;
; low toxicity against Drosophila melanogaster
;
_definition
; A free-text description of the biological properties of the
material.
;
data_chemical_properties_physical
_name '_chemical_properties_physical'
_category chemical
_type char
loop_ _example air-sensitive
moisture-sensitive
hygroscopic
deliquescent
oxygen-sensitive
photo-sensitive
pyrophoric
semiconductor
'ferromagnetic at low temperature'
'paramagnetic and thermochromic'
_definition
; A free-text description of the physical properties of the
material.
;
data_chemical_temperature_decomposition
_name '_chemical_temperature_decomposition'
_category chemical
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units K
_units_detail kelvin
_example 350
_definition
; The temperature in kelvins at which the solid decomposes.
;
data_chemical_temperature_decomposition_
loop_ _name '_chemical_temperature_decomposition_gt'
'_chemical_temperature_decomposition_lt'
_category chemical
_type numb
_enumeration_range 0.0:
_units K
_units_detail kelvin
_related_item '_chemical_temperature_decomposition'
_related_function alternate
_example 350
_definition
; A temperature in kelvins below which (*_lt) or above which
(*_gt) the solid is known to decompose. These items allow
a range of temperatures to be given.
_chemical_temperature_decomposition should always be used in
preference to these items whenever possible.
;
data_chemical_temperature_sublimation
_name '_chemical_temperature_sublimation'
_category chemical
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units K
_units_detail kelvin
_example 350
_definition
; The temperature in kelvins at which the solid sublimes.
;
data_chemical_temperature_sublimation_
loop_ _name '_chemical_temperature_sublimation_gt'
'_chemical_temperature_sublimation_lt'
_category chemical
_type numb
_enumeration_range 0.0:
_units K
_units_detail kelvin
_related_item '_chemical_temperature_sublimation'
_related_function alternate
_example 350
_definition
; A temperature in kelvins below which (*_lt) or above which
(*_gt) the solid is known to sublime. These items allow a
range of temperatures to be given.
_chemical_temperature_sublimation should always be used in
preference to these items whenever possible.
;
########################
## CHEMICAL_CONN_ATOM ##
########################
data_chemical_conn_atom_[]
_name '_chemical_conn_atom_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_chemical_conn_atom_number
_chemical_conn_atom_type_symbol
_chemical_conn_atom_display_x
_chemical_conn_atom_display_y
_chemical_conn_atom_NCA
_chemical_conn_atom_NH
1 S .39 .81 1 0
2 S .39 .96 2 0
3 N .14 .88 3 0
4 C .33 .88 3 0
5 C .11 .96 2 2
6 C .03 .96 2 2
7 C .03 .80 2 2
8 C .11 .80 2 2
9 S .54 .81 1 0
10 S .54 .96 2 0
11 N .80 .88 3 0
12 C .60 .88 3 0
13 C .84 .96 2 2
14 C .91 .96 2 2
15 C .91 .80 2 2
16 C .84 .80 2 2
;
;
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the _chemical_conn_atom_ and _chemical_conn_bond_
categories record details about the two-dimensional (2D)
chemical structure of the molecular species. They allow a 2D
chemical diagram to be reconstructed for use in a publication or
in a database search for structural and substructural
relationships.
The _chemical_conn_atom_ data items provide information about
the chemical properties of the atoms in the structure. In cases
where crystallographic and molecular symmetry elements coincide,
they must also contain symmetry-generated atoms, so that the
_chemical_conn_atom_ and _chemical_conn_bond_ data items will
always describe a complete chemical entity.
;
data_chemical_conn_atom_charge
_name '_chemical_conn_atom_charge'
_category chemical_conn_atom
_type numb
_list yes
_list_reference '_chemical_conn_atom_type_symbol'
_enumeration_range -6:6
_enumeration_default 0
loop_ _example
_example_detail 1 'for an ammonium nitrogen'
-1 'for a chloride ion'
_definition
; The net integer charge assigned to this atom. This is the
formal charge assignment normally found in chemical diagrams.
;
data_chemical_conn_atom_display_
loop_ _name '_chemical_conn_atom_display_x'
'_chemical_conn_atom_display_y'
_category chemical_conn_atom
_type numb
_list yes
_list_reference '_chemical_conn_atom_type_symbol'
_enumeration_range 0.0:1.0
_definition
; The 2D Cartesian coordinates (x,y) of the position of this atom
in a recognizable chemical diagram. The coordinate origin is at
the lower left corner, the x axis is horizontal and the y axis is
vertical. The coordinates must lie in the range 0.0 to 1.0. These
coordinates can be obtained from projections of a suitable
uncluttered view of the molecular structure.
;
data_chemical_conn_atom_NCA
_name '_chemical_conn_atom_NCA'
_category chemical_conn_atom
_type numb
_list yes
_list_reference '_chemical_conn_atom_type_symbol'
_enumeration_range 0:
_definition
; The number of connected atoms excluding terminal hydrogen atoms.
;
data_chemical_conn_atom_NH
_name '_chemical_conn_atom_NH'
_category chemical_conn_atom
_type numb
_list yes
_list_reference '_chemical_conn_atom_type_symbol'
_enumeration_range 0:
_definition
; The total number of hydrogen atoms attached to this atom,
regardless of whether they are included in the refinement or
the _atom_site_ list. This number will be the same as
_atom_site_attached_hydrogens only if none of the hydrogen
atoms appear in the _atom_site_ list.
;
data_chemical_conn_atom_number
_name '_chemical_conn_atom_number'
_category chemical_conn_atom
_type numb
_list yes
loop_ _list_link_child '_atom_site_chemical_conn_number'
'_chemical_conn_bond_atom_1'
'_chemical_conn_bond_atom_2'
_list_reference '_chemical_conn_atom_type_symbol'
_enumeration_range 1:
_definition
; The chemical sequence number to be associated with this atom.
;
data_chemical_conn_atom_type_symbol
_name '_chemical_conn_atom_type_symbol'
_category chemical_conn_atom
_type char
_list yes
_list_mandatory yes
_definition
; A code identifying the atom type. This code must match an
_atom_type_symbol code in the _atom_type_ list or be a
recognizable element symbol.
;
########################
## CHEMICAL_CONN_BOND ##
########################
data_chemical_conn_bond_[]
_name '_chemical_conn_bond_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_chemical_conn_bond_atom_1
_chemical_conn_bond_atom_2
_chemical_conn_bond_type
4 1 doub 4 3 sing
4 2 sing 5 3 sing
6 5 sing 7 6 sing
8 7 sing 8 3 sing
10 2 sing 12 9 doub
12 11 sing 12 10 sing
13 11 sing 14 13 sing
15 14 sing 16 15 sing
16 11 sing 17 5 sing
18 5 sing 19 6 sing
20 6 sing 21 7 sing
22 7 sing 23 8 sing
24 8 sing 25 13 sing
26 13 sing 27 14 sing
28 14 sing 29 15 sing
30 15 sing 31 16 sing
32 16 sing
;
;
Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar &
bin Shawkataly [Acta Cryst. (1996), C52, 951-953].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the _chemical_conn_atom_ and _chemical_conn_bond_
categories record details about the two-dimensional (2D)
chemical structure of the molecular species. They allow a 2D
chemical diagram to be reconstructed for use in a publication
or in a database search for structural and substructural
relationships.
The _chemical_conn_bond_ data items specify the connections
between the atoms in the _chemical_conn_atom_ list and the nature
of the chemical bond between these atoms.
;
data_chemical_conn_bond_atom_
loop_ _name '_chemical_conn_bond_atom_1'
'_chemical_conn_bond_atom_2'
_category chemical_conn_bond
_type numb
_list yes
_list_link_parent '_chemical_conn_atom_number'
_enumeration_range 1:
_definition
; Atom numbers which must match with chemical sequence numbers
specified as _chemical_conn_atom_number values. These link the
bond connection to the chemical numbering and atom sites.
;
data_chemical_conn_bond_type
_name '_chemical_conn_bond_type'
_category chemical_conn_bond
_type char
_list yes
_list_reference '_chemical_conn_bond_atom_'
loop_ _enumeration
_enumeration_detail sing 'single bond'
doub 'double bond'
trip 'triple bond'
quad 'quadruple bond'
arom 'aromatic bond'
poly 'polymeric bond'
delo 'delocalized double bond'
pi 'pi bond'
_enumeration_default sing
_definition
; The chemical bond type associated with the connection between
the two sites _chemical_conn_bond_atom_1 and *_2.
;
######################
## CHEMICAL_FORMULA ##
######################
data_chemical_formula_[]
_name '_chemical_formula_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_chemical_formula_moiety 'C18 H25 N O3'
_chemical_formula_sum 'C18 H25 N O3'
_chemical_formula_weight 303.40
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_chemical_formula_iupac '[Mo (C O)4 (C18 H33 P)2]'
_chemical_formula_moiety 'C40 H66 Mo O4 P2'
_chemical_formula_structural '((C O)4 (P (C6 H11)3)2)Mo'
_chemical_formula_sum 'C40 H66 Mo O4 P2'
_chemical_formula_weight 768.81
;
;
Example 2 - based on data set 9597gaus of Alyea, Ferguson & Kannan
[Acta Cryst. (1996), C52, 765-767].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; _chemical_formula_ items specify the composition and chemical
properties of the compound. The formula data items must agree
with those that specify the density, unit-cell and Z values.
The following rules apply to the construction of the data items
_chemical_formula_analytical, *_structural and *_sum. For the
data item *_moiety, the formula construction is broken up into
residues or moieties, i.e. groups of atoms that form a molecular
unit or molecular ion. The rules given below apply within each
moiety but different requirements apply to the way that moieties
are connected (see _chemical_formula_moiety).
(1) Only recognized element symbols may be used.
(2) Each element symbol is followed by a 'count' number. A
count of '1' may be omitted.
(3) A space or parenthesis must separate each cluster of (element
symbol + count).
(4) Where a group of elements is enclosed in parentheses, the
multiplier for the group must follow the closing parenthesis.
That is, all element and group multipliers are assumed to be
printed as subscripted numbers. (An exception to this rule
exists for *_moiety formulae where pre- and post-multipliers
are permitted for molecular units.)
(5) Unless the elements are ordered in a manner that corresponds
to their chemical structure, as in
_chemical_formula_structural, the order of the elements within
any group or moiety depends on whether carbon is present or
not. If carbon is present, the order should be: C, then H,
then the other elements in alphabetical order of their
symbol. If carbon is not present, the elements are listed
purely in alphabetical order of their symbol. This is the
'Hill' system used by Chemical Abstracts. This ordering is
used in _chemical_formula_moiety and _chemical_formula_sum.
;
data_chemical_formula_analytical
_name '_chemical_formula_analytical'
_category chemical_formula
_type char
_example 'Fe2.45(2) Ni1.60(3) S4'
_definition
; Formula determined by standard chemical analysis including trace
elements. See the _chemical_formula_[] category description for
rules for writing chemical formulae. Parentheses are used only
for standard uncertainties (e.s.d.'s).
;
data_chemical_formula_iupac
_name '_chemical_formula_iupac'
_category chemical_formula
_type char
_example '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H'
_definition
; Formula expressed in conformance with IUPAC rules for inorganic
and metal-organic compounds where these conflict with the rules
for any other _chemical_formula_ entries. Typically used for
formatting a formula in accordance with journal rules. This
should appear in the data block in addition to the most
appropriate of the other _chemical_formula_ data names.
Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry.
Oxford: Blackwell Scientific Publications.
;
data_chemical_formula_moiety
_name '_chemical_formula_moiety'
_category chemical_formula
_type char
loop_ _example 'C7 H4 Cl Hg N O3 S'
'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-'
'C12 H16 N2 O6, 5(H2 O1)'
"(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)"
_definition
; Formula with each discrete bonded residue or ion shown as a
separate moiety. See the _chemical_formula_[] category
description for rules for writing chemical formulae. In addition
to the general formulae requirements, the following rules apply:
(1) Moieties are separated by commas ','.
(2) The order of elements within a moiety follows general rule
(5) in the _chemical_formula_[] category description.
(3) Parentheses are not used within moieties but may surround
a moiety. Parentheses may not be nested.
(4) Charges should be placed at the end of the moiety. The
charge '+' or '-' may be preceded by a numerical multiplier
and should be separated from the last (element symbol +
count) by a space. Pre- or post-multipliers may be used for
individual moieties.
;
data_chemical_formula_structural
_name '_chemical_formula_structural'
_category chemical_formula
_type char
loop_ _example 'Ca ((Cl O3)2 O)2 (H2 O)6'
'(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2'
_definition
; See the _chemical_formula_[] category description for the rules
for writing chemical formulae for inorganics, organometallics,
metal complexes etc., in which bonded groups are preserved
as discrete entities within parentheses, with post-multipliers
as required. The order of the elements should give as much
information as possible about the chemical structure.
Parentheses may be used and nested as required. This formula
should correspond to the structure as actually reported,
i.e. trace elements not included in atom-type and atom-site
lists should not be included in this formula (see also
_chemical_formula_analytical).
;
data_chemical_formula_sum
_name '_chemical_formula_sum'
_category chemical_formula
_type char
loop_ _example 'C18 H19 N7 O8 S'
_definition
; See the _chemical_formula_[] category description for the rules
for writing chemical formulae in which all discrete bonded
residues and ions are summed over the constituent elements,
following the ordering given in general rule (5) in the
_chemical_formula_[] category description. Parentheses are not
normally used.
;
data_chemical_formula_weight
_name '_chemical_formula_weight'
_category chemical_formula
_type numb
_enumeration_range 1.0:
_units Da
_units_detail 'daltons'
_definition
; Formula mass in daltons. This mass should correspond to the
formulae given under _chemical_formula_structural, *_iupac,
*_moiety or *_sum and, together with the Z value and cell
parameters, should yield the density given as
_exptl_crystal_density_diffrn.
;
data_chemical_formula_weight_meas
_name '_chemical_formula_weight_meas'
_category chemical_formula
_type numb
_enumeration_range 1.0:
_units Da
_units_detail 'daltons'
_definition
; Formula mass in daltons measured by a non-diffraction experiment.
;
##############
## CITATION ##
##############
data_citation_[]
_name '_citation_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_citation_id
_citation_coordinate_linkage
_citation_title
_citation_country
_citation_page_first
_citation_page_last
_citation_year
_citation_journal_abbrev
_citation_journal_volume
_citation_journal_issue
_citation_journal_id_ASTM
_citation_journal_id_ISSN
_citation_book_title
_citation_book_publisher
_citation_book_id_ISBN
_citation_special_details
primary yes
; Crystallographic analysis of a complex between human
immunodeficiency virus type 1 protease and
acetyl-pepstatin at 2.0-Angstroms resolution.
;
US 14209 14219 1990 'J. Biol. Chem.' 265 .
HBCHA3 0021-9258 . . .
; The publication that directly relates to this coordinate
set.
;
2 no
; Three-dimensional structure of aspartyl-protease from
human immunodeficiency virus HIV-1.
;
UK 615 619 1989 'Nature' 337 .
NATUAS 0028-0836 . . .
; Determination of the structure of the unliganded enzyme.
;
3 no
; Crystallization of the aspartylprotease from human
immunodeficiency virus, HIV-1.
;
US 1919 1921 1989 'J. Biol. Chem.' 264 .
HBCHA3 0021-9258 . . .
; Crystallization of the unliganded enzyme.
;
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the CITATION category record details about the
literature cited as being relevant to the contents of the data
block.
;
data_citation_abstract
_name '_citation_abstract'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; Abstract for the citation. This is used most when the
citation is extracted from a bibliographic database that
contains full text or abstract information.
;
data_citation_abstract_id_CAS
_name '_citation_abstract_id_CAS'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The Chemical Abstracts Service (CAS) abstract identifier;
relevant for journal articles.
;
data_citation_book_id_ISBN
_name '_citation_book_id_ISBN'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The International Standard Book Number (ISBN) code assigned to
the book cited; relevant for books or book chapters.
;
data_citation_book_publisher
_name '_citation_book_publisher'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 'John Wiley'
_definition
; The name of the publisher of the citation; relevant
for books or book chapters.
;
data_citation_book_publisher_city
_name '_citation_book_publisher_city'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 'New York'
_definition
; The location of the publisher of the citation; relevant
for books or book chapters.
;
data_citation_book_title
_name '_citation_book_title'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The title of the book in which the citation appeared; relevant
for books or book chapters.
;
data_citation_coordinate_linkage
_name '_citation_coordinate_linkage'
_category citation
_type char
_list yes
_list_reference '_citation_id'
loop_ _enumeration
_enumeration_detail no 'citation unrelated to current coordinates'
n 'abbreviation for "no"'
yes 'citation related to current coordinates'
y 'abbreviation for "yes"'
_definition
; _citation_coordinate_linkage states whether or not this citation
is concerned with precisely the set of coordinates given in the
data block. If, for instance, the publication described the same
structure, but the coordinates had undergone further refinement
prior to creation of the data block, the value of this data item
would be 'no'.
;
data_citation_country
_name '_citation_country'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The country of publication; relevant for books and book
chapters.
;
data_citation_database_id_CSD
_name '_citation_database_id_CSD'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example LEKKUH
_definition
; Identifier ('refcode') of the database record in the Cambridge
Structural Database that contains details of the cited structure.
;
data_citation_database_id_Medline
_name '_citation_database_id_Medline'
_category citation
_type numb
_list yes
_list_reference '_citation_id'
_enumeration_range 1:
_example 89064067
_definition
; Accession number used by Medline to categorize a specific
bibliographic entry.
;
data_citation_id
_name '_citation_id'
_category citation
_type char
_list yes
_list_mandatory yes
loop_ _list_link_child '_citation_author_citation_id'
'_citation_editor_citation_id'
loop_ _example primary 1 2 3
_definition
; The value of _citation_id must uniquely identify a record in the
_citation_ list.
The _citation_id 'primary' should be used to indicate the
citation that the author(s) consider to be the most pertinent to
the contents of the data block.
Note that this item need not be a number; it can be any unique
identifier.
;
data_citation_journal_abbrev
_name '_citation_journal_abbrev'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 'J. Mol. Biol.'
_definition
; Abbreviated name of the journal cited as given in the Chemical
Abstracts Service Source Index.
;
data_citation_journal_id_ASTM
_name '_citation_journal_id_ASTM'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The American Society for Testing and Materials (ASTM) code
assigned to the journal cited (also referred to as the CODEN
designator of the Chemical Abstracts Service); relevant for
journal articles.
;
data_citation_journal_id_CSD
_name '_citation_journal_id_CSD'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example '0070'
_definition
; The Cambridge Structural Database (CSD) code assigned to the
journal cited; relevant for journal articles. This is also the
system used at the Protein Data Bank (PDB).
;
data_citation_journal_id_ISSN
_name '_citation_journal_id_ISSN'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The International Standard Serial Number (ISSN) code assigned to
the journal cited; relevant for journal articles.
;
data_citation_journal_full
_name '_citation_journal_full'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 'Journal of Molecular Biology'
_definition
; Full name of the journal cited; relevant for journal articles.
;
data_citation_journal_issue
_name '_citation_journal_issue'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 2
_definition
; Issue number of the journal cited; relevant for journal
articles.
;
data_citation_journal_volume
_name '_citation_journal_volume'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example 174
_definition
; Volume number of the journal cited; relevant for journal
articles.
;
data_citation_language
_name '_citation_language'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example German
_definition
; Language in which the cited article is written.
;
data_citation_page_
loop_ _name '_citation_page_first'
'_citation_page_last'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_definition
; The first and last pages of the citation; relevant for
journal articles, books and book chapters.
;
data_citation_special_details
_name '_citation_special_details'
_category citation
_type char
_list yes
_list_reference '_citation_id'
loop_ _example
; citation relates to this precise coordinate set
;
; citation relates to earlier low-resolution structure
;
; citation relates to further refinement of structure
reported in citation 2
;
_definition
; A description of special aspects of the relationship
of the contents of the data block to the literature item cited.
;
data_citation_title
_name '_citation_title'
_category citation
_type char
_list yes
_list_reference '_citation_id'
_example
; Structure of diferric duck ovotransferrin at 2.35 \%A
resolution.
;
_definition
; The title of the citation; relevant for journal articles, books
and book chapters.
;
data_citation_year
_name '_citation_year'
_category citation
_type numb
_list yes
_list_reference '_citation_id'
_example 1984
_definition
; The year of the citation; relevant for journal articles, books
and book chapters.
;
#####################
## CITATION_AUTHOR ##
#####################
data_citation_author_[]
_name '_citation_author_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_citation_author_citation_id
_citation_author_name
primary 'Fitzgerald, P.M.D.'
primary 'McKeever, B.M.'
primary 'Van Middlesworth, J.F.'
primary 'Springer, J.P.'
primary 'Heimbach, J.C.'
primary 'Leu, C.-T.'
primary 'Herber, W.K.'
primary 'Dixon, R.A.F.'
primary 'Darke, P.L.'
2 'Navia, M.A.'
2 'Fitzgerald, P.M.D.'
2 'McKeever, B.M.'
2 'Leu, C.-T.'
2 'Heimbach, J.C.'
2 'Herber, W.K.'
2 'Sigal, I.S.'
2 'Darke, P.L.'
2 'Springer, J.P.'
3 'McKeever, B.M.'
3 'Navia, M.A.'
3 'Fitzgerald, P.M.D.'
3 'Springer, J.P.'
3 'Leu, C.-T.'
3 'Heimbach, J.C.'
3 'Herber, W.K.'
3 'Sigal, I.S.'
3 'Darke, P.L.'
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the CITATION_AUTHOR category record details
about the authors associated with the citations in the
_citation_ list.
;
data_citation_author_citation_id
_name '_citation_author_citation_id'
_category citation_author
_type char
_list yes
_list_mandatory yes
_list_link_parent '_citation_id'
_definition
; The value of _citation_author_citation_id must match an
identifier specified by _citation_id in the _citation_ list.
;
data_citation_author_name
_name '_citation_author_name'
_category citation_author
_type char
_list yes
_list_mandatory yes
loop_ _example 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A.'
'M\"uller, H.A.'
'Ross II, C.R.'
_definition
; Name of an author of the citation; relevant for journal
articles, books and book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
data_citation_author_ordinal
_name '_citation_author_ordinal'
_category citation_author
_type char
_list yes
_definition
; This data name defines the order of the author's name in the
list of authors of a citation.
;
#####################
## CITATION_EDITOR ##
#####################
data_citation_editor_[]
_name '_citation_editor_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_citation_editor_citation_id
_citation_editor_name
5 'McKeever, B.M.'
5 'Navia, M.A.'
5 'Fitzgerald, P.M.D.'
5 'Springer, J.P.'
;
;
Example 1 - hypothetical example.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the CITATION_EDITOR category record details
about the editor associated with the book or book chapter
citations in the _citation_ list.
;
data_citation_editor_citation_id
_name '_citation_editor_citation_id'
_category citation_editor
_type char
_list yes
_list_mandatory yes
_list_link_parent '_citation_id'
_definition
; The value of _citation_editor_citation_id must match an
identifier specified by _citation_id in the _citation_ list.
;
data_citation_editor_name
_name '_citation_editor_name'
_category citation_editor
_type char
_list yes
_list_mandatory yes
loop_ _example 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A.'
'M\"uller, H.A.'
'Ross II, C.R.'
_definition
; Name of an editor of the citation; relevant for books and
book chapters.
The family name(s), followed by a comma and including any
dynastic components, precedes the first name(s) or initial(s).
;
data_citation_editor_ordinal
_name '_citation_editor_ordinal'
_category citation_editor
_type char
_list yes
_definition
; This data name defines the order of the editor's name in the
list of editors of a citation.
;
###############
## COMPUTING ##
###############
data_computing_[]
_name '_computing_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_computing_data_collection 'CAD-4 (Enraf-Nonius, 1989)'
_computing_cell_refinement 'CAD-4 (Enraf-Nonius, 1989)'
_computing_data_reduction 'CFEO (Solans, 1978)'
_computing_structure_solution 'SHELXS86 (Sheldrick, 1990)'
_computing_structure_refinement 'SHELXL93 (Sheldrick, 1993)'
_computing_molecular_graphics 'ORTEPII (Johnson, 1976)'
_computing_publication_material 'PARST (Nardelli, 1983)'
;
;
Example 1 - Rodr\'iguez-Romero, Ruiz-P\'erez & Solans
[Acta Cryst. (1996), C52, 1415-1417].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the COMPUTING category record details about the
computer programs used in the crystal structure analysis.
;
data_computing_
loop_ _name '_computing_cell_refinement'
'_computing_data_collection'
'_computing_data_reduction'
'_computing_molecular_graphics'
'_computing_publication_material'
'_computing_structure_refinement'
'_computing_structure_solution'
_category computing
_type char
loop_ _example 'CAD-4 (Enraf-Nonius, 1989)'
'DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990)'
'FRODO (Jones, 1986), ORTEP (Johnson, 1965)'
'CRYSTALS (Watkin, 1988)'
'SHELX85 (Sheldrick, 1985)'
_definition
; Software used in the processing of the data. Give the program
or package name and a brief reference.
;
##############
## DATABASE ##
##############
data_database_[]
_name '_database_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_database_code_CSD 'VOBYUG'
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DATABASE category record details about the
database identifiers of the data block.
These data items are assigned by database managers and should
only appear in a CIF if they originate from that source.
;
data_database_code_
loop_ _name '_database_code_CAS'
'_database_code_CSD'
'_database_code_ICSD'
'_database_code_MDF'
'_database_code_NBS'
'_database_code_PDB'
'_database_code_PDF'
_category database
_type char
_definition
; The codes are assigned by databases: Chemical Abstracts;
Cambridge Structural Database (organic and metal-organic
compounds); Inorganic Crystal Structure Database; Metals
Data File (metal structures); NBS (NIST) Crystal Data
Database (lattice parameters); Protein Data Bank; and the
Powder Diffraction File (JCPDS/ICDD).
;
data_database_code_depnum_ccdc_fiz
_name '_database_code_depnum_ccdc_fiz'
_category database
_type char
_definition
; Deposition numbers assigned by the Fachinformationszentrum
Karlsruhe (FIZ) to files containing structural information
archived by the Cambridge Crystallographic Data Centre (CCDC).
;
data_database_code_depnum_ccdc_journal
_name '_database_code_depnum_ccdc_journal'
_category database
_type char
_definition
; Deposition numbers assigned by various journals to files
containing structural information archived by the Cambridge
Crystallographic Data Centre (CCDC).
;
data_database_code_depnum_ccdc_archive
_name '_database_code_depnum_ccdc_archive'
_category database
_type char
_definition
; Deposition numbers assigned by the Cambridge Crystallographic
Data Centre (CCDC) to files containing structural information
archived by the CCDC.
;
data_database_CSD_history
_name '_database_CSD_history'
_category database
_type char
_definition
; A history of changes made by the Cambridge Crystallographic Data
Centre and incorporated into the Cambridge Structural Database
(CSD).
;
data_database_journal_
loop_ _name '_database_journal_ASTM'
'_database_journal_CSD'
_category database
_type char
_definition
; The ASTM CODEN designator for a journal as given in the
Chemical Source List maintained by the Chemical Abstracts
Service, and the journal code used in the Cambridge Structural
Database.
;
############
## DIFFRN ##
############
data_diffrn_[]
_name '_diffrn_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_special_details
; \q scan width (1.0 + 0.14tan\q)\%, \q scan rate
1.2\% min^-1^. Background counts for 5 s on each side
every scan.
;
_diffrn_ambient_temperature 293
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN category record details about the
intensity measurements.
;
data_diffrn_ambient_environment
_name '_diffrn_ambient_environment'
_category diffrn
_type char
loop_ _example He vacuum 'mother liquor'
_definition
; The gas or liquid surrounding the sample, if not air.
;
data_diffrn_ambient_pressure
_name '_diffrn_ambient_pressure'
_category diffrn
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units kPa
_units_detail 'kilopascals'
_definition
; The mean hydrostatic pressure in kilopascals at which the
intensities were measured.
;
data_diffrn_ambient_pressure_
loop_ _name '_diffrn_ambient_pressure_gt'
'_diffrn_ambient_pressure_lt'
_category diffrn
_type numb
_related_item '_diffrn_ambient_pressure'
_related_function alternate
_enumeration_range 0.0:
_units kPa
_units_detail 'kilopascals'
_definition
; The mean hydrostatic pressure in kilopascals above which (*_gt)
or below which (*_lt) the intensities were measured. These
items allow for a pressure range to be given.
_diffrn_ambient_pressure should always be used in
preference to these items whenever possible.
;
data_diffrn_ambient_temperature
_name '_diffrn_ambient_temperature'
_category diffrn
_type numb
_type_conditions esd
_enumeration_range 0.0:
_units K
_units_detail kelvin
_definition
; The mean temperature in kelvins at which the intensities
were measured.
;
data_diffrn_ambient_temperature_
loop_ _name '_diffrn_ambient_temperature_gt'
'_diffrn_ambient_temperature_lt'
_category diffrn
_type numb
_related_item '_diffrn_ambient_temperature'
_related_function alternate
_enumeration_range 0.0:
_units K
_units_detail kelvin
_definition
; The mean temperature in kelvins above which (*_gt) or below
which (*_lt) the intensities were measured. These items allow
a range of temperatures to be given.
_diffrn_ambient_temperature should always be used in preference
to these items whenever possible.
;
data_diffrn_crystal_treatment
_name '_diffrn_crystal_treatment'
_category diffrn
_type char
loop_ _example 'equilibrated in hutch for 24 hours'
'flash frozen in liquid nitrogen'
'slow cooled with direct air stream'
_definition
; Remarks about how the crystal was treated prior to the intensity
measurements. Particularly relevant when intensities were
measured at low temperature.
;
data_diffrn_measured_fraction_theta_full
_name '_diffrn_measured_fraction_theta_full'
_category diffrn
_type numb
_enumeration_range 0:1.0
_definition
; Fraction of unique (symmetry-independent) reflections measured
out to _diffrn_reflns_theta_full.
;
data_diffrn_measured_fraction_theta_max
_name '_diffrn_measured_fraction_theta_max'
_category diffrn
_type numb
_enumeration_range 0:1.0
_definition
; Fraction of unique (symmetry-independent) reflections measured
out to _diffrn_reflns_theta_max.
;
data_diffrn_special_details
_name '_diffrn_special_details'
_category diffrn
_type char
_example
; The results may not be entirely reliable
as the measurement was made during a heat
wave when the air-conditioning had failed.
;
_definition
; Special details of the intensity-measurement process. Should
include information about source instability, crystal motion,
degradation and so on.
;
data_diffrn_symmetry_description
_name '_diffrn_symmetry_description'
_category diffrn
_type char
_definition
; Observed diffraction point symmetry, systematic absences and
possible space group(s) or superspace group(s) compatible with
these.
;
#######################
## DIFFRN_ATTENUATOR ##
#######################
data_diffrn_attenuator_[]
_name '_diffrn_attenuator_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_attenuator_code
_diffrn_attenuator_scale
0 1.00
1 16.97
2 33.89
;
;
Example 1 - hypothetical example.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_ATTENUATOR category record details
about the diffraction attenuator scales employed.
;
data_diffrn_attenuator_code
_name '_diffrn_attenuator_code'
_category diffrn_attenuator
_type char
_list yes
_list_mandatory yes
_list_link_child '_diffrn_refln_attenuator_code'
_definition
; A code associated with a particular attenuator setting. This code
is referenced by the _diffrn_refln_attenuator_code which is
stored with the intensities. See _diffrn_attenuator_scale.
;
data_diffrn_attenuator_material
_name '_diffrn_attenuator_material'
_category diffrn_attenuator
_type char
_list yes
_list_reference '_diffrn_attenuator_code'
_definition
; Material from which the attenuator is made.
;
data_diffrn_attenuator_scale
_name '_diffrn_attenuator_scale'
_category diffrn_attenuator
_type numb
_list yes
_list_reference '_diffrn_attenuator_code'
_enumeration_range 1.0:
_definition
; The scale factor applied when an intensity measurement is
reduced by an attenuator identified by _diffrn_attenuator_code.
The measured intensity must be multiplied by this scale to
convert it to the same scale as unattenuated intensities.
;
#####################
## DIFFRN_DETECTOR ##
#####################
data_diffrn_detector_[]
_name '_diffrn_detector_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_detector 'multiwire'
_diffrn_detector_type 'Siemens'
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
data_diffrn_detector
_name '_diffrn_detector'
_category diffrn_detector
_type char
_related_item '_diffrn_radiation_detector'
_related_function alternate
loop_
_example 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
_definition
; The general class of the radiation detector.
;
data_diffrn_detector_area_resol_mean
_name '_diffrn_detector_area_resol_mean'
_category diffrn_detector
_type numb
_enumeration_range 0.0:
_units mm^-1^
_units_detail 'pixels per millimetre'
_definition
; The resolution of an area detector, in pixels/mm.
;
data_diffrn_detector_details
_name '_diffrn_detector_details'
_category diffrn_detector
_type char
_definition
; A description of special aspects of the radiation detector.
;
data_diffrn_detector_dtime
_name '_diffrn_detector_dtime'
_category diffrn_detector
_related_item '_diffrn_radiation_detector_dtime'
_related_function alternate
_type numb
_enumeration_range 0.0:
_definition
; The deadtime in microseconds of the detector used to measure
the diffraction intensities.
;
data_diffrn_detector_type
_name '_diffrn_detector_type'
_category diffrn_detector
_type char
_definition
; The make, model or name of the detector device used.
;
data_diffrn_radiation_detector
_name '_diffrn_radiation_detector'
_category diffrn_detector
_type char
_related_item '_diffrn_detector'
_related_function replace
_definition
; The detector used to measure the diffraction intensities.
;
data_diffrn_radiation_detector_dtime
_name '_diffrn_radiation_detector_dtime'
_category diffrn_detector
_type numb
_enumeration_range 0.0:
_related_item '_diffrn_detector_dtime'
_related_function replace
_definition
; The deadtime in microseconds of the detector used to measure
the diffraction intensities.
;
########################
## DIFFRN_MEASUREMENT ##
########################
data_diffrn_measurement_[]
_name '_diffrn_measurement_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_measurement_device_type
'Philips PW1100/20 diffractometer'
_diffrn_measurement_method \q/2\q
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_MEASUREMENT category refer to the
mounting of the sample and to the goniometer on which it is
mounted.
;
data_diffrn_measurement_details
_name '_diffrn_measurement_details'
_category diffrn_measurement
_type char
_example '440 frames of 0.25\%'
_definition
; A description of special aspects of the intensity measurement.
;
data_diffrn_measurement_device
_name '_diffrn_measurement_device'
_category diffrn_measurement
_type char
loop_
_example 'three-circle diffractometer'
'four-circle diffractometer'
'\k-geometry diffractometer'
'oscillation camera'
'precession camera'
_definition
; The general class of goniometer or device used to support
and orient the specimen.
;
data_diffrn_measurement_device_details
_name '_diffrn_measurement_device_details'
_category diffrn_measurement
_type char
_example
; commercial goniometer modified locally to
allow for 90\% \t arc
;
_definition
; A description of special aspects of the device used to measure
the diffraction intensities.
;
data_diffrn_measurement_device_type
_name '_diffrn_measurement_device_type'
_category diffrn_measurement
_type char
_definition
; The make, model or name of the measurement device
(goniometer) used.
;
data_diffrn_measurement_method
_name '_diffrn_measurement_method'
_category diffrn_measurement
_type char
_example 'profile data from \q/2\q scans'
_definition
; Method used to measure the intensities.
;
data_diffrn_measurement_specimen_support
_name '_diffrn_measurement_specimen_support'
_category diffrn_measurement
_type char
loop_ _example 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
_definition
; The physical device used to support the crystal during data
collection.
;
##########################
## DIFFRN_ORIENT_MATRIX ##
##########################
data_diffrn_orient_matrix_[]
_name '_diffrn_orient_matrix_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_orient_matrix_UB_11 -0.04170
_diffrn_orient_matrix_UB_12 -0.01429
_diffrn_orient_matrix_UB_13 -0.02226
_diffrn_orient_matrix_UB_21 -0.00380
_diffrn_orient_matrix_UB_22 -0.05578
_diffrn_orient_matrix_UB_23 -0.05048
_diffrn_orient_matrix_UB_31 0.00587
_diffrn_orient_matrix_UB_32 -0.13766
_diffrn_orient_matrix_UB_33 0.02277
_diffrn_orient_matrix_type 'TEXSAN convention (MSC, 1989)'
;
;
Example 1 - data set n-alkylation_C-4 of Hussain, Fleming, Norman & Chang
[Acta Cryst. (1996), C52, 1010-1012].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_ORIENT_MATRIX category record details
about the orientation matrix used in the measurement of the
diffraction intensities.
;
data_diffrn_orient_matrix_type
_name '_diffrn_orient_matrix_type'
_category diffrn_orient_matrix
_type char
_definition
; A description of the orientation matrix type and how it should
be applied to define the orientation of the crystal precisely
with respect to the diffractometer axes.
;
data_diffrn_orient_matrix_UB_
loop_ _name '_diffrn_orient_matrix_UB_11'
'_diffrn_orient_matrix_UB_12'
'_diffrn_orient_matrix_UB_13'
'_diffrn_orient_matrix_UB_21'
'_diffrn_orient_matrix_UB_22'
'_diffrn_orient_matrix_UB_23'
'_diffrn_orient_matrix_UB_31'
'_diffrn_orient_matrix_UB_32'
'_diffrn_orient_matrix_UB_33'
_category diffrn_orient_matrix
_type numb
_definition
; The elements of the diffractometer orientation matrix. These
define the dimensions of the reciprocal cell and its orientation
to the local diffractometer axes. See _diffrn_orient_matrix_type.
;
#########################
## DIFFRN_ORIENT_REFLN ##
#########################
data_diffrn_orient_refln_[]
_name '_diffrn_orient_refln_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_orient_refln_index_h
_diffrn_orient_refln_index_k
_diffrn_orient_refln_index_l
_diffrn_orient_refln_angle_theta
_diffrn_orient_refln_angle_phi
_diffrn_orient_refln_angle_omega
_diffrn_orient_refln_angle_kappa
-3 2 3 7.35 44.74 2.62 17.53
-4 1 0 9.26 83.27 8.06 5.79
0 0 6 5.85 -43.93 -25.36 86.20
2 1 3 7.36 -57.87 6.26 5.42
0 0 -6 5.85 -161.59 36.96 -86.79
-3 1 0 6.74 80.28 5.87 2.60
2 0 3 5.86 -76.86 -0.17 21.34
0 0 12 11.78 -44.02 -19.51 86.41
0 0 -12 11.78 -161.67 42.81 -86.61
-5 1 0 11.75 86.24 9.16 7.44
0 4 6 11.82 -19.82 10.45 4.19
5 0 6 14.13 -77.28 10.17 15.34
8 0 0 20.79 -77.08 25.30 -13.96
;
;
Example 1 - typical output listing from an Enraf-Nonius CAD-4
diffractometer.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_ORIENT_REFLN category record details
about the reflections that define the orientation matrix used in
the measurement of the diffraction intensities.
;
data_diffrn_orient_refln_angle_
loop_ _name '_diffrn_orient_refln_angle_chi'
'_diffrn_orient_refln_angle_kappa'
'_diffrn_orient_refln_angle_omega'
'_diffrn_orient_refln_angle_phi'
'_diffrn_orient_refln_angle_psi'
'_diffrn_orient_refln_angle_theta'
_category diffrn_orient_refln
_type numb
_list yes
_list_reference '_diffrn_orient_refln_index_'
_units deg
_units_detail 'degrees'
_definition
; Diffractometer angles of a reflection used to define
the orientation matrix in degrees. See
_diffrn_orient_matrix_UB_ and
_diffrn_orient_refln_index_h, *_k and *_l.
;
data_diffrn_orient_refln_index_
loop_ _name '_diffrn_orient_refln_index_h'
'_diffrn_orient_refln_index_k'
'_diffrn_orient_refln_index_l'
_category diffrn_orient_refln
_type numb
_list yes
_list_mandatory yes
_definition
; The indices of a reflection used to define the orientation
matrix. See _diffrn_orient_matrix_.
;
######################
## DIFFRN_RADIATION ##
######################
data_diffrn_radiation_[]
_name '_diffrn_radiation_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_radiation_type 'Cu K\a'
_diffrn_radiation_monochromator 'graphite'
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_RADIATION category describe the
radiation used in measuring the diffraction intensities, its
collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data items
in the DIFFRN_DETECTOR category.
;
data_diffrn_radiation_collimation
_name '_diffrn_radiation_collimation'
_category diffrn_radiation
_type char
loop_ _example '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
_definition
; The collimation or focusing applied to the radiation.
;
data_diffrn_radiation_filter_edge
_name '_diffrn_radiation_filter_edge'
_category diffrn_radiation
_type numb
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; Absorption edge in angstroms of the radiation filter used.
;
data_diffrn_radiation_inhomogeneity
_name '_diffrn_radiation_inhomogeneity'
_category diffrn_radiation
_type numb
_enumeration_range 0.0:
_definition
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
data_diffrn_radiation_monochromator
_name '_diffrn_radiation_monochromator'
_category diffrn_radiation
_type char
loop_ _example 'Zr filter' 'Ge 220' 'none'
'equatorial mounted graphite'
_definition
; The method used to obtain monochromatic radiation. If a mono-
chromator crystal is used, the material and the indices of the
Bragg reflection are specified.
;
data_diffrn_radiation_polarisn_norm
_name '_diffrn_radiation_polarisn_norm'
_category diffrn_radiation
_type numb
_enumeration_range -180.0:180.0
_units deg
_units_detail 'degrees'
_definition
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
data_diffrn_radiation_polarisn_ratio
_name '_diffrn_radiation_polarisn_ratio'
_category diffrn_radiation
_type numb
_enumeration_range 0.0:
_definition
; Polarization ratio of the diffraction beam incident on the
crystal. It is the ratio of the perpendicularly polarized to the
parallel polarized components of the radiation. The perpendicular
component forms an angle of _diffrn_radiation_polarisn_norm to
the normal to the diffraction plane of the sample (i.e. the plane
containing the incident and reflected beams).
;
data_diffrn_radiation_probe
_name '_diffrn_radiation_probe'
_category diffrn_radiation
_type char
loop_ _enumeration x-ray
neutron
electron
gamma
_definition
; The nature of the radiation used (i.e. the name of the
subatomic particle or the region of the electromagnetic
spectrum). It is strongly recommended that this information
be given, so that the probe radiation can be simply determined.
;
data_diffrn_radiation_type
_name '_diffrn_radiation_type'
_category diffrn_radiation
_type char
loop_ _example 'Cu K\a' 'Cu K\a~1~'
'Cu K-L~2,3~' white-beam
_definition
; The type of the radiation. This is used to give a more
detailed description than _diffrn_radiation_probe and is
typically a description of the X-ray wavelength in Siegbahn
notation.
;
data_diffrn_radiation_xray_symbol
_name '_diffrn_radiation_xray_symbol'
_category diffrn_radiation
_type char
loop_ _enumeration
_enumeration_detail
K-L~3~ 'K\a~1~ in older Siegbahn notation'
K-L~2~ 'K\a~2~ in older Siegbahn notation'
K-M~3~ 'K\b~1~ in older Siegbahn notation'
K-L~2,3~ 'use where K-L~3~ and K-L~2~ are not resolved'
_definition
; The IUPAC symbol for the X-ray wavelength for the probe
radiation.
;
###################################
### DIFFRN_RADIATION_WAVELENGTH ###
###################################
data_diffrn_radiation_wavelength_[]
_name '_diffrn_radiation_wavelength_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_radiation_wavelength 1.5418
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_RADIATION_WAVELENGTH category describe
the wavelength of the radiation used in measuring the diffraction
intensities. Items may be looped to identify and assign weights
to distinct wavelength components from a polychromatic beam.
;
data_diffrn_radiation_wavelength
_name '_diffrn_radiation_wavelength'
_category diffrn_radiation_wavelength
_type numb
_list both
_list_reference '_diffrn_radiation_wavelength_id'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The radiation wavelength in angstroms.
;
data_diffrn_radiation_wavelength_id
_name '_diffrn_radiation_wavelength_id'
_category diffrn_radiation_wavelength
_type char
_list yes
_list_mandatory yes
_list_link_child '_diffrn_refln_wavelength_id'
loop_ _example x1 x2 neut
_definition
; An arbitrary code identifying each value of
_diffrn_radiation_wavelength. Items in the DIFFRN_RADIATION
category are looped when multiple wavelengths are used.
This code is used to link with the _diffrn_refln_ list. It
must match with one of the _diffrn_refln_wavelength_id codes.
;
data_diffrn_radiation_wavelength_wt
_name '_diffrn_radiation_wavelength_wt'
_category diffrn_radiation_wavelength
_type numb
_list yes
_list_reference '_diffrn_radiation_wavelength_id'
_enumeration_range 0.0:1.0
_enumeration_default 1.0
_definition
; The relative weight of a wavelength identified by the code
_diffrn_radiation_wavelength_id in the list of wavelengths.
;
##################
## DIFFRN_REFLN ##
##################
data_diffrn_refln_[]
_name '_diffrn_refln_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_refln_index_h
_diffrn_refln_index_k
_diffrn_refln_index_l
_diffrn_refln_angle_chi
_diffrn_refln_scan_rate
_diffrn_refln_counts_bg_1
_diffrn_refln_counts_total
_diffrn_refln_counts_bg_2
_diffrn_refln_angle_theta
_diffrn_refln_angle_phi
_diffrn_refln_angle_omega
_diffrn_refln_angle_kappa
_diffrn_refln_scan_width
_diffrn_refln_elapsed_time
0 0 -16 0. 4.12 28 127 36 33.157 -75.846 16.404 50.170 1.516 19.43
0 0 -15 0. 4.12 38 143 28 30.847 -75.846 14.094 50.170 1.516 19.82
0 0 -14 0. 1.03 142 742 130 28.592 -75.846 11.839 50.170 1.516 21.32
0 0 -13 0. 4.12 26 120 37 26.384 -75.846 9.631 50.170 1.450 21.68
0 0 -12 0. 0.97 129 618 153 24.218 -75.846 7.464 50.170 1.450 23.20
0 0 -11 0. 4.12 33 107 38 22.087 -75.846 5.334 50.170 1.384 23.55
0 0 -10 0. 4.12 37 146 33 19.989 -75.846 3.235 50.170 1.384 23.90
0 0 -9 0. 4.12 50 179 49 17.918 -75.846 1.164 50.170 1.384 24.25
# - - - - data truncated for brevity - - - -
3 4 -4 0. 1.03 69 459 73 30.726 -53.744 46.543 -47.552 1.516 2082.58
3 4 -5 0. 1.03 91 465 75 31.407 -54.811 45.519 -42.705 1.516 2084.07
3 14 -6 0. 1.03 84 560 79 32.228 -55.841 44.745 -38.092 1.516 2085.57
# - - - - data truncated for brevity - - - -
;
;
Example 1 - extracted from the CAD-4 listing for Tl~2~Cd~2~(SO~4~)~3~ at
85 K (unpublished).
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_REFLN category record details about
the intensities measured in the diffraction experiment.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
(The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements. The DIFFRN_REFLNS data items
are not looped.)
;
data_diffrn_refln_angle_
loop_ _name '_diffrn_refln_angle_chi'
'_diffrn_refln_angle_kappa'
'_diffrn_refln_angle_omega'
'_diffrn_refln_angle_phi'
'_diffrn_refln_angle_psi'
'_diffrn_refln_angle_theta'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_units deg
_units_detail 'degrees'
_definition
; The diffractometer angles of a reflection in degrees. These
correspond to the specified orientation matrix and the original
measured cell before any subsequent cell transformations.
;
data_diffrn_refln_attenuator_code
_name '_diffrn_refln_attenuator_code'
_category diffrn_refln
_type char
_list yes
_list_reference '_diffrn_refln_index_'
_list_link_parent '_diffrn_attenuator_code'
_definition
; The code identifying the attenuator setting for this reflection.
This code must match one of the _diffrn_attenuator_code values.
;
data_diffrn_refln_class_code
_name '_diffrn_refln_class_code'
_category diffrn_refln
_type char
_list yes
_list_reference '_diffrn_refln_index_'
_list_link_parent '_diffrn_reflns_class_code'
_definition
; The code identifying the class to which this reflection has
been assigned. This code must match a value of
_diffrn_reflns_class_code. Reflections may be grouped into
classes for a variety of purposes. For example, for modulated
structures each reflection class may be defined by the
number m=sum|m~i~|, where the m~i~ are the integer coefficients
that, in addition to h,k,l, index the corresponding diffraction
vector in the basis defined for the reciprocal lattice.
;
data_diffrn_refln_counts_
loop_ _name '_diffrn_refln_counts_bg_1'
'_diffrn_refln_counts_bg_2'
'_diffrn_refln_counts_net'
'_diffrn_refln_counts_peak'
'_diffrn_refln_counts_total'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_definition
; The diffractometer counts for the measurements: background
before the peak, background after the peak, net counts after
background removed, counts for peak scan or position, and the
total counts (background plus peak).
;
data_diffrn_refln_crystal_id
_name '_diffrn_refln_crystal_id'
_category diffrn_refln
_type char
_list yes
_list_reference '_diffrn_refln_index_'
_list_link_parent '_exptl_crystal_id'
_definition
; Code identifying each crystal if multiple crystals are used. Is
used to link with _exptl_crystal_id in the _exptl_crystal_ list.
;
data_diffrn_refln_detect_slit_
loop_ _name '_diffrn_refln_detect_slit_horiz'
'_diffrn_refln_detect_slit_vert'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:90.0
_units deg
_units_detail 'degrees'
_definition
; Total slit apertures in degrees in the diffraction plane
(*_horiz) and perpendicular to the diffraction plane (*_vert).
;
data_diffrn_refln_elapsed_time
_name '_diffrn_refln_elapsed_time'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:
_units min
_units_detail 'minutes'
_definition
; Elapsed time in minutes from the start of the diffraction
experiment to the measurement of this intensity.
;
data_diffrn_refln_index_
loop_ _name '_diffrn_refln_index_h'
'_diffrn_refln_index_k'
'_diffrn_refln_index_l'
_category diffrn_refln
_type numb
_list yes
_list_mandatory yes
_definition
; Miller indices of a measured reflection. These need not match
the _refln_index_h, *_k, *_l values if a transformation of the
original measured cell has taken place. Details of the cell
transformation are given in _diffrn_reflns_reduction_process.
See also _diffrn_reflns_transf_matrix_.
;
data_diffrn_refln_intensity_net
_name '_diffrn_refln_intensity_net'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0:
_definition
; Net intensity calculated from the diffraction counts after
the attenuator and standard scales have been applied.
;
data_diffrn_refln_intensity_sigma
_name '_diffrn_refln_intensity_sigma'
_category diffrn_refln
_type numb
_related_item '_diffrn_refln_intensity_u'
_related_function replace
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0:
_definition
; Standard uncertainty (e.s.d.) of the net intensity calculated
from the diffraction counts after the attenuator and standard
scales have been applied.
;
data_diffrn_refln_intensity_u
_name '_diffrn_refln_intensity_u'
_category diffrn_refln
_type numb
_related_item '_diffrn_refln_intensity_sigma'
_related_function alternate
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0:
_definition
; Standard uncertainty of the net intensity calculated from
the diffraction counts after the attenuator and standard
scales have been applied.
;
data_diffrn_refln_scale_group_code
_name '_diffrn_refln_scale_group_code'
_category diffrn_refln
_type char
_list yes
_list_link_parent '_diffrn_scale_group_code'
_list_reference '_diffrn_refln_index_'
_definition
; The code identifying the scale applicable to this reflection.
This code must match with a specified _diffrn_scale_group_code
value.
;
data_diffrn_refln_scan_mode
_name '_diffrn_refln_scan_mode'
_category diffrn_refln
_type char
_list yes
_list_reference '_diffrn_refln_index_'
loop_ _enumeration
_enumeration_detail om 'omega scan'
ot 'omega/2theta scan'
q 'Q scans (arbitrary reciprocal directions)'
_definition
; The code identifying the mode of scanning for measurements
using a diffractometer. See _diffrn_refln_scan_width and
_diffrn_refln_scan_mode_backgd.
;
data_diffrn_refln_scan_mode_backgd
_name '_diffrn_refln_scan_mode_backgd'
_category diffrn_refln
_type char
_list yes
_list_reference '_diffrn_refln_index_'
loop_ _enumeration
_enumeration_detail st 'stationary counter background'
mo 'moving counter background'
_definition
; The code identifying the mode of scanning a reflection to measure
the background intensity.
;
data_diffrn_refln_scan_rate
_name '_diffrn_refln_scan_rate'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:
_units deg/min
_units_detail 'degrees per minute'
_definition
; The rate of scanning a reflection in
degrees per minute to measure the intensity.
;
data_diffrn_refln_scan_time_backgd
_name '_diffrn_refln_scan_time_backgd'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:
_units sec
_units_detail 'seconds'
_definition
; The time spent measuring each background in seconds.
;
data_diffrn_refln_scan_width
_name '_diffrn_refln_scan_width'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:90.0
_units deg
_units_detail 'degrees'
_definition
; The scan width in degrees of the scan mode defined by the code
_diffrn_refln_scan_mode.
;
data_diffrn_refln_sint/lambda
_name '_diffrn_refln_sint/lambda'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:
_units A^-1^
_units_detail 'reciprocal angstroms'
_definition
; The (sin theta)/lambda value in reciprocal angstroms for
this reflection.
;
data_diffrn_refln_standard_code
_name '_diffrn_refln_standard_code'
_category diffrn_refln
_type char
_list yes
_list_link_parent '_diffrn_standard_refln_code'
_list_reference '_diffrn_refln_index_'
loop_ _example 1 2 3 s1 s2 s3 A B C
_definition
; A code indicating that this reflection was measured as a
standard reflection. The value must be '.' or match one of
the _diffrn_standard_refln_code values.
;
data_diffrn_refln_wavelength
_name '_diffrn_refln_wavelength'
_category diffrn_refln
_type numb
_list yes
_list_reference '_diffrn_refln_index_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The mean wavelength in angstroms of the radiation used to measure
the intensity of this reflection. This is an important parameter
for reflections measured using energy-dispersive detectors or the
Laue method.
;
data_diffrn_refln_wavelength_id
_name '_diffrn_refln_wavelength_id'
_category diffrn_refln
_type char
_list yes
_list_link_parent '_diffrn_radiation_wavelength_id'
_list_reference '_diffrn_refln_index_'
loop_ _example x1 x2 neut
_definition
; Code identifying the wavelength in the _diffrn_radiation_ list.
;
###################
## DIFFRN_REFLNS ##
###################
data_diffrn_reflns_[]
_name '_diffrn_reflns_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_reflns_number 1592
_diffrn_reflns_av_R_equivalents 0
_diffrn_reflns_av_unetI/netI .027
_diffrn_reflns_limit_h_min 0
_diffrn_reflns_limit_h_max 6
_diffrn_reflns_limit_k_min -17
_diffrn_reflns_limit_k_max 0
_diffrn_reflns_limit_l_min 0
_diffrn_reflns_limit_l_max 22
_diffrn_reflns_theta_min 3.71
_diffrn_reflns_theta_max 61.97
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_REFLNS category record details about
the set of intensities measured in the diffraction experiment.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements. The DIFFRN_REFLNS data items
are not looped.
(The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.)
;
data_diffrn_reflns_av_R_equivalents
_name '_diffrn_reflns_av_R_equivalents'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:
_definition
; The residual [sum av|del(I)| / sum |av(I)|] for
symmetry-equivalent reflections used to calculate the
average intensity av(I). The av|del(I)| term is the
average absolute difference between av(I) and the
individual symmetry-equivalent intensities.
;
data_diffrn_reflns_av_sigmaI/netI
_name '_diffrn_reflns_av_sigmaI/netI'
_category diffrn_reflns
_type numb
_related_item '_diffrn_reflns_av_unetI/netI'
_related_function replace
_enumeration_range 0.0:
_definition
; Measure [sum u(net I)|/sum|net I|] for all measured reflections.
;
data_diffrn_reflns_av_unetI/netI
_name '_diffrn_reflns_av_unetI/netI'
_category diffrn_reflns
_type numb
_related_item '_diffrn_reflns_av_sigmaI/netI'
_related_function alternate
_enumeration_range 0.0:
_definition
; Measure [sum u(net I)|/sum|net I|] for all measured reflections.
;
data_diffrn_reflns_limit_
loop_ _name '_diffrn_reflns_limit_h_max'
'_diffrn_reflns_limit_h_min'
'_diffrn_reflns_limit_k_max'
'_diffrn_reflns_limit_k_min'
'_diffrn_reflns_limit_l_max'
'_diffrn_reflns_limit_l_min'
_category diffrn_reflns
_type numb
_definition
; The limits on the Miller indices of the intensities specified
by _diffrn_refln_index_h, *_k, *_l.
;
data_diffrn_reflns_number
_name '_diffrn_reflns_number'
_category diffrn_reflns
_type numb
_enumeration_range 0:
_definition
; The total number of measured intensities, excluding
reflections that are classed as systematically absent arising
from translational symmetry in the crystal unit cell.
;
data_diffrn_reflns_reduction_process
_name '_diffrn_reflns_reduction_process'
_category diffrn_reflns
_type char
_example 'data averaged using Fisher test'
_definition
; A description of the process used to reduce the intensities
into structure-factor magnitudes.
;
data_diffrn_reflns_resolution_full
_name '_diffrn_reflns_resolution_full'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:
_units A^-1^
_units_detail 'reciprocal angstroms'
_related_item '_diffrn_reflns_theta_full'
_related_function alternate
_definition
; The resolution in reciprocal angstroms at which the measured
reflection count is close to complete.
;
data_diffrn_reflns_resolution_max
_name '_diffrn_reflns_resolution_max'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:
_units A^-1^
_units_detail 'reciprocal angstroms'
_related_item '_diffrn_reflns_theta_max'
_related_function alternate
_definition
; Maximum resolution in reciprocal angstroms of the measured
diffraction pattern.
;
data_diffrn_reflns_theta_full
_name '_diffrn_reflns_theta_full'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:90.0
_units deg
_units_detail 'degrees'
_definition
; The theta angle (in degrees) at which the measured reflection
count is close to complete. The fraction of unique reflections
measured out to this angle is given by
_diffrn_measured_fraction_theta_full.
;
data_diffrn_reflns_theta_max
_name '_diffrn_reflns_theta_max'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:90.0
_units deg
_units_detail 'degrees'
_definition
; Maximum theta angle in degrees for the measured intensities.
;
data_diffrn_reflns_theta_min
_name '_diffrn_reflns_theta_min'
_category diffrn_reflns
_type numb
_enumeration_range 0.0:90.0
_units deg
_units_detail 'degrees'
_definition
; Minimum theta angle in degrees for the measured intensities.
;
data_diffrn_reflns_transf_matrix_
loop_ _name '_diffrn_reflns_transf_matrix_11'
'_diffrn_reflns_transf_matrix_12'
'_diffrn_reflns_transf_matrix_13'
'_diffrn_reflns_transf_matrix_21'
'_diffrn_reflns_transf_matrix_22'
'_diffrn_reflns_transf_matrix_23'
'_diffrn_reflns_transf_matrix_31'
'_diffrn_reflns_transf_matrix_32'
'_diffrn_reflns_transf_matrix_33'
_category diffrn_reflns
_type numb
_definition
; Elements of the matrix used to transform the diffraction
reflection indices _diffrn_refln_index_h, *_k, *_l into the
_refln_index_h, *_k, *_l indices.
|11 12 13|
(h k l) diffraction |21 22 23| = (h' k' l')
|31 32 33|
;
#########################
## DIFFRN_REFLNS_CLASS ##
#########################
data_diffrn_reflns_class_[]
_name '_diffrn_reflns_class_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_reflns_class_number
_diffrn_reflns_class_d_res_high
_diffrn_reflns_class_d_res_low
_diffrn_reflns_class_av_R_eq
_diffrn_reflns_class_code
_diffrn_reflns_class_description
1580 0.551 6.136 0.015 'Main'
'm=0; main reflections'
1045 0.551 6.136 0.010
'Sat1' 'm=1; first-order satellites'
;
;
Example 1 - example corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~. Each reflection class is
defined by the number m=sum|m~i~|, where the m~i~ are the
integer coefficients that, in addition to h,k,l, index the
corresponding diffraction vector in the basis defined for
the reciprocal lattice.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_REFLNS_CLASS category record details
about the classes of reflections measured in the diffraction
experiment.
;
data_diffrn_reflns_class_av_R_eq
_name '_diffrn_reflns_class_av_R_eq'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual
[sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections
used to calculate the average intensity av(I). The av|del(I)|
term is the average absolute difference between av(I) and the
individual intensities.
;
data_diffrn_reflns_class_av_sgI/I
_name '_diffrn_reflns_class_av_sgI/I'
_category diffrn_reflns_class
_type numb
_related_item '_diffrn_reflns_class_av_uI/I'
_related_function replace
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_definition
; Measure [sum|u(net I)|/sum|net I|] for all measured intensities
in a reflection class.
;
data_diffrn_reflns_class_av_uI/I
_name '_diffrn_reflns_class_av_uI/I'
_category diffrn_reflns_class
_type numb
_related_item '_diffrn_reflns_class_av_sgI/I'
_related_function alternate
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_definition
; Measure [sum|u(net I)|/sum|net I|] for all measured intensities
in a reflection class.
;
data_diffrn_reflns_class_code
_name '_diffrn_reflns_class_code'
_category diffrn_reflns_class
_type char
_list yes
_list_mandatory yes
_list_link_child '_diffrn_refln_class_code'
loop_ _example '1'
'm1'
's2'
_definition
; The code identifying a certain reflection class.
;
data_diffrn_reflns_class_description
_name '_diffrn_reflns_class_description'
_category diffrn_reflns_class
_type char
_list yes
_list_reference '_diffrn_reflns_class_code'
loop_ _example 'm=1 first order satellites'
'H0L0 common projection reflections'
_definition
; Description of each reflection class.
;
data_diffrn_reflns_class_d_res_high
_name '_diffrn_reflns_class_d_res_high'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; The smallest value in angstroms of the interplanar
spacings of the reflections in each reflection class.
This is called the highest resolution for this reflection class.
;
data_diffrn_reflns_class_d_res_low
_name '_diffrn_reflns_class_d_res_low'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; The highest value in angstroms of the interplanar
spacings of the reflections in each reflection class.
This is called the lowest resolution for this reflection class.
;
data_diffrn_reflns_class_number
_name '_diffrn_reflns_class_number'
_category diffrn_reflns_class
_type numb
_list yes
_list_reference '_diffrn_reflns_class_code'
_enumeration_range 0:
_definition
; The total number of measured intensities for each reflection
class, excluding the systematic absences arising from
centring translations.
;
########################
## DIFFRN_SCALE_GROUP ##
########################
data_diffrn_scale_group_[]
_name '_diffrn_scale_group_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_scale_group_code
_diffrn_scale_group_I_net
1 .86473
2 1.0654
;
;
Example 1 - hypothetical example.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_SCALE_GROUP category record details
of the scaling factors applied to place all intensities in
the reflection lists on a common scale.
Scaling groups might, for instance, correspond to each film
in a multi-film data set or each crystal in a multi-crystal
data set.
;
data_diffrn_scale_group_code
_name '_diffrn_scale_group_code'
_category diffrn_scale_group
_type char
_list yes
_list_mandatory yes
_list_link_child '_diffrn_refln_scale_group_code'
loop_ _example 1 2 3 s1 A B c1 c2 c3
_definition
; The code identifying a specific measurement group (e.g. for
multi-film or multi-crystal data). The code must match a
_diffrn_refln_scale_group_code in the reflection list.
;
data_diffrn_scale_group_I_net
_name '_diffrn_scale_group_I_net'
_category diffrn_scale_group
_type numb
_list yes
_list_reference '_diffrn_scale_group_code'
_enumeration_range 0.0:
_definition
; The scale for a specific measurement group which is to be
multiplied with the net intensity to place all intensities
in the _diffrn_refln_ or _refln_ list on a common scale.
;
###################
## DIFFRN_SOURCE ##
###################
data_diffrn_source_[]
_name '_diffrn_source_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_source 'rotating anode X-ray tube'
_diffrn_source_type 'Rigaku RU-200'
_diffrn_source_power 50
_diffrn_source_current 180
_diffrn_source_size '8 mm x 0.4 mm broad focus'
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_SOURCE category record details of
the source of radiation used in the diffraction experiment.
;
data_diffrn_radiation_source
_name '_diffrn_radiation_source'
_category diffrn_source
_type char
_related_item '_diffrn_source'
_related_function replace
_definition
; The source of radiation.
;
data_diffrn_source
_name '_diffrn_source'
_category diffrn_source
_type char
_related_item '_diffrn_radiation_source'
_related_function alternate
loop_
_example 'sealed X-ray tube'
'nuclear reactor'
'spallation source'
'electron microscope'
'rotating-anode X-ray tube'
'synchrotron'
_definition
; The general class of the source of radiation.
;
data_diffrn_source_current
_name '_diffrn_source_current'
_category diffrn_source
_type numb
_enumeration_range 0.0:
_units mA
_units_detail 'milliamperes'
_definition
; The current in milliamperes at which the radiation source was
operated.
;
data_diffrn_source_details
_name '_diffrn_source_details'
_category diffrn_source
_type char
_definition
; A description of special aspects of the source.
;
data_diffrn_source_power
_name '_diffrn_source_power'
_category diffrn_source
_type numb
_enumeration_range 0.0:
_units kW
_units_detail 'kilowatts'
_definition
; The power in kilowatts at which the radiation source was
operated.
;
data_diffrn_source_size
_name '_diffrn_source_size'
_category diffrn_source
_type char
loop_
_example '8mm x 0.4 mm fine-focus'
'broad focus'
_definition
; The dimensions of the source as viewed from the sample.
;
data_diffrn_source_take-off_angle
_name '_diffrn_source_take-off_angle'
_category diffrn_source
_type numb
_enumeration_range 0:90
_units degrees
_example 1.53
_definition
; The complement of the angle in degrees between the normal
to the surface of the X-ray tube target and the primary
X-ray beam for beams generated by traditional X-ray tubes.
;
data_diffrn_source_target
_name '_diffrn_source_target'
_category diffrn_source
_type char
loop_ _enumeration
H He Li Be B C N O F Ne Na Mg Al Si P S Cl
Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge
As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag
Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm
Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir
Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U
Np Pu Am Cm Bk Cf Es Fm Md No Lr
_definition
; The chemical element symbol for the X-ray target
(usually the anode) used to generate X-rays.
This can also be used for spallation sources.
;
data_diffrn_source_type
_name '_diffrn_source_type'
_category diffrn_source
_type char
loop_
_example 'NSLS beamline X8C'
'Rigaku RU200'
_definition
; The make, model or name of the source of radiation.
;
data_diffrn_source_voltage
_name '_diffrn_source_voltage'
_category diffrn_source
_type numb
_enumeration_range 0.0:
_units kV
_units_detail 'kilovolts'
_definition
; The voltage in kilovolts at which the radiation source was
operated.
;
###########################
## DIFFRN_STANDARD_REFLN ##
###########################
data_diffrn_standard_refln_[]
_name '_diffrn_standard_refln_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_diffrn_standard_refln_index_h
_diffrn_standard_refln_index_k
_diffrn_standard_refln_index_l
3 2 4 1 9 1 3 0 10
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_STANDARD_REFLN category record details
about the reflections treated as standards during the measurement
of the diffraction intensities.
Note that these are the individual standard reflections, not the
results of the analysis of the standard reflections.
;
data_diffrn_standard_refln_code
_name '_diffrn_standard_refln_code'
_category diffrn_standard_refln
_type char
_list yes
_list_link_child '_diffrn_refln_standard_code'
_list_reference '_diffrn_standard_refln_index_'
loop_ _example 1 2 3 s1 A B
_definition
; The code identifying a reflection measured as a standard
reflection with the indices _diffrn_standard_refln_index_.
This is the same code as the _diffrn_refln_standard_code in
the _diffrn_refln_ list.
;
data_diffrn_standard_refln_index_
loop_ _name '_diffrn_standard_refln_index_h'
'_diffrn_standard_refln_index_k'
'_diffrn_standard_refln_index_l'
_category diffrn_standard_refln
_type numb
_list yes
_list_mandatory yes
_definition
; Miller indices of standard reflections used in the diffraction
measurement process.
;
######################
## DIFFRN_STANDARDS ##
######################
data_diffrn_standards_[]
_name '_diffrn_standards_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_diffrn_standards_number 3
_diffrn_standards_interval_time 120
_diffrn_standards_decay_% 0
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the DIFFRN_STANDARDS category record details
about the set of standard reflections used to monitor intensity
stability during the measurement of diffraction intensities.
Note that these records describe properties common to the set of
standard reflections, not the standard reflections themselves.
;
data_diffrn_standards_decay_%
_name '_diffrn_standards_decay_%'
_category diffrn_standards
_type numb
_type_conditions esd
_enumeration_range :100
_definition
; The percentage decrease in the mean of the intensities
for the set of standard reflections from the start of the
measurement process to the end. This value usually
affords a measure of the overall decay in crystal quality
during the diffraction measurement process. Negative values
are used in exceptional instances where the final intensities
are greater than the initial ones.
;
data_diffrn_standards_interval_
loop_ _name '_diffrn_standards_interval_count'
'_diffrn_standards_interval_time'
_category diffrn_standards
_type numb
_enumeration_range 0:
_definition
; The number of reflection intensities, or the time in minutes,
between the measurement of standard reflection intensities.
;
data_diffrn_standards_number
_name '_diffrn_standards_number'
_category diffrn_standards
_type numb
_enumeration_range 0:
_definition
; The number of unique standard reflections used during the
measurement of the diffraction intensities.
;
data_diffrn_standards_scale_sigma
_name '_diffrn_standards_scale_sigma'
_category diffrn_standards
_type numb
_related_item '_diffrn_standards_scale_u'
_related_function replace
_enumeration_range 0.0:
_definition
; The standard uncertainty (e.s.d.) of the individual mean
standard scales applied to the intensity data.
;
data_diffrn_standards_scale_u
_name '_diffrn_standards_scale_u'
_category diffrn_standards
_type numb
_related_item '_diffrn_standards_scale_sigma'
_related_function alternate
_enumeration_range 0.0:
_definition
; The standard uncertainty of the individual mean
standard scales applied to the intensity data.
;
###########
## EXPTL ##
###########
data_exptl_[]
_name '_exptl_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_exptl_absorpt_coefficient_mu 0.962
_exptl_absorpt_correction_type psi-scan
_exptl_absorpt_process_details
'North, Phillips & Mathews (1968)'
_exptl_absorpt_correction_T_min 0.929
_exptl_absorpt_correction_T_max 0.997
;
;
Example 1 - based on a paper by Steiner [Acta Cryst. (1996), C52,
2554-2556].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the EXPTL category record details about the
experimental work prior to the intensity measurements and
details about the absorption-correction technique employed.
;
data_exptl_absorpt_coefficient_mu
_name '_exptl_absorpt_coefficient_mu'
_category exptl
_type numb
_enumeration_range 0.0:
_units mm^-1^
_units_detail 'reciprocal millimetres'
_definition
; The absorption coefficient mu in reciprocal millimetres
calculated from the atomic content of the cell, the density and
the radiation wavelength.
;
data_exptl_absorpt_correction_T_
loop_ _name '_exptl_absorpt_correction_T_max'
'_exptl_absorpt_correction_T_min'
_category exptl
_type numb
_enumeration_range 0.0:1.0
_definition
; The maximum and minimum transmission factors for the crystal
and radiation. These factors are also referred to as the
absorption correction A or 1/A*.
;
data_exptl_absorpt_correction_type
_name '_exptl_absorpt_correction_type'
_category exptl
_type char
loop_ _enumeration
_enumeration_detail analytical 'analytical from crystal shape'
cylinder 'cylindrical'
empirical 'empirical from intensities'
gaussian 'Gaussian from crystal shape'
integration 'integration from crystal shape'
multi-scan 'symmetry-related measurements'
none 'no absorption correction applied'
numerical 'numerical from crystal shape'
psi-scan 'psi-scan corrections'
refdelf 'refined from delta-F'
sphere 'spherical'
_definition
; The absorption-correction type and method. The value 'empirical'
should NOT be used unless more detailed information is not
available.
;
data_exptl_absorpt_process_details
_name '_exptl_absorpt_process_details'
_category exptl
_type char
loop_ _example 'Tompa analytical'
'MolEN (Fair, 1990)'
'(North, Phillips & Mathews, 1968)'
_definition
; Description of the absorption process applied to the
intensities. A literature reference should be supplied
for psi-scan techniques.
;
data_exptl_crystals_number
_name '_exptl_crystals_number'
_category exptl
_type numb
_enumeration_range 1:
_definition
; The total number of crystals used for the measurement of
intensities.
;
data_exptl_special_details
_name '_exptl_special_details'
_category exptl
_type char
_definition
; Any special information about the experimental work prior to the
intensity measurements. See also _exptl_crystal_preparation.
;
###################
## EXPTL_CRYSTAL ##
###################
data_exptl_crystal_[]
_name '_exptl_crystal_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_exptl_crystal_description prism
_exptl_crystal_colour colourless
_exptl_crystal_size_max 0.32
_exptl_crystal_size_mid 0.27
_exptl_crystal_size_min 0.10
_exptl_crystal_density_diffrn 1.146
_exptl_crystal_density_meas ?
_exptl_crystal_density_method 'not measured'
_exptl_crystal_F_000 656
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; _exptl_crystal_density_meas_gt 2.5
_exptl_crystal_density_meas_lt 5.0
;
;
Example 2 - using separate items to define upper and lower
limits for a value.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; _exptl_crystal_density_meas_temp_lt 300
;
;
Example 3 - here the density was measured at some
unspecified temperature below room temperature.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the EXPTL_CRYSTAL category record details about
experimental measurements on the crystal or crystals used,
such as shape, size or density.
;
data_exptl_crystal_colour
_name '_exptl_crystal_colour'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_
_related_item
_related_function '_exptl_crystal_colour_lustre' alternate
'_exptl_crystal_colour_modifier' alternate
'_exptl_crystal_colour_primary' alternate
_example 'dark green'
_definition
; The colour of the crystal.
;
data_exptl_crystal_colour_lustre
_name '_exptl_crystal_colour_lustre'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_ _enumeration metallic
dull
clear
_related_item '_exptl_crystal_colour'
_related_function alternate
_definition
; The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal_colour_modifier with
_exptl_crystal_colour_primary, as in 'dark-green' or
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
data_exptl_crystal_colour_modifier
_name '_exptl_crystal_colour_modifier'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_ _enumeration light
dark
whitish
blackish
grayish
brownish
reddish
pinkish
orangish
yellowish
greenish
bluish
_related_item '_exptl_crystal_colour'
_related_function alternate
_definition
; The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal_colour_modifier with
_exptl_crystal_colour_primary, as in 'dark-green' or
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
data_exptl_crystal_colour_primary
_name '_exptl_crystal_colour_primary'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_ _enumeration colourless
white
black
gray
brown
red
pink
orange
yellow
green
blue
violet
_related_item '_exptl_crystal_colour'
_related_function alternate
_definition
; The enumeration list of standardized names developed for the
International Centre for Diffraction Data.
The colour of a crystal is given by the combination of
_exptl_crystal_colour_modifier with
_exptl_crystal_colour_primary, as in 'dark-green' or
'bluish-violet', if necessary combined with
_exptl_crystal_colour_lustre, as in 'metallic-green'.
;
data_exptl_crystal_density_diffrn
_name '_exptl_crystal_density_diffrn'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units Mgm^-3^
_units_detail 'megagrams per cubic metre'
_definition
; Density values calculated from the crystal cell and contents. The
units are megagrams per cubic metre (grams per cubic centimetre).
;
data_exptl_crystal_density_meas
_name '_exptl_crystal_density_meas'
_category exptl_crystal
_type numb
_type_conditions esd
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units Mgm^-3^
_units_detail 'megagrams per cubic metre'
_definition
; Density values measured using standard chemical and physical
methods. The units are megagrams per cubic metre (grams per
cubic centimetre).
;
data_exptl_crystal_density_meas_gt
_name '_exptl_crystal_density_meas_gt'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units Mg^-3^
_units_detail 'megagrams per cubic metre'
_related_item '_exptl_crystal_density_meas'
_related_function alternate
loop_ _example
_example_detail
2.5
; lower limit for the density (only the range
within which the density lies was given in the
original paper)
;
_definition
; The value above which the density measured using standard
chemical and physical methods lies. The units are megagrams
per cubic metre (grams per cubic centimetre).
_exptl_crystal_density_meas_gt and
_exptl_crystal_density_meas_lt should not be used to
report new experimental work, for which
_exptl_crystal_density_meas should be used. These items
are intended for use in reporting information in
existing databases and archives which would be misleading if
reported under _exptl_crystal_density_meas.
;
data_exptl_crystal_density_meas_lt
_name '_exptl_crystal_density_meas_lt'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units Mg^-3^
_units_detail 'megagrams per cubic metre'
_related_item '_exptl_crystal_density_meas'
_related_function alternate
loop_ _example
_example_detail
1.0
'specimen floats in water'
5.0
; upper limit for the density (only the range
within which the density lies was given in the
original paper)
;
_definition
; The value below which the density measured using standard
chemical and physical methods lies. The units are megagrams
per cubic metre (grams per cubic centimetre).
_exptl_crystal_density_meas_gt and
_exptl_crystal_density_meas_lt should not be used to
report new experimental work, for which
_exptl_crystal_density_meas should be used. These items
are intended for use in reporting information in
existing databases and archives which would be misleading if
reported under _exptl_crystal_density_meas.
;
data_exptl_crystal_density_meas_temp
_name '_exptl_crystal_density_meas_temp'
_category exptl_crystal
_type numb
_type_conditions esd
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units K
_units_detail kelvin
_definition
; Temperature in kelvins at which _exptl_crystal_density_meas
was determined.
;
data_exptl_crystal_density_meas_temp_gt
_name '_exptl_crystal_density_meas_temp_gt'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units K
_units_detail kelvin
_related_item '_exptl_crystal_density_meas_temp'
_related_function alternate
_definition
; Temperature in kelvins above which _exptl_crystal_density_meas
was determined. _exptl_crystal_density_meas_temp_gt and
_exptl_crystal_density_meas_temp_lt should not be used for
reporting new work, for which the correct temperature of
measurement should be given. These items are intended for
use in reporting information stored in databases
or archives which would be misleading if reported under
_exptl_crystal_density_meas_temp.
;
data_exptl_crystal_density_meas_temp_lt
_name '_exptl_crystal_density_meas_temp_lt'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units K
_units_detail kelvin
_related_item '_exptl_crystal_density_meas_temp'
_related_function alternate
loop_ _example
_example_detail
300
; The density was measured at some unspecified
temperature below room temperature.
;
_definition
; Temperature in kelvins below which _exptl_crystal_density_meas
was determined. _exptl_crystal_density_meas_temp_gt and
_exptl_crystal_density_meas_temp_lt should not be used for
reporting new work, for which the correct temperature of
measurement should be given. These items are intended for
use in reporting information stored in databases
or archives which would be misleading if reported under
_exptl_crystal_density_meas_temp.
;
data_exptl_crystal_density_method
_name '_exptl_crystal_density_method'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
loop_ _example 'flotation in aqueous KI'
'not measured'
'Berman density torsion balance'
_definition
; The method used to measure _exptl_crystal_density_meas.
;
data_exptl_crystal_description
_name '_exptl_crystal_description'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_definition
; A description of the quality and habit of the crystal.
The crystal dimensions should not normally be reported here;
use instead _exptl_crystal_size_ for the gross dimensions of
the crystal and _exptl_crystal_face_ to describe the
relationship between individual faces.
;
data_exptl_crystal_F_000
_name '_exptl_crystal_F_000'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_definition
; The effective number of electrons in the crystal unit cell
contributing to F(000). This may contain dispersion contributions
and is calculated as
F(000) = [ (sum f~r~)^2^ + (sum f~i~)^2^ ]^1/2^
f~r~ = real part of the scattering factors at theta = 0
f~i~ = imaginary part of the scattering factors at theta = 0
the sum is taken over each atom in the unit cell
;
data_exptl_crystal_id
_name '_exptl_crystal_id'
_category exptl_crystal
_type char
_list yes
_list_mandatory yes
loop_ _list_link_child '_diffrn_refln_crystal_id'
'_refln_crystal_id'
_definition
; Code identifying each crystal if multiple crystals are used. It
is used to link with _diffrn_refln_crystal_id in the intensity
measurements and with _refln_crystal_id in the _refln_ list.
;
data_exptl_crystal_preparation
_name '_exptl_crystal_preparation'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_example 'mounted in an argon-filled quartz capillary'
_definition
; Details of crystal growth and preparation of the crystal (e.g.
mounting) prior to the intensity measurements.
;
data_exptl_crystal_pressure_history
_name '_exptl_crystal_pressure_history'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_definition
; Relevant details concerning the pressure history of the
sample.
;
data_exptl_crystal_recrystallization_method
_name '_exptl_crystal_recrystallization_method'
_category exptl_crystal
_type char
_definition
; Describes the method used to recrystallize the sample.
Sufficient details should be given for the procedure to be
repeated. The temperature or temperatures should be given as
well as details of the solvent, flux or carrier gas with
concentrations or pressures and ambient atmosphere.
;
data_exptl_crystal_size_
loop_ _name '_exptl_crystal_size_length'
'_exptl_crystal_size_max'
'_exptl_crystal_size_mid'
'_exptl_crystal_size_min'
'_exptl_crystal_size_rad'
_category exptl_crystal
_type numb
_list both
_list_reference '_exptl_crystal_id'
_enumeration_range 0.0:
_units mm
_units_detail 'millimetres'
_definition
; The maximum, medial and minimum dimensions in millimetres of
the crystal. If the crystal is a sphere, then the *_rad item is
its radius. If the crystal is a cylinder, then the *_rad item
is its radius and the *_length item is its length. These may
appear in a list with _exptl_crystal_id if multiple crystals
are used in the experiment.
;
data_exptl_crystal_thermal_history
_name '_exptl_crystal_thermal_history'
_category exptl_crystal
_type char
_list both
_list_reference '_exptl_crystal_id'
_definition
; Relevant details concerning the thermal history of the
sample.
;
########################
## EXPTL_CRYSTAL_FACE ##
########################
data_exptl_crystal_face_[]
_name '_exptl_crystal_face_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_exptl_crystal_face_index_h
_exptl_crystal_face_index_k
_exptl_crystal_face_index_l
_exptl_crystal_face_perp_dist
0 -1 -2 .18274
1 0 -2 .17571
-1 1 -2 .17845
-2 1 0 .21010
-1 0 2 .18849
1 -1 2 .20605
2 -1 0 .24680
-1 2 0 .19688
0 1 2 .15206
;
;
Example 1 - based on structure PAWD2 of Vittal & Dean [Acta
Cryst. (1996), C52, 1180-1182].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the EXPTL_CRYSTAL_FACE category record details
of the crystal faces.
;
data_exptl_crystal_face_diffr_
loop_ _name '_exptl_crystal_face_diffr_chi'
'_exptl_crystal_face_diffr_kappa'
'_exptl_crystal_face_diffr_phi'
'_exptl_crystal_face_diffr_psi'
_category exptl_crystal_face
_type numb
_list yes
_list_reference '_exptl_crystal_face_index_'
_units deg
_units_detail 'degrees'
_definition
; The goniometer angle settings in degrees when the perpendicular
to the specified crystal face is aligned along a specified
direction (e.g. the bisector of the incident and reflected beams
in an optical goniometer).
;
data_exptl_crystal_face_index_
loop_ _name '_exptl_crystal_face_index_h'
'_exptl_crystal_face_index_k'
'_exptl_crystal_face_index_l'
_category exptl_crystal_face
_type numb
_list yes
_list_mandatory yes
_definition
; Miller indices of the crystal face associated with the value
_exptl_crystal_face_perp_dist.
;
data_exptl_crystal_face_perp_dist
_name '_exptl_crystal_face_perp_dist'
_category exptl_crystal_face
_type numb
_list yes
_list_reference '_exptl_crystal_face_index_'
_enumeration_range 0.0:
_units mm
_units_detail 'millimetres'
_definition
; The perpendicular distance in millimetres from the face to the
centre of rotation of the crystal.
;
##########
## GEOM ##
##########
data_geom_[]
_name '_geom_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_geom_special_details
; All esds (except the esd in the dihedral angle between
two l.s. planes) are estimated using the full covariance
matrix. The cell esds are taken into account individually
in the estimation of esds in distances, angles and
torsion angles; correlations between esds in cell
parameters are only used when they are defined by crystal
symmetry. An approximate (isotropic) treatment of cell
esds is used for estimating esds involving l.s. planes.
;
;
;
Example 1 - based on data set bagan of Yamane & DiSalvo [Acta
Cryst. (1996), C52, 760-761].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM and related (GEOM_ANGLE,
GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION)
categories record details about the molecular and crystal
geometry as calculated from the ATOM,
CELL and SYMMETRY data.
Geometry data are usually redundant, in that they can be
calculated from other more fundamental quantities in the data
block. However, they serve the dual purposes of providing a
check on the correctness of both sets of data and of enabling
the most important geometric data to be identified for
publication by setting the appropriate publication flag.
;
data_geom_special_details
_name '_geom_special_details'
_category geom
_type char
_definition
; The description of geometrical information not covered by the
existing data names in the geometry categories, such as
least-squares planes.
;
################
## GEOM_ANGLE ##
################
data_geom_angle_[]
_name '_geom_angle_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_2
_geom_angle_site_symmetry_3
_geom_angle_publ_flag
C2 O1 C5 111.6(2) 1_555 1_555 1_555 yes
O1 C2 C3 110.9(2) 1_555 1_555 1_555 yes
O1 C2 O21 122.2(3) 1_555 1_555 1_555 yes
C3 C2 O21 127.0(3) 1_555 1_555 1_555 yes
C2 C3 N4 101.3(2) 1_555 1_555 1_555 yes
C2 C3 C31 111.3(2) 1_555 1_555 1_555 yes
C2 C3 H3 107(1) 1_555 1_555 1_555 no
N4 C3 C31 116.7(2) 1_555 1_555 1_555 yes
# - - - - data truncated for brevity - - - -
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM_ANGLE category record details about the
bond angles as calculated from the ATOM,
CELL and SYMMETRY data.
;
data_geom_angle
_name '_geom_angle'
_category geom_angle
_type numb
_type_conditions esd
_list yes
_list_reference '_geom_angle_atom_site_label_'
_units deg
_units_detail 'degrees'
_definition
; Angle in degrees defined by the three sites
_geom_angle_atom_site_label_1, *_2 and *_3. The site at *_2
is at the apex of the angle.
;
data_geom_angle_atom_site_label_
loop_ _name '_geom_angle_atom_site_label_1'
'_geom_angle_atom_site_label_2'
'_geom_angle_atom_site_label_3'
_category geom_angle
_type char
_list yes
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; The labels of the three atom sites which define the angle
given by _geom_angle. These must match labels specified as
_atom_site_label in the atom list. Label 2 identifies the site at
the apex of the angle.
;
data_geom_angle_publ_flag
_name '_geom_angle_publ_flag'
_category geom_angle
_type char
_list yes
_list_reference '_geom_angle_atom_site_label_'
loop_ _enumeration
_enumeration_detail no 'do not include angle in special list'
n 'abbreviation for "no"'
yes 'do include angle in special list'
y 'abbreviation for "yes"'
_enumeration_default no
_definition
; This code signals whether the angle is referred to in a
publication or should be placed in a table of significant
angles.
;
data_geom_angle_site_symmetry_
loop_ _name '_geom_angle_site_symmetry_1'
'_geom_angle_site_symmetry_2'
'_geom_angle_site_symmetry_3'
_category geom_angle
_type char
_list yes
_list_reference '_geom_angle_atom_site_label_'
loop_ _example
_example_detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
; The symmetry code of each atom site as the symmetry-equivalent
position number 'n' and the cell translation number 'klm'.
These numbers are combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
_space_group_symop_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry-transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
By adding 5 to the translations, the use of negative numbers
is avoided.
;
###############
## GEOM_BOND ##
###############
data_geom_bond_[]
_name '_geom_bond_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_1
_geom_bond_site_symmetry_2
_geom_bond_publ_flag
O1 C2 1.342(4) 1_555 1_555 yes
O1 C5 1.439(3) 1_555 1_555 yes
C2 C3 1.512(4) 1_555 1_555 yes
C2 O21 1.199(4) 1_555 1_555 yes
C3 N4 1.465(3) 1_555 1_555 yes
C3 C31 1.537(4) 1_555 1_555 yes
C3 H3 1.00(3) 1_555 1_555 no
N4 C5 1.472(3) 1_555 1_555 yes
# - - - - data truncated for brevity - - - -
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM_BOND category record details about
bonds as calculated from the ATOM, CELL
and SYMMETRY data.
;
data_geom_bond_atom_site_label_
loop_ _name '_geom_bond_atom_site_label_1'
'_geom_bond_atom_site_label_2'
_category geom_bond
_type char
_list yes
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; The labels of two atom sites that form a bond. These must match
labels specified as _atom_site_label in the atom list.
;
data_geom_bond_distance
_name '_geom_bond_distance'
_category geom_bond
_type numb
_type_conditions esd
_list yes
_list_reference '_geom_bond_atom_site_label_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The intramolecular bond distance in angstroms.
;
data_geom_bond_publ_flag
_name '_geom_bond_publ_flag'
_category geom_bond
_type char
_list yes
_list_reference '_geom_bond_atom_site_label_'
loop_ _enumeration
_enumeration_detail no 'do not include bond in special list'
n 'abbreviation for "no"'
yes 'do include bond in special list'
y 'abbreviation for "yes"'
_enumeration_default no
_definition
; This code signals whether the bond distance is referred to in a
publication or should be placed in a list of significant bond
distances.
;
data_geom_bond_site_symmetry_
loop_ _name '_geom_bond_site_symmetry_1'
'_geom_bond_site_symmetry_2'
_category geom_bond
_type char
_list yes
_list_reference '_geom_bond_atom_site_label_'
loop_ _example
_example_detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
; The symmetry code of each atom site as the symmetry-equivalent
position number 'n' and the cell translation number 'klm'.
These numbers are combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
_space_group_symop_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry-transformed coordinates to generate
the atom used in calculating the bond. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
By adding 5 to the translations, the use of negative numbers
is avoided.
;
data_geom_bond_valence
_name '_geom_bond_valence'
_category geom_bond
_type numb
_list yes
_list_reference '_geom_bond_atom_site_label_'
_definition
; The bond valence calculated from _geom_bond_distance.
;
##################
## GEOM_CONTACT ##
##################
data_geom_contact_[]
_name '_geom_contact_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_geom_contact_atom_site_label_1
_geom_contact_atom_site_label_2
_geom_contact_distance
_geom_contact_site_symmetry_1
_geom_contact_site_symmetry_2
_geom_contact_publ_flag
O(1) O(2) 2.735(3) . . yes
H(O1) O(2) 1.82 . . no
;
;
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
[Acta Cryst. (1992), C48, 2262-2264].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM_CONTACT category record details about
interatomic contacts as calculated from the
ATOM, CELL and SYMMETRY data.
;
data_geom_contact_atom_site_label_
loop_ _name '_geom_contact_atom_site_label_1'
'_geom_contact_atom_site_label_2'
_category geom_contact
_type char
_list yes
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; The labels of two atom sites that are within contact distance.
The labels must match _atom_site_label codes in the atom list.
;
data_geom_contact_distance
_name '_geom_contact_distance'
_category geom_contact
_type numb
_type_conditions esd
_list yes
_list_reference '_geom_contact_atom_site_label_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The interatomic contact distance in angstroms.
;
data_geom_contact_publ_flag
_name '_geom_contact_publ_flag'
_category geom_contact
_type char
_list yes
_list_reference '_geom_contact_atom_site_label_'
loop_ _enumeration
_enumeration_detail no 'do not include distance in special list'
n 'abbreviation for "no"'
yes 'do include distance in special list'
y 'abbreviation for "yes"'
_enumeration_default no
_definition
; This code signals whether the contact distance is referred to
in a publication or should be placed in a list of significant
contact distances.
;
data_geom_contact_site_symmetry_
loop_ _name '_geom_contact_site_symmetry_1'
'_geom_contact_site_symmetry_2'
_category geom_contact
_type char
_list yes
_list_reference '_geom_contact_atom_site_label_'
loop_ _example
_example_detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
; The symmetry code of each atom site as the symmetry-equivalent
position number 'n' and the cell translation number 'klm'.
These numbers are combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
_space_group_symop_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry-transformed coordinates to generate
the atom used in calculating the contact. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
By adding 5 to the translations, the use of negative numbers
is avoided.
;
################
## GEOM_HBOND ##
################
data_geom_hbond_[]
_name '_geom_hbond_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_publ_flag
N6 HN6 OW 0.888(8) 1.921(12) 2.801(8) 169.6(8) yes
OW HO2 O7 0.917(6) 1.923(12) 2.793(8) 153.5(8) yes
OW HO1 N10 0.894(8) 1.886(11) 2.842(8) 179.7(9) yes
;
;
Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer,
Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM_HBOND category record details about
hydrogen bonds as calculated from the ATOM,
CELL and SYMMETRY data.
;
data_geom_hbond_angle_DHA
_name '_geom_hbond_angle_DHA'
_category geom_hbond
_type numb
_type_conditions esd
_list yes
_list_reference '_geom_hbond_atom_site_label_'
_units deg
_units_detail 'degrees'
_definition
; Angle in degrees defined by the three sites
_geom_hbond_atom_site_label_D, *_H and *_A. The site at *_H
(the hydrogen atom participating in the interaction) is at
the apex of the angle.
;
data_geom_hbond_atom_site_label_
loop_ _name '_geom_hbond_atom_site_label_D'
'_geom_hbond_atom_site_label_H'
'_geom_hbond_atom_site_label_A'
_category geom_hbond
_type char
_list yes
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; The labels of three atom sites (respectively, the donor atom,
hydrogen atom and acceptor atom) participating in a hydrogen
bond. These must match labels specified as _atom_site_label
in the atom list.
;
data_geom_hbond_distance_
loop_ _name '_geom_hbond_distance_DH'
'_geom_hbond_distance_HA'
'_geom_hbond_distance_DA'
_category geom_hbond
_type numb
_type_conditions esd
_list yes
_list_reference '_geom_hbond_atom_site_label_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; Distances in angstroms between the donor and hydrogen (*_DH),
hydrogen and acceptor (*_HA) and donor and acceptor (*_DA)
sites in a hydrogen bond.
;
data_geom_hbond_publ_flag
_name '_geom_hbond_publ_flag'
_category geom_hbond
_type char
_list yes
_list_reference '_geom_hbond_atom_site_label_'
loop_ _enumeration
_enumeration_detail no 'do not include bond in special list'
n 'abbreviation for "no"'
yes 'do include bond in special list'
y 'abbreviation for "yes"'
_enumeration_default no
_definition
; This code signals whether the hydrogen-bond information
is referred to in a publication or should be placed in a
table of significant hydrogen-bond geometry.
;
data_geom_hbond_site_symmetry_
loop_ _name '_geom_hbond_site_symmetry_D'
'_geom_hbond_site_symmetry_H'
'_geom_hbond_site_symmetry_A'
_category geom_hbond
_type char
_list yes
_list_reference '_geom_hbond_atom_site_label_'
loop_ _example
_example_detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
; The symmetry code of each atom site as the symmetry-equivalent
position number 'n' and the cell translation number 'klm'.
These numbers are combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
_space_group_symop_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry-transformed coordinates to generate
the atom used in calculating the hydrogen bond. These
translations (x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
By adding 5 to the translations, the use of negative numbers
is avoided.
;
##################
## GEOM_TORSION ##
##################
data_geom_torsion_[]
_name '_geom_torsion_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_geom_torsion_atom_site_label_1
_geom_torsion_atom_site_label_2
_geom_torsion_atom_site_label_3
_geom_torsion_atom_site_label_4
_geom_torsion
_geom_torsion_site_symmetry_1
_geom_torsion_site_symmetry_2
_geom_torsion_site_symmetry_3
_geom_torsion_site_symmetry_4
_geom_torsion_publ_flag
C(9) O(2) C(7) C(2) 71.8(2) . . . . yes
C(7) O(2) C(9) C(10) -168.0(3) . . . 2_666 yes
C(10) O(3) C(8) C(6) -167.7(3) . . . . yes
C(8) O(3) C(10) C(9) -69.7(2) . . . 2_666 yes
O(1) C(1) C(2) C(3) -179.5(4) . . . . no
O(1) C(1) C(2) C(7) -0.6(1) . . . . no
;
;
Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne
[Acta Cryst. (1992), C48, 2262-2264].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the GEOM_TORSION category record details about
interatomic torsion angles as calculated from
the ATOM, CELL and SYMMETRY data.
;
data_geom_torsion
_name '_geom_torsion'
_category geom_torsion
_type numb
_type_conditions esd
_list yes
_list_reference '_geom_torsion_atom_site_label_'
_units deg
_units_detail 'degrees'
_definition
; The torsion angle in degrees bounded by the four atom sites
identified by the _geom_torsion_atom_site_label_ codes. These
must match labels specified as _atom_site_label in the atom list.
The torsion-angle definition should be that of Klyne and Prelog.
Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
;
data_geom_torsion_atom_site_label_
loop_ _name '_geom_torsion_atom_site_label_1'
'_geom_torsion_atom_site_label_2'
'_geom_torsion_atom_site_label_3'
'_geom_torsion_atom_site_label_4'
_category geom_torsion
_type char
_list yes
_list_mandatory yes
_list_link_parent '_atom_site_label'
_definition
; The labels of the four atom sites which define the torsion angle
specified by _geom_torsion. These must match codes specified as
_atom_site_label in the atom list. The torsion-angle definition
should be that of Klyne and Prelog. The vector direction
*_label_2 to *_label_3 is the viewing direction, and the torsion
angle is the angle of twist required to superimpose the
projection of the vector between site 2 and site 1 onto the
projection of the vector between site 3 and site 4. Clockwise
torsions are positive, anticlockwise torsions are negative.
Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
;
data_geom_torsion_publ_flag
_name '_geom_torsion_publ_flag'
_category geom_torsion
_type char
_list yes
_list_reference '_geom_torsion_atom_site_label_'
loop_ _enumeration
_enumeration_detail no 'do not include angle in special list'
n 'abbreviation for "no"'
yes 'do include angle in special list'
y 'abbreviation for "yes"'
_enumeration_default no
_definition
; This code signals whether the torsion angle is referred to in a
publication or should be placed in a table of significant
torsion angles.
;
data_geom_torsion_site_symmetry_
loop_ _name '_geom_torsion_site_symmetry_1'
'_geom_torsion_site_symmetry_2'
'_geom_torsion_site_symmetry_3'
'_geom_torsion_site_symmetry_4'
_category geom_torsion
_type char
_list yes
_list_reference '_geom_torsion_atom_site_label_'
loop_ _example
_example_detail . 'no symmetry or translation to site'
4 '4th symmetry operation applied'
7_645 '7th symm. posn.; +a on x; -b on y'
_definition
; The symmetry code of each atom site as the symmetry-equivalent
position number 'n' and the cell translation number 'klm'.
These numbers are combined to form the code 'n klm' or n_klm.
The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the
coordinates stored in _atom_site_fract_x, _atom_site_fract_y
and _atom_site_fract_z. It must match a number given in
_space_group_symop_id.
k, l and m refer to the translations that are subsequently
applied to the symmetry-transformed coordinates to generate
the atom used in calculating the angle. These translations
(x,y,z) are related to (k,l,m) by the relations
k = 5 + x
l = 5 + y
m = 5 + z
By adding 5 to the translations, the use of negative numbers
is avoided.
;
#############
## JOURNAL ##
#############
data_journal_[]
_name '_journal_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_journal_date_recd_electronic 91-04-15
_journal_date_from_coeditor 91-04-18
_journal_date_accepted 91-04-18
_journal_date_printers_first 91-08-07
_journal_date_proofs_out 91-08-07
_journal_coeditor_code HL0007
_journal_techeditor_code C910963
_journal_coden_ASTM ACSCEE
_journal_name_full 'Acta Crystallographica Section C'
_journal_year 1991
_journal_volume 47
_journal_issue NOV91
_journal_page_first 2276
_journal_page_last 2277
;
;
Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith
& Tozer (1991). Acta Cryst. C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the JOURNAL category record details about the
book-keeping by the journal staff when processing
a CIF submitted for publication.
The creator of a CIF will not normally specify these data items.
The data names are not defined in the dictionary because they are
for journal use only.
;
data_journal_
loop_ _name '_journal_coden_ASTM'
'_journal_coden_Cambridge'
'_journal_coeditor_address'
'_journal_coeditor_code'
'_journal_coeditor_email'
'_journal_coeditor_fax'
'_journal_coeditor_name'
'_journal_coeditor_notes'
'_journal_coeditor_phone'
'_journal_data_validation_number'
'_journal_date_accepted'
'_journal_date_from_coeditor'
'_journal_date_to_coeditor'
'_journal_date_printers_final'
'_journal_date_printers_first'
'_journal_date_proofs_in'
'_journal_date_proofs_out'
'_journal_date_recd_copyright'
'_journal_date_recd_electronic'
'_journal_date_recd_hard_copy'
'_journal_issue'
'_journal_language'
'_journal_name_full'
'_journal_page_first'
'_journal_page_last'
'_journal_paper_category'
'_journal_suppl_publ_number'
'_journal_suppl_publ_pages'
'_journal_techeditor_address'
'_journal_techeditor_code'
'_journal_techeditor_email'
'_journal_techeditor_fax'
'_journal_techeditor_name'
'_journal_techeditor_notes'
'_journal_techeditor_phone'
'_journal_volume'
'_journal_year'
_category journal
_type char
_definition
; Data items specified by the journal staff.
;
###################
## JOURNAL_INDEX ##
###################
data_journal_index_[]
_name '_journal_index_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_journal_index_type
_journal_index_term
_journal_index_subterm
O C16H19NO4 .
S alkaloids (-)-norcocaine
S (-)-norcocaine .
S
; [2R,3S-(2\b,3\b)]-methyl
3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate
; .
;
;
Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell
[Acta Cryst. (1994), C50, 2067-2069].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the JOURNAL_INDEX category are used to list
terms used to generate the journal indexes.
The creator of a CIF will not normally specify these data items.
;
data_journal_index_
loop_ _name '_journal_index_subterm'
'_journal_index_term'
'_journal_index_type'
_category journal_index
_type char
_definition
; Indexing terms supplied by the journal staff.
;
##########
## PUBL ##
##########
data_publ_[]
_name '_publ_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; _publ_section_title
; trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)-
1,3-oxazolidin-5-one
;
_publ_section_abstract
; The oxazolidinone ring is a shallow envelope
conformation with the tert-butyl and iso-butyl groups
occupying trans-positions with respect to the ring. The
angles at the N atom sum to 356.2\%, indicating a very
small degree of pyramidalization at this atom. This is
consistent with electron delocalization between the N
atom and the carbonyl centre [N-C=O = 1.374(3)\%A].
;
;
;
Example 1 - based on Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; _publ_section_title
; Hemiasterlin methyl ester
;
_publ_section_title_footnote
; IUPAC name: methyl 2,5-dimethyl-4-{2-[3-methyl-
2-methylamino-3-(N-methylbenzo[b]pyrrol-
3-yl)butanamido]-3,3-dimethyl-N-methyl-
butanamido}-2-hexenoate.
;
;
;
Example 2 - based on C~31~H~48~N~4~O~4~, reported by Coleman, Patrick,
Andersen & Rettig [Acta Cryst. (1996), C52, 1525-1527].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the PUBL category are used when submitting a
manuscript for publication. They refer either to the paper as
a whole, or to specific named elements within a paper (such as
the title and abstract, or the Comment and Experimental
sections of Acta Crystallographica Section C). The data items
in the PUBL_BODY category should be used for the text
of other submissions. Typically, each journal will
supply a list of the specific items it requires in its Notes
for Authors.
;
data_publ_contact_author
_name '_publ_contact_author'
_category publ
_type char
loop_
_example
; Professor George Ferguson
Department of Chemistry and Biochemistry
University of Guelph
Ontario
Canada
N1G 2W1
;
_definition
; The name and address of the author submitting the manuscript and
data block. This is the person contacted by the journal
editorial staff. It is preferable to use the separate data items
_publ_contact_author_name and _publ_contact_author_address.
;
data_publ_contact_author_address
_name '_publ_contact_author_address'
_category publ
_type char
_example
; Department of Chemistry and Biochemistry
University of Guelph
Ontario
Canada
N1G 2W1
;
_definition
; The address of the author submitting the manuscript and
data block. This is the person contacted by the journal
editorial staff.
;
data_publ_contact_author_email
_name '_publ_contact_author_email'
_category publ
_type char
loop_ _example name@host.domain.country
bm@iucr.org
_definition
; E-mail address in a form recognizable to international networks.
The format of e-mail addresses is given in Section 3.4, Address
Specification, of Internet Message Format, RFC 2822, P. Resnick
(Editor), Network Standards Group, April 2001.
;
data_publ_contact_author_fax
_name '_publ_contact_author_fax'
_category publ
_type char
loop_
_example '12(34)9477334'
'12()349477334'
_definition
; Facsimile telephone number of the author submitting the
manuscript and data block.
The recommended style is the international dialing
prefix, followed by the area code in parentheses, followed by
the local number with no spaces. The earlier convention of
including the international dialing prefix in parentheses is
no longer recommended.
;
data_publ_contact_author_id_iucr
_name '_publ_contact_author_id_iucr'
_category publ
_type char
_example 2985
_definition
; Identifier in the IUCr contact database of the author
submitting the manuscript and data block. This identifier may
be available from the World Directory of Crystallographers
(http://wdc.iucr.org).
;
data_publ_contact_author_name
_name '_publ_contact_author_name'
_category publ
_type char
_example 'Professor George Ferguson'
_definition
; The name of the author submitting the manuscript and
data block. This is the person contacted by the journal
editorial staff.
;
data_publ_contact_author_phone
_name '_publ_contact_author_phone'
_category publ
_type char
loop_
_example '12(34)9477330'
'12()349477330'
'12(34)9477330x5543'
_definition
; Telephone number of the author submitting the manuscript and
data block.
The recommended style is the international dialing
prefix, followed by the area code in parentheses, followed by the
local number and any extension number prefixed by 'x',
with no spaces. The earlier convention of including
the international dialing prefix in parentheses is no longer
recommended.
;
data_publ_contact_letter
_name '_publ_contact_letter'
_category publ
_type char
_definition
; A letter submitted to the journal editor by the contact author.
;
data_publ_manuscript_creation
_name '_publ_manuscript_creation'
_category publ
_type char
_example 'Tex file created by FrameMaker on a Sun 3/280'
_definition
; A description of the word-processor package and computer used to
create the word-processed manuscript stored as
_publ_manuscript_processed.
;
data_publ_manuscript_processed
_name '_publ_manuscript_processed'
_category publ
_type char
_definition
; The full manuscript of a paper (excluding possibly the figures
and the tables) output in ASCII characters from a word processor.
Information about the generation of this data item must be
specified in the data item _publ_manuscript_creation.
;
data_publ_manuscript_text
_name '_publ_manuscript_text'
_category publ
_type char
_definition
; The full manuscript of a paper (excluding figures and possibly
the tables) output as standard ASCII text.
;
data_publ_requested_category
_name '_publ_requested_category'
_category publ
_type char
loop_ _enumeration
_enumeration_detail
FA 'Full article'
FI 'Full submission - inorganic (Acta C)'
FO 'Full submission - organic (Acta C)'
FM 'Full submission - metal-organic (Acta C)'
CI 'CIF-access paper - inorganic (Acta C) (no longer in use)'
CO 'CIF-access paper - organic (Acta C) (no longer in use)'
CM 'CIF-access paper - metal-organic (Acta C) (no longer in use)'
EI 'Electronic submission - inorganic (Acta E)'
EO 'Electronic submission - organic (Acta E)'
EM 'Electronic submission - metal-organic (Acta E)'
AD 'Addenda and Errata (Acta C, Acta E)'
SC 'Short communication'
_enumeration_default FA
_definition
; The category of paper submitted. For submission to Acta
Crystallographica Section C or Acta Crystallographica
Section E, ONLY those codes indicated for use with those
journals should be used.
;
data_publ_requested_coeditor_name
_name '_publ_requested_coeditor_name'
_category publ
_type char
_definition
; The name of the co-editor whom the authors would like to
handle the submitted manuscript.
;
data_publ_requested_journal
_name '_publ_requested_journal'
_category publ
_type char
_definition
; The name of the journal to which the manuscript is being
submitted.
;
data_publ_section_
loop_ _name '_publ_section_title'
'_publ_section_title_footnote'
'_publ_section_synopsis'
'_publ_section_abstract'
'_publ_section_comment'
'_publ_section_introduction'
'_publ_section_experimental'
'_publ_section_exptl_prep'
'_publ_section_exptl_refinement'
'_publ_section_exptl_solution'
'_publ_section_discussion'
'_publ_section_acknowledgements'
'_publ_section_references'
'_publ_section_figure_captions'
'_publ_section_table_legends'
_category publ
_type char
_definition
; The sections of a manuscript if submitted in parts. As
an alternative, see _publ_manuscript_text and
_publ_manuscript_processed.
The _publ_section_exptl_prep, _publ_section_exptl_refinement
and _publ_section_exptl_solution items are preferred for
separating the chemical preparation, refinement and structure
solution aspects of the experimental description.
;
#################
## PUBL_AUTHOR ##
#################
data_publ_author_[]
_name '_publ_author_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_publ_author_name
_publ_author_address
'Willis, Anthony C.'
; Research School of Chemistry
Australian National University
GPO Box 4
Canberra, ACT
Australia 2601
;
;
;
Example 1 - based on Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the PUBL_AUTHOR category record details of
the authors of a manuscript submitted for publication.
;
data_publ_author_address
_name '_publ_author_address'
_category publ_author
_type char
_list both
_list_reference '_publ_author_name'
_example
; Department
Institute
Street
City and postcode
COUNTRY
;
_definition
; The address of a publication author. If there is more than one
author, this will be looped with _publ_author_name.
;
data_publ_author_footnote
_name '_publ_author_footnote'
_category publ_author
_type char
_list both
_list_reference '_publ_author_name'
loop_ _example 'On leave from U. Western Australia'
'Also at Department of Biophysics'
_definition
; A footnote accompanying an author's name in the list of authors
of a paper. Typically indicates sabbatical address, additional
affiliations or date of decease.
;
data_publ_author_email
_name '_publ_author_email'
_category publ_author
_type char
_list both
_list_reference '_publ_author_name'
loop_ _example name@host.domain.country
bm@iucr.org
_definition
; The e-mail address of a publication author. If there is more
than one author, this will be looped with _publ_author_name.
The format of e-mail addresses is given in Section 3.4, Address
Specification, of Internet Message Format, RFC 2822, P. Resnick
(Editor), Network Standards Group, April 2001.
;
data_publ_author_id_iucr
_name '_publ_author_id_iucr'
_category publ_author
_type char
_list both
_example 2985
_definition
; Identifier in the IUCr contact database of a publication
author. This identifier may be available from the World
Directory of Crystallographers (http://wdc.iucr.org).
;
data_publ_author_name
_name '_publ_author_name'
_category publ_author
_type char
_list both
_list_mandatory yes
loop_ _example 'Bleary, Percival R.'
"O'Neil, F.K."
'Van den Bossche, G.'
'Yang, D.-L.'
'Simonov, Yu.A.'
'M\"uller, H.A.'
'Ross II, C.R.'
_definition
; The name of a publication author. If there are multiple authors,
this will be looped with _publ_author_address. The family
name(s), followed by a comma and including any dynastic
components, precedes the first names or initials.
;
###############
## PUBL_BODY ##
###############
data_publ_body_[]
_name '_publ_body_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_publ_body_element
_publ_body_label
_publ_body_title
_publ_body_format
_publ_body_contents
section 1 Introduction cif
; X-ray diffraction from a crystalline material provides
information on the thermally and spatially averaged
electron density in the crystal...
;
section 2 Theory tex
; In the rigid-atom approximation, the dynamic electron
density of an atom is described by the convolution
product of the static atomic density and a probability
density function,
$\rho_{dyn}(\bf r) = \rho_{stat}(\bf r) * P(\bf r). \eqno(1)$
;
;
;
Example 1 - based on a paper by R. Restori & D. Schwarzenbach
[Acta Cryst. (1996), A52, 369-378].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_publ_body_element
_publ_body_label
_publ_body_title
_publ_body_contents
section 3
; The two-channel method for retrieval of the deformation
electron density
;
.
subsection 3.1 'The two-channel entropy S[\D\r(r)]'
; As the wide dynamic range involved in the total electron
density...
;
subsection 3.2
'Uniform vs informative prior model densities' .
subsubsection 3.2.1 'Use of uniform models'
; Straightforward algebra leads to expressions analogous
to...
;
;
;
Example 2 - based on a paper by R. J. Papoular, Y. Vekhter & P. Coppens
[Acta Cryst. (1996), A52, 397-407].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the PUBL_BODY category permit the labelling of
different text sections within the body of a paper.
Note that these should not be used in a paper which has
a standard format with sections tagged by specific data names
(such as in Acta Crystallographica Section C). Typically,
each journal will supply a list of the specific items it
requires in its Notes for Authors.
;
data_publ_body_contents
_name '_publ_body_contents'
_category publ_body
_type char
_list yes
_list_reference '_publ_body_label'
_definition
; A text section of a paper.
;
data_publ_body_element
_name '_publ_body_element'
_category publ_body
_type char
_list yes
_list_reference '_publ_body_label'
loop_ _enumeration
section
subsection
subsubsection
appendix
footnote
_definition
; The functional role of the associated text section.
;
data_publ_body_format
_name '_publ_body_format'
_category publ_body
_type char
_list yes
_list_reference '_publ_body_label'
loop_ _enumeration
_enumeration_detail
ascii 'no coding for special symbols'
cif 'CIF convention'
latex 'LaTeX'
rtf 'Rich Text Format'
sgml 'SGML (ISO 8879)'
tex 'TeX'
troff 'troff or nroff'
_enumeration_default cif
_definition
; Code indicating the appropriate typesetting conventions
for accented characters and special symbols in the text
section.
;
data_publ_body_label
_name '_publ_body_label'
_category publ_body
_type char
_list yes
_list_mandatory yes
_list_uniqueness '_publ_body_element'
loop_ _example 1 1.1 2.1.3
_definition
; Code identifying the section of text. The combination of this
with _publ_body_element must be unique.
;
data_publ_body_title
_name '_publ_body_title'
_category publ_body
_type char
_list yes
_list_reference '_publ_body_label'
_definition
; Title of the associated section of text.
;
##########################
## PUBL_MANUSCRIPT_INCL ##
##########################
data_publ_manuscript_incl_[]
_name '_publ_manuscript_incl_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_publ_manuscript_incl_extra_item
_publ_manuscript_incl_extra_info
_publ_manuscript_incl_extra_defn
#
# Include Hydrogen Bonding Geometry Description
# =============================================
# Name explanation standard?
# ---- ----------- ---------
'_geom_hbond_atom_site_label_D' 'H-bond donor' yes
'_geom_hbond_atom_site_label_H' 'H-bond hydrogen' yes
'_geom_hbond_atom_site_label_A' 'H-bond acceptor' yes
'_geom_hbond_distance_DH' 'H-bond D-H' yes
'_geom_hbond_distance_HA' 'H-bond H...A' yes
'_geom_hbond_distance_DA' 'H-bond D...A' yes
'_geom_hbond_angle_DHA' 'H-bond D-H...A' yes
;
;
Example 1 - directive to include a hydrogen-bonding table, including
cosmetic headings in comments.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_publ_manuscript_incl_extra_item
_publ_manuscript_incl_extra_info
_publ_manuscript_incl_extra_defn
'_atom_site_symmetry_multiplicity'
'to emphasise special sites' yes
'_chemical_compound_source'
'rare material, unusual source' yes
'_reflns_d_resolution_high'
'limited data is a problem here' yes
'_crystal_magnetic_permeability'
'unusual value for this material' no
;
;
Example 2 - hypothetical example including both standard CIF data items
and a non-CIF quantity which the author wishes to list.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the PUBL_MANUSCRIPT_INCL category allow
the authors of a manuscript submitted for publication to list
data names that should be added to the standard request list
used by the journal printing software. Although these fields are
primarily intended to identify CIF data items that the author
wishes to include in a published paper, they can also be used
to identify data names created so that non-CIF items can be
included in the publication. Note that *_item names MUST be
enclosed in single quotes.
;
data_publ_manuscript_incl_extra_defn
_name '_publ_manuscript_incl_extra_defn'
_category publ_manuscript_incl
_type char
_list yes
_list_reference '_publ_manuscript_incl_extra_item'
loop_ _enumeration
_enumeration_detail
no 'not a standard CIF data name'
n 'abbreviation for "no"'
yes 'a standard CIF data name'
y 'abbreviation for "yes"'
_enumeration_default yes
_definition
; Flags whether the corresponding data item marked for inclusion
in a journal request list is a standard CIF definition or not.
;
data_publ_manuscript_incl_extra_info
_name '_publ_manuscript_incl_extra_info'
_category publ_manuscript_incl
_type char
_list yes
_list_reference '_publ_manuscript_incl_extra_item'
_definition
; A short note indicating the reason why the author wishes the
corresponding data item marked for inclusion in the journal
request list to be published.
;
data_publ_manuscript_incl_extra_item
_name '_publ_manuscript_incl_extra_item'
_category publ_manuscript_incl
_type char
_list yes
_list_mandatory yes
_definition
; Specifies the inclusion of specific data into a manuscript
which are not normally requested by the journal. The values
of this item are the extra data names (which MUST be enclosed
in single quotes) that will be added to the journal request list.
;
############
## REFINE ##
############
data_refine_[]
_name '_refine_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_refine_special_details sfls:_F_calc_weight_full_matrix
_refine_ls_structure_factor_coef F
_refine_ls_matrix_type full
_refine_ls_weighting_scheme calc
_refine_ls_weighting_details 'w=1/(u^2^(F)+0.0004F^2^)'
_refine_ls_hydrogen_treatment refxyz
_refine_ls_extinction_method Zachariasen
_refine_ls_extinction_coef 3514(42)
_refine_ls_extinction_expression
; Larson, A. C. (1970). "Crystallographic Computing", edited
by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.
;
_refine_ls_abs_structure_details
; The absolute configuration was assigned to agree with that
of its precursor l-leucine at the chiral centre C3.
;
_refine_ls_number_reflns 1408
_refine_ls_number_parameters 272
_refine_ls_number_restraints 0
_refine_ls_number_constraints 0
_refine_ls_R_factor_all .038
_refine_ls_R_factor_gt .034
_refine_ls_wR_factor_all .044
_refine_ls_wR_factor_gt .042
_refine_ls_goodness_of_fit_all 1.462
_refine_ls_goodness_of_fit_gt 1.515
_refine_ls_shift/su_max .535
_refine_ls_shift/su_mean .044
_refine_diff_density_min -.108
_refine_diff_density_max .131
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFINE category record details about the
structure-refinement parameters.
;
data_refine_diff_density_
loop_ _name '_refine_diff_density_max'
'_refine_diff_density_min'
'_refine_diff_density_rms'
_category refine
_type numb
_type_conditions esd
_units e_A^-3^
_units_detail 'electrons per cubic angstrom'
_definition
; The largest and smallest values and the root-mean-square
deviation, in electrons per angstrom cubed, of the final
difference electron density. The *_rms value is measured with
respect to the arithmetic mean density and is derived from
summations over each grid point in the asymmetric unit of
the cell. This quantity is useful for assessing the
significance of *_min and *_max values, and also for
defining suitable contour levels.
;
data_refine_ls_abs_structure_details
_name '_refine_ls_abs_structure_details'
_category refine
_type char
_definition
; The nature of the absolute structure and how it was determined.
;
data_refine_ls_abs_structure_Flack
_name '_refine_ls_abs_structure_Flack'
_category refine
_type numb
_type_conditions esd
_enumeration_range 0.0:1.0
_definition
; The measure of absolute structure as defined by Flack (1983).
For centrosymmetric structures, the only permitted value, if the
data name is present, is 'inapplicable', represented by '.' .
For noncentrosymmetric structures, the value must lie in the
99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a
standard uncertainty (e.s.d.) u must be supplied. The
_enumeration_range of 0.0:1.0 is correctly interpreted as
meaning (0.0 - 3u) =< x =< (1.0 + 3u).
Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881.
;
data_refine_ls_abs_structure_Rogers
_name '_refine_ls_abs_structure_Rogers'
_category refine
_type numb
_type_conditions esd
_enumeration_range -1.0:1.0
_definition
; The measure of absolute structure as defined by Rogers (1981).
The value must lie in the 99.97% Gaussian confidence interval
-1 -3u =< \h =< 1 + 3u and a standard uncertainty (e.s.d.) u must
be supplied. The _enumeration_range of -1.0:1.0 is correctly
interpreted as meaning (-1.0 - 3u) =< \h =< (1.0 + 3u).
Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741.
;
data_refine_ls_d_res_high
_name '_refine_ls_d_res_high'
_category refine
_type numb
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The smallest value in angstroms of the interplanar spacings
of the reflections used in the refinement. This is called
the highest resolution.
;
data_refine_ls_d_res_low
_name '_refine_ls_d_res_low'
_category refine
_type numb
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The largest value in angstroms of the interplanar spacings
of the reflections used in the refinement. This is called
the lowest resolution.
;
data_refine_ls_extinction_coef
_name '_refine_ls_extinction_coef'
_category refine
_type numb
_type_conditions esd
_example 3472(52)
_example_detail 'Zachariasen coefficient r* = 0.347(5) E04'
_definition
; The extinction coefficient used to calculate the correction
factor applied to the structure-factor data. The nature of the
extinction coefficient is given in the definitions of
_refine_ls_extinction_expression and
_refine_ls_extinction_method.
For the 'Zachariasen' method it is the r* value; for the
'Becker-Coppens type 1 isotropic' method it is the 'g' value
and for 'Becker-Coppens type 2 isotropic' corrections it is
the 'rho' value. Note that the magnitude of these values is
usually of the order of 10000.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-147, 148-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
data_refine_ls_extinction_expression
_name '_refine_ls_extinction_expression'
_category refine
_type char
_example
; Larson, A. C. (1970). "Crystallographic Computing",
edited by F. R. Ahmed. Eq. (22), p. 292.
Copenhagen: Munksgaard.
;
_definition
; A description of or reference to the extinction-correction
equation used to apply the data item _refine_ls_extinction_coef.
This information must be sufficient to reproduce the
extinction-correction factors applied to the structure factors.
;
data_refine_ls_extinction_method
_name '_refine_ls_extinction_method'
_category refine
_type char
_enumeration_default 'Zachariasen'
loop_ _example 'B-C type 2 Gaussian isotropic'
'none'
_definition
; A description of the extinction-correction method applied.
This description should
include information about the correction method, either
'Becker-Coppens' or 'Zachariasen'. The latter is sometimes
referred to as the 'Larson' method even though it employs
Zachariasen's formula.
The Becker-Coppens procedure is referred to as 'type 1' when
correcting secondary extinction dominated by the mosaic spread;
as 'type 2' when secondary extinction is dominated by particle
size and includes a primary extinction component; and as 'mixed'
when there is a mixture of types 1 and 2.
For the Becker-Coppens method, it is also necessary to set the
mosaic distribution as either 'Gaussian' or 'Lorentzian' and
the nature of the extinction as 'isotropic' or 'anisotropic'.
Note that if either the 'mixed' or 'anisotropic' corrections
are applied, the multiple coefficients cannot be contained in
*_extinction_coef and must be listed in _refine_special_details.
Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30,
129-147, 148-153.
Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564.
Larson, A. C. (1967). Acta Cryst. 23, 664-665.
;
data_refine_ls_goodness_of_fit_all
_name '_refine_ls_goodness_of_fit_all'
_category refine
_type numb
_type_conditions esd
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S for all
reflections after the final cycle of refinement.
Ideally, account should be taken of parameters restrained
in the least-squares refinement. See also
_refine_ls_restrained_S_ definitions.
{ sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = the standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
data_refine_ls_goodness_of_fit_gt
_name '_refine_ls_goodness_of_fit_gt'
_category refine
_type numb
_type_conditions esd
_related_item '_refine_ls_goodness_of_fit_obs'
_related_function alternate
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S for
significantly intense reflections (see
_reflns_threshold_expression) after the final cycle of
refinement. Ideally, account should be taken of parameters
restrained in the least-squares refinement. See also
_refine_ls_restrained_S_ definitions.
{ sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
data_refine_ls_goodness_of_fit_obs
_name '_refine_ls_goodness_of_fit_obs'
_category refine
_type numb
_type_conditions esd
_related_item '_refine_ls_goodness_of_fit_gt'
_related_function replace
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S for observed
reflections (see _reflns_observed_criterion) after the final
cycle of refinement. Ideally, account should be taken of
parameters restrained in the least-squares refinement. See also
_refine_ls_restrained_S_ definitions.
{ sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty (e.s.d.)
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
data_refine_ls_goodness_of_fit_ref
_name '_refine_ls_goodness_of_fit_ref'
_category refine
_type numb
_type_conditions esd
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S for all
reflections included in the refinement after the final cycle
of refinement. Ideally, account should be taken of parameters
restrained in the least-squares refinement. See also
_refine_ls_restrained_S_ definitions.
{ sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^
S = { ----------------------------------- }
{ Nref - Nparam }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/(u^2^)]
u = standard uncertainty
Nref = the number of reflections used in the refinement
Nparam = the number of refined parameters
and the sum is taken over the specified reflections
;
data_refine_ls_hydrogen_treatment
_name '_refine_ls_hydrogen_treatment'
_category refine
_type char
loop_ _enumeration
_enumeration_detail refall 'refined all H-atom parameters'
refxyz 'refined H-atom coordinates only'
refU 'refined H-atom U's only'
noref 'no refinement of H-atom parameters'
constr 'H-atom parameters constrained'
mixed 'some constrained, some independent'
undef 'H-atom parameters not defined'
_enumeration_default undef
_definition
; Treatment of hydrogen atoms in the least-squares refinement.
;
data_refine_ls_matrix_type
_name '_refine_ls_matrix_type'
_category refine
_type char
loop_ _enumeration
_enumeration_detail full 'full'
fullcycle 'full with fixed elements per cycle'
atomblock 'block diagonal per atom'
userblock 'user-defined blocks'
diagonal 'diagonal elements only'
sparse 'selected elements only'
_enumeration_default full
_definition
; Type of matrix used to accumulate the least-squares derivatives.
;
data_refine_ls_number_constraints
_name '_refine_ls_number_constraints'
_category refine
_type numb
_enumeration_range 0:
_enumeration_default 0
_definition
; The number of constrained (non-refined or dependent) parameters
in the least-squares process. These may be due to symmetry or any
other constraint process (e.g. rigid-body refinement). See also
_atom_site_constraints and _atom_site_refinement_flags. A general
description of constraints may appear in _refine_special_details.
;
data_refine_ls_number_parameters
_name '_refine_ls_number_parameters'
_category refine
_type numb
_enumeration_range 0:
_definition
; The number of parameters refined in the least-squares process.
If possible, this number should include some contribution from
the restrained parameters. The restrained parameters are
distinct from the constrained parameters (where one or more
parameters are linearly dependent on the refined value of
another). Least-squares restraints often depend on geometry or
energy considerations and this makes their direct contribution
to this number, and to the goodness-of-fit calculation,
difficult to assess.
;
data_refine_ls_number_reflns
_name '_refine_ls_number_reflns'
_category refine
_type numb
_enumeration_range 0:
_definition
; The number of unique reflections contributing to the
least-squares refinement calculation.
;
data_refine_ls_number_restraints
_name '_refine_ls_number_restraints'
_category refine
_type numb
_enumeration_range 0:
_definition
; The number of restrained parameters. These are parameters which
are not directly dependent on another refined parameter.
Restrained parameters often involve geometry or energy
dependencies.
See also _atom_site_constraints and _atom_site_refinement_flags.
A general description of refinement constraints may appear in
_refine_special_details.
;
data_refine_ls_R_factor_all
_name '_refine_ls_R_factor_all'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Residual factor for all reflections satisfying the
resolution limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. This is the conventional R
factor. See also _refine_ls_wR_factor_ definitions.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
;
data_refine_ls_R_factor_gt
_name '_refine_ls_R_factor_gt'
_category refine
_type numb
_related_item '_refine_ls_R_factor_obs'
_related_function alternate
_enumeration_range 0.0:
_definition
; Residual factor for the reflections (with number given by
_reflns_number_gt) judged significantly intense (i.e. satisfying
the threshold specified by _reflns_threshold_expression)
and included in the refinement. The reflections also satisfy
the resolution limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. This is the conventional R
factor. See also _refine_ls_wR_factor_ definitions.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
;
data_refine_ls_R_factor_obs
_name '_refine_ls_R_factor_obs'
_category refine
_type numb
_related_item '_refine_ls_R_factor_gt'
_related_function replace
_enumeration_range 0.0:
_definition
; Residual factor for the reflections classified as 'observed'
(see _reflns_observed_criterion) and included in the
refinement. The reflections also satisfy the resolution limits
established by _refine_ls_d_res_high and
_refine_ls_d_res_low. This is the conventional R
factor. See also _refine_ls_wR_factor_ definitions.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the specified reflections
;
data_refine_ls_R_Fsqd_factor
_name '_refine_ls_R_Fsqd_factor'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Residual factor R(Fsqd), calculated on the squared amplitudes
of the observed and calculated structure factors, for
significantly intense reflections (satisfying
_reflns_threshold_expression) and included in the refinement.
The reflections also satisfy the resolution limits established
by _refine_ls_d_res_high and _refine_ls_d_res_low.
sum | F(obs)^2^ - F(calc)^2^ |
R(Fsqd) = -------------------------------
sum F(obs)^2^
F(obs)^2^ = squares of the observed structure-factor amplitudes
F(calc)^2^ = squares of the calculated structure-factor
amplitudes
and the sum is taken over the specified reflections
;
data_refine_ls_R_I_factor
_name '_refine_ls_R_I_factor'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Residual factor R(I) for significantly intense reflections
(satisfying _reflns_threshold_expression) and included in
the refinement.
This is most often calculated in Rietveld refinements against
powder data, where it is referred to as R~B~ or R~Bragg~.
sum | I(obs) - I(calc) |
R(I) = ------------------------
sum | I(obs) |
I(obs) = the net observed intensities
I(calc) = the net calculated intensities
and the sum is taken over the specified reflections
;
data_refine_ls_restrained_S_all
_name '_refine_ls_restrained_S_all'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S' for all
reflections after the final cycle of least-squares refinement.
This parameter explicitly includes the restraints applied in the
least-squares process. See also _refine_ls_goodness_of_fit_
definitions.
{sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
{ + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } }
S' = { -------------------------------------------------- }
{ N~ref~ + N~restr~ - N~param~ }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/square of standard uncertainty (e.s.d.)]
P(calc) = the calculated restraint values
P(targ) = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see _refine_ls_number_reflns)
N~restr~ = the number of restraints
(see _refine_ls_number_restraints)
N~param~ = the number of refined parameters
(see _refine_ls_number_parameters)
sum is taken over the specified reflections
sum~r~ is taken over the restraints
;
data_refine_ls_restrained_S_gt
_name '_refine_ls_restrained_S_gt'
_category refine
_type numb
_related_item '_refine_ls_restrained_S_obs'
_related_function alternate
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S' for
significantly intense reflections (satisfying
_reflns_threshold_expression) after the final cycle
of least-squares refinement. This parameter explicitly includes
the restraints applied in the least-squares process.
See also _refine_ls_goodness_of_fit_ definitions.
{sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
{ + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } }
S' = { -------------------------------------------------- }
{ N~ref~ + N~restr~ - N~param~ }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/square of standard uncertainty (e.s.d.)]
P(calc) = the calculated restraint values
P(targ) = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see _refine_ls_number_reflns)
N~restr~ = the number of restraints
(see _refine_ls_number_restraints)
N~param~ = the number of refined parameters
(see _refine_ls_number_parameters)
sum is taken over the specified reflections
sum~r~ is taken over the restraints
;
data_refine_ls_restrained_S_obs
_name '_refine_ls_restrained_S_obs'
_category refine
_type numb
_related_item '_refine_ls_restrained_S_gt'
_related_function replace
_enumeration_range 0.0:
_definition
; The least-squares goodness-of-fit parameter S' for observed
reflections after the final cycle of least-squares refinement.
This parameter explicitly includes the restraints applied in the
least-squares process. See also _refine_ls_goodness_of_fit_
definitions.
{sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^
{ + sum~r~ { w~r~ [ P(calc) - P(targ) ]^2^ } }
S' = { -------------------------------------------------- }
{ N~ref~ + N~restr~ - N~param~ }
Y(obs) = the observed coefficients
(see _refine_ls_structure_factor_coef)
Y(calc) = the calculated coefficients
(see _refine_ls_structure_factor_coef)
w = the least-squares reflection weight
[1/square of standard uncertainty (e.s.d.)]
P(calc) = the calculated restraint values
P(targ) = the target restraint values
w~r~ = the restraint weight
N~ref~ = the number of reflections used in the refinement
(see _refine_ls_number_reflns)
N~restr~ = the number of restraints
(see _refine_ls_number_restraints)
N~param~ = the number of refined parameters
(see _refine_ls_number_parameters)
sum is taken over the specified reflections
sum~r~ is taken over the restraints
;
data_refine_ls_shift/esd_max
_name '_refine_ls_shift/esd_max'
_category refine
_type numb
_related_item '_refine_ls_shift/su_max'
_related_function replace
_enumeration_range 0.0:
_definition
; The largest ratio of the final least-squares parameter
shift to the final standard uncertainty (s.u.,
formerly described as estimated standard deviation, e.s.d.).
;
data_refine_ls_shift/esd_mean
_name '_refine_ls_shift/esd_mean'
_category refine
_type numb
_related_item '_refine_ls_shift/su_mean'
_related_function replace
_enumeration_range 0.0:
_definition
; The average ratio of the final least-squares parameter
shift to the final standard uncertainty (s.u.,
formerly described as estimated standard deviation, e.s.d.).
;
data_refine_ls_shift/su_max
_name '_refine_ls_shift/su_max'
_category refine
_type numb
_related_item '_refine_ls_shift/esd_max'
_related_function alternate
_enumeration_range 0.0:
_definition
; The largest ratio of the final least-squares parameter
shift to the final standard uncertainty.
;
data_refine_ls_shift/su_max_lt
_name '_refine_ls_shift/su_max_lt'
_category refine
_type numb
_related_item '_refine_ls_shift/su_max'
_related_function alternate
_enumeration_range 0.0:
_definition
; An upper limit for the largest ratio of the final
least-squares parameter shift to the final
standard uncertainty. This item is used when the largest
value of the shift divided by the final standard uncertainty
is too small to measure.
;
data_refine_ls_shift/su_mean
_name '_refine_ls_shift/su_mean'
_category refine
_type numb
_related_item '_refine_ls_shift/esd_mean'
_related_function alternate
_enumeration_range 0.0:
_definition
; The average ratio of the final least-squares parameter
shift to the final standard uncertainty.
;
data_refine_ls_shift/su_mean_lt
_name '_refine_ls_shift/su_mean_lt'
_category refine
_type numb
_related_item '_refine_ls_shift/su_mean'
_related_function alternate
_enumeration_range 0.0:
_definition
; An upper limit for the average ratio of the final
least-squares parameter shift to the
final standard uncertainty. This
item is used when the average value of the shift divided by
the final standard uncertainty is too small to measure.
;
data_refine_ls_structure_factor_coef
_name '_refine_ls_structure_factor_coef'
_category refine
_type char
loop_ _enumeration
_enumeration_detail F 'structure-factor magnitude'
Fsqd 'structure factor squared'
Inet 'net intensity'
_enumeration_default F
_definition
; Structure-factor coefficient |F|, F^2^ or I used in the
least-squares refinement process.
;
data_refine_ls_weighting_details
_name '_refine_ls_weighting_details'
_category refine
_type char
_example
; Sigdel model of Konnert-Hendrickson:
Sigdel = Afsig + Bfsig*(sin(\q)/\l - 1/6)
Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement.
Afsig = 16.0, Bfsig = 60.0 at the end of refinement.
;
_definition
; A description of special aspects of the weighting scheme used
in the least-squares refinement. Used to describe the weighting
when the value of _refine_ls_weighting_scheme is specified
as 'calc'.
;
data_refine_ls_weighting_scheme
_name '_refine_ls_weighting_scheme'
_category refine
_type char
loop_ _enumeration
_enumeration_detail sigma "based on measured s.u.'s"
unit 'unit or no weights applied'
calc 'calculated weights applied'
_enumeration_default sigma
_definition
; The weighting scheme applied in the least-squares process. The
standard code may be followed by a description of the weight
(but see _refine_ls_weighting_details for a preferred approach).
;
data_refine_ls_wR_factor_all
_name '_refine_ls_wR_factor_all'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Weighted residual factors for all reflections.
The reflections also satisfy the resolution limits established
by _refine_ls_d_res_high and _refine_ls_d_res_low.
See also the _refine_ls_R_factor_ definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitude specified by
_refine_ls_structure_factor_coef
w = the least-squares weight
and the sum is taken over the specified reflections
;
data_refine_ls_wR_factor_gt
_name '_refine_ls_wR_factor_gt'
_category refine
_type numb
_related_item '_refine_ls_wR_factor_obs'
_related_function alternate
_enumeration_range 0.0:
_definition
; Weighted residual factors for significantly intense reflections
(satisfying _reflns_threshold_expression) included in the
refinement. The reflections also satisfy the resolution
limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. See also the _refine_ls_R_factor_
definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitude specified by
_refine_ls_structure_factor_coef
w = the least-squares weight
and the sum is taken over the specified reflections
;
data_refine_ls_wR_factor_obs
_name '_refine_ls_wR_factor_obs'
_category refine
_type numb
_related_item '_refine_ls_wR_factor_gt'
_related_function replace
_enumeration_range 0.0:
_definition
; Weighted residual factors for the reflections classified as
'observed' (see _reflns_observed_criterion) and included
in the refinement. The reflections also satisfy the resolution
limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. See also the _refine_ls_R_factor_
definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitude specified by
_refine_ls_structure_factor_coef
w = the least-squares weight
and the sum is taken over the specified reflections
;
data_refine_ls_wR_factor_ref
_name '_refine_ls_wR_factor_ref'
_category refine
_type numb
_enumeration_range 0.0:
_definition
; Weighted residual factors for all reflections included in the
refinement. The reflections also satisfy the resolution
limits established by _refine_ls_d_res_high and
_refine_ls_d_res_low. See also the _refine_ls_R_factor_
definitions.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitude specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitude specified by
_refine_ls_structure_factor_coef
w = the least-squares weight
and the sum is taken over the specified reflections
;
data_refine_special_details
_name '_refine_special_details'
_category refine
_type char
_definition
; Description of special aspects of the refinement process.
;
#####################
## REFINE_LS_CLASS ##
#####################
data_refine_ls_class_[]
_name '_refine_ls_class_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_refine_ls_class_R_factor_gt
_refine_ls_class_code
0.057 'Main'
0.074 'Com'
0.064 'NbRefls'
0.046 'LaRefls'
0.112 'Sat1'
0.177 'Sat2'
;
;
Example 1 - example for a modulated structure extracted from van Smaalen
[J. Phys. Condens. Matter (1991), 3, 1247-1263.]
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFINE_LS_CLASS category record details
(for each reflection class separately) about the reflections
used for the structure refinement.
;
data_refine_ls_class_code
_name '_refine_ls_class_code'
_category refine_ls_class
_type char
_list yes
_list_link_parent '_reflns_class_code'
loop_ _example '1'
'm1'
's2'
_definition
; The code identifying a certain reflection class. This code must
match a _reflns_class_code.
;
data_refine_ls_class_d_res_high
_name '_refine_ls_class_d_res_high'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class, the highest resolution in angstroms
for the reflections used in the refinement. This is
the lowest d value in a reflection class.
;
data_refine_ls_class_d_res_low
_name '_refine_ls_class_d_res_low'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class, the lowest resolution in angstroms
for the reflections used in the refinement. This is
the highest d value in a reflection class.
;
data_refine_ls_class_R_factor_
loop_ _name '_refine_ls_class_R_factor_all'
'_refine_ls_class_R_factor_gt'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factors for all
reflections, and for significantly intense reflections (see
_reflns_threshold_expression), included in the refinement.
The reflections also satisfy the resolution limits established by
_refine_ls_class_d_res_high and _refine_ls_class_d_res_low.
This is the conventional R factor.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class. See also
_refine_ls_class_wR_factor_all definitions.
;
data_refine_ls_class_R_Fsqd_factor
_name '_refine_ls_class_R_Fsqd_factor'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factor R(F^2^) calculated
on the squared amplitudes of the observed and calculated
structure factors for the reflections judged significantly
intense (i.e. satisfying the threshold specified by
_reflns_threshold_expression) and included in the refinement.
The reflections also satisfy the resolution limits established
by _refine_ls_class_d_res_high and _refine_ls_class_d_res_low.
sum | F(obs)^2^ - F(calc)^2^ |
R(Fsqd) = -------------------------------
sum F(obs)^2^
F(obs)^2^ = squares of the observed structure-factor amplitudes
F(calc)^2^ = squares of the calculated structure-factor
amplitudes
and the sum is taken over the reflections of this class.
;
data_refine_ls_class_R_I_factor
_name '_refine_ls_class_R_I_factor'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factor R(I) for the
reflections judged significantly intense (i.e. satisfying the
threshold specified by _reflns_threshold_expression) and
included in the refinement.
This is most often calculated in Rietveld refinements
against powder data, where it is referred to as R~B~ or R~Bragg~.
sum | I(obs) - I(calc) |
R(I) = ------------------------
sum | I(obs) |
I(obs) = the net observed intensities
I(calc) = the net calculated intensities
and the sum is taken over the reflections of this class.
;
data_refine_ls_class_wR_factor_all
_name '_refine_ls_class_wR_factor_all'
_category refine_ls_class
_type numb
_list yes
_list_reference '_refine_ls_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the weighted residual factors for all
reflections included in the refinement. The reflections also
satisfy the resolution limits established by
_refine_ls_class_d_res_high and _refine_ls_class_d_res_low.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitudes specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitudes specified by
_refine_ls_structure_factor_coef
w = the least-squares weights
and the sum is taken over the reflections of this class. See
also _refine_ls_class_R_factor_ definitions.
;
###########
## REFLN ##
###########
data_refln_[]
_name '_refln_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_refln_index_h
_refln_index_k
_refln_index_l
_refln_F_squared_calc
_refln_F_squared_meas
_refln_F_squared_sigma
_refln_include_status
2 0 0 85.57 58.90 1.45 o
3 0 0 15718.18 15631.06 30.40 o
4 0 0 55613.11 49840.09 61.86 o
5 0 0 246.85 241.86 10.02 o
6 0 0 82.16 69.97 1.93 o
7 0 0 1133.62 947.79 11.78 o
8 0 0 2558.04 2453.33 20.44 o
9 0 0 283.88 393.66 7.79 o
10 0 0 283.70 171.98 4.26 o
;
;
Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov
[Acta Cryst. (1993), C49, 1352-1354].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_refln_index_h
_refln_index_k
_refln_index_l
_refln_F_meas
_refln_F_calc
_refln_F_sigma
_refln_include_status
_refln_scale_group_code
0 0 6 34.935 36.034 3.143 o 1
0 0 12 42.599 40.855 2.131 o 1
0 1 0 42.500 42.507 4.719 o 1
0 1 1 59.172 57.976 4.719 o 1
0 1 2 89.694 94.741 4.325 o 1
0 1 3 51.743 52.241 3.850 o 1
0 1 4 9.294 10.318 2.346 o 1
0 1 5 41.160 39.951 3.313 o 1
0 1 6 6.755 7.102 .895 < 1
0 1 7 30.693 31.171 2.668 o 1
0 1 8 12.324 12.085 2.391 o 1
0 1 9 15.348 15.122 2.239 o 1
0 1 10 17.622 19.605 1.997 o 1
;
;
Example 2 - based on standard test data set p6122 of the Xtal distribution
[Hall, King & Stewart (1995). Xtal3.4 User's Manual. University
of Western Australia].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFLN category record details about the
reflections used to determine the ATOM_SITE data items.
The REFLN data items refer to individual reflections and must
be included in looped lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
;
data_refln_A_
loop_ _name '_refln_A_calc'
'_refln_A_meas'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_definition
; The calculated and measured structure-factor component A
(in electrons for X-ray diffraction).
A =|F|cos(phase)
;
data_refln_B_
loop_ _name '_refln_B_calc'
'_refln_B_meas'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_definition
; The calculated and measured structure-factor component B
(in electrons for X-ray diffraction).
B =|F|sin(phase)
;
data_refln_class_code
_name '_refln_class_code'
_category refln
_type char
_list yes
_list_reference '_refln_index_'
_list_link_parent '_reflns_class_code'
_definition
; The code identifying the class to which this reflection has been
assigned. This code must match a value of _reflns_class_code.
Reflections may be grouped into classes for a variety of
purposes. For example, for modulated structures each reflection
class may be defined by the number m=sum|m~i~|, where the m~i~
are the integer coefficients that, in addition to h,k,l, index
the corresponding diffraction vector in the basis defined
for the reciprocal lattice.
;
data_refln_d_spacing
_name '_refln_d_spacing'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The d spacing in angstroms for this reflection. This is related
to the (sin theta)/lambda value by the expression
_refln_d_spacing = 2/(_refln_sint/lambda)
;
data_refln_crystal_id
_name '_refln_crystal_id'
_category refln
_type char
_list yes
_list_link_parent '_exptl_crystal_id'
_list_reference '_refln_index_'
_definition
; Code identifying each crystal if multiple crystals are used. Is
used to link with _exptl_crystal_id in the _exptl_crystal_ list.
;
data_refln_F_
loop_ _name '_refln_F_calc'
'_refln_F_meas'
'_refln_F_sigma'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_definition
; The calculated, measured and standard uncertainty (derived from
measurement) of the structure factors (in electrons for
X-ray diffraction).
;
data_refln_F_squared_
loop_ _name '_refln_F_squared_calc'
'_refln_F_squared_meas'
'_refln_F_squared_sigma'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_definition
; Calculated, measured and estimated standard uncertainty (derived
from measurement) of the squared structure factors (in electrons
squared for X-ray diffraction).
;
data_refln_include_status
_name '_refln_include_status'
_category refln
_type char
_related_item '_refln_observed_status'
_related_function alternate
_list yes
_list_reference '_refln_index_'
loop_ _enumeration
_enumeration_detail o
; (lower-case letter o for 'observed')
satisfies _refine_ls_d_res_high
satisfies _refine_ls_d_res_low
exceeds _reflns_threshold_expression
;
<
; satisfies _refine_ls_d_res_high
satisfies _refine_ls_d_res_low
does not exceed
_reflns_threshold_expression
;
- 'systematically absent reflection'
x 'unreliable measurement -- not used'
h 'does not satisfy _refine_ls_d_res_high'
l 'does not satisfy _refine_ls_d_res_low'
_enumeration_default o
_definition
; Classification of a reflection indicating its status with
respect to inclusion in the refinement and the calculation
of R factors.
;
data_refln_index_
loop_ _name '_refln_index_h'
'_refln_index_k'
'_refln_index_l'
_category refln
_type numb
_list yes
_list_mandatory yes
_definition
; Miller indices of the reflection. The values of the Miller
indices in the REFLN category must correspond to the cell
defined by the cell lengths and cell angles in the CELL category.
;
data_refln_intensity_
loop_ _name '_refln_intensity_calc'
'_refln_intensity_meas'
'_refln_intensity_sigma'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_definition
; The calculated, measured and standard uncertainty (derived from
measurement) of the intensity, all in the same arbitrary units
as _refln_intensity_meas.
;
data_refln_mean_path_length_tbar
_name '_refln_mean_path_length_tbar'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_enumeration_range 0.0:
_units mm
_units_detail 'millimetres'
_definition
; Mean path length in millimetres through the crystal for this
reflection.
;
data_refln_observed_status
_name '_refln_observed_status'
_category refln
_type char
_related_item '_refln_include_status'
_related_function replace
_list yes
_list_reference '_refln_index_'
loop_ _enumeration
_enumeration_detail o
; satisfies _refine_ls_d_res_high
satisfies _refine_ls_d_res_low
observed by _reflns_observed_criterion
;
<
; satisfies _refine_ls_d_res_high
satisfies _refine_ls_d_res_low
unobserved by _reflns_observed_criterion
;
- 'systematically absent reflection'
x 'unreliable measurement -- not used'
h 'does not satisfy _refine_ls_d_res_high'
l 'does not satisfy _refine_ls_d_res_low'
_enumeration_default o
_definition
; Classification of a reflection indicating its status with
respect to inclusion in the refinement and the calculation
of R factors.
;
data_refln_phase_calc
_name '_refln_phase_calc'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_units deg
_units_detail 'degrees'
_definition
; The calculated structure-factor phase in degrees.
;
data_refln_phase_meas
_name '_refln_phase_meas'
_category refln
_type numb
_type_conditions esd
_list yes
_list_reference '_refln_index_'
_units deg
_units_detail 'degrees'
_definition
; The measured structure-factor phase in degrees.
;
data_refln_refinement_status
_name '_refln_refinement_status'
_category refln
_type char
_list yes
_list_reference '_refln_index_'
loop_ _enumeration
_enumeration_detail incl 'included in ls process'
excl 'excluded from ls process'
extn 'excluded due to extinction'
_enumeration_default incl
_definition
; Status of a reflection in the structure-refinement process.
;
data_refln_scale_group_code
_name '_refln_scale_group_code'
_category refln
_type char
_list yes
_list_link_parent '_reflns_scale_group_code'
_list_reference '_refln_index_'
loop_ _example 1 2 3 s1 A B c1 c2 c3
_definition
; Code identifying the structure-factor scale. This code must
correspond to one of the _reflns_scale_group_code values.
;
data_refln_sint/lambda
_name '_refln_sint/lambda'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_enumeration_range 0.0:
_units A^-1^
_units_detail 'reciprocal angstroms'
_definition
; The (sin theta)/lambda value in reciprocal angstroms for this
reflection.
;
data_refln_symmetry_epsilon
_name '_refln_symmetry_epsilon'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_enumeration_range 1:48
_definition
; The symmetry reinforcement factor corresponding to the number of
times the reflection indices are generated identically from the
space-group symmetry operations.
;
data_refln_symmetry_multiplicity
_name '_refln_symmetry_multiplicity'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_enumeration_range 1:48
_definition
; The number of reflections symmetry-equivalent under the Laue
symmetry to the present reflection. In the Laue symmetry, Friedel
opposites (h k l and -h -k -l) are equivalent. Tables of
symmetry-equivalent reflections are available in International
Tables for Crystallography Volume A (2002), Chapter 10.1.
;
data_refln_wavelength
_name '_refln_wavelength'
_category refln
_type numb
_list yes
_list_reference '_refln_index_'
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The mean wavelength in angstroms of the radiation used to measure
this reflection. This is an important parameter for data
collected using energy-dispersive detectors or the Laue method.
;
data_refln_wavelength_id
_name '_refln_wavelength_id'
_category refln
_type char
_list yes
_list_link_parent '_diffrn_radiation_wavelength_id'
_list_reference '_refln_index_'
_definition
; Code identifying the wavelength in the _diffrn_radiation_ list.
See _diffrn_radiation_wavelength_id.
;
############
## REFLNS ##
############
data_reflns_[]
_name '_reflns_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_reflns_limit_h_min 0
_reflns_limit_h_max 6
_reflns_limit_k_min 0
_reflns_limit_k_max 17
_reflns_limit_l_min 0
_reflns_limit_l_max 22
_reflns_number_total 1592
_reflns_number_gt 1408
_reflns_threshold_expression 'F > 6.0u(F)'
_reflns_d_resolution_high 0.8733
_reflns_d_resolution_low 11.9202
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFLNS category record details about the
reflections used to determine the ATOM_SITE data items.
The REFLN data items refer to individual reflections and must
be included in looped lists.
The REFLNS data items specify the parameters that apply to all
reflections. The REFLNS data items are not looped.
;
data_reflns_d_resolution_
loop_ _name '_reflns_d_resolution_high'
'_reflns_d_resolution_low'
_category reflns
_type numb
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The highest and lowest resolution in angstroms for the
reflections. These are the smallest and largest d values.
;
data_reflns_Friedel_coverage
_name '_reflns_Friedel_coverage'
_category reflns
_type numb
_enumeration_range 0.0:1.0
_definition
; The proportion of Friedel-related reflections present in
the number of 'independent' reflections specified by
the item _reflns_number_total.
This proportion is calculated as the ratio:
[N(crystal class) - N(Laue symmetry)] / N(Laue symmetry)
where, working from the _diffrn_refln_ list,
N(crystal class) is the number of reflections obtained on
averaging under the symmetry of the crystal class
N(Laue symmetry) is the number of reflections obtained on
averaging under the Laue symmetry.
Examples:
(a) For centrosymmetric structures, _reflns_Friedel_coverage
is necessarily equal to 0.0 as the crystal class
is identical to the Laue symmetry.
(b) For whole-sphere data for a crystal in the space
group P1, _reflns_Friedel_coverage is equal to 1.0,
as no reflection h k l is equivalent to -h -k -l
in the crystal class and all Friedel pairs
{h k l; -h -k -l} have been measured.
(c) For whole-sphere data in space group Pmm2,
_reflns_Friedel_coverage will be < 1.0 because
although reflections h k l and
-h -k -l are not equivalent when h k l indices are
nonzero, they are when l=0.
(d) For a crystal in the space group Pmm2, measurements of the
two inequivalent octants h >= 0, k >=0, l lead to the
same value as in (c), whereas measurements of the
two equivalent octants h >= 0, k, l >= 0 will lead to
a value of zero for _reflns_Friedel_coverage.
;
data_reflns_limit_
loop_ _name '_reflns_limit_h_max'
'_reflns_limit_h_min'
'_reflns_limit_k_max'
'_reflns_limit_k_min'
'_reflns_limit_l_max'
'_reflns_limit_l_min'
_category reflns
_type numb
_definition
; Miller indices limits for the reported reflections. These need
not be the same as the _diffrn_reflns_limit_ values.
;
data_reflns_number_gt
_name '_reflns_number_gt'
_category reflns
_type numb
_related_item '_reflns_number_observed'
_related_function alternate
_enumeration_range 0:
_definition
; The number of reflections in the _refln_ list (not the
_diffrn_refln_ list) that are significantly intense, satisfying
the criterion specified by _reflns_threshold_expression. This may
include Friedel-equivalent reflections (i.e. those which are
symmetry-equivalent under the Laue symmetry but inequivalent
under the crystal class) according to the nature of the
structure and the procedures used. Special characteristics
of the reflections included in the _refln_ list should be given
in the item _reflns_special_details.
;
data_reflns_number_observed
_name '_reflns_number_observed'
_category reflns
_type numb
_related_item '_reflns_number_gt'
_related_function replace
_enumeration_range 0:
_definition
; The number of 'observed' reflections in the _refln_ list (not
the _diffrn_refln_ list). The observed reflections satisfy the
threshold criterion specified by _reflns_threshold_expression
(or the deprecated item _reflns_observed_criterion). They may
include Friedel-equivalent reflections according to the nature
of the structure and the procedures used. Special characteristics
of the reflections included in the _refln_ list should be given
in the item _reflns_special_details.
;
data_reflns_number_total
_name '_reflns_number_total'
_category reflns
_type numb
_enumeration_range 0:
_definition
; The total number of reflections in the _refln_ list (not the
_diffrn_refln_ list). This may include Friedel-equivalent
reflections (i.e. those which are symmetry-equivalent under the
Laue symmetry but inequivalent under the crystal class)
according to the nature of the structure and the procedures
used. Special characteristics of the reflections included
in the _refln_ list should be given in the item
_reflns_special_details.
;
data_reflns_observed_criterion
_name '_reflns_observed_criterion'
_category reflns
_type char
_related_item '_reflns_threshold_expression'
_related_function replace
_example 'I>2u(I)'
_definition
; The criterion used to classify a reflection as 'observed'. This
criterion is usually expressed in terms of a sigma(I) or sigma(F)
threshold.
;
data_reflns_special_details
_name '_reflns_special_details'
_category reflns
_type char
_definition
; Description of the properties of the reported reflection list
that are not given in other data items. In particular, this
should include information about the averaging (or not) of
symmetry-equivalent reflections including Friedel pairs.
;
data_reflns_threshold_expression
_name '_reflns_threshold_expression'
_category reflns
_type char
_related_item '_reflns_observed_criterion'
_related_function alternate
_example 'I>2u(I)'
_definition
; The threshold, usually based on multiples of u(I), u(F^2^)
or u(F), that serves to identify significantly intense
reflections, the number of which is given by _reflns_number_gt.
These reflections are used in the calculation of
_refine_ls_R_factor_gt.
;
##################
## REFLNS_CLASS ##
##################
data_reflns_class_[]
_name '_reflns_class_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_reflns_class_number_gt
_reflns_class_code
584 'Main'
226 'Sat1'
50 'Sat2'
;
;
Example 1 - corresponding to the one-dimensional incommensurately
modulated structure of K~2~SeO~4~.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFLNS_CLASS category record details, for
each reflection class, about the reflections used to determine
the structural parameters.
;
data_reflns_class_code
_name '_reflns_class_code'
_category reflns_class
_type char
_list yes
loop_ _list_link_child '_refln_class_code'
'_refine_ls_class_code'
loop_ _example '1'
'm1'
's2'
_definition
; The code identifying a certain reflection class.
;
data_reflns_class_description
_name '_reflns_class_description'
_category reflns_class
_type char
_list yes
_list_reference '_reflns_class_code'
loop_ _example 'm=1 first order satellites'
'H0L0 common projection reflections'
_definition
; Description of each reflection class.
;
data_reflns_class_d_res_high
_name '_reflns_class_d_res_high'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class, the highest resolution in angstroms
for the reflections used in the refinement. This is the smallest
d value.
;
data_reflns_class_d_res_low
_name '_reflns_class_d_res_low'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_units A
_units_detail 'Angstroms'
_definition
; For each reflection class, the lowest resolution in angstroms
for the reflections used in the refinement. This is the largest
d value.
;
data_reflns_class_number_gt
_name '_reflns_class_number_gt'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the number of significantly intense
reflections (see _reflns_threshold_expression) in the _refln_
list (not the _diffrn_refln_ list). This may include Friedel-
equivalent reflections (i.e. those which are symmetry-equivalent
under the Laue symmetry but inequivalent under the crystal
class) according to the nature of the structure and the
procedures used. Special characteristics of the reflections
included in the _refln_ list should be given in the item
_reflns_special_details.
;
data_reflns_class_number_total
_name '_reflns_class_number_total'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the total number of reflections
in the _refln_ list (not the _diffrn_refln_ list). This may
include Friedel-equivalent reflections (i.e. those which are
symmetry-equivalent under the Laue symmetry but inequivalent
under the crystal class) according to the nature of the
structure and the procedures used. Special characteristics
of the reflections included in the _refln_ list should be given
in the item _reflns_special_details.
;
data_reflns_class_R_factor_
loop_ _name '_reflns_class_R_factor_all'
'_reflns_class_R_factor_gt'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factors for all
reflections, and for significantly intense reflections (see
_reflns_threshold_expression), included in the refinement.
The reflections also satisfy the resolution limits established by
_reflns_class_d_res_high and _reflns_class_d_res_low.
This is the conventional R factor.
sum | F(obs) - F(calc) |
R = ------------------------
sum | F(obs) |
F(obs) = the observed structure-factor amplitudes
F(calc) = the calculated structure-factor amplitudes
and the sum is taken over the reflections of this class. See also
_reflns_class_wR_factor_all definitions.
;
data_reflns_class_R_Fsqd_factor
_name '_reflns_class_R_Fsqd_factor'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factor R(F^2^) calculated
on the squared amplitudes of the observed and calculated
structure factors, for the reflections judged significantly
intense (i.e. satisfying the threshold specified by
_reflns_threshold_expression) and included in the refinement.
The reflections also satisfy the resolution limits established
by _reflns_class_d_res_high and _reflns_class_d_res_low.
sum | F(obs)^2^ - F(calc)^2^ |
R(Fsqd) = -------------------------------
sum F(obs)^2^
F(obs)^2^ = squares of the observed structure-factor amplitudes
F(calc)^2^ = squares of the calculated structure-factor
amplitudes
and the sum is taken over the reflections of this class.
;
data_reflns_class_R_I_factor
_name '_reflns_class_R_I_factor'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the residual factor R(I) for the
reflections judged significantly intense (i.e. satisfying the
threshold specified by _reflns_threshold_expression) and
included in the refinement.
This is most often calculated in Rietveld refinements
against powder data, where it is referred to as R~B~ or R~Bragg~.
sum | I(obs) - I(calc) |
R(I) = ------------------------
sum | I(obs) |
I(obs) = the net observed intensities
I(calc) = the net calculated intensities
and the sum is taken over the reflections of this class.
;
data_reflns_class_wR_factor_all
_name '_reflns_class_wR_factor_all'
_category reflns_class
_type numb
_list yes
_list_reference '_reflns_class_code'
_enumeration_range 0.0:
_definition
; For each reflection class, the weighted residual factors for all
reflections included in the refinement. The reflections also
satisfy the resolution limits established by
_reflns_class_d_res_high and _reflns_class_d_res_low.
( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^
wR = ( ------------------------------ )
( sum w Y(obs)^2^ )
Y(obs) = the observed amplitudes specified by
_refine_ls_structure_factor_coef
Y(calc) = the calculated amplitudes specified by
_refine_ls_structure_factor_coef
w = the least-squares weights
and the sum is taken over the reflections of this class. See
also _reflns_class_R_factor_ definitions.
;
##################
## REFLNS_SCALE ##
##################
data_reflns_scale_[]
_name '_reflns_scale_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_reflns_scale_group_code
_reflns_scale_meas_F
1 .895447
2 .912743
;
;
Example 1 - based on standard test data set p6122 of the Xtal distribution
[Hall, King & Stewart (1995). Xtal3.4 User's Manual. University
of Western Australia].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFLNS_SCALE category record details about
the structure-factor scales. They are referenced from within
the REFLN list through _refln_scale_group_code.
;
data_reflns_scale_group_code
_name '_reflns_scale_group_code'
_category reflns_scale
_type char
_list yes
_list_mandatory yes
_list_link_child '_refln_scale_group_code'
_definition
; The code identifying a scale _reflns_scale_meas_. These are
linked to the _refln_ list by the _refln_scale_group_code. These
codes need not correspond to those in the _diffrn_scale_ list.
;
data_reflns_scale_meas_
loop_ _name '_reflns_scale_meas_F'
'_reflns_scale_meas_F_squared'
'_reflns_scale_meas_intensity'
_category reflns_scale
_type numb
_type_conditions esd
_enumeration_range 0.0:
_list yes
_list_reference '_reflns_scale_group_code'
_definition
; Scales associated with _reflns_scale_group_code.
;
##################
## REFLNS_SHELL ##
##################
data_reflns_shell_[]
_name '_reflns_shell_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_reflns_shell_d_res_high
_reflns_shell_d_res_low
_reflns_shell_meanI_over_uI_gt
_reflns_shell_number_measured_gt
_reflns_shell_number_unique_gt
_reflns_shell_percent_possible_gt
_reflns_shell_Rmerge_F_gt
31.38 3.82 69.8 9024 2540 96.8 1.98
3.82 3.03 26.1 7413 2364 95.1 3.85
3.03 2.65 10.5 5640 2123 86.2 6.37
2.65 2.41 6.4 4322 1882 76.8 8.01
2.41 2.23 4.3 3247 1714 70.4 9.86
2.23 2.10 3.1 1140 812 33.3 13.99
;
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the REFLNS_SHELL category record details about
the reflections used to determine the ATOM_SITE data items,
as broken down by shells of resolution.
;
data_reflns_shell_d_res_high
_name '_reflns_shell_d_res_high'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The highest resolution in angstroms for the reflections in
this shell. This is the smallest d value.
;
data_reflns_shell_d_res_low
_name '_reflns_shell_d_res_low'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_units A
_units_detail 'angstroms'
_definition
; The lowest resolution in angstroms for the
reflections in this shell. This is the largest d value.
;
data_reflns_shell_meanI_over_sigI_all
_name '_reflns_shell_meanI_over_sigI_all'
_category reflns_shell
_type numb
_related_item '_reflns_shell_meanI_over_uI_all'
_related_function replace
_list yes
_definition
; The ratio of the mean of the intensities of all reflections
in this shell to the mean of the standard uncertainties of the
intensities of all reflections in the resolution shell.
;
data_reflns_shell_meanI_over_sigI_gt
_name '_reflns_shell_meanI_over_sigI_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_meanI_over_uI_gt'
_related_function replace
_list yes
_definition
; The ratio of the mean of the intensities of the significantly
intense reflections (see _reflns_threshold_expression) in
this shell to the mean of the standard uncertainties of the
intensities of the significantly intense reflections in the
resolution shell.
;
data_reflns_shell_meanI_over_sigI_obs
_name '_reflns_shell_meanI_over_sigI_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_meanI_over_sigI_gt'
_related_function replace
_list yes
_definition
; The ratio of the mean of the intensities of the reflections
classified as 'observed' (see _reflns_observed_criterion) in
this shell to the mean of the standard uncertainties of the
intensities of the 'observed' reflections in the resolution
shell.
;
data_reflns_shell_meanI_over_uI_all
_name '_reflns_shell_meanI_over_uI_all'
_category reflns_shell
_type numb
_related_item '_reflns_shell_meanI_over_sigI_all'
_related_function alternate
_list yes
_definition
; The ratio of the mean of the intensities of all reflections
in this shell to the mean of the standard uncertainties of the
intensities of all reflections in the resolution shell.
;
data_reflns_shell_meanI_over_uI_gt
_name '_reflns_shell_meanI_over_uI_gt'
_category reflns_shell
_type numb
loop_ _related_item
_related_function '_reflns_shell_meanI_over_sigI_gt' alternate
'_reflns_shell_meanI_over_sigI_obs' alternate
_list yes
_definition
; The ratio of the mean of the intensities of the significantly
intense reflections (see _reflns_threshold_expression) in
this shell to the mean of the standard uncertainties of the
intensities of the significantly intense reflections in the
resolution shell.
;
data_reflns_shell_number_measured_all
_name '_reflns_shell_number_measured_all'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_definition
; The total number of reflections measured for this
resolution shell.
;
data_reflns_shell_number_measured_gt
_name '_reflns_shell_number_measured_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_number_measured_obs'
_related_function alternate
_list yes
_enumeration_range 0.0:
_definition
; The number of significantly intense reflections
(see _reflns_threshold_expression) measured for this
resolution shell.
;
data_reflns_shell_number_measured_obs
_name '_reflns_shell_number_measured_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_number_measured_gt'
_related_function replace
_list yes
_enumeration_range 0.0:
_definition
; The number of reflections classified as 'observed'
(see _reflns_observed_criterion) measured for this
resolution shell.
;
data_reflns_shell_number_possible
_name '_reflns_shell_number_possible'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0:
_definition
; The number of unique reflections it is possible to measure in
this reflection shell.
;
data_reflns_shell_number_unique_all
_name '_reflns_shell_number_unique_all'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0:
_definition
; The total number of measured reflections resulting from
merging measured symmetry-equivalent reflections for this
resolution shell.
;
data_reflns_shell_number_unique_gt
_name '_reflns_shell_number_unique_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_number_unique_obs'
_related_function alternate
_list yes
_enumeration_range 0:
_definition
; The total number of significantly intense reflections
(see _reflns_threshold_expression) resulting from merging
measured symmetry-equivalent reflections for this resolution
shell.
;
data_reflns_shell_number_unique_obs
_name '_reflns_shell_number_unique_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_number_unique_gt'
_related_function replace
_list yes
_enumeration_range 0:
_definition
; The total number of reflections classified as
'observed' (see _reflns_observed_criterion) resulting from
merging measured symmetry-equivalent reflections for this
resolution shell.
;
data_reflns_shell_percent_possible_all
_name '_reflns_shell_percent_possible_all'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:100.0
_definition
; The percentage of geometrically possible reflections
represented by all reflections measured for this
resolution shell.
;
data_reflns_shell_percent_possible_gt
_name '_reflns_shell_percent_possible_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_percent_possible_obs'
_related_function alternate
_list yes
_enumeration_range 0.0:100.0
_definition
; The percentage of geometrically possible reflections
represented by significantly intense reflections
(see _reflns_threshold_expression) measured for this
resolution shell.
;
data_reflns_shell_percent_possible_obs
_name '_reflns_shell_percent_possible_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_percent_possible_gt'
_related_function replace
_list yes
_enumeration_range 0.0:100.0
_definition
; The percentage of geometrically possible reflections
represented by reflections classified as 'observed'
(see _reflns_observed_criterion) measured for this
resolution shell.
;
data_reflns_shell_Rmerge_F_all
_name '_reflns_shell_Rmerge_F_all'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(F) for all reflections in a given shell.
sum~i~ ( sum~j~ | F~j~ - | )
Rmerge(F) = --------------------------------
sum~i~ ( sum~j~ )
F~j~ = the amplitude of the jth observation of reflection i
= the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
data_reflns_shell_Rmerge_F_gt
_name '_reflns_shell_Rmerge_F_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_Rmerge_F_obs'
_related_function alternate
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(F) for significantly intense reflections
(see _reflns_threshold_expression) in a given shell.
sum~i~ ( sum~j~ | F~j~ - | )
Rmerge(F) = --------------------------------
sum~i~ ( sum~j~ )
F~j~ = the amplitude of the jth observation of reflection i
= the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
data_reflns_shell_Rmerge_F_obs
_name '_reflns_shell_Rmerge_F_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_Rmerge_F_gt'
_related_function replace
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(F) for reflections classified as 'observed'
(see _reflns_observed_criterion) in a given shell.
sum~i~ ( sum~j~ | F~j~ - | )
Rmerge(F) = --------------------------------
sum~i~ ( sum~j~ )
F~j~ = the amplitude of the jth observation of reflection i
= the mean of the amplitudes of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
data_reflns_shell_Rmerge_I_all
_name '_reflns_shell_Rmerge_I_all'
_category reflns_shell
_type numb
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(I) for all reflections in a given shell.
sum~i~ ( sum~j~ | I~j~ - | )
Rmerge(I) = --------------------------------
sum~i~ ( sum~j~ )
I~j~ = the intensity of the jth observation of reflection i
= the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
data_reflns_shell_Rmerge_I_gt
_name '_reflns_shell_Rmerge_I_gt'
_category reflns_shell
_type numb
_related_item '_reflns_shell_Rmerge_I_obs'
_related_function alternate
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(I) for significantly intense reflections
(see _reflns_threshold_expression) in a given shell.
sum~i~ ( sum~j~ | I~j~ - | )
Rmerge(I) = --------------------------------
sum~i~ ( sum~j~ )
I~j~ = the intensity of the jth observation of reflection i
= the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
data_reflns_shell_Rmerge_I_obs
_name '_reflns_shell_Rmerge_I_obs'
_category reflns_shell
_type numb
_related_item '_reflns_shell_Rmerge_I_gt'
_related_function replace
_list yes
_enumeration_range 0.0:
_definition
; The value of Rmerge(I) for reflections classified as 'observed'
(see _reflns_observed_criterion) in a given shell.
sum~i~ ( sum~j~ | I~j~ - | )
Rmerge(I) = --------------------------------
sum~i~ ( sum~j~ )
I~j~ = the intensity of the jth observation of reflection i
= the mean of the intensities of all observations of
reflection i
sum~i~ is taken over all reflections
sum~j~ is taken over all observations of each reflection.
;
#################
## SPACE_GROUP ##
#################
data_space_group_[]
_name '_space_group_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_space_group_id 1
_space_group_name_H-M_alt 'C 2/c'
_space_group_IT_number 15
_space_group_name_Hall '-C 2yc'
_space_group_crystal_system monoclinic
;
;
Example 1 - the monoclinic space group No. 15 with unique axis b.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Contains all the data items that refer to the space group as a
whole, such as its name or crystal system. They may be looped,
for example, in a list of space groups and their properties.
Only a subset of the SPACE_GROUP category items appear in the
core dictionary. The remainder are found in the symmetry CIF
dictionary.
Space-group types are identified by their number as given in
International Tables for Crystallography Vol. A. Specific
settings of the space groups can be identified either by their
Hall symbol or by specifying their symmetry operations.
The commonly used Hermann-Mauguin symbol determines the
space-group type uniquely but several different Hermann-Mauguin
symbols may refer to the same space-group type. A
Hermann-Mauguin symbol contains information on the choice of
the basis, but not on the choice of origin. Different formats
for the Hermann-Mauguin symbol are found in the symmetry CIF
dictionary.
;
data_space_group_crystal_system
_name '_space_group_crystal_system'
_category space_group
_type char
_list both
_list_reference '_space_group_id'
_related_item '_symmetry_cell_setting'
_related_function alternate
loop_ _enumeration triclinic
monoclinic
orthorhombic
tetragonal
trigonal
hexagonal
cubic
_definition
; The name of the system of geometric crystal classes of space
groups (crystal system) to which the space group belongs.
Note that rhombohedral space groups belong to the
trigonal system.
;
data_space_group_id
_name '_space_group_id'
_category space_group
_type char
_list yes
_list_mandatory yes
_list_link_child '_space_group_symop_sg_id'
_definition
; This is an identifier needed if _space_group_ items are looped.
;
data_space_group_IT_number
_name '_space_group_IT_number'
_category space_group
_type numb
_list both
_list_reference '_space_group_id'
_related_item '_symmetry_Int_Tables_number'
_related_function alternate
_enumeration_range 1:230
_definition
; The number as assigned in International Tables for
Crystallography Vol. A, specifying the proper affine class (i.e.
the orientation-preserving affine class) of space groups
(crystallographic space-group type) to which the space group
belongs. This number defines the space-group type but not
the coordinate system in which it is expressed.
;
data_space_group_name_Hall
_name '_space_group_name_Hall'
_category space_group
_type char
_list both
_list_reference '_space_group_id'
_related_item '_symmetry_space_group_name_Hall'
_related_function alternate
loop_ _example
_example_detail 'P 2c -2ac' 'equivalent to Pca21'
'-I 4bd 2ab 3' 'equivalent to Ia-3d'
_definition
; Space-group symbol defined by Hall.
Each component of the space-group name is separated by a
space or an underscore. The use of a space is strongly
recommended. The underscore is only retained because it
was used in older files. It should not be
used in new CIFs.
_space_group_name_Hall uniquely defines the space group and
its reference to a particular coordinate system.
Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
(1981), A37, 921.
[See also International Tables for Crystallography,
Vol. B (2001), Chapter 1.4, Appendix 1.4.2]
;
data_space_group_name_H-M_alt
_name '_space_group_name_H-M_alt'
_category space_group
_type char
_list both
_list_reference '_space_group_id'
_related_item '_symmetry_space_group_name_H-M'
_related_function alternate
loop_ _example
_example_detail
; loop_
_space_group_id
_space_group_name_H-M_alt
1 'C m c m'
2 'C 2/c 2/m 21/m'
3 'A m a m'
;
'three examples for space group No. 63'
_definition
; _space_group_name_H-M_alt allows any Hermann-Mauguin symbol
to be given. The way in which this item is used is determined
by the user and in general is not intended to be interpreted by
computer. It may, for example, be used to give one of the
extended Hermann-Mauguin symbols given in Table 4.3.2.1 of
International Tables for Crystallography Vol. A (2002) or
a Hermann-Mauguin symbol for a conventional or unconventional
setting.
Each component of the space-group name is separated by a
space or an underscore. The use of a space is strongly
recommended. The underscore is only retained because it
was used in older files. It should not be
used in new CIFs. Subscripts should appear without special
symbols. Bars should be given as negative signs before the
numbers to which they apply.
The commonly used Hermann-Mauguin symbol determines the space-
group type uniquely but a given space-group type may be
described by more than one Hermann-Mauguin symbol. The space-
group type is best described using _space_group_IT_number.
The Hermann-Mauguin symbol may contain information on the
choice of basis, but not on the choice of origin. To
define the setting uniquely, use _space_group_name_Hall or
list the symmetry operations.
;
#######################
## SPACE_GROUP_SYMOP ##
#######################
data_space_group_symop_[]
_name '_space_group_symop_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 x,y,z
2 -x,-y,-z
3 -x,1/2+y,1/2-z
4 x,1/2-y,1/2+z
;
;
Example 1 - the symmetry operations for the space group P21/c.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Contains information about the symmetry operations of the
space group.
;
data_space_group_symop_id
_name '_space_group_symop_id'
_type char
_category space_group_symop
_list yes
_list_mandatory yes
_related_item '_symmetry_equiv_pos_site_id'
_related_function alternate
_definition
; An arbitrary identifier that uniquely labels each symmetry
operation in the list.
;
data_space_group_symop_operation_xyz
_name '_space_group_symop_operation_xyz'
_category space_group_symop
_type char
_list both
_list_reference '_space_group_symop_id'
_enumeration_default 'x,y,z'
_related_item '_symmetry_equiv_pos_as_xyz'
_related_function alternate
loop_ _example
_example_detail 'x,1/2-y,1/2+z'
; glide reflection through the plane (x,1/4,z),
with glide vector (1/2)c
;
_definition
; A parsable string giving one of the symmetry operations of the
space group in algebraic form. If W is a matrix representation
of the rotational part of the symmetry operation defined by the
positions and signs of x, y and z, and w is a column of
translations defined by fractions, an equivalent position
X' is generated from a given position X by the equation
X' = WX + w
(Note: X is used to represent bold_italics_x in International
Tables for Crystallography Vol. A, Part 5)
When a list of symmetry operations is given, it must contain
a complete set of coordinate representatives which generates
all the operations of the space group by the addition of
all primitive translations of the space group. Such
representatives are to be found as the coordinates of
the general-equivalent position in International Tables for
Crystallography Vol. A (2002), to which it is necessary to
add any centring translations shown above the
general-equivalent position.
That is to say, it is necessary to list explicitly all the
symmetry operations required to generate all the atoms in
the unit cell defined by the setting used.
;
data_space_group_symop_sg_id
_name '_space_group_symop_sg_id'
_category space_group_symop
_type numb
_list both
_list_mandatory no
_list_reference '_space_group_symop_id'
_list_link_parent '_space_group_id'
_definition
; This must match a particular value of _space_group_id, allowing
the symmetry operation to be identified with a particular space
group.
;
##############
## SYMMETRY ##
##############
data_symmetry_[]
_name '_symmetry_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
_symmetry_cell_setting orthorhombic
_symmetry_space_group_name_H-M 'P 21 21 21'
_symmetry_space_group_name_Hall 'P 2ac 2ab'
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the SYMMETRY category record details about the
space-group symmetry.
;
data_symmetry_cell_setting
_name '_symmetry_cell_setting'
_category symmetry
_type char
loop_ _enumeration triclinic
monoclinic
orthorhombic
tetragonal
rhombohedral
trigonal
hexagonal
cubic
_related_item '_space_group_crystal_system'
_related_function replace
_definition
; The cell settings for this space-group symmetry.
;
data_symmetry_Int_Tables_number
_name '_symmetry_Int_Tables_number'
_category symmetry
_type numb
_enumeration_range 1:230
_related_item '_space_group_IT_number'
_related_function replace
_definition
; Space-group number from International Tables for Crystallography
Vol. A (2002).
;
data_symmetry_space_group_name_Hall
_name '_symmetry_space_group_name_Hall'
_category symmetry
_type char
_related_item '_space_group_name_Hall'
_related_function replace
loop_ _example '-P 2ac 2n'
'-R 3 2"'
'P 61 2 2 (0 0 -1)'
_definition
; Space-group symbol as described by Hall. This symbol gives the
space-group setting explicitly. Leave spaces between the separate
components of the symbol.
Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum
(1981), A37, 921.
;
data_symmetry_space_group_name_H-M
_name '_symmetry_space_group_name_H-M'
_category symmetry
_type char
_related_item '_space_group_name_H-M_alt'
_related_function replace
loop_ _example 'P 1 21/m 1'
'P 2/n 2/n 2/n (origin at -1)'
'R -3 2/m'
_definition
; Hermann-Mauguin space-group symbol. Note that the Hermann-Mauguin
symbol does not necessarily contain complete information
about the symmetry and the space-group origin. If used, always
supply the FULL symbol from International Tables for
Crystallography Vol. A (2002) and indicate the origin and
the setting if it is not implicit. If there is any doubt
that the equivalent positions can be uniquely deduced from
this symbol, specify the _symmetry_equiv_pos_as_xyz
or *_Hall data items as well. Leave spaces between
symbols referring to different axes.
;
####################
## SYMMETRY_EQUIV ##
####################
data_symmetry_equiv_[]
_name '_symmetry_equiv_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_symmetry_equiv_pos_as_xyz
+x,+y,+z 1/2-x,-y,1/2+z 1/2+x,1/2-y,-z -x,1/2+y,1/2-z
;
;
Example 1 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 1/2-x,-y,1/2+z
3 1/2+x,1/2-y,-z
4 -x,1/2+y,1/2-z
;
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277]. Formally, the value of
_symmetry_equiv_pos_site_id can be any unique character string;
it is recommended that it be assigned the sequence number of
the list of equivalent positions for compatibility with
older files in which it did not appear.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the SYMMETRY_EQUIV category list the
symmetry-equivalent positions for the space group.
;
data_symmetry_equiv_pos_as_xyz
_name '_symmetry_equiv_pos_as_xyz'
_category symmetry_equiv
_type char
_list both
_example -y+x,-y,1/3+z
_related_item '_space_group_symop_operation_xyz'
_related_function replace
_definition
; Symmetry-equivalent position in the 'xyz' representation. Except
for the space group P1, these data will be repeated in a loop.
The format of the data item is as per International Tables for
Crystallography Vol. A. (2002). All equivalent positions should
be entered, including those for lattice centring and a centre of
symmetry, if present.
;
data_symmetry_equiv_pos_site_id
_name '_symmetry_equiv_pos_site_id'
_category symmetry_equiv
_type numb
_list yes
_list_reference '_symmetry_equiv_pos_as_xyz'
_related_item '_space_group_symop_id'
_related_function replace
_definition
; A code identifying each entry in the _symmetry_equiv_pos_as_xyz
list. It is normally the sequence number of the entry in that
list, and should be identified with the code 'n' in
_geom_*_symmetry_ codes of the form 'n_klm'.
;
###################
## VALENCE_PARAM ##
###################
data_valence_param_[]
_name '_valence_param_[]'
_category category_overview
_type null
loop_ _example
_example_detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
loop_
_valence_param_id
_valence_param_atom_1
_valence_param_atom_1_valence
_valence_param_atom_2
_valence_param_atom_2_valence
_valence_param_Ro
_valence_param_B
_valence_param_ref_id
_valence_param_details
1 Cu 2 O -2 1.679 0.37 a .
2 Cu 2 O -2 1.649 0.37 j .
3 Cu 2 N -3 1.64 0.37 m '2-coordinate N'
4 Cu 2 N -3 1.76 0.37 m '3-coordinate N'
loop_
_valence_ref_id
_valence_ref_reference
a 'Brown & Altermatt (1985), Acta Cryst. B41, 244-247'
j 'Liu & Thorp (1993), Inorg. Chem. 32, 4102-4205'
m 'See, Krause & Strub (1998), Inorg. Chem. 37, 5369-5375'
;
;
Example 1 - a bond-valence parameter list with accompanying references.
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_definition
; Data items in the VALENCE_PARAM category define the
parameters used for calculating bond valences from bond
lengths. In addition to the parameters, a pointer
is given to the reference (in VALENCE_REF) from which
the bond-valence parameters were taken.
;
data_valence_param_atom_1
_name '_valence_param_atom_1'
_category valence_param
_type char
_list yes
_list_reference '_valence_param_id'
_definition
; The element symbol of the first atom forming the bond whose
bond-valence parameters are given in this category.
;
data_valence_param_atom_1_valence
_name '_valence_param_atom_1_valence'
_category valence_param
_type numb
_list yes
_list_reference '_valence_param_id'
_definition
; The valence (formal charge) of the first atom whose
bond-valence parameters are given in this category.
;
data_valence_param_atom_2
_name '_valence_param_atom_2'
_category valence_param
_type char
_list yes
_list_reference '_valence_param_id'
_definition
; The element symbol of the second atom forming the bond whose
bond-valence parameters are given in this category.
;
data_valence_param_atom_2_valence
_name '_valence_param_atom_2_valence'
_category valence_param
_type numb
_list yes
_list_reference '_valence_param_id'
_definition
; The valence (formal charge) of the second atom whose
bond-valence parameters are given in this category.
;
data_valence_param_B
_name '_valence_param_B'
_category valence_param
_type numb
_list yes
_list_reference '_valence_param_id'
_units A
_units_detail Angstrom
_definition
; The bond-valence parameter B used in the expression
s = exp[(Ro - R)/B]
where s is the valence of a bond of length R.
;
data_valence_param_details
_name '_valence_param_details'
_category valence_param
_type char
_list yes
_list_reference '_valence_param_id'
_definition
; Details of or comments on the bond-valence parameters.
;
data_valence_param_id
_name '_valence_param_id'
_category valence_param
_type char
_list yes
_definition
; An identifier for the valence parameters of a bond between
the given atoms.
;
data_valence_param_ref_id
_name '_valence_param_ref_id'
_category valence_param
_type char
_list yes
_list_reference '_valence_param_id'
_list_link_parent '_valence_ref_id'
_definition
; An identifier which links to the reference to the source
from which the bond-valence parameters are taken. A child
of _valence_ref_id, which it must match.
;
data_valence_param_Ro
_name '_valence_param_Ro'
_category valence_param
_type numb
_list yes
_list_reference '_valence_param_id'
_units A
_units_detail Angstrom
_definition
; The bond-valence parameter Ro used in the expression
s = exp[(Ro - R)/B]
where s is the valence of a bond of length R.
;
#################
## VALENCE_REF ##
#################
data_valence_ref_[]
_name '_valence_ref_[]'
_category category_overview
_type null
_definition
; Data items in the VALENCE_REF category list the references
from which the bond-valence parameters have been taken.
;
data_valence_ref_id
_name '_valence_ref_id'
_category valence_ref
_type char
_list yes
_list_reference '_valence_ref_id'
_list_link_child '_valence_param_ref_id'
_definition
; An identifier for items in this category. Parent of
_valence_param_ref_id, which must have the same value.
;
data_valence_ref_reference
_name '_valence_ref_reference'
_type char
_category valence_ref
_list yes
_list_reference '_valence_ref_id'
_definition
; Literature reference from which the valence parameters
identified by _valence_param_id were taken.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
./CBFlib-0.9.2.2/doc/Idiffrn_scan_frame_axis.displacement_increment.html 0000644 0000765 0000765 00000006037 11603702115 024535 0 ustar yaya yaya
(IUCr) CIF Definition save__diffrn_scan_frame_axis.displacement_increment
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
Type: code
Mandatory item: yes
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Image dictionary (imgCIF) version 1.5.4 definitions
##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.5.4 #
# of 2007-07-28 #
# ################################################################### #
# # *** WARNING *** THIS IS A DRAFT FOR DISCUSSSION *** WARNING *** # #
# # SUBJECT TO CHANGE WITHOUT NOTICE # #
# # SEND COMMENTS TO imgcif-l@iucr.org CITING THE VERSION # #
# ################################################################### #
# This draft edited by H. J. Bernstein #
# #
# by Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook #
# #
# This dictionary was adapted from format discussed at the imgCIF Workshop, #
# held at BNL Oct 1997 and the Crystallographic Binary File Format Draft #
# Proposal by Andrew Hammersley. The first DDL 2.1 Version was created by #
# John Westbrook. This version was drafted by Herbert J. Bernstein and #
# incorporates comments by I. David Brown, John Westbrook, Brian McMahon, #
# Bob Sweet, Paul Ellis, Harry Powell, Wilfred Li, Gotzon Madariaga, #
# Frances C. Bernstein, Chris Nielsen, Nicola Ashcroft and others. #
##############################################################################
Definitions are arranged alphabetically by category and within category.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Data items in the ARRAY_DATA category are the containers for
the array data items described in the category ARRAY_STRUCTURE.
It is recognized that the data in this category needs to be used in
two distinct ways. During a data collection the lack of ancillary
data and timing constraints in processing data may dictate the
need to make a 'miniCBF' nothing more than an essential minimum
of information to record the results of the data collection. In that
case it is proper to use the ARRAY_DATA category as a
container for just a single image and a compacted, beam-line
dependent list of data collection parameter values. In such
a case, only the tags '_array_data.header_convention',
'_array_data.header_contents' and '_array_data.data' need be
populated.
For full processing and archiving, most of the tags in this
dictionary will need to be populated.
Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
_array_intensities.gain. If raw, uncorrected values
are presented (e.g. for calibration experiments), the
value of _array_intensities.linearity will be 'raw'
and _array_intensities.gain will not be used.
Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets of axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axes: one for the angular
direction and one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one
set.
Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection or the axes defining the
coordinate system of an image.
The location of each axis is specified by two vectors: the axis
itself, given by a unit vector in the direction of the axis, and
an offset to the base of the unit vector.
The vectors defining an axis are referenced to an appropriate
coordinate system. The axis vector, itself, is a dimensionless
unit vector. Where meaningful, the offset vector is given in
millimetres. In coordinate systems not measured in metres,
the offset is not specified and is taken as zero.
The available coordinate systems are:
The imgCIF standard laboratory coordinate system
The direct lattice (fractional atomic coordinates)
The orthogonal Cartesian coordinate system (real space)
The reciprocal lattice
An abstract orthogonal Cartesian coordinate frame
DIFFRN_GROUP
Categories that describe details of the diffraction experiment.
Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases but should not be used for new work.
Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the
diffraction data were measured.
Data items in the DIFFRN_RADIATION category describe
the radiation used for measuring diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
Data items in the DIFFRN_REFLN category record details about
the intensities in the diffraction data set
identified by _diffrn_refln.diffrn_id.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in the particular diffraction
data set identified by _diffrn_reflns.diffrn_id and
_diffrn_refln.frame_id
Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the
settings of axes for particular frames. Unspecified axes are
assumed to be at their zero points. If, for any given frame,
nonzero values apply for any of the data items in this category,
those values should be given explicitly in this category and not
simply inferred from values in DIFFRN_SCAN_AXIS.
A single frame may have more than one monitor value, and each
monitor value may be the result of integration over the entire
frame integration time given by the value of
_diffrn_scan_frame.integration_time
or many monitor values may be reported over shorter times given
by the value of _diffrn_scan_frame_monitor.integration_time. If
only one monitor value for a given monitor is collected during
the integration time of the frame, the value of
_diffrn_scan_frame_monitor.id may be
omitted.
Data items in the MAP category record
the details of a maps. Maps record values of parameters,
such as density, that are functions of position within
a cell or are functions of orthogonal coordinates in
three space.
A map may is composed of one or more map segments
specified in the MAP_SEGMENT category.
Data items in the VARIANT category record
the details about sets of variants of data items.
There is sometimes a need to allow for multiple versions of the
same data items in order to allow for refinements and corrections
to earlier assumptions, observations and calculations. In order
to allow data sets to contain more than one variant of the same
information, an optional ...variant data item as a pointer to
_variant.variant has been added to the key of every category,
as an implicit data item with a null (empty) default value.
All rows in a category with the same variant value are considered
to be related to one another and to all rows in other categories
with the same variant value. For a given variant, all such rows
are also considered to be related to all rows with a null variant
value, except that a row with a null variant value is for which
all other components of its key are identical to those entries
in another row with a non-null variant value is not related the
the rows with that non-null variant value. This behavior is
similar to the convention for identifying alternate conformers
in an atom list.
An optional role may be specified for a variant as the value of
_variant.role. Possible roles are null, "preferred",
"raw data", "unsuccessful trial".
Variants may carry an optional timestamp as the value of
_variant.timestamp.
Variants may be related to other variants from which they were
derived by the value of _variant.variant_of
Further details about the variant may be specified as the value
of _variant.details.
In order to allow variant information from multiple datasets to
be combined, _variant.diffrn_id and/or _variant.entry_id may
be used.
;
_dictionary.title cif_img.dic
_dictionary.version 1.6.4
_dictionary.datablock_id cif_img.dic
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
'map_group'
'inclusive_group'
; Categories that describe details of map data.
;
'variant_group'
'inclusive_group'
; Categories that describe details of map data.
;
##################
## SUB_CATEGORY ##
##################
loop_
_sub_category.id
_sub_category.description
'matrix'
; The collection of elements of a matrix.
;
'vector'
; The collection of elements of a vector.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
; Data items in the ARRAY_DATA category are the containers for
the array data items described in the category ARRAY_STRUCTURE.
It is recognized that the data in this category needs to be used in
two distinct ways. During a data collection the lack of ancillary
data and timing constraints in processing data may dictate the
need to make a 'miniCBF' nothing more than an essential minimum
of information to record the results of the data collection. In that
case it is proper to use the ARRAY_DATA category as a
container for just a single image and a compacted, beam-line
dependent list of data collection parameter values. In such
a case, only the tags '_array_data.header_convention',
'_array_data.header_contents' and '_array_data.data' need be
populated.
For full processing and archiving, most of the tags in this
dictionary will need to be populated.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
'_array_data.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and is
presented as hexadecimal data. The first character 'H' on the
data lines means hexadecimal. It could have been 'O' for octal
or 'D' for decimal. The second character on the line shows
the number of bytes in each word (in this case '4'), which then
requires eight hexadecimal digits per word. The third character
gives the order of octets within a word, in this case '<'
for the ordering 4321 (i.e. 'big-endian'). Alternatively, the
character '>' could have been used for the ordering 1234
(i.e. 'little-endian'). The block has a 'message digest'
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id_array_data.binary_id_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 2
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
This example shows a single image in a miniCBF, provided by
E. Eikenberry. The entire CBF consists of one data block
containing one category and three tags. The CBFlib
program convert_miniCBF and a suitable template file
can be used to convert this miniCBF to a full imgCIF
file.
;
;
###CBF: VERSION 1.5
# CBF file written by CBFlib v0.7.8
data_insulin_pilatus6m
_array_data.header_convention SLS_1.0
_array_data.header_contents
;
# Detector: PILATUS 6M SN: 60-0001
# 2007/Jun/17 15:12:36.928
# Pixel_size 172e-6 m x 172e-6 m
# Silicon sensor, thickness 0.000320 m
# Exposure_time 0.995000 s
# Exposure_period 1.000000 s
# Tau = 194.0e-09 s
# Count_cutoff 1048575 counts
# Threshold_setting 5000 eV
# Wavelength 1.2398 A
# Energy_range (0, 0) eV
# Detector_distance 0.15500 m
# Detector_Voffset -0.01003 m
# Beam_xy (1231.00, 1277.00) pixels
# Flux 22487563295 ph/s
# Filter_transmission 0.0008
# Start_angle 13.0000 deg.
# Angle_increment 1.0000 deg.
# Detector_2theta 0.0000 deg.
# Polarization 0.990
# Alpha 0.0000 deg.
# Kappa 0.0000 deg.
# Phi 0.0000 deg.
# Chi 0.0000 deg.
# Oscillation_axis X, CW
# N_oscillations 1
;
_array_data.data
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_BYTE_OFFSET"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 6247567
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
X-Binary-Element-Byte-Order: LITTLE_ENDIAN
Content-MD5: 8wO6i2+899lf5iO8QPdgrw==
X-Binary-Number-of-Elements: 6224001
X-Binary-Size-Fastest-Dimension: 2463
X-Binary-Size-Second-Dimension: 2527
X-Binary-Size-Padding: 4095
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
If not given, it defaults to 1.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code implicit
_item_default.value 1
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id, should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-ID, the value of _array_data.binary_id
should be equal to the value given for X-Binary-ID.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
'\n--CIF-BINARY-FORMAT-SECTION--' (including the
required initial '\n--').
The Content-Type may be any of the discrete types permitted
in RFC 2045; 'application/octet-stream' is recommended
for diffraction images in the ARRAY_DATA category.
Note: When appropriate in other categories, e.g. for
photographs of crystals, more precise types, such as
'image/jpeg', 'image/tiff', 'image/png', etc. should be used.
If an octet stream was compressed, the compression should
be specified by the parameter
'conversions="X-CBF_PACKED"'
or the parameter
'conversions="X-CBF_CANONICAL"'
or the parameter
'conversions="X-CBF_BYTE_OFFSET"'
or the parameter
'conversions="X-CBF_BACKGROUND_OFFSET_DELTA"'
If the parameter
'conversions="X-CBF_PACKED"'
is given it may be further modified with the parameters
'"uncorrelated_sections"'
or
'"flat"'
If the '"uncorrelated_sections"' parameter is
given, each section will be compressed without using
the prior section for averaging.
If the '"flat"' parameter is given, each the
image will be treated as one long row.
Note that the X-CBF_CANONICAL and X-CBF_PACKED are
slower but more efficient compressions that the others.
The X-CBF_BYTE_OFFSET compression is a good compromise
between speed and efficiency for ordinary diffraction
images. The X-CBF_BACKGROUND_OFFSET_DELTA compression
is oriented towards sparse data, such as masks and
tables of replacement pixel values for images with
overloaded spots.
The Content-Transfer-Encoding may be 'BASE64',
'Quoted-Printable', 'X-BASE8', 'X-BASE10',
'X-BASE16' or 'X-BASE32K', for an imgCIF or 'BINARY'
for a CBF. The octal, decimal and hexadecimal transfer
encodings are provided for convenience in debugging and
are not recommended for archiving and data interchange.
In a CIF, one of the parameters 'charset=us-ascii',
'charset=utf-8' or 'charset=utf-16' may be used on the
Content-Transfer-Encoding to specify the character set
used for the external presentation of the encoded data.
If no charset parameter is given, the character set of
the enclosing CIF is assumed. In any case, if a BOM
flag is detected (FE FF for big-endian UTF-16, FF FE for
little-endian UTF-16 or EF BB BF for UTF-8) is detected,
the indicated charset will be assumed until the end of the
encoded data or the detection of a different BOM. The
charset of the Content-Transfer-Encoding is not the character
set of the encoded data, only the character set of the
presentation of the encoded data and should be respecified
for each distinct STAR string.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In an imgCIF file,
the encoded binary data ends with the terminating boundary
delimiter '\n--CIF-BINARY-FORMAT-SECTION----'
in the currently effective charset or with the '\n; '
that terminates the STAR string.
In a CBF, the raw binary data begins after an empty line
terminating the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of
the message size or in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. An adjustment is made for
the deprecated binary formats in which eight bytes of binary
header are used for the compression type. In this case,
the eight bytes used for the compression type are subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is 'unsigned 32-bit integer'.
An MD5 message digest may, optionally, be used. The 'RSA Data
Security, Inc. MD5 Message-Digest Algorithm' should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is 'X-BASE8', 'X-BASE10' or
'X-BASE16', the data are presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ('big-
endian') or 1234... ('little-endian'). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as '==' for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is 'H', 'O' or 'D' for hexadecimal, octal or
decimal, n is the number of octets per word and d is '<'
or '>' for the '...4321' and '1234...' octet orderings,
respectively. The '==' padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hexadecimal, octal and decimal formats only,
comments beginning with '#' are permitted to improve
readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three: c1, c2, c3. The resulting 24 bits
are broken into four six-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order four bits of the second octet [(c1 & 3)<<4 | (c2>>4)],
then the bottom four bits of the second octet followed by the
high-order two bits of the last octet [(c2 & 15)<<2 | (c3>>6)],
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
With short groups of octets padded on the right with one '='
if c3 is missing, and with '==' if both c2 and c3 are missing.
X-BASE32K encoding is similar to BASE64 encoding, except that
sets of 15 octets are encoded as sets of 8 16-bit unicode
characters, by breaking the 120 bits into 8 15-bit quantities.
256 is added to each 15 bit quantity to bring it into a
printable uncode range. When encoding, zero padding is used
to fill out the last 15 bit quantity. If 8 or more bits of
padding are used, a single equals sign (hexadecimal 003D) is
appended. Embedded whitespace and newlines are introduced
to produce lines of no more than 80 characters each. On
decoding, all printable ascii characters and ascii whitespace
characters are ignored except for any trailing equals signs.
The number of trailing equals signs indicated the number of
trailing octets to be trimmed from the end of the decoded data.
(see Georgi Darakev, Vassil Litchev, Kostadin Z. Mitev, Herbert
J. Bernstein, 'Efficient Support of Binary Data in the XML
Implementation of the NeXus File Format',absract W0165,
ACA Summer Meeting, Honolulu, HI, July 2006).
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32...38,
42, 48...57, 59, 60, 62, 64...126 and the octet is not a ';'
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
'wrapped' with a terminating '=' (i.e. the MIME conventions
for an implicit line terminator are never used).
The "X-Binary-Element-Byte-Order" can specify either
'"BIG_ENDIAN"' or '"LITTLE_ENDIAN"' byte order of the imaage
data. Only LITTLE_ENDIAN is recommended. Processors
may treat BIG_ENDIAN as a warning of data that can
only be processed by special software.
The "X-Binary-Number-of-Elements" specifies the number of
elements (not the number of octets) in the decompressed, decoded
image.
The optional "X-Binary-Size-Fastest-Dimension" specifies the
number of elements (not the number of octets) in one row of the
fastest changing dimension of the binary data array. This
information must be in the MIME header for proper operation of
some of the decompression algorithms.
The optional "X-Binary-Size-Second-Dimension" specifies the
number of elements (not the number of octets) in one column of
the second-fastest changing dimension of the binary data array.
This information must be in the MIME header for proper operation
of some of the decompression algorithms.
The optional "X-Binary-Size-Third-Dimension" specifies the
number of sections for the third-fastest changing dimension of
the binary data array.
The optional "X-Binary-Size-Padding" specifies the size in
octets of an optional padding after the binary array data and
before the closing flags for a binary section.
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
save__array_data.header_contents
_item_description.description
; This item is an text field for use in minimal CBF files to carry
essential header information to be kept with image data
in _array_data.data when the tags that normally carry the
structured metadata for the image have not been populated.
Normally this data item should not appear when the full set
of tags have been populated and _diffrn_data_frame.details
appears.
;
_item.name '_array_data.header_contents'
_item.category_id array_data
_item.mandatory_code no
_item_type.code text
save_
save__array_data.header_convention
_item_description.description
; This item is an identifier for the convention followed in
constructing the contents of _array_data.header_contents
The permitted values are of the of an image creator identifier
followed by an underscore and a version string. To avoid
confusion about conventions, all creator identifiers
should be registered with the IUCr and the conventions
for all identifiers and versions should be posted on
the MEDSBIO.org web site.
;
_item.name '_array_data.header_convention'
_item.category_id array_data
_item.mandatory_code no
_item_type.code code
save_
save__array_data.variant
_item_description.description
; The value of _array_data.variant gives the variant
to which the given array_data row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_data.variant'
_item.category_id array_data
_item.mandatory_code no
_item_type.code code
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
; Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
'_array_element_size.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code implicit
_item_type.code code
save_
save__array_element_size.index
_item_description.description
; This item is a pointer to _array_structure_list.index in
the ARRAY_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
; The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__array_element_size.variant
_item_description.description
; The value of _array_element_size.variant gives the variant
to which the given array_element_size row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_element_size.variant'
_item.category_id array_element_size
_item.mandatory_code no
_item_type.code code
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
; Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
_array_intensities.gain. If raw, uncorrected values
are presented (e.g. for calibration experiments), the
value of _array_intensities.linearity will be 'raw'
and _array_intensities.gain will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
'_array_intensities.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id_array_intensities.linearity_array_intensities.gain_array_intensities.overload_array_intensities.undefined_value_array_intensities.pixel_fast_bin_size_array_intensities.pixel_slow_bin_size_array_intensities.pixel_binning_method
image_1 linear 1.2 655535 0 2 2 hardware
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
; Detector 'gain'. The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
; The estimated standard deviation in detector 'gain'.
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
; The intensity linearity scaling method used to convert
from the raw intensity to the stored element value:
'linear' is linear.
'offset' means that the value defined by
_array_intensities.offset should be added to each
element value.
'scaling' means that the value defined by
_array_intensities.scaling should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by _array_intensities.scaling is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
'logarithmic_scaled' means that the logarithm base 10 of
raw intensities multiplied by _array_intensities.scaling
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and calculating 10
to the power of this number.
'raw' means that the data are a set of raw values straight
from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
; The value defined by _array_intensities.offset should
be added to each element value.
;
'scaling'
; The value defined by _array_intensities.scaling should be
multiplied with each element value.
;
'scaling_offset'
; The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
; The square root of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
;
'logarithmic_scaled'
; The logarithm base 10 of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
_array_intensities.scaling and calculating 10 to the
power of this number.
;
'raw'
; The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data-fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
; Offset value to add to array element values in the manner
described by the item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
; The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.pixel_fast_bin_size
_item_description.description
; The value of _array_intensities.pixel_fast_bin_size specifies
the number of pixels that compose one element in the direction
of the most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_fast_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_slow_bin_size
_item_description.description
; The value of _array_intensities.pixel_slow_bin_size specifies
the number of pixels that compose one element in the direction
of the second most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_slow_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_binning_method
_item_description.description
; The value of _array_intensities.pixel_binning_method specifies
the method used to derive array elements from multiple pixels.
;
_item.name '_array_intensities.pixel_binning_method'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'hardware'
; The element intensities were derived from the raw data of one
or more pixels by used of hardware in the detector, e.g. by use
of shift registers in a CCD to combine pixels into super-pixels.
;
'software'
; The element intensities were derived from the raw data of more
than one pixel by use of software.
;
'combined'
; The element intensities were derived from the raw data of more
than one pixel by use of both hardware and software, as when
hardware binning is used in one direction and software in the
other.
;
'none'
; In the both directions, the data has not been binned. The
number of pixels is equal to the number of elements.
When the value of _array_intensities.pixel_binning_method is
'none' the values of _array_intensities.pixel_fast_bin_size
and _array_intensities.pixel_slow_bin_size both must be 1.
;
'unspecified'
; The method used to derive element intensities is not specified.
;
_item_default.value 'unspecified'
save_
save__array_intensities.scaling
_item_description.description
; Multiplicative scaling value to be applied to array data
in the manner described by item
_array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.undefined_value
_item_description.description
; A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.variant
_item_description.description
; The value of _array_intensities.variant gives the variant
to which the given array_intensities row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_intensities.variant'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code code
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
; Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data that may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
loop_
_category_key.name '_array_structure.id'
'_array_structure.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
; The order of bytes for integer values which require more
than 1 byte.
(IBM-PC's and compatibles and DEC VAXs use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. DEC Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
; The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
; The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
; Type of data-compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'byte_offset'
; Using the 'byte_offset' compression scheme as per A. Hammersley
and the CBFlib manual, section 3.3.3
;
'canonical'
; Using the 'canonical' compression scheme (International Tables
for Crystallography Volume G, Section 5.6.3.1) and CBFlib
manual section 3.3.1
;
'none'
; Data are stored in normal format as defined by
_array_structure.encoding_type and
_array_structure.byte_order.
;
'packed'
; Using the 'packed' compression scheme, a CCP4-style packing
as per J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
'packed_v2'
; Using the 'packed' compression scheme, version 2, as per
J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
save_
save__array_structure.compression_type_flag
_item_description.description
; Flags modifying the type of data-compression method used to
compress the arraydata.
;
_item.name '_array_structure.compression_type_flag'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'uncorrelated_sections'
; When applying packed or packed_v2 compression on an array with
uncorrelated sections, do not average in points from the prior
section.
;
'flat'
; When applying packed or packed_v2 compression on an array with
treat the entire image as a single line set the maximum number
of bits for an offset to 65 bits.
The flag is included for compatibility with software prior to
CBFlib_0.7.7, and should not be used for new data sets.
;
save_
save__array_structure.encoding_type
_item_description.description
; Data encoding of a single element of array data.
The type 'unsigned 1-bit integer' is used for
packed Booleans arrays for masks. Each element
of the array corresponds to a single bit
packed in unsigned 8-bit data.
In several cases, the IEEE format is referenced.
See IEEE Standard 754-1985 (IEEE, 1985).
Ref: IEEE (1985). IEEE Standard for Binary Floating-Point
Arithmetic. ANSI/IEEE Std 754-1985. New York: Institute of
Electrical and Electronics Engineers.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 1-bit integer'
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
This item has been made implicit and given a default value of 1
as a convenience in writing miniCBF files. Normally an
explicit name with useful content should be used.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure implicit
'_array_data.array_id' array_data implicit
'_array_structure_list.array_id' array_structure_list implicit
'_array_intensities.array_id' array_intensities implicit
'_diffrn_data_frame.array_id' diffrn_data_frame implicit
_item_default.value 1
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
save__array_structure.variant
_item_description.description
; The value of _array_structure.variant gives the variant
to which the given array_structure row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_structure.variant'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code code
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
; Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
'_array_structure_list.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left to right (increasing) in the
first dimension and bottom to top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differs
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the 'poise' of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
; The number of elements stored in the array structure in
this dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
; Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
; Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
; Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
; Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
; Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.variant
_item_description.description
; The value of _array_structure_list.variant gives the variant
to which the given array_structure_list row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_structure_list.variant'
_item.category_id array_structure_list
_item.mandatory_code no
_item_type.code code
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
; Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets of axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axes: one for the angular
direction and one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one
set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
'_array_structure_list_axis.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes in the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
; The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to
_array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list_axis.angle
_item_description.description
; The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified for this case.
See _array_structure_list_axis.angular_pitch.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement
_item_description.description
; The setting of the specified axis as a decimal fraction of
the axis unit vector for the first data point of the array
index with the corresponding value of
_array_structure_list.axis_set_id.
If the index is specified as 'increasing', this will be the
centre of the pixel with index value 1. If the index is
specified as 'decreasing', this will be the centre of the
pixel with maximum index value.
;
_item.name '_array_structure_list_axis.fract_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis as a decimal fraction of the
axis unit vector.
;
_item.name
'_array_structure_list_axis.fract_displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
; The pixel-centre-to-pixel-centre distance for a one-step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans
or for uncoupled angular scans at a constant radius
(cylindrical scans) and should not be specified for cases
in which the angle between pixels (rather than the distance
between pixels) is uniform.
See _array_structure_list_axis.angle_increment.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
; The radial distance from one 'cylinder' of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of _array_structure_list_axis.displacement_increment.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.reference_angle
_item_description.description
; The value of _array_structure_list_axis.reference_angle
specifies the setting of the angle of this axis used for
determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the
value of _array_structure_list.angle.
;
_item.name '_array_structure_list_axis.reference_angle'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.reference_displacement
_item_description.description
; The value of _array_structure_list_axis.reference_displacement
specifies the setting of the displacement of this axis used
for determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the value
of _array_structure_list.displacement.
;
_item.name '_array_structure_list_axis.reference_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.variant
_item_description.description
; The value of _array_structure_list_axis.variant gives the variant
to which the given array_structure_list_axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_structure_list_axis.variant'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_type.code code
save_
########
# AXIS #
########
save_AXIS
_category.description
; Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection or the axes defining the
coordinate system of an image.
The location of each axis is specified by two vectors: the axis
itself, given by a unit vector in the direction of the axis, and
an offset to the base of the unit vector.
The vectors defining an axis are referenced to an appropriate
coordinate system. The axis vector, itself, is a dimensionless
unit vector. Where meaningful, the offset vector is given in
millimetres. In coordinate systems not measured in metres,
the offset is not specified and is taken as zero.
The available coordinate systems are:
The imgCIF standard laboratory coordinate system
The direct lattice (fractional atomic coordinates)
The orthogonal Cartesian coordinate system (real space)
The reciprocal lattice
An abstract orthogonal Cartesian coordinate frame
For consistency in this discussion, we call the three coordinate
system axes X, Y and Z. This is appropriate for the imgCIF
standard laboratory coordinate system, and last two Cartesian
coordinate systems, but for the direct lattice, X corresponds
to a, Y to b and Z to c, while for the reciprocal lattice,
X corresponds to a*, Y to b* and Z to c*.
For purposes of visualization, all the coordinate systems are
taken as right-handed, i.e., using the convention that the extended
thumb of a right hand could point along the first (X) axis, the
straightened pointer finger could point along the second (Y) axis
and the middle finger folded inward could point along the third (Z)
axis.
THE IMGCIF STANDARD LABORATORY COORDINATE SYSTEM
The imgCIF standard laboratory coordinate system is a right-handed
orthogonal coordinate similar to the MOSFLM coordinate system,
but imgCIF puts Z along the X-ray beam, rather than putting X along the
X-ray beam as in MOSFLM.
The vectors for the imgCIF standard laboratory coordinate system
form a right-handed Cartesian coordinate system with its origin
in the sample or specimen. The origin of the axis system should,
if possible, be defined in terms of mechanically stable axes to be
be both in the sample and in the beam. If the sample goniometer or other
sample positioner has two axes the intersection of which defines a
unique point at which the sample should be mounted to be bathed
by the beam, that will be the origin of the axis system. If no such
point is defined, then the midpoint of the line of intersection
between the sample and the center of the beam will define the origin.
For this definition the sample positioning system will be set at
its initial reference position for the experiment.
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer or
sample positioning system if the sample positioning system has an axis
that intersects the origin and which form an angle of more than 22.5
degrees with the beam axis.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
If the conditions for the X-axis can be met, the coordinate system
will be based on the goniometer or other sample positioning system
and the beam and not on the orientation of the detector, gravity etc.
The vectors necessary to specify all other axes are given by sets of
three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right-handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to but significantly
different from the choice in MOSFLM (Leslie & Powell, 2004). In MOSFLM,
X is along the X-ray beam (the CBF/imgCIF Z axis) and Z is along the
rotation axis.
In some experimental techniques, there is no goniometer or the principal
axis of the goniometer is at a small acute angle with respect to
the source axis. In such cases, other reference axes are needed
to define a useful coordinate system. The order of priority in
defining directions in such cases is to use the detector, then
gravity, then north.
If the X-axis cannot be defined as above, then the
direction (not the origin) of the X-axis should be parallel to the axis
of the primary detector element corresponding to the most rapidly
varying dimension of that detector element's data array, with its
positive sense corresponding to increasing values of the index for
that dimension. If the detector is such that such a direction cannot
be defined (as with a point detector) or that direction forms an
angle of less than 22.5 degrees with respect to the source axis, then
the X-axis should be chosen so that if the Y-axis is chosen
in the direction of gravity, and the Z-axis is chosen to be along
the source axis, a right-handed orthogonal coordinate system is chosen.
In the case of a vertical source axis, as a last resort, the
X-axis should be chosen to point North.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam centre.
The location of the beam centre on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected millimetres from
the (0,0) corner of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, it is necessary to
specify the location of the beam centre on the detector in terms
of the origin of the detector, which is, of course, not coincident
with the centre of the sample.
The unit cell, reciprocal cell and crystallographic orthogonal
Cartesian coordinate system are defined by the CELL and the matrices
in the ATOM_SITES category.
THE DIRECT LATTICE (FRACTIONAL COORDINATES)
The direct lattice coordinate system is a system of fractional
coordinates aligned to the crystal, rather than to the laboratory.
This is a natural coordinate system for maps and atomic coordinates.
It is the simplest coordinate system in which to apply symmetry.
The axes are determined by the cell edges, and are not necessarily
othogonal. This coordinate system is not uniquely defined and
depends on the cell parameters in the CELL category and the
settings chosen to index the crystal.
Molecules in a crystal studied by X-ray diffracraction are organized
into a repeating regular array of unit cells. Each unit cell is defined
by three vectors, a, b and c. To quote from Drenth,
"The choice of the unit cell is not unique and therefore, guidelines
have been established for selecting the standard basis vectors and
the origin. They are based on symmetry and metric considerations:
"(1) The axial system should be right handed.
(2) The basis vectors should coincide as much as possible with
directions of highest symmetry."
(3) The cell taken should be the smallest one that satisfies
condition (2)
(4) Of all the lattice vectors, none is shorter than a.
(5) Of those not directed along a, none is shorter than b.
(6) Of those not lying in the ab plane, none is shorter than c.
(7) The three angles between the basis vectors a, b and c are
either all acute (<90\%) or all obtuse (≥90\%)."
These rules do not produce a unique result that is stable under
the assumption of experimental errors, and the the resulting cell
may not be primitive.
In this coordinate system, the vector (.5, .5, .5) is in the middle
of the given unit cell.
Grid coordinates are an important variation on fractional coordinates
used when working with maps. In imgCIF, the conversion from
fractional to grid coordinates is implicit in the array indexing
specified by _array_structure_list.dimension. Note that this
implicit grid-coordinate scheme is 1-based, not zero-based, i.e.
the origin of the cell for axes along the cell edges with no
specified _array_structure_list_axis.displacement will have
grid coordinates of (1,1,1), i.e. array indices of (1,1,1).
THE ORTHOGONAL CARTESIAN COORDINATE SYSTEM (REAL SPACE)
The orthogonal Cartesian coordinate system is a transformation of
the direct lattice to the actual physical coordinates of atoms in
space. It is similar to the laboratory coordinate system, but
is anchored to and moves with the crystal, rather than being
schored to the laboratory. The transformation from fractional
to orthogonal cartesian coordinates is given by the
_atom_sites.Cartn_transf_matrix[i][j] and
_atom_sites.Cartn_transf_vector[i]
tags. A common choice for the matrix of the transformation is
given in the 1992 PDB format document
| a b cos(\g) c cos(\b) |
| 0 b sin(\g) c (cos(\a) - cos(\b)cos(\g))/sin(\g) |
| 0 0 V/(a b sin(\g)) |
This is a convenient coordinate system in which to do fitting
of models to maps and in which to understand the chemistry of
a molecule.
THE RECIPROCAL LATTICE
The reciprocal lattice coordinate system is used for diffraction
intensitities. It is based on the reciprocal cell, the dual of the cell,
in which reciprocal cell edges are derived from direct cell faces:
a* = bc sin(\a)/V b* = ac sin(\b)/V c* = ab sin(\g)/V
cos(\a*) = (cos(\b) cos(\g) - cos(\a))/(sin(\b) sin(\g))
cos(\b*) = (cos(\a) cos(\g) - cos(\b))/(sin(\a) sin(\g))
cos(\g*) = (cos(\a) cos(\b) - cos(\g))/(sin(\a) sin(\b))
V = abc SQRT(1 - cos(\a)^2^
- cos(\b)^2^
- cos(\g)^2^
+ 2 cos(\a) cos(\b) cos(\g) )
In this form the dimensions of the reciprocal lattice are in reciprocal
\%Angstroms (\%A^-1^). A dimensionless form can be obtained by
multiplying by the wavelength. Reflections are commonly indexed against
this coordinate system as (h, k, l) triples.
References:
Drenth, J., "Introduction to basic crystallography." chapter
2.1 in Rossmann, M. G. and Arnold, E. "Crystallography of
biological macromolecules", Volume F of the IUCr's "International
tables for crystallography", Kluwer, Dordrecht 2001, pp 44 -- 63
Leslie, A. G. W. and Powell, H. (2004). MOSFLM v6.11.
MRC Laboratory of Molecular Biology, Hills Road, Cambridge, England.
http://www.CCP4.ac.uk/dist/X-windows/Mosflm/.
Stout, G. H. and Jensen, L. H., "X-ray structure determination",
2nd ed., Wiley, New York, 1989, 453 pp.
__, "PROTEIN DATA BANK ATOMIC COORDINATE AND BIBLIOGRAPHIC ENTRY
FORMAT DESCRIPTION," Brookhaven National Laboratory, February 1992.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
'_axis.variant'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
This example shows the axis specification of the axes of a kappa-
geometry goniometer [see Stout, G. H. & Jensen, L. H. (1989). X-ray
structure determination. A practical
guide, 2nd ed. p. 134. New York: Wiley Interscience].
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X axis. The next innermost axis, kappa,
is at a 50 degree angle to the X axis, pointed away from the source.
The innermost axis, phi, aligns with the X axis when omega and
phi are at their zero points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
X' = (T-omega) (T-kappa) (T-phi) X
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 -
This example shows the axis specification of the axes of a
detector, source and gravity. The order has been changed as a
reminder that the ordering of presentation of tokens is not
significant. The centre of rotation of the detector has been taken
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 3 -
This example show the axis specification of the axes for a map,
using fractional coordinates. Each cell edge has been divided
into a grid of 50 divisions in the ARRAY_STRUCTURE_LIST_AXIS
category. The map is using only the first octant of the grid
in the ARRAY_STRUCTURE_LIST category.
The fastest changing axis is the gris along A, then along B,
and the slowest is along C.
The map sampling is being done in the middle of each grid
division
;
;
loop_
_axis.id_axis.system_axis.vector[1]_axis.vector[2]_axis.vector[3]
CELL_A_AXIS fractional 1 0 0
CELL_B_AXIS fractional 0 1 0
CELL_C_AXIS fractional 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing CELL_A_AXIS
MAP 1 25 2 increasing CELL_B_AXIS
MAP 1 25 3 increasing CELL_C_AXIS
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.fract_displacement
_array_structure_list_axis.fract_displacement_increment
CELL_A_AXIS 0.01 0.02
CELL_B_AXIS 0.01 0.02
CELL_C_AXIS 0.01 0.02
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 4 -
This example show the axis specification of the axes for a map,
this time as orthogonal \%Angstroms, using the same coordinate system
as for the atomic coordinates. The map is sampling every 1.5
\%Angstroms (1.5e-7 millimeters) in a map segment 37.5 \%Angstroms on
a side.
;
;
loop_
_axis.id_axis.system_axis.vector[1]_axis.vector[2]_axis.vector[3]
X orthogonal 1 0 0
Y orthogonal 0 1 0
Z orthogonal 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing X
MAP 2 25 2 increasing Y
MAP 3 25 3 increasing Z
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
X 7.5e-8 1.5e-7
Y 7.5e-8 1.5e-7
Z 7.5e-8 1.5e-7
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.depends_on specifies the next outermost
axis upon which this axis depends.
This item is a pointer to _axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.equipment specifies the type of
equipment using the axis: 'goniometer', 'detector',
'gravity', 'source' or 'general'.
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.system
_item_description.description
; The value of _axis.system specifies the coordinate
system used to define the axis: 'laboratory', 'direct',
'orthogonal', 'reciprocal' or 'abstract'.
;
_item.name '_axis.system'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value laboratory
loop_
_item_enumeration.value
_item_enumeration.detail
laboratory
; the axis is referenced to the imgCIF standard laboratory Cartesian
coordinate system
;
direct
; the axis is referenced to the direct lattice
;
orthogonal
; the axis is referenced to the cell Cartesian orthogonal coordinates
;
reciprocal
; the axis is referenced to the reciprocal lattice
;
abstract
; the axis is referenced to abstract Cartesian cooridinate system
;
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: 'rotation' or 'translation' (or 'general' when
the type is not relevant, as for gravity).
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.variant
_item_description.description
; The value of _axis.variant gives the variant
to which the given axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_axis.variant'
_item.category_id axis
_item.mandatory_code no
_item_type.code code
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
; Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
'_diffrn_data_frame.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element are
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id.
;
;
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.center_fast
_item_description.description
; The value of _diffrn_data_frame.center_fast is
the fast index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_data_frame.center_units' along the fast
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement the current setting of detector
positioner given frame are used.
It is important to note that for measurements in millimetres,
the sense of the axis is used, rather than the sign of the
pixel-to-pixel increments.
;
_item.name '_diffrn_data_frame.center_fast'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_data_frame.center_slow
_item_description.description
; The value of _diffrn_data_frame.center_slow is
the slow index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_data_frame.center_units' along the slow
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement the current setting of detector
positioner given frame are used.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
;
_item.name '_diffrn_data_frame.center_slow'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_data_frame.center_units
_item_description.description
; The value of _diffrn_data_frame.center_units
specifies the units in which the values of
'_diffrn_data_frame.center_fast' and
'_diffrn_data_frame.center_slow'
are presented. The default is 'mm' for millimetres. The
alternatives are 'pixels' and 'bins'. In all cases the
center distances are measured from the center of the
first pixel, i.e. in a 2x2 binning, the measuring origin
is offset from the centers of the bins by one half pixel
towards the first pixel.
If 'bins' is specified, the data in
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size', and
'_array_intensities.pixel_binning_method'
is used to define the binning scheme.
;
_item.name '_diffrn_data_frame.center_units'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
mm 'millimetres'
pixels 'detector pixels'
bins 'detector bins'
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.id
_item_description.description
; The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
'_diffrn_scan_frame_monitor.frame_id'
diffrn_scan_frame_monitor
implicit
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
'_diffrn_scan_frame_monitor.frame_id'
'_diffrn_data_frame.id'
save_
save__diffrn_data_frame.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
This is an appropriate location in which to record
information from vendor headers as presented in those
headers, but it should never be used as a substitute
for providing the fully parsed information within
the appropriate imgCIF/CBF categories.
Normally, when a conversion from a miniCBF has been done
the data from '_array_data.header_convention'
should be transferred to this data item and
'_array_data.header_convention'
should be removed.
;
_item.name '_diffrn_data_frame.details'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_frame_data.details'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.4
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
;
HEADER_BYTES = 512;
DIM = 2;
BYTE_ORDER = big_endian;
TYPE = unsigned_short;
SIZE1 = 3072;
SIZE2 = 3072;
PIXEL_SIZE = 0.102588;
BIN = 2x2;
DETECTOR_SN = 901;
TIME = 29.945155;
DISTANCE = 200.000000;
PHI = 85.000000;
OSC_START = 85.000000;
OSC_RANGE = 1.000000;
WAVELENGTH = 0.979381;
BEAM_CENTER_X = 157.500000;
BEAM_CENTER_Y = 157.500000;
PIXEL SIZE = 0.102588;
OSCILLATION RANGE = 1;
EXPOSURE TIME = 29.9452;
TWO THETA = 0;
BEAM CENTRE = 157.5 157.5;
;
; Example of header information extracted from an ADSC Quantum
315 detector header by CBFlib_0.7.6. Image provided by Chris
Nielsen of ADSC from a data collection at SSRL beamline 1-5.
;
save_
save__diffrn_data_frame.variant
_item_description.description
; The value of _diffrn_data_frame.variant gives the variant
to which the given diffrn_data_frame row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_data_frame.variant'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code code
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
'_diffrn_detector.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'slow mode'
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detector(s) used to
measure the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
; The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of
_diffrn_detector.diffrn_id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
'_diffrn_scan_frame_monitor.detector_id'
diffrn_scan_frame_monitor yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
'_diffrn_scan_frame_monitor.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
; The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id.
The word 'positioner' is a general term used in
instrumentation design for devices that are used to change
the positions of portions of apparatus by linear
translation, rotation or combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__diffrn_detector.variant
_item_description.description
; The value of _diffrn_detector.variant gives the variant
to which the given diffrn_detector row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_detector.variant'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_type.code code
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
; Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
'_diffrn_detector_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named _diffrn_detector_axis.id
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_detector_axis.variant
_item_description.description
; The value of _diffrn_detector_axis.variant gives the variant
to which the given diffrn_detector_axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_detector_axis.variant'
_item.category_id diffrn_detector_axis
_item.mandatory_code no
_item_type.code code
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
; Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, giving more detailed information
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
is preferable to simply providing the centre of the
detector element.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
'_diffrn_detector_element.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square, in the pattern
1 2
*
3 4
Note that the beam centre is slightly displaced from each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4. For each element, the detector
face coordiate system, is assumed to have the fast axis
running from left to right and the slow axis running from
top to bottom with the origin at the top left corner.
;
;
loop_
_diffrn_detector_element.detector_id_diffrn_detector_element.id_diffrn_detector_element.reference_center_fast_diffrn_detector_element.reference_center_slow_diffrn_detector_element.reference_center_units
d1 d1_ccd_1 201.5 201.5 mm
d1 d1_ccd_2 -1.8 201.5 mm
d1 d1_ccd_3 201.6 -1.4 mm
d1 d1_ccd_4 -1.7 -1.5 mm
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.id
_item_description.description
; The value of _diffrn_detector_element.id must uniquely
identify each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
; This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_element.reference_center_fast
_item_description.description
; The value of _diffrn_detector_element.reference_center_fast is
the fast index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_detector_element.reference_center_units' along the fast
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value given whould be
representive of the beam center as determined from the ensemble
of settings.
It is important to note that for measurements in millimetres,
the sense of the axis is used, rather than the sign of the
pixel-to-pixel increments.
;
_item.name '_diffrn_detector_element.reference_center_fast'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_detector_element.reference_center_slow
_item_description.description
; The value of _diffrn_detector_element.reference_center_slow is
the slow index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_detector_element.reference_center_units' along the slow
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value givien whould be
representive of the beam center as determined from the ensemble
of settings.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
;
_item.name '_diffrn_detector_element.reference_center_slow'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_detector_element.reference_center_units
_item_description.description
; The value of _diffrn_detector_element.reference_center_units
specifies the units in which the values of
'_diffrn_detector_element.reference_center_fast' and
'_diffrn_detector_element.reference_center_slow'
are presented. The default is 'mm' for millimetres. The
alternatives are 'pixels' and 'bins'. In all cases the
center distances are measured from the center of the
first pixel, i.e. in a 2x2 binning, the measuring origin
is offset from the centers of the bins by one half pixel
towards the first pixel.
If 'bins' is specified, the data in
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size', and
'_array_intensities.pixel_binning_method'
is used to define the binning scheme.
;
_item.name '_diffrn_detector_element.reference_center_units'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
mm 'millimetres'
pixels 'detector pixels'
bins 'detector bins'
save_
save__diffrn_detector_element.variant
_item_description.description
; The value of _diffrn_detector_element.variant gives the variant
to which the given diffrn_detector_element row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_detector_element.variant'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code code
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the
diffraction data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
'_diffrn_measurement.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model X'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector
angle 22.5 degrees
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support
and orient the specimen.
If the value of _diffrn_measurement.device is not given,
it is implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to
measure the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'home-made'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity
measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
; The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during the collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
; The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id.
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
# _diffrn_measurement.sample_detector_distance
# _diffrn_measurement.sample_detector_voffset
save__diffrn_measurement.sample_detector_distance
_item_description.description
; The value of _diffrn_measurement.sample_detector_distance gives
the unsigned distance in millimetres from the sample to the
detector along the beam.
;
_item.name '_diffrn_measurement.sample_detector_distance'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
_item_type.code float
_item_units.code mm
save_
save__diffrn_measurement.sample_detector_voffset
_item_description.description
; The value of _diffrn_measurement.sample_detector_voffset gives
the signed distance in millimetres in the vertical
direction (positive for up) from the center of
the beam to the center of the detector.
;
_item.name '_diffrn_measurement.sample_detector_voffset'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . .
. .
_item_type.code float
_item_units.code mm
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
save__diffrn_measurement.variant
_item_description.description
; The value of _diffrn_measurement.variant gives the variant
to which the given diffrn_measurement row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_measurement.variant'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_type.code code
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
; Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
'_diffrn_measurement_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
; This data item is a pointer to _diffrn_measurement.device
in the DIFFRN_MEASUREMENT category.
;
_item.name
'_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_type.code text
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named _diffrn_measurement_axis.id,
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_measurement_axis.variant
_item_description.description
; The value of _diffrn_measurement_axis.variant gives the variant
to which the given diffrn_measurement_axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_measurement_axis.variant'
_item.category_id diffrn_measurement_axis
_item.mandatory_code no
_item_type.code code
save_
####################
# DIFFRN_RADIATION #
####################
save_DIFFRN_RADIATION
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used for measuring diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
loop_
_category_key.name '_diffrn_radiation.diffrn_id'
'_diffrn_radiation.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions of
photons in the XZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions
of photons in the YZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation degrees^2^ between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
direction of each photon in XZ plane times the deviations
of the direction of the same photon in the YZ plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons, this value is specified in
milliradians^2^, in which case a conversion would be needed.
To go from a value in milliradians^2^ to a value in
degrees^2^, multiply by 0.180^2^ and divide by \p^2^.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in \%Angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a
monochromator crystal is used, the material and the
indices of the Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarization ratio of the diffraction beam incident on the
crystal. This is the ratio of the perpendicularly polarized to
the parallel polarized component of the radiation. The
perpendicular component forms an angle of
_diffrn_radiation.polarisn_norm to the normal to the
diffraction plane of the sample (i.e. the plane containing
the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between
the normal to the polarization plane and the laboratory Y
axis as defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monochromater.
This differs from the value of
_diffrn_radiation.polarisn_norm
in that _diffrn_radiation.polarisn_norm refers to
polarization relative to the diffraction plane rather than
to the laboratory axis system.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane should be taken
as the XZ plane and the angle as 0.
See _diffrn_radiation.polarizn_source_ratio.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared)
of the electric vector in the plane of the normal to the
plane of polarization.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane is to be taken
as the XZ plane and the normal is parallel to the Y axis.
Thus, if there was complete polarization in the plane of
polarization, the value of
_diffrn_radiation.polarizn_source_ratio would be 1, and
for an unpolarized beam
_diffrn_radiation.polarizn_source_ratio would have a
value of 0.
If the X axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of 'MONOCHROMATOR' in the Denzo glossary, and values of near
1 should be expected for a bending-magnet source. However,
if the X axis were perpendicular to the polarization plane
(not a common choice), then the Denzo value would be the
negative of _diffrn_radiation.polarizn_source_ratio.
See http://www.hkl-xray.com for information on Denzo and
Otwinowski & Minor (1997).
This differs both in the choice of ratio and choice of
orientation from _diffrn_radiation.polarisn_ratio, which,
unlike _diffrn_radiation.polarizn_source_ratio, is
unbounded.
Reference: Otwinowski, Z. & Minor, W. (1997). 'Processing of
X-ray diffraction data collected in oscillation mode.' Methods
Enzymol. 276, 307-326.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly
recommended that this be given so that the
probe radiation is clearly specified.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'X-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for the probe
radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to
_diffrn_radiation_wavelength.id in the
DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.category_id diffrn_radiation
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_radiation.variant
_item_description.description
; The value of _diffrn_radiation.variant gives the variant
to which the given diffrn_radiation row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_radiation.variant'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code code
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
; This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
Data items in the DIFFRN_REFLN category record details about
the intensities in the diffraction data set
identified by _diffrn_refln.diffrn_id.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in the particular diffraction
data set identified by _diffrn_reflns.diffrn_id and
_diffrn_refln.frame_id
;
_category.id diffrn_refln
_category.mandatory_code no
loop_
_category_key.name '_diffrn_refln.diffrn_id'
'_diffrn_refln.id'
'_diffrn_refln.frame_id'
'_diffrn_refln.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
; This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_refln.variant
_item_description.description
; The value of _diffrn_refln.variant gives the variant
to which the given diffrn_refln row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_refln.variant'
_item.category_id diffrn_refln
_item.mandatory_code no
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
; Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
loop_
_category_key.name '_diffrn_scan.id'
'_diffrn_scan.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. In this example, three rotation axes and one translation axis
at nonzero values are specified, with one axis stepping. There is no
reason why more axes could not have been specified to step. Range
information has been specified, but note that it can be calculated from
the number of frames and the increment, so the data item
_diffrn_scan_axis.angle_range could be dropped.
Both the sweep data and the data for a single frame are specified.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
_diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
_diffrn_scan_frame.integration_time and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustments are made to
scan times and nonlinear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.angle_increment_diffrn_scan_frame_axis.displacement_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
; Example 2 - a more extensive example (R. M. Sweet, P. J. Ellis &
H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the goniometer.
This leads to a choice: either the axes of
the detector are defined at the origin, and then a Z setting of -240
is entered, or the axes are defined with the necessary Z offset.
In this case, the setting is used and the offset is left as zero.
This axis is called DETECTOR_Z.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm X 0.150mm, the centre of the first pixel is at (0.075,
0.075) in this coordinate system.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.displacement_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
; Example 3 - Example 2 revised for a spiral scan (R. M. Sweet,
P. J. Ellis & H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the
goniometer, as in Example 2 above, but in this example the
image plate is scanned in a spiral pattern from the outside edge in.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. The rotation axis is called ELEMENT_ROT and the
radial axis is called ELEMENT_RAD. A 150 micrometre radial pitch
and a 75 micrometre 'constant velocity' angular pitch are assumed.
Indexing is carried out first on the rotation axis and the radial axis
is made to be dependent on it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.angle_array_structure_list_axis.displacement_array_structure_list_axis.angular_pitch_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
; The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
; The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
; Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
_diffrn_scan_frame.integration_time, even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
; The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frame_id_end
_item_description.description
; The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frames
_item_description.description
; The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
save__diffrn_scan.time_period
_item_description.description
; Approximate average time in seconds between the start
of each step of the scan. The precise start-to-start
time increment of each particular step may be provided in
_diffrn_scan_frame.time_period.
;
_item.name '_diffrn_scan.time_period'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.time_rstrt_incr
_item_description.description
; Approximate average time in seconds between the end
of integration of each step of the scan than the start
of integration of the next step.
In general, this will agree with
_diffrn_scan_frame.time_rstrt_incr. The
sum of the values of _diffrn_scan_frame.integration_time
and _diffrn_scan_frame.time_rstrt_incr is the
time from the start of integration of one frame and the start of
integration for the next frame and should equal the value of
_diffrn_scan_frame.time_period for this
frame. If the individual frame values vary, then the value of
_diffrn_scan.time_rstrt_incr will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.time_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan.time_period'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.variant
_item_description.description
; The value of _diffrn_scan.variant gives the variant
to which the given diffrn_scan row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan.variant'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code code
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
; Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
'_diffrn_scan_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
; The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.angle_start
_item_description.description
; The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
; The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
; The increment for each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_increment. The
sum of the values of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
; The increment after each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_rstrt_incr. The
sum of the values of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment
and _diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.angle for this
next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
; The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
; The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_increment.
The sum of the values of
_diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_rstrt_incr.
The sum of the values of
_diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.displacement
for this next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_angle.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_angle will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_angle (e.g.
the mean).
If not specified, the value defaults to zero.
;
_item.name '_diffrn_scan_axis.reference_angle'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_displacement.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_displacement will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_displacement (e.g.
the mean).
If not specified, the value defaults to to the value of
_diffrn_scan_axis.displacement.
;
_item.name '_diffrn_scan_axis.reference_displacement'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.variant
_item_description.description
; The value of _diffrn_scan_axis.variant gives the variant
to which the given diffrn_scan_axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_axis.variant'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_type.code code
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
; Data items in the DIFFRN_SCAN_FRAME category describe
the relationships of particular frames to scans.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
'_diffrn_scan_frame.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
; The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame.frame_number
_item_description.description
; The value of this data item is the number of the frame
within the scan, starting with 1. It is not necessarily
the same as the value of _diffrn_scan_frame.frame_id,
but it may be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
; The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of _diffrn_scan.integration_time.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame.time_period
_item_description.description
; The time in seconds between the start of this frame and the
start of the next frame, if any. If there is no next frame,
a null value should be given.
;
_item.name '_diffrn_scan_frame.time_period'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.time_rstrt_incr
_item_description.description
; The time in seconds between the end of integration of this step of the scan
and the start of integration of the next step.
The sum of the values of _diffrn_scan_frame.integration_time
and _diffrn_scan_frame.time_rstrt_incr is the
time from the start of integration of one frame and the start of
integration for the next frame and should equal the value of
_diffrn_scan_frame.time_period for this
frame. The value of _diffrn_scan.time_rstrt_incr will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.time_rstrt_incr (e.g.
the mean).
If there is no next frame, a null value should be given.
;
_item.name '_diffrn_scan.time_period'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.variant
_item_description.description
; The value of _diffrn_scan_frame.variant gives the variant
to which the given diffrn_scan_frame row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_frame.variant'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code code
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
; Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the
settings of axes for particular frames. Unspecified axes are
assumed to be at their zero points. If, for any given frame,
nonzero values apply for any of the data items in this category,
those values should be given explicitly in this category and not
simply inferred from values in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
'_diffrn_scan_frame_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
; The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
; The increment for this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
; The increment after this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment and
_diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.angle for this next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.displacement for this next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be zero.
;
_item.name '_diffrn_scan_frame_axis.reference_angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be equal to
_diffrn_scan_frame_axis.displacement.
;
_item.name '_diffrn_scan_frame_axis.reference_displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.variant
_item_description.description
; The value of _diffrn_scan_frame_axis.variant gives the variant
to which the given diffrn_scan_frame_axis row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_frame_axis.variant'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_type.code code
save_
#############################
# DIFFRN_SCAN_FRAME_MONITOR #
#############################
save_DIFFRN_SCAN_FRAME_MONITOR
_category.description
; Data items in the DIFFRN_SCAN_FRAME_MONITOR category record
the values and details about each monitor for each frame of data
during a scan.
Each monitor value is uniquely identified by the combination of
the scan_id given by _diffrn_scan_frame.scan_id
the frame_id given by _diffrn_scan_frame_monitor.frame_id,
the monitor's detector_id given by
_diffrn_scan_frame_monitor.monitor_id,
and a 1-based ordinal given by _diffrn_scan_frame_monitor.id.
If there is only one frame for the scan, the value of
_diffrn_scan_frame_monitor.frame_id may be
omitted.
A single frame may have more than one monitor value, and each
monitor value may be the result of integration over the entire
frame integration time given by the value of
_diffrn_scan_frame.integration_time
or many monitor values may be reported over shorter times given
by the value of _diffrn_scan_frame_monitor.integration_time. If
only one monitor value for a given monitor is collected during
the integration time of the frame, the value of
_diffrn_scan_frame_monitor.id may be
omitted.
;
_category.id diffrn_data_frame_monitor
_category.mandatory_code no
loop_
_category_key.name '_diffrn_scan_frame_monitor.id'
'_diffrn_scan_frame_monitor.detector_id'
'_diffrn_scan_frame_monitor.scan_id'
'_diffrn_data_frame_monitor.frame_id'
'_diffrn_data_frame_monitor.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - The beam intensity for frame FRAME1 is being tracked
by a beamstop monitor detector BSM01, made from metal foil and
a PIN diode, locate 20 mm in front of a MAR345 detector and being
sampled every 2 seconds in a 20 second scan.
;
;
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
P6MB BSM01 'metal foil and PIN diode' 1
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
BSM01 MONITOR_Z
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
SCAN1 MONITOR_Z 0.0 0.0 0.0 -220.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_MONITOR
loop_
_diffrn_scan_frame_monitor.id_diffrn_scan_frame_monitor.detector_id_diffrn_scan_frame_monitor.scan_id_diffrn_data_frame_monitor.frame_id_diffrn_data_frame_monitor.integration_time_diffrn_data_frame_monitor.monitor_value
1 BSM01 SCAN1 FRAME1 2.0 23838345642
2 BSM01 SCAN1 FRAME1 2.0 23843170669
3 BSM01 SCAN1 FRAME1 2.0 23839478690
4 BSM01 SCAN1 FRAME1 2.0 23856642085
5 BSM01 SCAN1 FRAME1 2.0 23781717656
6 BSM01 SCAN1 FRAME1 2.0 23788850775
7 BSM01 SCAN1 FRAME1 2.0 23815576677
8 BSM01 SCAN1 FRAME1 2.0 23789299964
9 BSM01 SCAN1 FRAME1 2.0 23830195536
10 BSM01 SCAN1 FRAME1 2.0 23673082270
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
FRAME1 MONITOR_Z 0.0 -220.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
MONITOR_Z translation detector . 0 0 1 0 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan_frame_monitor.id
_item_description.description
; This item is an integer identifier which, along with
_diffrn_scan_frame_monitor.detector_id,
_diffrn_scan_frame_monitor.scan_id, and
_diffrn_data_frame_monitor.frame_id
should uniquely identify the monitor value being recorded
If _array_data.binary_id is not explicitly given,
it defaults to 1.
;
loop_
_item.name '_diffrn_scan_frame_monitor.id'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code implicit
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__diffrn_scan_frame_monitor.detector_id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_scan_frame_monitor.detector_id'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_monitor.frame_id
_item_description.description
; This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_monitor.frame_id'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_monitor.integration_time
_item_description.description
; The precise time for integration of the monitor value given in
_diffrn_scan_frame_monitor.value
must be given in _diffrn_scan_frame_monitor.integration_time.
;
_item.name '_diffrn_scan_frame_monitor.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame_monitor.value
_item_description.description
; The value reported by the monitor detector should be given in
_diffrn_scan_frame_monitor.value.
The value is typed as float to allow of monitors for very intense beams
that cannot report all digits, but when available, all digits of the
monitor should be recorded.
;
_item.name '_diffrn_scan_frame_monitor.value'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame_monitor.variant
_item_description.description
; The value of _diffrn_scan_frame_monitor.variant gives the variant
to which the given diffrn_scan_frame_monitor row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_frame_monitor.variant'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code no
_item_type.code code
save_
#######
# MAP #
#######
save_MAP
_category.description
; Data items in the MAP category record
the details of a maps. Maps record values of parameters,
such as density, that are functions of position within
a cell or are functions of orthogonal coordinates in
three space.
A map may is composed of one or more map segments
specified in the MAP_SEGMENT category.
Examples are given in the MAP_SEGMENT category.
;
_category.id map
_category.mandatory_code no
loop_
_category_key.name '_map.id'
'_map.diffrn_id'
'_map.entry_id'
'_map.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'map_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.details
_item_description.description
; The value of _map.details should give a
description of special aspects of each map.
;
_item.name '_map.details'
_item.category_id map
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.diffrn_id
_item_description.description
; This item is a pointer to _diffrn.id in the
DIFFRN category.
;
_item.name '_map.diffrn_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.entry_id
_item_description.description
; This item is a pointer to _entry.id in the
ENTRY category.
;
_item.name '_map.entry_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.id
_item_description.description
; The value of _map.id must uniquely identify
each map for the given diffrn.id or entry.id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map.id' map yes
'_map_segment.id' map_segment yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_segment.id' '_map.id'
save_
save__map.variant
_item_description.description
; The value of _map.variant gives the variant
to which the given map row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_map.variant'
_item.category_id map
_item.mandatory_code no
_item_type.code code
save_
###############
# MAP_SEGMENT #
###############
save_MAP_SEGMENT
_category.description
; Data items in the MAP_SEGMENT category record
the details about each segment (section or brick) of a map.
;
_category.id map_segment
_category.mandatory_code no
loop_
_category_key.name '_map_segment.id'
'_map_segment.map_id'
'_map_segment.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'map_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map, each consisting of one
segment, both using the same array structure
and mask.
;
;
loop_
_map.id_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
loop_
_map_segment.map_id
_map_segment.id
_map_segment.array_id
_map_segment.binary_id
_map_segment.mask_array_id
_map_segment.mask_binary_id
rho_calc rho_calc map_structure 1 mask_structure 1
rho_obs rho_obs map_structure 2 mask_structure 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map_segment.array_id
_item_description.description
; The value of _map_segment.array_id identifies the array
structure into which the map is organized.
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.array_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code code
save_
save__map_segment.binary_id
_item_description.description
; The value of _map_segment.binary_id distinguishes the particular
set of data organized according to _map_segment.array_id in
which the data values of the map are stored.
This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.mask_array_id
_item_description.description
; The value of _map_segment.mask_array_id, if given, the array
structure into which the mask for the map is organized. If no
value is given, then all elements of the map are valid. If a
value is given, then only elements of the map for which the
corresponding element of the mask is non-zero are valid. The
value of _map_segment.mask_array_id differs from the value of
_map_segment.array_id in order to permit the mask to be given
as, say, unsigned 8-bit integers, while the map is given as
a data type with more range. However, the two array structures
must be aligned, using the same axes in the same order with the
same displacements and increments
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.mask_array_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code code
save_
save__map_segment.mask_binary_id
_item_description.description
; The value of _map_segment.mask_binary_id identifies the
particular set of data organized according to
_map_segment.mask_array_id specifying the mask for the map.
This item is a pointer to _array_data.mask_binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.mask_binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.id
_item_description.description
; The value of _map_segment.id must uniquely
identify each segment of a map.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map_segment.id'
map_segment
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_data_frame.map_segment_id'
'_map_segment.id'
save_
save__map_segment.map_id
_item_description.description
; This item is a pointer to _map.id
in the MAP category.
;
_item.name '_map_segment.map_id'
_item.category_id map_segment
_item.mandatory_code yes
_item_type.code code
save_
save__map_segment.details
_item_description.description
; The value of _map_segment.details should give a
description of special aspects of each segment of a map.
;
_item.name '_map_segment.details'
_item.category_id map_segment
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
; Example to be provided
;
;
;
save_
save__map_segment.variant
_item_description.description
; The value of _map_segment.variant gives the variant
to which the given map segment is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_map_segment.variant'
_item.category_id map_segment
_item.mandatory_code no
_item_type.code code
save_
###########
# VARIANT #
###########
save_VARIANT
_category.description
; Data items in the VARIANT category record
the details about sets of variants of data items.
There is sometimes a need to allow for multiple versions of the
same data items in order to allow for refinements and corrections
to earlier assumptions, observations and calculations. In order
to allow data sets to contain more than one variant of the same
information, an optional ...variant data item as a pointer to
_variant.variant has been added to the key of every category,
as an implicit data item with a null (empty) default value.
All rows in a category with the same variant value are considered
to be related to one another and to all rows in other categories
with the same variant value. For a given variant, all such rows
are also considered to be related to all rows with a null variant
value, except that a row with a null variant value is for which
all other components of its key are identical to those entries
in another row with a non-null variant value is not related the
the rows with that non-null variant value. This behavior is
similar to the convention for identifying alternate conformers
in an atom list.
An optional role may be specified for a variant as the value of
_variant.role. Possible roles are null, "preferred",
"raw data", "unsuccessful trial".
Variants may carry an optional timestamp as the value of
_variant.timestamp.
Variants may be related to other variants from which they were
derived by the value of _variant.variant_of
Further details about the variant may be specified as the value
of _variant.details.
In order to allow variant information from multiple datasets to
be combined, _variant.diffrn_id and/or _variant.entry_id may
be used.
;
_category.id variant
_category.mandatory_code no
loop_
_category_key.name '_variant.variant'
'_variant.diffrn_id'
'_variant.entry_id'
loop_
_category_group.id 'inclusive_group'
'variant_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Distinguishing between a raw beam center and a refined beam
center inferred after indexing. Detector d1 is composed of
four CCD detector elements, each 200 mm by 200 mm, arranged
in a square, in the pattern
1 2
*
3 4
Note that the beam centre is slightly displaced from each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4. For each element, the detector
face coordiate system, is assumed to have the fast axis
running from left to right and the slow axis running from
top to bottom with the origin at the top left corner.
After indexing and refinement, the center is shifted by .2 mm
left and .1 mm down.
;
;
loop_
_variant.variant
_variant.role
_variant.timestamp
_variant.variant_of
_variant.details
. "raw data" 2007-08-03T23:20:00 . .
indexed "preferred" 2007-08-04T01:17:28 .
"indexed cell and refined beam center"
loop_
_diffrn_detector_element.detector_id_diffrn_detector_element.id_diffrn_detector_element.reference_center_fast_diffrn_detector_element.reference_center_slow_diffrn_detector_element.reference_center_units_diffrn_detector_element.variant
d1 d1_ccd_1 201.5 201.5 mm .
d1 d1_ccd_2 -1.8 201.5 mm .
d1 d1_ccd_3 201.6 -1.4 mm .
d1 d1_ccd_4 -1.7 -1.5 mm .
d1 d1_ccd_1 201.3 201.6 mm indexed
d1 d1_ccd_2 -2.0 201.6 mm indexed
d1 d1_ccd_3 201.3 -1.5 mm indexed
d1 d1_ccd_4 -1.9 -1.6 mm indexed
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__variant.details
_item_description.description
; A description of special aspects of the variant.
;
_item.name '_variant.details'
_item.category_id variant
_item.mandatory_code no
_item_type.code text
_item_examples.case
; indexed cell and refined beam center
;
save_
save__variant.role
_item_description.description
; The value of _variant.role specified a role
for this variant. Possible roles are null, "preferred",
"raw data", and "unsuccessful trial".
;
_item.name '_variant.role'
_item.category_id variant
_item.mandatory_code no
_item_type.code uline
loop_
_item_enumeration.value
_item_enumeration.detail
.
; A null value for _variant.role leaves the precise role of
the variant unspecified. No inference should be made that the variant
with the latest time stamp is preferred.
;
"preferred"
; A value of "preferred" indicates that rows of any categories specifying
this variant should be used in preference to rows with the same key
specifying other variants or the null variant. It is an error to specify
two variants that appear in the same category with the same key as being
preferred, but it is not an error to specify more than one variant as
preferred in other cases.
;
"raw data"
; A value of "raw data" indicates data prior to any corrections,
calculations or refinements. It is not necessarily an error for raw data
to also be a variant of an earlier variant. It may be replacement raw
data for earlier data believed to be erroneous.
;
"unsuccessful trial"
; A value of "unsuccessful trial" indicates data that should not be used
for further calculation.
;
save_
save__variant.timestamp
_item_description.description
; The date and time identifying a variant. This is not
necessarily the precise time of the measurement or calculation
of the individual related data items, but a timestamp that
reflects the order in which the variants were defined.
;
_item.name '_variant.timestamp'
_item.category_id variant
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__variant.variant
_item_description.description
; The value of _variant.variant must uniquely identify
each variant for the given diffraction experiment and/or entry
This item has been made implicit and given a default value of
null.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_variant.variant' variant implicit
'_variant.variant_of' variant implicit
'_array_data.variant' array_data implicit
'_array_element_size.variant' array_element_size implicit
'_array_intensities.variant' array_intensities implicit
'_array_structure.variant' array_structure implicit
'_array_structure_list.variant' array_structure_list
implicit
'_array_structure_list_axis.variant' array_structure_list_axis
implicit
'_axis.variant' axis implicit
'_diffrn_data_frame.variant' diffrn_data_frame implicit
'_diffrn_detector.variant' diffrn_detector implicit
'_diffrn_detector_axis.variant' diffrn_detector_axis
implicit
'_diffrn_detector_element.variant' diffrn_detector_element
implicit
'_diffrn_measurement.variant' diffrn_measurement implicit
'_diffrn_measurement_axis.variant' diffrn_measurement_axis
implicit
'_diffrn_radiation.variant' diffrn_radiation implicit
'_diffrn_refln.variant' diffrn_refln implicit
'_diffrn_scan.variant' diffrn_scan implicit
'_diffrn_scan_axis.variant' diffrn_scan_axis implicit
'_diffrn_scan_frame.variant' diffrn_scan_frame implicit
'_diffrn_scan_frame_axis.variant' diffrn_scan_frame_axis
implicit
'_diffrn_scan_frame_monitor.variant' diffrn_scan_frame_monitor
implicit
'_map.variant' map implicit
'_map_segment.variant' map_segment implicit
_item_default.value .
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.variant' '_variant.variant'
'_array_data.variant_of' '_variant.variant'
'_array_element_size.variant' '_variant.variant'
'_array_intensities.variant' '_variant.variant'
'_array_structure.variant' '_variant.variant'
'_array_structure_list.variant' '_variant.variant'
'_array_structure_list_axis.variant' '_variant.variant'
'_axis.variant' '_variant.variant'
'_diffrn_data_frame.variant' '_variant.variant'
'_diffrn_detector.variant' '_variant.variant'
'_diffrn_detector_axis.variant' '_variant.variant'
'_diffrn_detector_element.variant' '_variant.variant'
'_diffrn_measurement.variant' '_variant.variant'
'_diffrn_measurement_axis.variant' '_variant.variant'
'_diffrn_radiation.variant' '_variant.variant'
'_diffrn_refln.variant' '_variant.variant'
'_diffrn_scan.variant' '_variant.variant'
'_diffrn_scan_axis.variant' '_variant.variant'
'_diffrn_scan_frame.variant' '_variant.variant'
'_diffrn_scan_frame_axis.variant' '_variant.variant'
'_diffrn_scan_frame_monitor.variant' '_variant.variant'
'_map.variant' '_variant.variant'
'_map_segment.variant' '_variant.variant'
save_
save__variant.variant_of
_item_description.description
; The value of _variant.variant_of gives the variant
from which this variant was derived. If this value is not given,
the variant is assumed to be derived from the default null
variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_variant.variant_of'
_item.category_id variant
_item.mandatory_code no
_item_type.code code
save_
######################## DEPRECATED DATA ITEMS ########################
save__diffrn_detector_axis.id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_detector_axis.id'
_item.category_id diffrn_detector_axis
_item.mandatory_code no
_item_type.code code
save_
save__diffrn_detector_element.center[1]
_item_description.description
; The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
Because of ambiguity about the setting used to determine this
center, use of this data item is deprecated. The data item
_diffrn_data_frame.center_fast
which is referenced to the detector coordinate system and not
directly to the laboratory coordinate system should be used
instead.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
; The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
Because of ambiguity about the setting used to determine this
center, use of this data item is deprecated. The data item
_diffrn_data_frame.center_slow
which is referenced to the detector coordinate system and not
directly to the laboratory coordinate system should be used
instead.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_measurement_axis.id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_measurement_axis.id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code no
_item_type.code code
save_
######################### DEPRECATED CATEGORY #########################
#####################
# DIFFRN_FRAME_DATA #
#####################
save_DIFFRN_FRAME_DATA
_category.description
; Data items in the DIFFRN_FRAME_DATA category record
the details about each frame of data.
The items in this category are now in the
DIFFRN_DATA_FRAME category.
The items in the DIFFRN_FRAME_DATA category
are now deprecated. The items from this category
are provided as aliases in the 1.0 dictionary
or, in the case of _diffrn_frame_data.details,
in the 1.4 dictionary. THESE ITEMS SHOULD NOT
BE USED FOR NEW WORK.
The items from the old category are provided
in this dictionary for completeness
but should not be used or cited. To avoid
confusion, the example has been removed
and the redundant parent-child links to other
categories have been removed.
All _item.mandatory_code values have been changed to no
;
_category.id diffrn_frame_data
_category.mandatory_code no
loop_
_category_key.name '_diffrn_frame_data.id'
'_diffrn_frame_data.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
THE DIFFRN_FRAME_DATA category is deprecated and should not be used.
;
;
# EXAMPLE REMOVED #
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_frame_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.array_id'
_item.category_id diffrn_frame_data
_item.mandatory_code no
_item_type.code code
save_
save__diffrn_frame_data.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.binary_id'
_item.category_id diffrn_frame_data
_item.mandatory_code no
_item_type.code int
save_
save__diffrn_frame_data.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.detector_element_id'
_item.category_id diffrn_frame_data
_item.mandatory_code no
_item_type.code code
save_
save__diffrn_frame_data.id
_item_description.description
; The value of _diffrn_frame_data.id must uniquely identify
each complete frame of data.
DEPRECATED -- DO NOT USE
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_frame_data.id' diffrn_frame_data yes
_item_type.code code
save_
save__diffrn_frame_data.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.details'
_item.category_id diffrn_frame_data
_item.mandatory_code no
_item_type.code text
save_
################ END DEPRECATED SECTION ###########
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive) ...
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items (case insensitive)...
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
point numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9]?[0-9]\
((T[0-2][0-9](:[0-5][0-9](:[0-5][0-9](.[0-9]+)?)?)?)?\
([+-][0-5][0-9]:[0-5][0-9]))?
;
;
Standard format for CIF date and time strings (see
http://www.iucr.org/iucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character 'T' followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
decimal fraction on the seconds of time.
Time is local time if no time-zone offset is given.
Note that this type extends the mmCIF yyyy-mm-dd type
but does not conform to the mmCIF yyyy-mm-dd:hh:mm
type that uses a ':' in place if the 'T' specified
by the IUCr standard. For reading, both forms should
be accepted, but for writing, only the IUCr form should
be used.
For maximal compatibility, the special time zone
indicator 'Z' (for 'zulu') should be accepted on
reading in place of '+00:00' for GMT.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2)^)'
'millimetres' 'millimetres (metres * 10^( -3)^)'
'nanometres' 'nanometres (metres * 10^( -9)^)'
'angstroms' '\%Angstroms (metres * 10^(-10)^)'
'picometres' 'picometres (metres * 10^(-12)^)'
'femtometres' 'femtometres (metres * 10^(-15)^)'
#
'reciprocal_metres' 'reciprocal metres (metres^(-1)^)'
'reciprocal_centimetres'
'reciprocal centimetres ((metres * 10^( -2)^)^(-1)^)'
'reciprocal_millimetres'
'reciprocal millimetres ((metres * 10^( -3)^)^(-1)^)'
'reciprocal_nanometres'
'reciprocal nanometres ((metres * 10^( -9)^)^(-1)^)'
'reciprocal_angstroms'
'reciprocal \%Angstroms ((metres * 10^(-10)^)^(-1)^)'
'reciprocal_picometres'
'reciprocal picometres ((metres * 10^(-12)^)^(-1)^)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9)^)^2^'
'angstroms_squared' '\%Angstroms squared (metres * 10^(-10)^)^2^'
'8pi2_angstroms_squared'
'8\p^2^ * \%Angstroms squared (metres * 10^(-10)^)^2^'
'picometres_squared' 'picometres squared (metres * 10^(-12)^)^2^'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9)^)^3^'
'angstroms_cubed' '\%Angstroms cubed (metres * 10^(-10)^)^3^'
'picometres_cubed' 'picometres cubed (metres * 10^(-12)^)^3^'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^( -9)^)^(-3)^)
;
'electrons_per_angstroms_cubed'
; electrons per \%Angstroms cubed (electrons/(metres * 10^(-10)^)^(-3)^)
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (electrons/(metres * 10^(-12)^)^(-3)^)
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'pixels_per_element' '(image) pixels per (array) element'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.6.4 2011-07-02
; Corrections to support DLS Dectris header as per G. Winter (HJB)
+ Define new tags _diffrn_scan.time_period,
_diffrn_scan.time_rstrt_incr,
_diffrn_scan_frame.time_period,
_diffrn_scan_frame.time_rstrt_incr
+ fix bad category name in loop in _diffrn_detector.id
+ remove stray text field terminator at line 4642
+ fix unquoted tag as a value in _diffrn_scan_frame_monitor.id
+ make formerly mandatory and implicit deprecated items non-mandatory
;
1.6.3 2010-08-26
; Cummulative corrections from 1.6.0, 1, 2 drafts (HJB)
+ Move descriptive dictionary comments into
_datablock.description with catgeory tree described
+ add default _array_data.array_id value of 1
+ add option of CBF_BACKGROUND_OFFSET_DELTA compression
+ add VARIANT catgeory and tags
+ add DIFFRN_SCAN_FRAME_MONITOR category
;
1.5.4 2007-07-28
; Typographics corrections (HJB)
+ Corrected embedded degree characters to \%
+ Corrected embedded Aring to \%A
+ Added trailing ^ for a power
+ Removed 2 cases of a space after an underscore
in tag name.
;
1.5.3 2007-07-08
; Changes to support SLS miniCBF and suggestions
from the 24 May 07 BNL imgCIF workshop (HJB)
+ Added new data items
'_array_data.header_contents',
'_array_data.header_convention',
'_diffrn_data_frame.center_fast',
'_diffrn_data_frame.center_slow',
'_diffrn_data_frame.center_units',
'_diffrn_measurement.sample_detector_distance',
'_diffrn_measurement.sample_detector_voffset
+ Deprecated data items
'_diffrn_detector_element.center[1]',
'_diffrn_detector_element.center[2]'
+ Added comments and example on miniCBF
+ Changed all array_id data items to implicit
;
1.5.2 2007-05-06
; Further clarifications of the coordinate system. (HJB)
;
1.5.1 2007-04-26
; Improve defintion of X-axis to cover the case of no goniometer
and clean up more line folds (HJB)
;
1.5 2007-07-25
; This is a cummulative list of the changes proposed since the
imgCIF workshop in Hawaii in July 2006. It is the result
of contributions by H. J. Bernstein, A. Hammersley,
J. Wright and W. Kabsch.
2007-02-19 Consolidated changes (edited by HJB)
+ Added new data items
'_array_structure.compression_type_flag',
'_array_structure_list_axis.fract_displacement',
'_array_structure_list_axis.displacement_increment',
'_array_structure_list_axis.reference_angle',
'_array_structure_list_axis.reference_displacement',
'_axis.system',
'_diffrn_detector_element.reference_center_fast',
'_diffrn_detector_element.reference_center_slow',
'_diffrn_scan_axis.reference_angle',
'_diffrn_scan_axis.reference_displacement',
'_map.details', '_map.diffrn_id',
'_map.entry_id', '_map.id',
'_map_segment.array_id', '_map_segment.binary_id',
'_map_segment.mask_array_id', '_map_segment.mask_binary_id',
'_map_segment.id', '_map_segment.map_id',
'_map_segment.details.
+ Change type of
'_array_structure.byte_order' and
'_array_structure.compression_type'
to ucode to make these values case-insensitive
+ Add values 'packed_v2' and 'byte_offset' to enumeration of values for
'_array_structure.compression_type'
+ Add to definitions for the binary data type to handle new compression
types, maps, and a variety of new axis types.
2007-07-25 Cleanup of typos for formal release (HJB)
+ Corrected text fields for reference_ tag descriptions that
were off by one column
+ Fix typos in comments listing fract_ tags
+ Changed name of release from 1.5_DRAFT to 1.5
+ Fix unclosed text fields in various map definitions
;
1.4 2006-07-04
; This is a change to reintegrate all changes made in the course of
publication of ITVG, by the RCSB from April 2005 through
August 2008 and changes for the 2006 imgCIF workshop in
Hawaii.
2006-07-04 Consolidated changes for the 2006 imgCIF workshop (edited by HJB)
+ Correct type of '_array_structure_list.direction' from 'int' to 'code'.
+ Added new data items suggested by CN
'_diffrn_data_frame.details'
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size and
'_array_intensities.pixel_binning_method
+ Added deprecated item for completeness
'_diffrn_frame_data.details'
+ Added entry for missing item in contents list
'_array_structure_list_axis.displacement'
+ Added new MIME type X-BASE32K based on work by VL, KM, GD, HJB
+ Correct description of MIME boundary delimiter to start in
column 1.
+ General cleanup of text fields to conform to changes for ITVG
by removing empty lines at start and finish of text field.
+ Amend example for ARRAY_INTENSITIES to include binning.
+ Add local copy of type specification (as 'code') for all children
of '_diffrn.id'.
+ For consistency, change all references to 'pi' to '\p' and all
references to 'Angstroms' to '\%Angstroms'.
+ Clean up all powers to use IUCr convention of '^power^', as in
'10^3^' for '10**3'.
+ Update 'yyyy-mm-dd' type regex to allow truncation from the right
and improve comments to explain handling of related mmCIF
'yyyy-mm-dd:hh:mm' type, and use of 'Z' for GMT time zone.
2005-03-08 and
2004-08-08 fixed cases where _item_units.code used
instead of _item_type.code (JDW)
2004-04-15 fixed item ordering in
_diffrn_measurement_axis.measurement_id
added sub_category 'vector' (JDW)
;
1.3.2 2005-06-25
; 2005-06-25 ITEM_TYPE_LIST: code, ucode, line, uline regexps updated
to those of current mmCIF; float modified by allowing integers
terminated by a point as valid. The 'time' part of
yyyy-mm-dd types made optional in the regexp. (BM)
2005-06-17 Minor corrections as for proofs for IT G Chapter 4.6
(NJA)
2005-02-21 Minor corrections to spelling and punctuation
(NJA)
2005-01-08 Changes as per Nicola Ashcroft.
+ Updated example 1 for DIFFRN_MEASUREMENT to agree with mmCIF.
+ Spelled out "micrometres" for "um" and "millimetres" for "mm".
+ Removed phrase "which may be stored" from ARRAY_STRUCTURE
description.
+ Removed unused 'byte-offsets' compressions and updated
cites to ITVG for '_array_structure.compression_type'.
(HJB)
;
1.3.1 2003-08-13
;
Changes as per Frances C. Bernstein.
+ Identify initials.
+ Adopt British spelling for centre in text.
+ Set \p and \%Angstrom and powers.
+ Clean up commas and unclear wordings.
+ Clean up tenses in history.
Changes as per Gotzon Madariaga.
+ Fix the ARRAY_DATA example to align '_array_data.binary_id'
and X-Binary-ID.
+ Add a range to '_array_intensities.gain_esd'.
+ In the example of DIFFRN_DETECTOR_ELEMENT,
'_diffrn_detector_element.id' and
'_diffrn_detector_element.detector_id' interchanged.
+ Fix typos for direction, detector and axes.
+ Clarify description of polarisation.
+ Clarify axes in '_diffrn_detector_element.center[1]'
'_diffrn_detector_element.center[2]'.
+ Add local item types for items that are pointers.
(HJB)
;
1.3.0 2003-07-24
;
Changes as per Brian McMahon.
+ Consistently quote tags embedded in text.
+ Clean up introductory comments.
+ Adjust line lengths to fit in 80 character window.
+ Fix several descriptions in AXIS category which
referred to '_axis.type' instead of the current item.
+ Fix erroneous use of deprecated item
'_diffrn_detector_axis.id' in examples for
DIFFRN_SCAN_AXIS.
+ Add deprecated items '_diffrn_detector_axis.id'
and '_diffrn_measurement_axis.id'.
(HJB)
;
1.2.4 2003-07-14
;
Changes as per I. David Brown.
+ Enhance descriptions in DIFFRN_SCAN_AXIS to make them less
dependent on the descriptions in DIFFRN_SCAN_FRAME_AXIS.
+ Provide a copy of the deprecated DIFFRN_FRAME_DATA
category for completeness.
(HJB)
;
1.2.3 2003-07-03
;
Cleanup to conform to ITVG.
+ Correct sign error in ..._cubed units.
+ Correct '_diffrn_radiation.polarisn_norm' range.
(HJB)
;
1.2.2 2003-03-10
;
Correction of typos in various DIFFRN_SCAN_AXIS descriptions.
(HJB)
;
1.2.1 2003-02-22
;
Correction of ATOM_ for ARRAY_ typos in various descriptions.
(HJB)
;
1.2 2003-02-07
;
Corrections to encodings (remove extraneous hyphens) remove
extraneous underscore in '_array_structure.encoding_type'
enumeration. Correct typos in items units list. (HJB)
;
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB.
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li.
;
1.1.1 2001-02-16
;
Several typo corrections by JW.
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS. (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME.
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to
'_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source',
'_diffrn_radiation.polarizn_source_norm',
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add '_diffrn_measurement.device' to category key.
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to
allow for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up. (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes. (JW)
+ Correct spelling of diffrn_measurement_axis in '_axis.id'
+ Correct ordering of uses of '_item.mandatory_code' and
'_item_default.value'.
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown. (HJB)
+ Add further comments on '\n' and '\t'.
+ Update ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Change 'meter' to 'metre' throughout.
+ Add missing enumerations to '_array_structure.compression_type'
and make 'none' the default.
+ Remove parent-child relationship between
'_array_structure_list.index' and '_array_structure_list.precedence'.
+ Improve alphabetization.
+ Fix '_array_intensities_gain.esd' related function.
+ Improve comments in AXIS.
+ Fix DIFFRN_FRAME_DATA example.
+ Remove erroneous DIFFRN_MEASUREMENT example.
+ Add '_diffrn_measurement_axis.id' to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data. (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors. (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for '_diffrn_scan.id' definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header. (HJB)
+ Restore '_diffrn_detector.diffrn_id' to DIFFRN_DETECTOR KEY.
+ Add AXIS category.
+ Bring in complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
from cif_mm.dic for clarity.
+ Change '_array_structure.encoding_type' from type code to uline and
added X-Binary-Element-Type to MIME header.
+ Add detector beam centre '_diffrn_detector_element.center[1]' and
'_diffrn_detector_element.center[2]'.
+ Correct item name of '_diffrn_refln.frame_id'.
+ Replace reference to '_array_intensities.undefined' by
'_array_intensities.undefined_value'.
+ Replace references to '_array_intensity.scaling' with
'_array_intensities.scaling'.
+ Add DIFFRN_SCAN... categories.
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft. (HJB)
+ Reflow comment lines over 80 characters and corrected typos.
+ Update examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF. (HJB)
+ Add binary type, which is a text field containing a variant on
MIME encoded data.
+ Change type of '_array_data.data' to binary and specify internal
structure of raw binary data.
+ Add '_array_data.binary_id', and make
'_diffrn_frame_data.binary_id' and '_array_intensities.binary_id'
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft. (JW)
+ Add category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes are made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA is renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE is renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for '_diffrn_frame_data.array_id' is changed from
'_array_structure_list.array_id' to '_array_structure.id'. Item
'_diffrn_detector.array_id' is deleted.
+ Add data item '_diffrn_frame_data.binary_id' to identify data
groups within a binary section. The formal identification of the
binary section is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version is adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley
(AH).
Modifications to the CBF draft. (JW)
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories
have been generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category
ARRAY_DATA. This departs from the CBF notion of data existing
in some special comment. In this description, data are handled as an
ordinary data item encapsulated in a character data type. Although
data this manner deviates from CIF conventions, it does not violate
any DDL 2.1 rules. DDL 2.1 regular expressions can be used to define
the binary representation which will permit some level of data
validation. In this version, the placeholder type code "any" has
been used. This translates to a regular expression which will match
any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary.
It may be possible to use the DDL 2.1 ITEM_STRUCTURE and
ITEM_STRUCTURE_LIST categories to provide the information that is
carried in by the ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By
moving the array structure to the DDL level it would be possible to
define an array type as well as a regular expression defining the
data format.
+ Multiple array sections can be properly handled within a single
datablock.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases but should not be used for new work.
Example:
Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element are
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
./CBFlib-0.9.2.2/doc/ddl2.dic 0000644 0000765 0000765 00000314352 11603702115 013661 0 ustar yaya yaya ###########################################################################
#
# File: mmcif_ddl.dic
# Date: Mon Aug 9 02:48:08 EDT 2004
#
# Created from files in CVS module dict-mmcif_ddl.dic unless noted:
# mmcif_ddl-header.dic
# mmcif_ddl-data.dic
# mmcif_ddl-def-1.dic
# mmcif_ddl-def-2.dic
#
###########################################################################
###########################################################################
#
# File: mmcif_ddl-header.dic
#
# mmCIF DDL Core Dictionary with NDB extensions
#
# This DDL dictionary is a mirror of ddl_core.dic-org with all implicit
# data items fully expanded and with NDB extensions added.
#
# Header Section
#
#
###########################################################################
data_mmcif_ddl.dic
_datablock.id mmcif_ddl.dic
_datablock.description
;
This data block holds the core DDL.
;
_dictionary.datablock_id mmcif_ddl.dic
_dictionary.title mmcif_ddl.dic
_dictionary.version 2.1.6
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.1 1994-07-25
;
DDL 1.1 from Syd Hall et. al.
;
1.2.1 1994-09-18
;
Changes:.........etc. etc. John Westbrook
;
1.2.9 1994-10-05
;
Reflect the results of the Treaty of Brussels. JW.
;
2.0.1 1994-10-15
;
Adapted for closer mapping to DDL1.3 and clearer presentation. SRH/NS.
;
2.0.2 1994-10-16
;
Even closer................... SRH/NS.
;
2.0.3 1994-10-17
;
Coming to grips with the links and dependencies..... SRH/NS.
;
2.0.4 1994-10-20
;
Backed in changes from mm-ddl 1.2.12
Many other changes ... (JW)
;
2.0.5 1994-10-20
;
Some small adjustments..........SRH.
;
2.0.6 1994-10-20
;
More small adjustments..........JW.
;
2.0.7 1994-11-03
;
Changes: (JW)
+ Place all item and item_linked category definitions with the parent
item.
+ Fixed a number of not so trivial typos.
+ Corrected errors in the data type conversion table.
+ Corrected key item inconsistencies.
+ Added the item_aliases category.
;
2.0.8 1994-11-10
;
Miscellaneous corrections: (JW)
+ defined sub_category_group
+ corrected typo in category_examples.id definition
+ added _item_type_conditions.name in item category
+ added _item_structure.name in item category
+ corrected typo in item_aliases category definition
+ corrected typo in sub_category.method_id definition
;
2.0.9 1994-11-14
;
Changes: (JW)
+ added ITEM_UNITS, ITEM_UNITS_LIST, and UNITS_CONVERSION
categories.
+ added an additional primitive type for character type items
for which comparisons must be case insensitive.
Since it is customary to permit item names and category
identifiers to be specified in mixed case, it is necessary
to declare that case should NOT be considered in any
comparisons of these items.
;
2.0.10 1994-11-23
;
Changes: (JW)
+ Several name category changes for the sake of consistency:
enumeration -> item_enumeration
enumeration_default -> item_enumeration_default
enumeration_limit -> item_enumeration_limit
units_conversion -> item_units_conversion
+ Added _item_related.function_code alternate_exclusive
to identify mutually exclusive alternative declarations
of the same item.
+ Added structure options for real symmetric matrices.
+ Changed from zero based indices to one based indices
for compatibility with existing matrix component
definitions.
+ Add _item_linked.parent_name to the key of the item_linked
category.
+ Reorder items in the DDL so be alphabetical within
category groups.
;
2.0.11 1994-11-28
;
Changes: (JW)
+ Corrected spelling error for the data type code in
the DICTIONARY_HISTORY category.
+ Add category BLOCK to hold the data block name and data
block description. The block identifier was also added
to the key of the item category. The block identifier
can be implicitly derived from the STAR "data_" delimiter.
This identifier is required to form the key for categories
which are conceptually related to the data block as a
whole.
;
2.0.12 1994-11-30
;
Changes: (JW)
+ Added a data item _block.scope to indicate the scope of
data item names defined within included data blocks.
;
2.0.13 1994-12-12
;
Changes: (JW)
+ Deleted data item _block.scope.
+ Changed DICTIONARY category key to _dictionary.block_id
to guarantee only one dictionary definition per block.
+ Deleted data item _item.block_id as this will be replaced
by an item address syntax that will include block, save
frame, and url.
;
2.0.14 1994-12-15
;
Changes: (JW)
+ Made some terminology changes suggested by PMDF
_item_enumeration.code -> _item_enumeration.value
ITEM_ENUMERATION_DEFAULT -> ITEM_DEFAULT
ITEM_ENUMERATION_LIMIT -> ITEM_RANGE
+ Added item _item_type_list.detail
+ Version 2.0.14 is being frozen and exported.
;
2.0.15 1995-02-13
;
Changes: (JW)
+ Added '_' prefix to all data item save frame names.
References to data item names now always include
a leading underscore independent of the usage context.
+ A few miscellaneous corrections.
;
2.0.16 1995-06-18
;
Changes: (JW)
+ Revised the block level categories in the following ways:
Changed category BLOCK to DATA_BLOCK.
Added connection from _data_block.id to _category.implicit_key
in order to provide a formal means of merging the contents
of categories between data blocks.
+ Moved ennumerations for _method_list.code and
method_list.language to examples.
+ Removed symmetric matrix options from the ennumerations
for _item_structure.organization.
+ Added _item_related.function codes for 'associated_value',
'associated_esd', 'replaces' and 'replacedby'
+ Added data items _item_aliases.dictionary and
_item_aliases.dictionary_version.
+ Reorganized method categories such that multiple methods can
be applied at each level of data structure. Introduced a
consistent set of categories to hold method associations:
ITEM_METHODS, CATEGORY_METHODS, SUB_CATEGORY_METHODS, and
DATA_BLOCK_METHODS. Removed data items _category.method_id
_sub_category.method_id.
;
2.0.17 1995-06-22
;
Changes: (JW)
+ Quoted data vaules containing the leading string 'data_'.
;
2.1.0 1995-07-20
;
Changes: (JW)
Final adjustments before the first release of the mmCIF dictionary:
+ changed data_block to datablock to avoid any problems with
the STAR data_ reserved token.
+ created new category to hold item subcategory associations
and deleted the subcategory attribute from ITEM category.
+ modified regular expressions to reflect limitations observed
on several platforms.
+ expanded the ennumeration of _item_related.function_code.
+ removed default value from _item.manadatory_code.
+ removed type construct for date and changed date data type
to yyyy-mm-dd
+ added less restrictive data type for alias names.
;
2.1.1 1995-09-26
;
Changes: (JW)
+ Changed regular expressions for type code to permit
single quote.
+ Corrected regular expression syntax for type name and
type date.
+ Corrected lower bound description for item_range.minimum.
The incorrect <= condition is changed to <.
+ _item_mandatory.code has been now a mandatory item.
+ _item_aliases.dictionary and _item_aliases.dictionary_version
are added to the composite key for category ITEM_ALIASES.
+ _datablock.id data type changes to type code.
+ Shortened the name _item_aliases.dictionary_version to
_item_aliases.version
;
2.1.2 1997-01-24
;
Changes: (JW)
+ Added associated_error to the enumeration list of
_item_related.function_code.
;
2.1.3 2000-10-16
;
Changes: (JW)
+ Changed data type for regular expression in
_item_type_list.construct to type text.
;
2.1.5 2003-06-23
; Changes: (JW)
+ NDB extensions adopted into ddl_core
+ New partitioning scheme implemented
;
2.1.6 2004-04-15
; Changes: (JW)
+ Name changed to mmcif_ddl.dic
;
### EOF mmcif_ddl-header.dic ####
###########################################################################
#
# File: mmcif_ddl-data.dic
#
# mmCIF DDL Core Dictionary with NDB extensions
#
# This DDL dictionary is a mirror of ddl_core.dic-org with all implicit
# data items fully expanded and with NDB extensions added.
#
# Data Section
#
#
###########################################################################
# DATA TYPE CONVERSION TABLE
# --------------------------
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.detail
_item_type_list.construct
code char 'A single word'
'[^\t\n "]*'
char char 'A single line of text'
'[^\n]*'
text char 'Text which may span lines'
'.*'
int numb 'Unsigned integer data'
'[0-9]+'
name uchar 'A data item name (restrictive type)'
'_[_A-Za-z0-9]+[.][][_A-Za-z0-9\<\>%/-]+'
aliasname uchar 'A DDL 1.4 data item name (less restrictive type)'
'_[^\t\n "]+'
idname uchar 'A data item name component or identifier'
'[_A-Za-z0-9]+'
any char 'Any data type'
'.*'
yyyy-mm-dd char 'A date format'
'[0-9][0-9][0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]'
#
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'ddl_group' .
;
Component categories of the macromolecular DDL
;
'datablock_group' 'ddl_group'
;
Categories that describe the characteristics of data blocks.
;
'category_group' 'ddl_group'
;
Categories that describe the characteristics of categories.
;
'sub_category_group' 'ddl_group'
;
Categories that describe the characteristics of subcategories.
;
'item_group' 'ddl_group'
;
Categories that describe the characteristics of data items.
;
'dictionary_group' 'ddl_group'
;
Categories that describe the dictionary.
;
'compliance_group' 'ddl_group'
;
Categories that are retained specifically for compliance with
older versions of the DDL.
;
### EOF mmcif_ddl-data.dic
###########################################################################
#
# File: mmcif_ddl-def-1.dic
#
# mmCIF DDL Core Dictionary with NDB extensions
#
# This DDL dictionary is a mirror of ddl_core.dic-org with all implicit
# data items fully expanded and with NDB extensions added.
#
# Definition Section 1.
# (Core Definitions)
#
#
###########################################################################
# ----------------------------------------------------------------------------
save_DATABLOCK
_category.description
;
Attributes defining the characteristics of a data block.
;
_category.id datablock
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id datablock
_category_key.name '_datablock.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' datablock
'datablock_group' datablock
save_
save__datablock.id
_item_description.name '_datablock.id'
_item_description.description
;
The identity of the data block.
;
_item.name '_datablock.id'
_item.category_id datablock
_item.mandatory_code implicit
_item_type.name '_datablock.id'
_item_type.code code
loop_
_item_linked.parent_name
_item_linked.child_name
'_datablock.id' '_datablock_methods.datablock_id'
'_datablock.id' '_dictionary.datablock_id'
'_datablock.id' '_category.implicit_key'
save_
save__datablock.description
_item_description.name '_datablock.description'
_item_description.description
;
Text description of the data block.
;
_item.name '_datablock.description'
_item.category_id datablock
_item.mandatory_code yes
_item_type.name '_datablock.description'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_DATABLOCK_METHODS
_category.description
;
Attributes specifying the association between data blocks and methods.
;
_category.id datablock_methods
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
datablock_methods '_datablock_methods.method_id'
datablock_methods '_datablock_methods.datablock_id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' datablock_methods
'datablock_group' datablock_methods
save_
save__datablock_methods.datablock_id
_item_description.name '_datablock_methods.datablock_id'
_item_description.description
;
Identifier of data block.
;
_item.name '_datablock_methods.datablock_id'
_item.category_id datablock_methods
_item.mandatory_code implicit
_item_type.name '_datablock_methods.datablock_id'
_item_type.code code
save_
save__datablock_methods.method_id
_item_description.name '_datablock_methods.method_id'
_item_description.description
;
Unique method identifier associated with a data block.
;
_item.name '_datablock_methods.method_id'
_item.category_id datablock_methods
_item.mandatory_code yes
_item_type.name '_datablock_methods.method_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_CATEGORY
_category.description
;
Attributes defining the functionality for the entire category.
;
_category.id category
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id category
_category_key.name '_category.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' category
'category_group' category
save_
save__category.id
_item_description.name '_category.id'
_item_description.description
;
The identity of the data category. Data items may only be looped
with items of the same category.
;
_item.name '_category.id'
_item.category_id category
_item.mandatory_code yes
_item_type.name '_category.id'
_item_type.code idname
loop_
_item_linked.child_name
_item_linked.parent_name
'_category_examples.id' '_category.id'
'_category_group.category_id' '_category.id'
'_category_key.id' '_category.id'
'_category_methods.category_id' '_category.id'
'_item.category_id' '_category.id'
save_
save__category.description
_item_description.name '_category.description'
_item_description.description
;
Text description of a category.
;
_item.name '_category.description'
_item.category_id category
_item.mandatory_code yes
_item_type.name '_category.description'
_item_type.code text
save_
save__category.implicit_key
_item_description.name '_category.implicit_key'
_item_description.description
;
An identifier that may be used to distinguish the contents of
like categories between data blocks.
;
_item.name '_category.implicit_key'
_item.category_id category
_item.mandatory_code implicit
_item_type.name '_category.implicit_key'
_item_type.code code
save_
save__category.mandatory_code
_item_description.name '_category.mandatory_code'
_item_description.description
;
Whether the category must be specified in a dictionary.
;
_item.name '_category.mandatory_code'
_item.category_id category
_item.mandatory_code yes
_item_type.name '_category.mandatory_code'
_item_type.code code
save_
# ----------------------------------------------------------------------------
save_CATEGORY_EXAMPLES
_category.description
;
Example applications and descriptions of data items in this category.
;
_category.id category_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
category_examples '_category_examples.id'
category_examples '_category_examples.case'
save_
save__category_examples.id
_item_description.name '_category_examples.id'
_item_description.description
;
The name of category.
;
_item.name '_category_examples.id'
_item.category_id category_examples
_item.mandatory_code implicit
_item_type.name '_category_examples.id'
_item_type.code idname
save_
save__category_examples.case
_item_description.name '_category_examples.case'
_item_description.description
;
A case of examples involving items in this category.
;
_item.name '_category_examples.case'
_item.category_id category_examples
_item.mandatory_code yes
_item_type.name '_category_examples.case'
_item_type.code text
save_
save__category_examples.detail
_item_description.name '_category_examples.detail'
_item_description.description
;
A description of an example _category_examples.case
;
_item.name '_category_examples.detail'
_item.category_id category_examples
_item.mandatory_code no
_item_type.name '_category_examples.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_CATEGORY_KEY
_category.description
;
This category holds a list of the item names that uniquely
identify the elements of the category.
;
_category.id category_key
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
category_key '_category_key.name'
category_key '_category_key.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' category_key
'category_group' category_key
save_
save__category_key.name
_item_description.name '_category_key.name'
_item_description.description
;
The name of a data item that serves as a key identifier for the
category (eg. a component of the primary key).
;
_item.name '_category_key.name'
_item.category_id category_key
_item.mandatory_code yes
_item_type.name '_category_key.name'
_item_type.code name
save_
save__category_key.id
_item_description.name '_category_key.id'
_item_description.description
;
The identifier of the category (eg. a component of the primary key).
;
_item.name '_category_key.id'
_item.category_id category_key
_item.mandatory_code implicit
_item_type.name '_category_key.id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_CATEGORY_GROUP
_category.description
;
Provides a list of category groups to which the base category
belongs.
;
_category.id category_group
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
category_group '_category_group.id'
category_group '_category_group.category_id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' category_group
'category_group' category_group
save_
save__category_group.id
_item_description.name '_category_group.id'
_item_description.description
;
The name of a category group ...
;
_item.name '_category_group.id'
_item.category_id category_group
_item.mandatory_code yes
_item_type.name '_category_group.id'
_item_type.code idname
save_
save__category_group.category_id
_item_description.name '_category_group.category_id'
_item_description.description
;
The name of a category ...
;
_item.name '_category_group.category_id'
_item.category_id category_group
_item.mandatory_code implicit
_item_type.name '_category_group.category_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_CATEGORY_GROUP_LIST
_category.description
;
This category provides the definition of each category group.
A category group is a collection of related categories.
;
_category.id category_group_list
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id category_group_list
_category_key.name '_category_group_list.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' category_group_list
'category_group' category_group_list
save_
save__category_group_list.id
_item_description.name '_category_group_list.id'
_item_description.description
;
The name of a category group ...
;
_item.name '_category_group_list.id'
_item.category_id category_group_list
_item.mandatory_code yes
_item_type.name '_category_group_list.id'
_item_type.code idname
loop_
_item_linked.child_name
_item_linked.parent_name
'_category_group.id' '_category_group_list.id'
'_category_group_list.parent_id' '_category_group_list.id'
save_
save__category_group_list.description
_item_description.name '_category_group_list.description'
_item_description.description
;
Text description of a category group...
;
_item.name '_category_group_list.description'
_item.category_id category_group_list
_item.mandatory_code yes
_item_type.name '_category_group_list.description'
_item_type.code text
save_
save__category_group_list.parent_id
_item_description.name '_category_group_list.parent_id'
_item_description.description
;
The name of the optional parent category group.
;
_item.name '_category_group_list.parent_id'
_item.category_id category_group_list
_item.mandatory_code no
_item_type.name '_category_group_list.parent_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_CATEGORY_METHODS
_category.description
;
Attributes specifying the association between categories and methods.
;
_category.id category_methods
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
category_methods '_category_methods.method_id'
category_methods '_category_methods.category_id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' category_methods
'category_group' category_methods
save_
save__category_methods.category_id
_item_description.name '_category_methods.category_id'
_item_description.description
;
The name of the category
;
_item.name '_category_methods.category_id'
_item.category_id category_methods
_item.mandatory_code implicit
_item_type.name '_category_methods.category_id'
_item_type.code idname
save_
save__category_methods.method_id
_item_description.name '_category_methods.method_id'
_item_description.description
;
The name of the method
;
_item.name '_category_methods.method_id'
_item.category_id category_methods
_item.mandatory_code yes
_item_type.name '_category_methods.method_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_SUB_CATEGORY
_category.description
;
The purpose of a sub-category is to define an association between
data items within a category and optionally provide a method to
validate the collection of items. The sub-category named
'cartesian' might be applied to the data items for the coordinates
x, y, and z.
;
_category.id sub_category
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id sub_category
_category_key.name '_sub_category.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' sub_category
'sub_category_group' sub_category
save_
save__sub_category.id
_item_description.name '_sub_category.id'
_item_description.description
;
The identity of the sub-category.
;
_item.name '_sub_category.id'
_item.category_id sub_category
_item.mandatory_code yes
_item_type.name '_sub_category.id'
_item_type.code idname
loop_
_item_linked.child_name
_item_linked.parent_name
'_sub_category_examples.id' '_sub_category.id'
'_sub_category_methods.sub_category_id' '_sub_category.id'
'_item_sub_category.id' '_sub_category.id'
save_
save__sub_category.description
_item_description.name '_sub_category.description'
_item_description.description
;
Description of the sub-category.
;
_item.name '_sub_category.description'
_item.category_id sub_category
_item.mandatory_code yes
_item_type.name '_sub_category.description'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_SUB_CATEGORY_EXAMPLES
_category.description
;
Example applications and descriptions of data items in this subcategory.
;
_category.id sub_category_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
sub_category_examples '_sub_category_examples.id'
sub_category_examples '_sub_category_examples.case'
loop_
_category_group.id
_category_group.category_id
'ddl_group' sub_category_examples
'sub_category_group' sub_category_examples
save_
save__sub_category_examples.id
_item_description.name '_sub_category_examples.id'
_item_description.description
;
The name for the subcategory.
;
_item.name '_sub_category_examples.id'
_item.category_id sub_category_examples
_item.mandatory_code yes
_item_type.name '_sub_category_examples.id'
_item_type.code idname
save_
save__sub_category_examples.case
_item_description.name '_sub_category_examples.case'
_item_description.description
;
An example involving items in this subcategory.
;
_item.name '_sub_category_examples.case'
_item.category_id sub_category_examples
_item.mandatory_code yes
_item_type.name '_sub_category_examples.case'
_item_type.code text
save_
save__sub_category_examples.detail
_item_description.name '_sub_category_examples.detail'
_item_description.description
;
A description of an example _sub_category_examples.case
;
_item.name '_sub_category_examples.detail'
_item.category_id sub_category_examples
_item.mandatory_code no
_item_type.name '_sub_category_examples.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_SUB_CATEGORY_METHODS
_category.description
;
Attributes specifying the association between subcategories and methods.
;
_category.id sub_category_methods
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
sub_category_methods '_sub_category_methods.method_id'
sub_category_methods '_sub_category_methods.sub_category_id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' sub_category_methods
'sub_category_group' sub_category_methods
save_
save__sub_category_methods.sub_category_id
_item_description.name '_sub_category_methods.sub_category_id'
_item_description.description
;
The name of the subcategory
;
_item.name '_sub_category_methods.sub_category_id'
_item.category_id sub_category_methods
_item.mandatory_code yes
_item_type.name '_sub_category_methods.sub_category_id'
_item_type.code idname
save_
save__sub_category_methods.method_id
_item_description.name '_sub_category_methods.method_id'
_item_description.description
;
The name of the method
;
_item.name '_sub_category_methods.method_id'
_item.category_id sub_category_methods
_item.mandatory_code yes
_item_type.name '_sub_category_methods.method_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_ITEM
_category.description
;
Attributes which describe the characteristics of a data item.
;
_category.id item
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item
_category_key.name '_item.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item
'item_group' item
save_
save__item.name
_item_description.name '_item.name'
_item_description.description
;
Data name of the defined item.
;
_item_type.name '_item.name'
_item_type.code name
_item.name '_item.name'
_item.category_id item
_item.mandatory_code implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_category_key.name' '_item.name'
'_item_aliases.name' '_item.name'
'_item_default.name' '_item.name'
'_item_dependent.name' '_item.name'
'_item_dependent.dependent_name' '_item.name'
'_item_description.name' '_item.name'
'_item_enumeration.name' '_item.name'
'_item_examples.name' '_item.name'
'_item_linked.child_name' '_item.name'
'_item_linked.parent_name' '_item.name'
'_item_methods.name' '_item.name'
'_item_range.name' '_item.name'
'_item_related.name' '_item.name'
'_item_related.related_name' '_item.name'
'_item_type.name' '_item.name'
'_item_type_conditions.name' '_item.name'
'_item_structure.name' '_item.name'
'_item_sub_category.name' '_item.name'
'_item_units.name' '_item.name'
save_
save__item.mandatory_code
_item_description.name '_item.mandatory_code'
_item_description.description
;
Signals if the defined item is mandatory for the proper description
of its category.
;
_item.name '_item.mandatory_code'
_item.category_id item
_item.mandatory_code yes
_item_type.name '_item.mandatory_code'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item.mandatory_code'
yes 'required item in this category'
'_item.mandatory_code'
no 'optional item in this category'
'_item.mandatory_code'
implicit 'required item but may be determined from context'
save_
save__item.category_id
_item_description.name '_item.category_id'
_item_description.description
;
This is category id of the item.
;
_item.name '_item.category_id'
_item.category_id item
_item.mandatory_code implicit
_item_type.name '_item.category_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_ITEM_ALIASES
_category.description
;
This category holds a list of possible alias names or synonyms for
each data item. Each alias name is identified by the name and
version of the dictionary to which it belongs.
;
_category.id item_aliases
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_aliases '_item_aliases.alias_name'
item_aliases '_item_aliases.dictionary'
item_aliases '_item_aliases.version'
save_
save__item_aliases.name
_item_description.name '_item_aliases.name'
_item_description.description
;
Name for the data item.
;
_item.name '_item_aliases.name'
_item.category_id item_aliases
_item.mandatory_code implicit
_item_type.name '_item_aliases.name'
_item_type.code name
save_
save__item_aliases.alias_name
_item_description.name '_item_aliases.alias_name'
_item_description.description
;
Alias name for the data item.
;
_item.name '_item_aliases.alias_name'
_item.category_id item_aliases
_item.mandatory_code yes
_item_type.name '_item_aliases.alias_name'
_item_type.code aliasname
save_
save__item_aliases.dictionary
_item_description.name '_item_aliases.dictionary'
_item_description.description
;
The dictionary in which the alias name is defined.
;
_item.name '_item_aliases.dictionary'
_item.category_id item_aliases
_item.mandatory_code yes
_item_type.name '_item_aliases.dictionary'
_item_type.code char
save_
save__item_aliases.version
_item_description.name '_item_aliases.version'
_item_description.description
;
The version of the dictionary in which the alias name is defined.
;
_item.name '_item_aliases.version'
_item.category_id item_aliases
_item.mandatory_code yes
_item_type.name '_item_aliases.version'
_item_type.code char
save_
# ----------------------------------------------------------------------------
save_ITEM_DEFAULT
_category.description
;
Attributes specifying the default value for a data item.
;
_category.id item_default
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_default
_category_key.name '_item_default.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_default
'item_group' item_default
save_
save__item_default.name
_item_description.name '_item_default.name'
_item_description.description
;
The name of item for which the default value is defined
;
_item.name '_item_default.name'
_item.category_id item_default
_item.mandatory_code implicit
_item_type.name '_item_default.name'
_item_type.code name
save_
save__item_default.value
_item_description.name '_item_default.value'
_item_description.description
;
The default value for the defined item if it is not specified
explicitly. If a data value is not declared, the default is
assumed to be the most likely or natural value.
;
_item.name '_item_default.value'
_item.category_id item_default
_item.mandatory_code no
_item_type.name '_item_default.value'
_item_type.code any
save_
# ----------------------------------------------------------------------------
save_ITEM_DEPENDENT
_category.description
;
Attributes which identify other data items that must be specified
for the defined data item to be valid.
;
_category.id item_dependent
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_dependent '_item_dependent.name'
item_dependent '_item_dependent.dependent_name'
save_
save__item_dependent.name
_item_description.name '_item_dependent.name'
_item_description.description
;
Item name of a dependent item.
;
_item.name '_item_dependent.name'
_item.category_id item_dependent
_item.mandatory_code implicit
_item_type.name '_item_dependent.name'
_item_type.code name
save_
save__item_dependent.dependent_name
_item_description.name '_item_dependent.dependent_name'
_item_description.description
;
Data name of a dependent item.
;
_item.name '_item_dependent.dependent_name'
_item.category_id item_dependent
_item.mandatory_code yes
_item_type.name '_item_dependent.dependent_name'
_item_type.code name
save_
# ----------------------------------------------------------------------------
save_ITEM_DESCRIPTION
_category.description
;
This category holds the descriptions of each data item.
;
_category.id item_description
_category.mandatory_code yes
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_description '_item_description.name'
item_description '_item_description.description'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_description
'item_group' item_description
save_
save__item_description.name
_item_description.name '_item_description.name'
_item_description.description
;
Tne name of data item.
;
_item.name '_item_description.name'
_item.category_id item_description
_item.mandatory_code implicit
_item_type.name '_item_description.name'
_item_type.code name
save_
save__item_description.description
_item_description.name '_item_description.description'
_item_description.description
;
Text decription of the defined data item.
;
_item.name '_item_description.description'
_item.category_id item_description
_item.mandatory_code yes
_item_type.name '_item_description.description'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_ITEM_ENUMERATION
_category.description
;
Attributes which specify the permitted enumeration of the items.
;
_category.id item_enumeration
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_enumeration '_item_enumeration.name'
item_enumeration '_item_enumeration.value'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_enumeration
'item_group' item_enumeration
save_
save__item_enumeration.name
_item_description.name '_item_enumeration.name'
_item_description.description
;
Name of data item.
;
_item.name '_item_enumeration.name'
_item.category_id item_enumeration
_item.mandatory_code implicit
_item_type.name '_item_enumeration.name'
_item_type.code name
save_
save__item_enumeration.value
_item_description.name '_item_enumeration.value'
_item_description.description
;
A permissible value, character or number, for the defined item.
;
_item.name '_item_enumeration.value'
_item.category_id item_enumeration
_item.mandatory_code yes
_item_type.name '_item_enumeration.value'
_item_type.code any
save_
save__item_enumeration.detail
_item_description.name '_item_enumeration.detail'
_item_description.description
;
A description of a permissible value for the defined item.
;
_item.name '_item_enumeration.detail'
_item.category_id item_enumeration
_item.mandatory_code no
_item_type.name '_item_enumeration.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_ITEM_EXAMPLES
_category.description
;
Attributes for describing application examples of the data item.
;
_category.id item_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_examples '_item_examples.name'
item_examples '_item_examples.case'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_examples
'item_group' item_examples
save_
save__item_examples.name
_item_description.name '_item_examples.name'
_item_description.description
;
The name of data item for the example.
;
_item.name '_item_examples.name'
_item.category_id item_examples
_item.mandatory_code implicit
_item_type.name '_item_examples.name'
_item_type.code name
save_
save__item_examples.case
_item_description.name '_item_examples.case'
_item_description.description
;
An example application of the defined data item.
;
_item.name '_item_examples.case'
_item.category_id item_examples
_item.mandatory_code no
_item_type.name '_item_examples.case'
_item_type.code text
save_
save__item_examples.detail
_item_description.name '_item_examples.detail'
_item_description.description
;
A description of an example specified in _item_example.case
;
_item.name '_item_examples.detail'
_item.category_id item_examples
_item.mandatory_code no
_item_type.name '_item_examples.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_ITEM_LINKED
_category.description
;
Attributes which describe how equivalent data items are linked
within categories and across different categories.
;
_category.id item_linked
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_linked '_item_linked.child_name'
item_linked '_item_linked.parent_name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_linked
'item_group' item_linked
save_
save__item_linked.child_name
_item_description.name '_item_linked.child_name'
_item_description.description
;
Name of the child data item.
;
_item.name '_item_linked.child_name'
_item.category_id item_linked
_item.mandatory_code yes
_item_type.name '_item_linked.child_name'
_item_type.code name
save_
save__item_linked.parent_name
_item_description.name '_item_linked.parent_name'
_item_description.description
;
Name of the parent data item.
;
_item.name '_item_linked.parent_name'
_item.category_id item_linked
_item.mandatory_code implicit
_item_type.name '_item_linked.parent_name'
_item_type.code name
save_
# ----------------------------------------------------------------------------
save_ITEM_METHODS
_category.description
;
Attributes specifying the association between data items and methods.
;
_category.id item_methods
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_methods '_item_methods.method_id'
item_methods '_item_methods.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_methods
'item_group' item_methods
save_
save__item_methods.name
_item_description.name '_item_methods.name'
_item_description.description
;
The name of the item
;
_item.name '_item_methods.name'
_item.category_id item_methods
_item.mandatory_code implicit
_item_type.name '_item_methods.name'
_item_type.code name
save_
save__item_methods.method_id
_item_description.name '_item_methods.method_id'
_item_description.description
;
The name of itemthe method
;
_item.name '_item_methods.method_id'
_item.category_id item_methods
_item.mandatory_code yes
_item_type.name '_item_methods.method_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_ITEM_RANGE
_category.description
;
The range of permissible values of a data item. When multiple
ranges are specified they are interpreted sequentially
using a logical OR. To specify that an item value may be
equal to a boundary value, specify an item range where the
maximum and mimimum values equal the boundary value.
;
_category.id item_range
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_range '_item_range.name'
item_range '_item_range.minimum'
item_range '_item_range.maximum'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_range
'item_group' item_range
save_
save__item_range.name
_item_description.name '_item_range.name'
_item_description.description
;
Name of data item ...
;
_item.name '_item_range.name'
_item.category_id item_range
_item.mandatory_code implicit
_item_type.name '_item_range.name'
_item_type.code name
save_
save__item_range.minimum
_item_description.name '_item_range.minimum'
_item_description.description
;
Minimum permissible value of a data item or the lower bound
of a permissible range. ( minimum value < data value)
;
_item.name '_item_range.minimum'
_item.category_id item_range
_item.mandatory_code no
_item_type.name '_item_range.minimum'
_item_type.code any
save_
save__item_range.maximum
_item_description.name '_item_range.maximum'
_item_description.description
;
Maximum permissible value of a data item or the upper bound
of a permissible range. ( maximum value > data value)
;
_item.name '_item_range.maximum'
_item.category_id item_range
_item.mandatory_code no
_item_type.name '_item_range.maximum'
_item_type.code any
save_
# ----------------------------------------------------------------------------
save_ITEM_RELATED
_category.description
;
Attributes which specify recognized relationships between data items.
;
_category.id item_related
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_related '_item_related.name'
item_related '_item_related.related_name'
item_related '_item_related.function_code'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_related
'item_group' item_related
save_
save__item_related.name
_item_description.name '_item_related.name'
_item_description.description
;
Identifies a defined data item ...
;
_item.name '_item_related.name'
_item.category_id item_related
_item.mandatory_code implicit
_item_type.name '_item_related.name'
_item_type.code name
save_
save__item_related.related_name
_item_description.name '_item_related.related_name'
_item_description.description
;
Identifies a data item by name which is closely related to the
defined data item by the manner described by _item_related.function_code
;
_item.name '_item_related.related_name'
_item.category_id item_related
_item.mandatory_code yes
_item_type.name '_item_related.related_name'
_item_type.code name
save_
save__item_related.function_code
_item_description.name '_item_related.function_code'
_item_description.description
;
The code for the type of relationship of the item identified by
_item_related.name and the defined item.
ALTERNATE indicates that the item identified in
_item_related.related_name is an alternative expression in terms
of its application and attributes to the item in this definition.
ALTERNATE_EXCLUSIVE indicates that the item identified in
_item_related.related_name is an alternative expression in terms
of its application and attributes to the item in this definition.
Only one of the alternative forms may be specified.
CONVENTION indicates that the item identified in
_item_related.related_name differs from the defined item only
in terms of a convention in its expression.
CONVERSION_CONSTANT indicates that the item identified in
_item_related.related_name differs from the defined item only
by a known constant.
CONVERSION_ARBITRARY indicates that the item identified in
_item_related.related_name differs from the defined item only
by a arbitrary constant.
REPLACES indicates that the defined item replaces the item identified
in _item_related.related_name.
REPLACEDBY indicates that the defined item is replaced by the
item identified in _item_related.related_name.
ASSOCIATED_VALUE indicates that the item identified in
_item_related.related_name is meaningful when associated with the
defined item.
ASSOCIATED_ESD indicates that the item identified in
_item_related.related_name is the estimated standard deviation of
of the defined item.
;
_item.name '_item_related.function_code'
_item.category_id item_related
_item.mandatory_code yes
_item_type.name '_item_related.function_code'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item_related.function_code'
alternate 'alternate form of the item'
'_item_related.function_code'
alternate_exclusive 'mutually exclusive alternate form of the item'
'_item_related.function_code'
convention 'depends on defined convention'
'_item_related.function_code'
conversion_constant 'related by a known conversion factor'
'_item_related.function_code'
conversion_arbitrary 'related by a arbitrary conversion factor'
'_item_related.function_code'
replaces 'a replacement definition'
'_item_related.function_code'
replacedby 'an obsolete definition'
'_item_related.function_code'
associated_value 'a meaningful value when related to the item'
'_item_related.function_code'
associated_esd 'an estimated standard deviation of the item'
'_item_related.function_code'
associated_error 'an estimated error of the item'
save_
# ----------------------------------------------------------------------------
save_ITEM_STRUCTURE
_category.description
;
This category holds the association between data items and
named vector/matrix declarations.
;
_category.id item_structure
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_structure
_category_key.name '_item_structure.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_structure
'item_group' item_structure
save_
save__item_structure.name
_item_description.name '_item_structure.name'
_item_description.description
;
The name of data item
;
_item.name '_item_structure.name'
_item.category_id item_structure
_item.mandatory_code implicit
_item_type.name '_item_structure.name'
_item_type.code name
save_
save__item_structure.code
_item_description.name '_item_structure.code'
_item_description.description
;
Provides an indirect reference into the list of structure
type definition in category item_structure_list.
;
_item.name '_item_structure.code'
_item.category_id item_structure
_item.mandatory_code yes
_item_type.name '_item_structure.code'
_item_type.code code
save_
save__item_structure.organization
_item_description.name '_item_structure.organization'
_item_description.description
;
Identifies if the struct is defined in column or row major order.
Only the unique elements of symmetric matrices are specified.
;
_item.name '_item_structure.organization'
_item.category_id item_structure
_item.mandatory_code yes
_item_type.name '_item_structure.organization'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item_structure.organization' 'columnwise' 'column major order'
'_item_structure.organization' 'rowwise' 'row major order'
save_
# ----------------------------------------------------------------------------
save_ITEM_STRUCTURE_LIST
_category.description
;
This category holds a description for each structure type.
;
_category.id item_structure_list
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_structure_list '_item_structure_list.code'
item_structure_list '_item_structure_list.index'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_structure_list
'item_group' item_structure_list
save_
save__item_structure_list.code
_item_description.name '_item_structure_list.code'
_item_description.description
;
The name of the matrix/vector structure declaration.
;
_item.name '_item_structure_list.code'
_item.category_id item_structure_list
_item.mandatory_code yes
_item_linked.parent_name '_item_structure_list.code'
_item_linked.child_name '_item_structure.code'
_item_type.name '_item_structure_list.code'
_item_type.code code
save_
save__item_structure_list.index
_item_description.name '_item_structure_list.index'
_item_description.description
;
Identifies the one based index of a row/column of the structure.
;
_item.name '_item_structure_list.index'
_item.category_id item_structure_list
_item.mandatory_code yes
loop_
_item_range.name
_item_range.minimum
_item_range.maximum
'_item_structure_list.index' 1 1
'_item_structure_list.index' 1 .
_item_type.name '_item_structure_list.index'
_item_type.code int
save_
save__item_structure_list.dimension
_item_description.name '_item_structure_list.dimension'
_item_description.description
;
Identifies the length of this row/column of the structure.
;
_item.name '_item_structure_list.dimension'
_item.category_id item_structure_list
_item.mandatory_code yes
loop_
_item_range.name
_item_range.minimum
_item_range.maximum
'_item_structure_list.dimension' 1 1
'_item_structure_list.dimension' 1 .
_item_type.name '_item_structure_list.dimension'
_item_type.code int
save_
# ----------------------------------------------------------------------------
save_ITEM_SUB_CATEGORY
_category.description
;
This category assigns data items to subcategories.
;
_category.id item_sub_category
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_sub_category '_item_sub_category.id'
item_sub_category '_item_sub_category.name'
loop_
_category_group.id
_category_group.category_id
'sub_category_group' item_sub_category
'item_group' item_sub_category
save_
save__item_sub_category.name
_item_description.name '_item_sub_category.name'
_item_description.description
;
The name of data item
;
_item.name '_item_sub_category.name'
_item.category_id item_sub_category
_item.mandatory_code implicit
_item_type.name '_item_sub_category.name'
_item_type.code name
save_
save__item_sub_category.id
_item_description.name '_item_sub_category.id'
_item_description.description
;
The identifier of subcategory
;
_item.name '_item_sub_category.id'
_item.category_id item_sub_category
_item.mandatory_code yes
_item_type.name '_item_sub_category.id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_ITEM_TYPE
_category.description
;
Attributes for specifying the data type code for each data item.
;
_category.id item_type
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_type
_category_key.name '_item_type.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_type
'item_group' item_type
save_
save__item_type.name
_item_description.name '_item_type.name'
_item_description.description
;
The name of data item
;
_item.name '_item_type.name'
_item.category_id item_type
_item.mandatory_code implicit
_item_type.name '_item_type.name'
_item_type.code name
save_
save__item_type.code
_item_description.name '_item_type.code'
_item_description.description
;
Data type of defined data item
;
_item.name '_item_type.code'
_item.category_id item_type
_item.mandatory_code yes
_item_type.name '_item_type.code'
_item_type.code code
save_
# ----------------------------------------------------------------------------
save_ITEM_TYPE_CONDITIONS
_category.description
;
Attributes for specifying additional conditions associated with
the data type of the item.
;
_category.id item_type_conditions
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_type_conditions
_category_key.name '_item_type_conditions.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_type_conditions
'item_group' item_type_conditions
'compliance_group' item_type_conditions
save_
save__item_type_conditions.name
_item_description.name '_item_type_conditions.name'
_item_description.description
;
The name of data item
;
_item.name '_item_type_conditions.name'
_item.category_id item_type_conditions
_item.mandatory_code implicit
_item_type.name '_item_type_conditions.name'
_item_type.code name
save_
save__item_type_conditions.code
_item_description.name '_item_type_conditions.code'
_item_description.description
;
Codes defining conditions on the _item_type.code specification.
'esd' permits a number string to contain an appended standard
deviation number enclosed within parentheses. E.g. 4.37(5)
'seq' permits data to be declared as a sequence of values
separated by a comma <,> or a colon <:>.
* The sequence v1,v2,v3,. signals that v1, v2, v3, etc.
are alternative values or the data item.
* The sequence v1:v2 signals that v1 and v2 are the boundary
values of a continuous range of values. This mechanism
was used to specify permitted ranges of an item in
previous DDL versions.
Combinations of alternate and range sequences are permitted.
;
_item.name '_item_type_conditions.code'
_item.category_id item_type_conditions
_item.mandatory_code yes
_item_type.name '_item_type_conditions.code'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item_type_conditions.code'
none 'no extra conditions apply to this data item'
'_item_type_conditions.code'
esd 'numbers may have esd values appended within ()'
'_item_type_conditions.code'
seq 'data may be declared as a comma or colon separated sequence'
save_
# ----------------------------------------------------------------------------
save_ITEM_TYPE_LIST
_category.description
;
Attributes which define each type code.
;
_category.id item_type_list
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_type_list
_category_key.name '_item_type_list.code'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_type_list
'item_group' item_type_list
save_
save__item_type_list.code
_item_description.name '_item_type_list.code'
_item_description.description
;
The codes specifying the nature of the data value.
;
_item.name '_item_type_list.code'
_item.category_id item_type_list
_item.mandatory_code yes
_item_type.name '_item_type_list.code'
_item_type.code code
_item_linked.child_name '_item_type.code'
_item_linked.parent_name '_item_type_list.code'
save_
save__item_type_list.primitive_code
_item_description.name '_item_type_list.primitive_code'
_item_description.description
;
The codes specifying the primitive type of the data value.
;
_item.name '_item_type_list.primitive_code'
_item.category_id item_type_list
_item.mandatory_code yes
_item_type.name '_item_type_list.primitive_code'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item_type_list.primitive_code'
numb 'numerically-interpretable string'
'_item_type_list.primitive_code'
char 'character or text string (case-sensitive)'
'_item_type_list.primitive_code'
uchar 'character or text string (case-insensitive)'
'_item_type_list.primitive_code'
null 'for dictionary purposes only'
save_
save__item_type_list.construct
_item_description.name '_item_type_list.construct'
_item_description.description
;
When a data value can be defined as a pre-determined sequence of
characters, or optional characters, or data names (for which the
definition is also available), it is specified as a construction.
The rules of construction conform to the the regular expression
(REGEX) specificatiopns detailed in the IEEE document P1003.2
Draft 11.2 Sept 1991 (ftp file '/doc/POSIX/1003.2/p121-140').
Resolved data names for which _item_type_list.construct
specifications exist are replaced by these constructions,
otherwise the data name string is not replaced.
;
_item.name '_item_type_list.construct'
_item.category_id item_type_list
_item.mandatory_code no
_item_type.name '_item_type_list.construct'
_item_type.code text
_item_examples.name '_item_type_list.construct'
_item_examples.case '{_year}-{_month}-{_day}'
_item_examples.detail 'typical construction for _date'
save_
save__item_type_list.detail
_item_description.name '_item_type_list.detail'
_item_description.description
;
An optional description of the data type
;
_item.name '_item_type_list.detail'
_item.category_id item_type_list
_item.mandatory_code no
_item_type.name '_item_type_list.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_ITEM_UNITS
_category.description
;
Specifies the physical units in which data items are expressed.
;
_category.id item_units
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_units
_category_key.name '_item_units.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_units
'item_group' item_units
save_
save__item_units.name
_item_description.name '_item_units.name'
_item_description.description
;
The name of data item
;
_item.name '_item_units.name'
_item.category_id item_units
_item.mandatory_code implicit
_item_type.name '_item_units.name'
_item_type.code name
save_
save__item_units.code
_item_description.name '_item_units.code'
_item_description.description
;
The identifier of unit in which the data item is expressed.
;
_item.name '_item_units.code'
_item.category_id item_units
_item.mandatory_code yes
_item_type.name '_item_units.code'
_item_type.code code
save_
# ----------------------------------------------------------------------------
save_ITEM_UNITS_CONVERSION
_category.description
;
Conversion factors between the various units of measure defined
in the ITEM_UNITS_LIST category.
;
_category.id item_units_conversion
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_units_conversion '_item_units_conversion.from_code'
item_units_conversion '_item_units_conversion.to_code'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_units_conversion
'item_group' item_units_conversion
save_
save__item_units_conversion.from_code
_item_description.name '_item_units_conversion.from_code'
_item_description.description
;
The unit system on which the conversion operation is applied
to produce the unit system specified in _item_units_conversion.to_code.
=
;
_item.name '_item_units_conversion.from_code'
_item.category_id item_units_conversion
_item.mandatory_code yes
_item_type.name '_item_units_conversion.from_code'
_item_type.code code
save_
save__item_units_conversion.to_code
_item_description.name '_item_units_conversion.to_code'
_item_description.description
;
The unit system produced after an operation is applied to the unit
system specified by _item_units_conversion.from_code.
=
;
_item.name '_item_units_conversion.to_code'
_item.category_id item_units_conversion
_item.mandatory_code yes
_item_type.name '_item_units_conversion.to_code'
_item_type.code code
save_
save__item_units_conversion.operator
_item_description.name '_item_units_conversion.operator'
_item_description.description
;
The arithmetic operator required to convert between the
unit systems:
=
;
_item.name '_item_units_conversion.operator'
_item.category_id item_units_conversion
_item.mandatory_code yes
_item_type.name '_item_units_conversion.operator'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item_units_conversion.operator' '+' 'addition'
'_item_units_conversion.operator' '-' 'subtraction'
'_item_units_conversion.operator' '*' 'multiplication'
'_item_units_conversion.operator' '/' 'division'
save_
save__item_units_conversion.factor
_item_description.name '_item_units_conversion.factor'
_item_description.description
;
The arithmetic operation required to convert between the
unit systems:
=
;
_item.name '_item_units_conversion.factor'
_item.category_id item_units_conversion
_item.mandatory_code yes
_item_type.name '_item_units_conversion.factor'
_item_type.code any
save_
# ----------------------------------------------------------------------------
save_ITEM_UNITS_LIST
_category.description
;
Attributes which describe the physical units of measure
in which data items may be expressed.
;
_category.id item_units_list
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_units_list
_category_key.name '_item_units_list.code'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_units_list
'item_group' item_units_list
save_
save__item_units_list.code
_item_description.name '_item_units_list.code'
_item_description.description
;
The code specifying the name of the unit of measure.
;
_item.name '_item_units_list.code'
_item.category_id item_units_list
_item.mandatory_code yes
_item_type.name '_item_units_list.code'
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_item_units.code' '_item_units_list.code'
'_item_units_conversion.from_code' '_item_units_list.code'
'_item_units_conversion.to_code' '_item_units_list.code'
save_
save__item_units_list.detail
_item_description.name '_item_units_list.detail'
_item_description.description
;
A description of the unit of measure.
;
_item.name '_item_units_list.detail'
_item.category_id item_units_list
_item.mandatory_code no
_item_type.name '_item_units_list.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_METHOD_LIST
_category.description
;
Attributes specifying the list of methods applicable to data items,
sub-categories, and categories.
;
_category.id method_list
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id method_list
_category_key.name '_method_list.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' method_list
'item_group' method_list
'category_group' method_list
save_
save__method_list.id
_item_description.name '_method_list.id'
_item_description.description
;
Identity of method in the list referenced by _method.id
;
_item.name '_method_list.id'
_item.category_id method_list
_item.mandatory_code yes
_item_type.name '_method_list.id'
_item_type.code idname
loop_
_item_linked.child_name
_item_linked.parent_name
'_item_methods.method_id' '_method_list.id'
'_category_methods.method_id' '_method_list.id'
'_sub_category_methods.method_id' '_method_list.id'
'_datablock_methods.method_id' '_method_list.id'
save_
save__method_list.detail
_item_description.name '_method_list.detail'
_item_description.description
;
Description of application method in _method_list.id
;
_item.name '_method_list.detail'
_item.category_id method_list
_item.mandatory_code no
_item_type.name '_method_list.detail'
_item_type.code text
save_
save__method_list.inline
_item_description.name '_method_list.inline'
_item_description.description
;
Inline text of a method associated with the data item.
;
_item.name '_method_list.inline'
_item.category_id method_list
_item.mandatory_code yes
_item_type.name '_method_list.inline'
_item_type.code text
save_
save__method_list.code
_item_description.name '_method_list.code'
_item_description.description
;
A code that describes the function of the method.
;
_item.name '_method_list.code'
_item.category_id method_list
_item.mandatory_code yes
_item_type.name '_method_list.code'
_item_type.code code
loop_
_item_examples.name
_item_examples.case
_item_examples.detail
'_method_list.code' calculation 'method to calculate the item '
'_method_list.code' verification 'method to verify the data item '
'_method_list.code' cast 'method to provide cast conversion '
'_method_list.code' addition 'method to define item + item '
'_method_list.code' division 'method to define item / item '
'_method_list.code' multiplication 'method to define item * item '
'_method_list.code' equivalence 'method to define item = item '
'_method_list.code' other 'miscellaneous method '
save_
save__method_list.language
_item_description.name '_method_list.language'
_item_description.description
;
Language in which the method is expressed.
;
_item.name '_method_list.language'
_item.category_id method_list
_item.mandatory_code yes
_item_type.name '_method_list.language'
_item_type.code code
loop_
_item_examples.name
_item_examples.case
_item_examples.detail
'_method_list.language' BNF ?
'_method_list.language' C ?
'_method_list.language' C++ ?
'_method_list.language' FORTRAN ?
'_method_list.language' LISP ?
'_method_list.language' PASCAL ?
'_method_list.language' PEARL ?
'_method_list.language' TCL ?
'_method_list.language' OTHER ?
save_
# ----------------------------------------------------------------------------
save_DICTIONARY
_category.description
;
Attributes for specifying the dictionary title, version and
data block identifier.
;
_category.id dictionary
_category.mandatory_code yes
_category.implicit_key mmcif_ddl.dic
_category_key.id dictionary
_category_key.name '_dictionary.datablock_id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' dictionary
'datablock_group' dictionary
'dictionary_group' dictionary
save_
save__dictionary.datablock_id
_item_description.name '_dictionary.datablock_id'
_item_description.description
;
The identifier for the data block containing the dictionary.
;
_item.name '_dictionary.datablock_id'
_item.category_id dictionary
_item.mandatory_code implicit
_item_type.name '_dictionary.datablock_id'
_item_type.code code
save_
save__dictionary.title
_item_description.name '_dictionary.title'
_item_description.description
;
Title identification of the dictionary.
;
_item.name '_dictionary.title'
_item.category_id dictionary
_item.mandatory_code yes
_item_type.name '_dictionary.title'
_item_type.code char
save_
save__dictionary.version
_item_description.name '_dictionary.version'
_item_description.description
;
A unique version identifier for the dictionary.
;
_item.name '_dictionary.version'
_item.category_id dictionary
_item.mandatory_code yes
_item_type.name '_dictionary.version'
_item_type.code char
save_
# ----------------------------------------------------------------------------
save_DICTIONARY_HISTORY
_category.description
;
Attributes for specifying the revision history of the dictionary.
;
_category.id dictionary_history
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id dictionary_history
_category_key.name '_dictionary_history.version'
loop_
_category_group.id
_category_group.category_id
'ddl_group' dictionary_history
'dictionary_group' dictionary_history
save_
save__dictionary_history.version
_item_description.name '_dictionary_history.version'
_item_description.description
;
A unique version identifier for the dictionary revision.
;
_item.name '_dictionary_history.version'
_item.category_id dictionary_history
_item.mandatory_code yes
_item_type.name '_dictionary_history.version'
_item_type.code char
_item_linked.child_name '_dictionary.version'
_item_linked.parent_name '_dictionary_history.version'
save_
save__dictionary_history.update
_item_description.name '_dictionary_history.update'
_item_description.description
;
The date that the last dictionary revision took place.
;
_item.name '_dictionary_history.update'
_item.category_id dictionary_history
_item.mandatory_code yes
_item_type.name '_dictionary_history.update'
_item_type.code yyyy-mm-dd
save_
save__dictionary_history.revision
_item_description.name '_dictionary_history.revision'
_item_description.description
;
Text description of the dictionary revision.
;
_item.name '_dictionary_history.revision'
_item.category_id dictionary_history
_item.mandatory_code yes
_item_type.name '_dictionary_history.revision'
_item_type.code text
save_
### EOF mmcif_ddl-def-1.dic
###########################################################################
#
# File: mmcif_ddl-def-1.dic
#
# mmCIF DDL Core Dictionary with NDB extensions
#
# This DDL dictionary is a mirror of ddl_core.dic-org with all implicit
# data items fully expanded and with NDB extensions added.
#
# Definition Section 2.
# (NDB Extension Definitions)
#
#
###########################################################################
save_NDB_CATEGORY_DESCRIPTION
_category.description
;
NDB description of data items in this category.
;
_category.id ndb_category_description
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
ndb_category_description '_ndb_category_description.id'
ndb_category_description '_ndb_category_description.description'
save_
save__ndb_category_description.id
_item.name '_ndb_category_description.id'
_item.category_id ndb_category_description
_item.mandatory_code implicit
_item_type.name '_ndb_category_description.id'
_item_type.code idname
_item_linked.child_name '_ndb_category_description.id'
_item_linked.parent_name '_category.id'
save_
save__ndb_category_description.description
_item_description.name '_ndb_category_description.description'
_item_description.description
;
NDB text description of a category.
;
_item.name '_ndb_category_description.description'
_item.category_id ndb_category_description
_item.mandatory_code yes
_item_type.name '_ndb_category_description.description'
_item_type.code text
save_
# --------------------------------------------------------------------------
save_NDB_CATEGORY_EXAMPLES
_category.description
;
NDB example applications and descriptions of data items in this
category.
;
_category.id ndb_category_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
ndb_category_examples '_ndb_category_examples.id'
ndb_category_examples '_ndb_category_examples.case'
save_
save__ndb_category_examples.id
_item.name '_ndb_category_examples.id'
_item.category_id ndb_category_examples
_item.mandatory_code implicit
_item_type.name '_ndb_category_examples.id'
_item_type.code idname
_item_linked.child_name '_ndb_category_examples.id'
_item_linked.parent_name '_category.id'
save_
save__ndb_category_examples.case
_item_description.name '_ndb_category_examples.case'
_item_description.description
;
NDB case of examples involving items in this category.
;
_item.name '_ndb_category_examples.case'
_item.category_id ndb_category_examples
_item.mandatory_code yes
_item_type.name '_ndb_category_examples.case'
_item_type.code text
save_
save__ndb_category_examples.detail
_item_description.name '_ndb_category_examples.detail'
_item_description.description
;
NDB description of an example _category_examples.case
;
_item.name '_ndb_category_examples.detail'
_item.category_id ndb_category_examples
_item.mandatory_code no
_item_type.name '_ndb_category_examples.detail'
_item_type.code text
save_
#--------------------------------------------------------------------------
save_NDB_ITEM_DESCRIPTION
_category.description
;
This category holds the NDB descriptions of each data item.
;
_category.id ndb_item_description
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
ndb_item_description '_ndb_item_description.name'
ndb_item_description '_ndb_item_description.description'
loop_
_category_group.id
_category_group.category_id
'ddl_group' ndb_item_description
'item_group' ndb_item_description
save_
save__ndb_item_description.name
_item_description.name '_ndb_item_description.name'
_item_description.description
;
Data name of the defined item.
;
_item.name '_ndb_item_description.name'
_item.category_id ndb_item_description
_item.mandatory_code implicit
_item_type.name '_ndb_item_description.name'
_item_type.code name
_item_linked.child_name '_ndb_item_description.name'
_item_linked.parent_name '_item.name'
save_
save__ndb_item_description.description
_item_description.name '_ndb_item_description.description'
_item_description.description
;
NDB text description of the defined data item.
;
_item.name '_ndb_item_description.description'
_item.category_id ndb_item_description
_item.mandatory_code yes
_item_type.name '_ndb_item_description.description'
_item_type.code text
save_
# --------------------------------------------------------------------------
save_NDB_ITEM_ENUMERATION
_category.description
;
Attributes which specify the permitted enumeration of the items.
;
_category.id ndb_item_enumeration
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
ndb_item_enumeration '_ndb_item_enumeration.name'
ndb_item_enumeration '_ndb_item_enumeration.value'
loop_
_category_group.category_id
_category_group.id
ndb_item_enumeration 'ddl_group'
ndb_item_enumeration 'item_group'
save_
save__ndb_item_enumeration.name
_item.name '_ndb_item_enumeration.name'
_item.category_id ndb_item_enumeration
_item.mandatory_code implicit
_item_type.name '_ndb_item_enumeration.name'
_item_type.code name
_item_linked.child_name '_ndb_item_enumeration.name'
_item_linked.parent_name '_item.name'
save_
save__ndb_item_enumeration.value
_item_description.name '_ndb_item_enumeration.value'
_item_description.description
;
A permissible value, character or number, for the defined item.
;
_item.name '_ndb_item_enumeration.value'
_item.category_id ndb_item_enumeration
_item.mandatory_code yes
_item_type.name '_ndb_item_enumeration.value'
_item_type.code any
save_
save__ndb_item_enumeration.detail
_item_description.name '_ndb_item_enumeration.detail'
_item_description.description
;
A description of a permissible value for the defined item.
;
_item.name '_ndb_item_enumeration.detail'
_item.category_id ndb_item_enumeration
_item.mandatory_code no
_item_type.name '_ndb_item_enumeration.detail'
_item_type.code text
save_
# --------------------------------------------------------------------------
save_NDB_ITEM_EXAMPLES
_category.description
;
Attributes for describing application examples of the data item.
;
_category.id ndb_item_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
ndb_item_examples '_ndb_item_examples.name'
ndb_item_examples '_ndb_item_examples.case'
loop_
_category_group.id
_category_group.category_id
'ddl_group' ndb_item_examples
'item_group' ndb_item_examples
save_
save__ndb_item_examples.case
_item_description.name '_ndb_item_examples.case'
_item_description.description
;
NDB example application of the defined data item.
;
_item.name '_ndb_item_examples.case'
_item.category_id ndb_item_examples
_item.mandatory_code yes
_item_type.name '_ndb_item_examples.case'
_item_type.code text
save_
save__ndb_item_examples.detail
_item_description.name '_ndb_item_examples.detail'
_item_description.description
;
NDB description of an example specified in _ndb_item_example.case
;
_item.name '_ndb_item_examples.detail'
_item.category_id ndb_item_examples
_item.mandatory_code yes
_item_type.name '_ndb_item_examples.detail'
_item_type.code text
save_
save__ndb_item_examples.name
_item.name '_ndb_item_examples.name'
_item.category_id ndb_item_examples
_item.mandatory_code implicit
_item_type.name '_ndb_item_examples.name'
_item_type.code name
_item_linked.child_name '_ndb_item_examples.name'
_item_linked.parent_name '_item.name'
save_
#### EOF mmcif_ddl-def-2.dic
./CBFlib-0.9.2.2/doc/Idiffrn_radiation.xray_symbol.html 0000644 0000765 0000765 00000006441 11603702115 021220 0 ustar yaya yaya
(IUCr) CIF Definition save__diffrn_radiation.xray_symbol
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
./CBFlib-0.9.2.2/doc/cif_img_1.5.3_8Jul07.dic 0000644 0000765 0000765 00000746652 11603702115 016242 0 ustar yaya yaya ##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.5.3 #
# of 2007-07-08 #
# ################################################################### #
# # *** WARNING *** THIS IS A DRAFT FOR DISCUSSSION *** WARNING *** # #
# # SUBJECT TO CHANGE WITHOUT NOTICE # #
# # SEND COMMENTS TO imgcif-l@iucr.org CITING THE VERSION # #
# ################################################################### #
# This draft edited by H. J. Bernstein #
# #
# by Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook #
# #
# This dictionary was adapted from format discussed at the imgCIF Workshop, #
# held at BNL Oct 1997 and the Crystallographic Binary File Format Draft #
# Proposal by Andrew Hammersley. The first DDL 2.1 Version was created by #
# John Westbrook. This version was drafted by Herbert J. Bernstein and #
# incorporates comments by I. David Brown, John Westbrook, Brian McMahon, #
# Bob Sweet, Paul Ellis, Harry Powell, Wilfred Li, Gotzon Madariaga, #
# Frances C. Bernstein, Chris Nielsen, Nicola Ashcroft and others. #
##############################################################################
data_cif_img.dic
_dictionary.title cif_img.dic
_dictionary.version 1.5.3
_dictionary.datablock_id cif_img.dic
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
# SUB_CATEGORY
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
# _array_data.header_contents
# _array_data.header_convention
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.gain
# _array_intensities.gain_esd
# _array_intensities.linearity
# _array_intensities.offset
# _array_intensities.scaling
# _array_intensities.overload
# _array_intensities.undefined_value
# _array_intensities.pixel_fast_bin_size
# _array_intensities.pixel_slow_bin_size
# _array_intensities.pixel_binning_method
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.compression_type_flag
# _array_structure.encoding_type
# _array_structure.id
#
# category ARRAY_STRUCTURE_LIST
#
# _array_structure_list.axis_set_id
# _array_structure_list.array_id
# _array_structure_list.dimension
# _array_structure_list.direction
# _array_structure_list.index
# _array_structure_list.precedence
#
# category ARRAY_STRUCTURE_LIST_AXIS
#
# _array_structure_list_axis.axis_id
# _array_structure_list_axis.axis_set_id
# _array_structure_list_axis.angle
# _array_structure_list_axis.angle_increment
# _array_structure_list_axis.displacement
# _array_structure_list_axis.fract_displacement
# _array_structure_list_axis.displacement_increment
# _array_structure_list_axis.fract_displacement_increment
# _array_structure_list_axis.angular_pitch
# _array_structure_list_axis.radial_pitch
# _array_structure_list_axis.reference_angle
# _array_structure_list_axis.reference_displacement
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.type
# _axis.system
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
#
# category DIFFRN_DATA_FRAME
#
# _diffrn_data_frame.array_id
# _diffrn_data_frame.binary_id
# _diffrn_data_frame.center_fast
# _diffrn_data_frame.center_slow
# _diffrn_data_frame.center_units
# _diffrn_data_frame.detector_element_id
# _diffrn_data_frame.id
# _diffrn_data_frame.details
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.id
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.axis_id
# _diffrn_detector_axis.detector_id
#
# category DIFFRN_DETECTOR_ELEMENT
#
# _diffrn_detector_element.id
# _diffrn_detector_element.detector_id
# _diffrn_detector_element.reference_center_fast
# _diffrn_detector_element.reference_center_slow
# _diffrn_detector_element.reference_center_units
#
# category DIFFRN_MEASUREMENT
#
# _diffrn_measurement.diffrn_id
# _diffrn_measurement.details
# _diffrn_measurement.device
# _diffrn_measurement.device_details
# _diffrn_measurement.device_type
# _diffrn_measurement.id
# _diffrn_measurement.method
# _diffrn_measurement.number_of_axes
# _diffrn_measurement.sample_detector_distance
# _diffrn_measurement.sample_detector_voffset
# _diffrn_measurement.specimen_support
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.axis_id
# _diffrn_measurement_axis.measurement_device
# _diffrn_measurement_axis.measurement_id
#
# category DIFFRN_RADIATION
#
# _diffrn_radiation.collimation
# _diffrn_radiation.diffrn_id
# _diffrn_radiation.div_x_source
# _diffrn_radiation.div_y_source
# _diffrn_radiation.div_x_y_source
# _diffrn_radiation.filter_edge'
# _diffrn_radiation.inhomogeneity
# _diffrn_radiation.monochromator
# _diffrn_radiation.polarisn_norm
# _diffrn_radiation.polarisn_ratio
# _diffrn_radiation.polarizn_source_norm
# _diffrn_radiation.polarizn_source_ratio
# _diffrn_radiation.probe
# _diffrn_radiation.type
# _diffrn_radiation.xray_symbol
# _diffrn_radiation.wavelength_id
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.date_end
# _diffrn_scan.date_start
# _diffrn_scan.integration_time
# _diffrn_scan.frame_id_start
# _diffrn_scan.frame_id_end
# _diffrn_scan.frames
#
# category DIFFRN_SCAN_AXIS
#
# _diffrn_scan_axis.axis_id
# _diffrn_scan_axis.angle_start
# _diffrn_scan_axis.angle_range
# _diffrn_scan_axis.angle_increment
# _diffrn_scan_axis.angle_rstrt_incr
# _diffrn_scan_axis.displacement_start
# _diffrn_scan_axis.displacement_range
# _diffrn_scan_axis.displacement_increment
# _diffrn_scan_axis.displacement_rstrt_incr
# _diffrn_scan_axis.reference_angle
# _diffrn_scan_axis.reference_displacement
# _diffrn_scan_axis.scan_id
#
# category DIFFRN_SCAN_FRAME
#
# _diffrn_scan_frame.date
# _diffrn_scan_frame.frame_id
# _diffrn_scan_frame.frame_number
# _diffrn_scan_frame.integration_time
# _diffrn_scan_frame.scan_id
#
# category DIFFRN_SCAN_FRAME_AXIS
#
# _diffrn_scan_frame_axis.axis_id
# _diffrn_scan_frame_axis.angle
# _diffrn_scan_frame_axis.angle_increment
# _diffrn_scan_frame_axis.angle_rstrt_incr
# _diffrn_scan_frame_axis.displacement
# _diffrn_scan_frame_axis.displacement_increment
# _diffrn_scan_frame_axis.displacement_rstrt_incr
# _diffrn_scan_frame_axis.reference_angle
# _diffrn_scan_frame_axis.reference_displacement
# _diffrn_scan_frame_axis.frame_id
#
# categor MAP
#
# _map.details
# _map.diffrn_id
# _map.entry_id
# _map.id
#
# categor MAP_SEGMENT
#
# _map_segment.array_id
# _map_segment.binary_id
# _map_segment.mask_array_id
# _map_segment.mask_binary_id
# _map_segment.id
# _map_segment.map_id
# _map_segment.details
#
# ***DEPRECATED*** data items
#
# _diffrn_detector_axis.id
# _diffrn_detector_element.center[1]
# _diffrn_detector_element.center[2]
# _diffrn_measurement_axis.id
#
# ***DEPRECATED*** category DIFFRN_FRAME_DATA
#
# _diffrn_frame_data.array_id
# _diffrn_frame_data.binary_id
# _diffrn_frame_data.detector_element_id
# _diffrn_frame_data.id
# _diffrn_frame_data.details
#
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
##################
## SUB_CATEGORY ##
##################
loop_
_sub_category.id
_sub_category.description
'matrix'
; The collection of elements of a matrix.
;
'vector'
; The collection of elements of a vector.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
; Data items in the ARRAY_DATA category are the containers for
the array data items described in the category ARRAY_STRUCTURE.
It is recognized that the data in this category needs to be used in
two distinct ways. During a data collection the lack of ancillary
data and timing constraints in processing data may dictate the
need to make a 'miniCBF' nothing more than an essential minimum
of information to record the results of the data collection. In that
case it is proper to use the ARRAY_DATA category as a
container for just a single image and a compacted, beam-line
dependent list of data collection parameter values. In such
a case, only the tags '_array_data.header_convention',
'_array_data.header_contents' and '_array_data.data' need be
populated.
For full processing and archiving, most of the tags in this
dictionary will need to be populated.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and is
presented as hexadecimal data. The first character 'H' on the
data lines means hexadecimal. It could have been 'O' for octal
or 'D' for decimal. The second character on the line shows
the number of bytes in each word (in this case '4'), which then
requires eight hexadecimal digits per word. The third character
gives the order of octets within a word, in this case '<'
for the ordering 4321 (i.e. 'big-endian'). Alternatively, the
character '>' could have been used for the ordering 1234
(i.e. 'little-endian'). The block has a 'message digest'
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 2
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
This example shows a single image in a miniCBF, provided by
E. Eikenberry. The entire CBF consists of one data block
containing one category and three tags. The CBFlib
program convert_miniCBF and a suitable template file
can be used to convert this miniCBF to a full imgCIF
file.
;
;
###CBF: VERSION 1.5
# CBF file written by CBFlib v0.7.8
data_insulin_pilatus6m
_array_data.header_convention SLS_1.0
_array_data.header_contents
;
# Detector: PILATUS 6M SN: 60-0001
# 2007/Jun/17 15:12:36.928
# Pixel_size 172e-6 m x 172e-6 m
# Silicon sensor, thickness 0.000320 m
# Exposure_time 0.995000 s
# Exposure_period 1.000000 s
# Tau = 194.0e-09 s
# Count_cutoff 1048575 counts
# Threshold_setting 5000 eV
# Wavelength 1.2398 A
# Energy_range (0, 0) eV
# Detector_distance 0.15500 m
# Detector_Voffset -0.01003 m
# Beam_xy (1231.00, 1277.00) pixels
# Flux 22487563295 ph/s
# Filter_transmission 0.0008
# Start_angle 13.0000 deg.
# Angle_increment 1.0000 deg.
# Detector_2theta 0.0000 deg.
# Polarization 0.990
# Alpha 0.0000 deg.
# Kappa 0.0000 deg.
# Phi 0.0000 deg.
# Chi 0.0000 deg.
# Oscillation_axis X, CW
# N_oscillations 1
;
_array_data.data
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_BYTE_OFFSET"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 6247567
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
X-Binary-Element-Byte-Order: LITTLE_ENDIAN
Content-MD5: 8wO6i2+899lf5iO8QPdgrw==
X-Binary-Number-of-Elements: 6224001
X-Binary-Size-Fastest-Dimension: 2463
X-Binary-Size-Second-Dimension: 2527
X-Binary-Size-Padding: 4095
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
If not given, it defaults to 1.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code implicit
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id, should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-ID, the value of _array_data.binary_id
should be equal to the value given for X-Binary-ID.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
'\n--CIF-BINARY-FORMAT-SECTION--' (including the
required initial '\n--').
The Content-Type may be any of the discrete types permitted
in RFC 2045; 'application/octet-stream' is recommended
for diffraction images in the ARRAY_DATA category.
Note: When appropriate in other categories, e.g. for
photographs of crystals, more precise types, such as
'image/jpeg', 'image/tiff', 'image/png', etc. should be used.
If an octet stream was compressed, the compression should
be specified by the parameter
'conversions="X-CBF_PACKED"'
or the parameter
'conversions="X-CBF_CANONICAL"'
or the parameter
'conversions="X-CBF_BYTE_OFFSET"'
If the parameter
'conversions="X-CBF_PACKED"'
is given it may be further modified with the parameters
'"uncorrelated_sections"'
or
'"flat"'
If the '"uncorrelated_sections"' parameter is
given, each section will be compressed without using
the prior section for averaging.
If the '"flat"' parameter is given, each the
image will be treated as one long row.
The Content-Transfer-Encoding may be 'BASE64',
'Quoted-Printable', 'X-BASE8', 'X-BASE10',
'X-BASE16' or 'X-BASE32K', for an imgCIF or 'BINARY'
for a CBF. The octal, decimal and hexadecimal transfer
encodings are provided for convenience in debugging and
are not recommended for archiving and data interchange.
In a CIF, one of the parameters 'charset=us-ascii',
'charset=utf-8' or 'charset=utf-16' may be used on the
Content-Transfer-Encoding to specify the character set
used for the external presentation of the encoded data.
If no charset parameter is given, the character set of
the enclosing CIF is assumed. In any case, if a BOM
flag is detected (FE FF for big-endian UTF-16, FF FE for
little-endian UTF-16 or EF BB BF for UTF-8) is detected,
the indicated charset will be assumed until the end of the
encoded data or the detection of a different BOM. The
charset of the Content-Transfer-Encoding is not the character
set of the encoded data, only the character set of the
presentation of the encoded data and should be respecified
for each distinct STAR string.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In an imgCIF file,
the encoded binary data ends with the terminating boundary
delimiter '\n--CIF-BINARY-FORMAT-SECTION----'
in the currently effective charset or with the '\n; '
that terminates the STAR string.
In a CBF, the raw binary data begins after an empty line
terminating the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of
the message size or in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. An adjustment is made for
the deprecated binary formats in which eight bytes of binary
header are used for the compression type. In this case,
the eight bytes used for the compression type are subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is 'unsigned 32-bit integer'.
An MD5 message digest may, optionally, be used. The 'RSA Data
Security, Inc. MD5 Message-Digest Algorithm' should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is 'X-BASE8', 'X-BASE10' or
'X-BASE16', the data are presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ('big-
endian') or 1234... ('little-endian'). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as '==' for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is 'H', 'O' or 'D' for hexadecimal, octal or
decimal, n is the number of octets per word and d is '<'
or '>' for the '...4321' and '1234...' octet orderings,
respectively. The '==' padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hexadecimal, octal and decimal formats only,
comments beginning with '#' are permitted to improve
readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three: c1, c2, c3. The resulting 24 bits
are broken into four six-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order four bits of the second octet [(c1 & 3)<<4 | (c2>>4)],
then the bottom four bits of the second octet followed by the
high-order two bits of the last octet [(c2 & 15)<<2 | (c3>>6)],
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
With short groups of octets padded on the right with one '='
if c3 is missing, and with '==' if both c2 and c3 are missing.
X-BASE32K encoding is similar to BASE64 encoding, except that
sets of 15 octets are encoded as sets of 8 16-bit unicode
characters, by breaking the 120 bits into 8 15-bit quantities.
256 is added to each 15 bit quantity to bring it into a
printable uncode range. When encoding, zero padding is used
to fill out the last 15 bit quantity. If 8 or more bits of
padding are used, a single equals sign (hexadecimal 003D) is
appended. Embedded whitespace and newlines are introduced
to produce lines of no more than 80 characters each. On
decoding, all printable ascii characters and ascii whitespace
characters are ignored except for any trailing equals signs.
The number of trailing equals signs indicated the number of
trailing octets to be trimmed from the end of the decoded data.
(see Georgi Darakev, Vassil Litchev, Kostadin Z. Mitev, Herbert
J. Bernstein, 'Efficient Support of Binary Data in the XML
Implementation of the NeXus File Format',absract W0165,
ACA Summer Meeting, Honolulu, HI, July 2006).
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32...38,
42, 48...57, 59, 60, 62, 64...126 and the octet is not a ';'
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
'wrapped' with a terminating '=' (i.e. the MIME conventions
for an implicit line terminator are never used).
The "X-Binary-Element-Byte-Order" can specify either
'"BIG_ENDIAN"' or '"LITTLE_ENDIAN"' byte order of the imaage
data. Only LITTLE_ENDIAN is recommended. Processors
may treat BIG_ENDIAN as a warning of data that can
only be processed by special software.
The "X-Binary-Number-of-Elements" specifies the number of
elements (not the number of octets) in the decompressed, decoded
image.
The optional "X-Binary-Size-Fastest-Dimension" specifies the
number of elements (not the number of octets) in one row of the
fastest changing dimension of the binary data array. This
information must be in the MIME header for proper operation of
some of the decompression algorithms.
The optional "X-Binary-Size-Second-Dimension" specifies the
number of elements (not the number of octets) in one column of
the second-fastest changing dimension of the binary data array.
This information must be in the MIME header for proper operation
of some of the decompression algorithms.
The optional "X-Binary-Size-Third-Dimension" specifies the number
of sections for the third-fastest changing dimension of the
binary data array.
The optional "X-Binary-Size-Padding" specifies the size in
octets of an optional padding after the binary array data and
before the closing flags for a binary section.
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
save__array_data.header_contents
_item_description.description
; This item is an text field for use in minimal CBF files to carry
essential header information to be kept with image data
in _array_data.data when the tags that normally carry the
structured metadata for the image have not been populated.
Normally this data item should not appear when the full set
of tags have been populated and _diffrn_data_frame.details
appears.
;
_item.name '_array_data.header_contents'
_item.category_id array_data
_item.mandatory_code no
_item_type.code text
save_
save__array_data.header_convention
_item_description.description
; This item is an identifier for the convention followed in
constructing the contents of _array_data.header_contents
The permitted values are of the of an image creator identifier
followed by an underscore and a version string. To avoid
confusion about conventions, all creator identifiers
should be registered with the IUCr and the conventions
for all identifiers and versions should be posted on
the MEDSBIO.org web site.
;
_item.name '_array_data.header_convention'
_item.category_id array_data
_item.mandatory_code no
_item_type.code code
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
; Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code implicit
_item_type.code code
save_
save__array_element_size.index
_item_description.description
; This item is a pointer to _array_structure_list.index in
the ARRAY_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
; The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
; Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
_array_intensities.gain. If raw, uncorrected values
are presented (e.g. for calibration experiments), the
value of _array_intensities.linearity will be 'raw'
and _array_intensities.gain will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.overload
_array_intensities.undefined_value
_array_intensities.pixel_fast_bin_size
_array_intensities.pixel_slow_bin_size
_array_intensities.pixel_binning_method
image_1 linear 1.2 655535 0 2 2 hardware
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
; Detector 'gain'. The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
; The estimated standard deviation in detector 'gain'.
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
; The intensity linearity scaling method used to convert
from the raw intensity to the stored element value:
'linear' is linear.
'offset' means that the value defined by
_array_intensities.offset should be added to each
element value.
'scaling' means that the value defined by
_array_intensities.scaling should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by _array_intensities.scaling is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
'logarithmic_scaled' means that the logarithm base 10 of
raw intensities multiplied by _array_intensities.scaling
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and calculating 10
to the power of this number.
'raw' means that the data are a set of raw values straight
from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
; The value defined by _array_intensities.offset should
be added to each element value.
;
'scaling'
; The value defined by _array_intensities.scaling should be
multiplied with each element value.
;
'scaling_offset'
; The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
; The square root of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
;
'logarithmic_scaled'
; The logarithm base 10 of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
_array_intensities.scaling and calculating 10 to the
power of this number.
;
'raw'
; The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data-fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
; Offset value to add to array element values in the manner
described by the item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
; The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.pixel_fast_bin_size
_item_description.description
; The value of _array_intensities.pixel_fast_bin_size specifies
the number of pixels that compose one element in the direction
of the most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_fast_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_slow_bin_size
_item_description.description
; The value of _array_intensities.pixel_slow_bin_size specifies
the number of pixels that compose one element in the direction
of the second most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_slow_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_binning_method
_item_description.description
; The value of _array_intensities.pixel_binning_method specifies
the method used to derive array elements from multiple pixels.
;
_item.name '_array_intensities.pixel_binning_method'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'hardware'
; The element intensities were derived from the raw data of one
or more pixels by used of hardware in the detector, e.g. by use
of shift registers in a CCD to combine pixels into super-pixels.
;
'software'
; The element intensities were derived from the raw data of more
than one pixel by use of software.
;
'combined'
; The element intensities were derived from the raw data of more
than one pixel by use of both hardware and software, as when
hardware binning is used in one direction and software in the
other.
;
'none'
; In the both directions, the data has not been binned. The
number of pixels is equal to the number of elements.
When the value of _array_intensities.pixel_binning_method is
'none' the values of _array_intensities.pixel_fast_bin_size
and _array_intensities.pixel_slow_bin_size both must be 1.
;
'unspecified'
; The method used to derive element intensities is not specified.
;
_item_default.value 'unspecified'
save_
save__array_intensities.scaling
_item_description.description
; Multiplicative scaling value to be applied to array data
in the manner described by item
_array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.undefined_value
_item_description.description
; A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
; Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data that may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
_category_key.name '_array_structure.id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
; The order of bytes for integer values which require more
than 1 byte.
(IBM-PC's and compatibles and DEC VAXs use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. DEC Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
; The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
; The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
; Type of data-compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'byte_offset'
; Using the 'byte_offset' compression scheme as per A. Hammersley
and the CBFlib manual, section 3.3.3
;
'canonical'
; Using the 'canonical' compression scheme (International Tables
for Crystallography Volume G, Section 5.6.3.1) and CBFlib
manual section 3.3.1
;
'none'
; Data are stored in normal format as defined by
_array_structure.encoding_type and
_array_structure.byte_order.
;
'packed'
; Using the 'packed' compression scheme, a CCP4-style packing
as per J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
'packed_v2'
; Using the 'packed' compression scheme, version 2, as per
J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
save_
save__array_structure.compression_type_flag
_item_description.description
; Flags modifying the type of data-compression method used to
compress the arraydata.
;
_item.name '_array_structure.compression_type_flag'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'uncorrelated_sections'
; When applying packed or packed_v2 compression on an array with
uncorrelated sections, do not average in points from the prior
section.
;
'flat'
; When applying packed or packed_v2 compression on an array with
treat the entire image as a single line set the maximum number
of bits for an offset to 65 bits.
The flag is included for compatibility with software prior to
CBFlib_0.7.7, and should not be used for new data sets.
;
save_
save__array_structure.encoding_type
_item_description.description
; Data encoding of a single element of array data.
The type 'unsigned 1-bit integer' is used for
packed Booleans arrays for masks. Each element
of the array corresponds to a single bit
packed in unsigned 8-bit data.
In several cases, the IEEE format is referenced.
See IEEE Standard 754-1985 (IEEE, 1985).
Ref: IEEE (1985). IEEE Standard for Binary Floating-Point
Arithmetic. ANSI/IEEE Std 754-1985. New York: Institute of
Electrical and Electronics Engineers.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 1-bit integer'
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
This item has been made implicit and given a default value of 1
as a convenience in writing miniCBF files. Normally an
explicit name with useful content should be used.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure implicit
'_array_data.array_id' array_data implicit
'_array_structure_list.array_id' array_structure_list implicit
'_array_intensities.array_id' array_intensities implicit
'_diffrn_data_frame.array_id' diffrn_data_frame implicit
_item_default.value 1
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
; Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left to right (increasing) in the
first dimension and bottom to top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differs
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the 'poise' of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
; The number of elements stored in the array structure in this
dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
; Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
; Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
; Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
; Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
; Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
; Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets of axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axes: one for the angular
direction and one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes in the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
; The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to
_array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list_axis.angle
_item_description.description
; The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified for this case.
See _array_structure_list_axis.angular_pitch.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement
_item_description.description
; The setting of the specified axis as a decimal fraction of
the axis unit vector for the first data point of the array
index with the corresponding value of
_array_structure_list.axis_set_id.
If the index is specified as 'increasing', this will be the
centre of the pixel with index value 1. If the index is
specified as 'decreasing', this will be the centre of the
pixel with maximum index value.
;
_item.name '_array_structure_list_axis.fract_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis as a decimal fraction of the
axis unit vector.
;
_item.name
'_array_structure_list_axis.fract_displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
; The pixel-centre-to-pixel-centre distance for a one-step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans
or for uncoupled angular scans at a constant radius
(cylindrical scans) and should not be specified for cases
in which the angle between pixels (rather than the distance
between pixels) is uniform.
See _array_structure_list_axis.angle_increment.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
; The radial distance from one 'cylinder' of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of _array_structure_list_axis.displacement_increment.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.reference_angle
_item_description.description
; The value of _array_structure_list_axis.reference_angle
specifies the setting of the angle of this axis used for
determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the
value of _array_structure_list.angle.
;
_item.name '_array_structure_list_axis.reference_angle'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.reference_displacement
_item_description.description
; The value of _array_structure_list_axis.reference_displacement
specifies the setting of the displacement of this axis used
for determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the value
of _array_structure_list.displacement.
;
_item.name '_array_structure_list_axis.reference_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
########
# AXIS #
########
save_AXIS
_category.description
; Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection or the axes defining the
coordinate system of an image.
The location of each axis is specified by two vectors: the axis
itself, given by a unit vector in the direction of the axis, and
an offset to the base of the unit vector.
The vectors defining an axis are referenced to an appropriate
coordinate system. The axis vector, itself, is a dimensionless
unit vector. Where meaningful, the offset vector is given in
millimetres. In coordinate systems not measured in metres,
the offset is not specified and is taken as zero.
The available coordinate systems are:
The imgCIF standard laboratory coordinate system
The direct lattice (fractional atomic coordinates)
The orthogonal Cartesian coordinate system (real space)
The reciprocal lattice
An abstract orthogonal Cartesian coordinate frame
For consistency in this discussion, we call the three coordinate
system axes X, Y and Z. This is appropriate for the imgCIF
standard laboratory coordinate system, and last two Cartesian
coordinate systems, but for the direct lattice, X corresponds
to a, Y to b and Z to c, while for the reciprocal lattice,
X corresponds to a*, Y to b* and Z to c*.
For purposes of visualization, all the coordinate systems are
taken as right-handed, i.e., using the convention that the extended
thumb of a right hand could point along the first (X) axis, the
straightened pointer finger could point along the second (Y) axis
and the middle finger folded inward could point along the third (Z)
axis.
THE IMGCIF STANDARD LABORATORY COORDINATE SYSTEM
The imgCIF standard laboratory coordinate system is a right-handed
orthogonal coordinate similar to the MOSFLM coordinate system,
but imgCIF puts Z along the X-ray beam, rather than putting X along the
X-ray beam as in MOSFLM.
The vectors for the imgCIF standard laboratory coordinate system
form a right-handed Cartesian coordinate system with its origin
in the sample or specimen. The origin of the axis system should,
if possible, be defined in terms of mechanically stable axes to be
be both in the sample and in the beam. If the sample goniometer or other
sample positioner has two axes the intersection of which defines a
unique point at which the sample should be mounted to be bathed
by the beam, that will be the origin of the axis system. If no such
point is defined, then the midpoint of the line of intersection
between the sample and the center of the beam will define the origin.
For this definition the sample positioning system will be set at
its initial reference position for the experiment.
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer or
sample positioning system if the sample positioning system has an axis that
intersects the origin and which form an angle of more than 22.5 degrees
with the beam axis.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
If the conditions for the X-axis can be met, the coordinate system
will be based on the goniometer or other sample positioning system
and the beam and not on the orientation of the detector, gravity etc.
The vectors necessary to specify all other axes are given by sets of
three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right-handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to but significantly
different from the choice in MOSFLM (Leslie & Powell, 2004). In MOSFLM,
X is along the X-ray beam (the CBF/imgCIF Z axis) and Z is along the
rotation axis.
In some experimental techniques, there is no goniometer or the principal
axis of the goniometer is at a small acute angle with respect to
the source axis. In such cases, other reference axes are needed
to define a useful coordinate system. The order of priority in
defining directions in such cases is to use the detector, then
gravity, then north.
If the X-axis cannot be defined as above, then the
direction (not the origin) of the X-axis should be parallel to the axis
of the primary detector element corresponding to the most rapidly
varying dimension of that detector element's data array, with its
positive sense corresponding to increasing values of the index for
that dimension. If the detector is such that such a direction cannot
be defined (as with a point detector) or that direction forms an
angle of less than 22.5 degrees with respect to the source axis, then
the X-axis should be chosen so that if the Y-axis is chosen
in the direction of gravity, and the Z-axis is chosen to be along
the source axis, a right-handed orthogonal coordinate system is chosen.
In the case of a vertical source axis, as a last resort, the
X-axis should be chosen to point North.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam centre.
The location of the beam centre on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected millimetres from
the (0,0) corner of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, it is necessary to
specify the location of the beam centre on the detector in terms
of the origin of the detector, which is, of course, not coincident
with the centre of the sample.
The unit cell, reciprocal cell and crystallographic orthogonal
Cartesian coordinate system are defined by the CELL and the matrices
in the ATOM_SITES category.
THE DIRECT LATTICE (FRACTIONAL COORDINATES)
The direct lattice coordinate system is a system of fractional
coordinates aligned to the crystal, rather than to the laboratory.
This is a natural coordinate system for maps and atomic coordinates.
It is the simplest coordinate system in which to apply symmetry.
The axes are determined by the cell edges, and are not necessarily
othogonal. This coordinate system is not uniquely defined and
depends on the cell parameters in the CELL category and the
settings chosen to index the crystal.
Molecules in a crystal studied by X-ray diffracraction are organized
into a repeating regular array of unit cells. Each unit cell is defined
by three vectors, a, b and c. To quote from Drenth,
"The choice of the unit cell is not unique and therefore, guidelines
have been established for selecting the standard basis vectors and
the origin. They are based on symmetry and metric considerations:
"(1) The axial system should be right handed.
(2) The basis vectors should coincide as much as possible with
directions of highest symmetry."
(3) The cell taken should be the smallest one that satisfies
condition (2)
(4) Of all the lattice vectors, none is shorter than a.
(5) Of those not directed along a, none is shorter than b.
(6) Of those not lying in the ab plane, none is shorter than c.
(7) The three angles between the basis vectors a, b and c are
either all acute (<90°) or all obtuse (>=90°)."
These rules do not produce a unique result that is stable under
the assumption of experimental errors, and the the resulting cell
may not be primitive.
In this coordinate system, the vector (.5, .5, .5) is in the middle
of the given unit cell.
Grid coordinates are an important variation on fractional coordinates
used when working with maps. In imgCIF, the conversion from
fractional to grid coordinates is implicit in the array indexing
specified by _array_structure_list.dimension. Note that this
implicit grid-coordinate scheme is 1-based, not zero-based, i.e.
the origin of the cell for axes along the cell edges with no
specified _array_structure_list_axis.displacement will have
grid coordinates of (1,1,1), i.e. array indices of (1,1,1).
THE ORTHOGONAL CARTESIAN COORDINATE SYSTEM (REAL SPACE)
The orthogonal Cartesian coordinate system is a transformation of
the direct lattice to the actual physical coordinates of atoms in
space. It is similar to the laboratory coordinate system, but
is anchored to and moves with the crystal, rather than being
schored to the laboratory. The transformation from fractional
to orthogonal cartesian coordinates is given by the
_atom_sites.Cartn_transf_matrix[i][j] and
_atom_sites.Cartn_transf_vector[i]
tags. A common choice for the matrix of the transformation is
given in the 1992 PDB format document
| a b cos(g) c cos(b) |
| 0 b sin(g) c (cos(a) - cos(b)cos(g))/sin(g) |
| 0 0 V/(a b sin(g)) |
This is a convenient coordinate system in which to do fitting
of models to maps and in which to understand the chemistry of
a molecule.
THE RECIPROCAL LATTICE
The reciprocal lattice coordinate system is used for diffraction
intensitities. It is based on the reciprocal cell, the dual of the cell,
in which reciprocal cell edges are derived from direct cell faces:
a* = bc sin(a)/V b* = ac sin(b)/V c* = ab sin(g)/V
cos(a*) = (cos(b) cos(g) - cos(a))/(sin(b) sin(g))
cos(b*) = (cos(g) cos(g) - cos(b) )/(sin(a) sin(g))
cos(g*) = (cos(a) cos(b) - cos(g))/(sin(a) sin(b))
V = abc SQRT (1 - cos(a)2 - cos(b)2 - cos(g)2
+ 2 cos(a) cos(b) cos(g) )
In this form the dimensions of the reciprocal lattice are in reciprocal
Ångstroms (&A^-1). A dimensionless form can be obtained by
multiplying by the wavelength. Reflections are commonly indexed against
this coordinate system as (h, k, l) triples.
References:
Drenth, J., "Introduction to basic crystallography." chapter
2.1 in Rossmann, M. G. and Arnold, E. "Crystallography of
biological macromolecules", Volume F of the IUCr's "International
tables for crystallography", Kluwer, Dordrecht 2001, pp 44 -- 63
Leslie, A. G. W. and Powell, H. (2004). MOSFLM v6.11.
MRC Laboratory of Molecular Biology, Hills Road, Cambridge, England.
http://www.CCP4.ac.uk/dist/X-windows/Mosflm/.
Stout, G. H. and Jensen, L. H., "X-ray structure determination",
2nd ed., Wiley, New York, 1989, 453 pp.
__, "PROTEIN DATA BANK ATOMIC COORDINATE AND BIBLIOGRAPHIC ENTRY
FORMAT DESCRIPTION," Brookhaven National Laboratory, February 1992.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
This example shows the axis specification of the axes of a kappa-
geometry goniometer [see Stout, G. H. & Jensen, L. H. (1989). X-ray
structure determination. A practical
guide, 2nd ed. p. 134. New York: Wiley Interscience].
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X axis. The next innermost axis, kappa,
is at a 50 degree angle to the X axis, pointed away from the source.
The innermost axis, phi, aligns with the X axis when omega and
phi are at their zero points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
X' = (T-omega) (T-kappa) (T-phi) X
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 -
This example shows the axis specification of the axes of a
detector, source and gravity. The order has been changed as a
reminder that the ordering of presentation of tokens is not
significant. The centre of rotation of the detector has been taken
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 3 -
This example show the axis specification of the axes for a map,
using fractional coordinates. Each cell edge has been divided
into a grid of 50 divisions in the ARRAY_STRUCTURE_LIST_AXIS
category. The map is using only the first octant of the grid
in the ARRAY_STRUCTURE_LIST category.
The fastest changing axis is the gris along A, then along B,
and the slowest is along C.
The map sampling is being done in the middle of each grid
division
;
;
loop_
_axis.id
_axis.system
_axis.vector[1] _axis.vector[2] _axis.vector[3]
CELL_A_AXIS fractional 1 0 0
CELL_B_AXIS fractional 0 1 0
CELL_C_AXIS fractional 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing CELL_A_AXIS
MAP 1 25 2 increasing CELL_B_AXIS
MAP 1 25 3 increasing CELL_C_AXIS
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.fract_displacement
_array_structure_list_axis.fract_displacement_increment
CELL_A_AXIS 0.01 0.02
CELL_B_AXIS 0.01 0.02
CELL_C_AXIS 0.01 0.02
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 4 -
This example show the axis specification of the axes for a map,
this time as orthogonal Angstroms, using the same coordinate system
as for the atomic coordinates. The map is sampling every 1.5
Angstroms (1.5e-7 millimeters) in a map segment 37.5 Angstroms on
a side.
;
;
loop_
_axis.id
_axis.system
_axis.vector[1] _axis.vector[2] _axis.vector[3]
X orthogonal 1 0 0
Y orthogonal 0 1 0
Z orthogonal 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing X
MAP 2 25 2 increasing Y
MAP 3 25 3 increasing Z
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
X 7.5e-8 1.5e-7
Y 7.5e-8 1.5e-7
Z 7.5e-8 1.5e-7
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.depends_on specifies the next outermost
axis upon which this axis depends.
This item is a pointer to _axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.equipment specifies the type of
equipment using the axis: 'goniometer', 'detector',
'gravity', 'source' or 'general'.
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.system
_item_description.description
; The value of _axis.system specifies the coordinate
system used to define the axis: 'laboratory', 'direct',
'orthogonal', 'reciprocal' or 'abstract'.
;
_item.name '_axis.system'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value laboratory
loop_
_item_enumeration.value
_item_enumeration.detail
laboratory
; the axis is referenced to the imgCIF standard laboratory Cartesian
coordinate system
;
direct
; the axis is referenced to the direct lattice
;
orthogonal
; the axis is referenced to the cell Cartesian orthogonal coordinates
;
reciprocal
; the axis is referenced to the reciprocal lattice
;
abstract
; the axis is referenced to abstract Cartesian cooridinate system
;
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: 'rotation' or 'translation' (or 'general' when
the type is not relevant, as for gravity).
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
; Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element are
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id.
;
;
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.center_fast
_item_description.description
; The value of _diffrn_data_frame.center_fast is
the fast index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_data_frame.center_units' along the fast
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement the current setting of detector
positioner given frame are used.
It is important to note that for measurements in millimetres,
the sense of the axis is used, rather than the sign of the
pixel-to-pixel increments.
;
_item.name '_diffrn_data_frame.center_fast'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_data_frame.center_slow
_item_description.description
; The value of _diffrn_data_frame.center_slow is
the slow index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_data_frame.center_units' along the slow
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement the current setting of detector
positioner given frame are used.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
;
_item.name '_diffrn_data_frame.center_slow'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_data_frame.center_units
_item_description.description
; The value of _diffrn_data_frame.center_units
specifies the units in which the values of
'_diffrn_data_frame.center_fast' and
'_diffrn_data_frame.center_slow'
are presented. The default is 'mm' for millimetres. The
alternatives are 'pixels' and 'bins'. In all cases the
center distances are measured from the center of the
first pixel, i.e. in a 2x2 binning, the measuring origin
is offset from the centers of the bins by one half pixel
towards the first pixel.
If 'bins' is specified, the data in
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size', and
'_array_intensities.pixel_binning_method'
is used to define the binning scheme.
;
_item.name '_diffrn_data_frame.center_units'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code code
loop_
_ item_enumeration.value
_ item_enumeration.detail
mm 'millimetres'
pixels 'detector pixels'
bins 'detector bins'
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.id
_item_description.description
; The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
save_
save__diffrn_data_frame.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
This is an appropriate location in which to record
information from vendor headers as presented in those
headers, but it should never be used as a substitute
for providing the fully parsed information within
the appropriate imgCIF/CBF categories.
Normally, when a conversion from a miniCBF has been done
the data from '_array_data.header_convention'
should be transferred to this data item and
'_array_data.header_convention'
should be removed.
;
_item.name '_diffrn_data_frame.details'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_frame_data.details'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.4
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
;
HEADER_BYTES = 512;
DIM = 2;
BYTE_ORDER = big_endian;
TYPE = unsigned_short;
SIZE1 = 3072;
SIZE2 = 3072;
PIXEL_SIZE = 0.102588;
BIN = 2x2;
DETECTOR_SN = 901;
TIME = 29.945155;
DISTANCE = 200.000000;
PHI = 85.000000;
OSC_START = 85.000000;
OSC_RANGE = 1.000000;
WAVELENGTH = 0.979381;
BEAM_CENTER_X = 157.500000;
BEAM_CENTER_Y = 157.500000;
PIXEL SIZE = 0.102588;
OSCILLATION RANGE = 1;
EXPOSURE TIME = 29.9452;
TWO THETA = 0;
BEAM CENTRE = 157.5 157.5;
;
; Example of header information extracted from an ADSC Quantum
315 detector header by CBFlib_0.7.6. Image provided by Chris
Nielsen of ADSC from a data collection at SSRL beamline 1-5.
;
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'slow mode'
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detector(s) used to
measure the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
; The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of
_diffrn_detector.diffrn_id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
; The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id.
The word 'positioner' is a general term used in
instrumentation design for devices that are used to change
the positions of portions of apparatus by linear
translation, rotation or combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
; Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named _diffrn_detector_axis.id
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
; Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, giving more detailed information
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
is preferable to simply providing the centre of the
detector element.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square, in the pattern
1 2
*
3 4
Note that the beam centre is slightly displaced from each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4. For each element, the detector
face coordiate system, is assumed to have the fast axis
running from left to right and the slow axis running from
top to bottom with the origin at the top left corner.
;
;
loop_
_diffrn_detector_element.detector_id
_diffrn_detector_element.id
_diffrn_detector_element.reference_center_fast
_diffrn_detector_element.reference_center_slow
_diffrn_detector_element.reference_center_units
d1 d1_ccd_1 201.5 201.5 mm
d1 d1_ccd_2 -1.8 201.5 mm
d1 d1_ccd_3 201.6 -1.4 mm
d1 d1_ccd_4 -1.7 -1.5 mm
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.id
_item_description.description
; The value of _diffrn_detector_element.id must uniquely
identify each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
; This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_element.reference_center_fast
_item_description.description
; The value of _diffrn_detector_element.reference_center_fast is
the fast index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_detector_element.reference_center_units' along the fast
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value given whould be
representive of the beam center as determined from the ensemble
of settings.
It is important to note that for measurements in millimetres,
the sense of the axis is used, rather than the sign of the
pixel-to-pixel increments.
;
_item.name '_diffrn_detector_element.reference_center_fast'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_detector_element.reference_center_slow
_item_description.description
; The value of _diffrn_detector_element.reference_center_slow is
the slow index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_detector_element.reference_center_units' along the slow
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value givien whould be
representive of the beam center as determined from the ensemble
of settings.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
;
_item.name '_diffrn_detector_element.reference_center_slow'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_detector_element.reference_center_units
_item_description.description
; The value of _diffrn_detector_element.reference_center_units
specifies the units in which the values of
'_diffrn_detector_element.reference_center_fast' and
'_diffrn_detector_element.reference_center_slow'
are presented. The default is 'mm' for millimetres. The
alternatives are 'pixels' and 'bins'. In all cases the
center distances are measured from the center of the
first pixel, i.e. in a 2x2 binning, the measuring origin
is offset from the centers of the bins by one half pixel
towards the first pixel.
If 'bins' is specified, the data in
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size', and
'_array_intensities.pixel_binning_method'
is used to define the binning scheme.
;
_item.name '_diffrn_detector_element.reference_center_units'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code code
loop_
_ item_enumeration.value
_ item_enumeration.detail
mm 'millimetres'
pixels 'detector pixels'
bins 'detector bins'
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the
diffraction data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model X'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector
angle 22.5 degrees
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support
and orient the specimen.
If the value of _diffrn_measurement.device is not given,
it is implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to
measure the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'home-made'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity
measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
; The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during the collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
; The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id.
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
# _diffrn_measurement.sample_detector_distance
# _diffrn_measurement.sample_detector_voffset
save__diffrn_measurement.sample_detector_distance
_item_description.description
; The value of _diffrn_measurement.sample_detector_distance gives
the unsigned distance in millimetres from the sample to the
detector along the beam.
;
_item.name '_diffrn_measurement.sample_detector_distance'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
_item_type.code float
_item_units.code mm
save_
save__diffrn_measurement.sample_detector_voffset
_item_description.description
; The value of _diffrn_measurement.sample_detector_voffset gives
the signed distance in millimetres in the vertical
direction (positive for up) from the center of
the beam to the center of the detector.
;
_item.name '_diffrn_measurement.sample_detector_voffset'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . .
. .
_item_type.code float
_item_units.code mm
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
; Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
; This data item is a pointer to _diffrn_measurement.device
in the DIFFRN_MEASUREMENT category.
;
_item.name
'_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_type.code text
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named _diffrn_measurement_axis.id,
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
####################
# DIFFRN_RADIATION #
####################
save_DIFFRN_RADIATION
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used for measuring diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
_category_key.name '_diffrn_radiation.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions of
photons in the XZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions
of photons in the YZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation degrees^2^ between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
direction of each photon in XZ plane times the deviations
of the direction of the same photon in the YZ plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons, this value is specified in
milliradians^2^, in which case a conversion would be needed.
To go from a value in milliradians^2^ to a value in
degrees^2^, multiply by 0.180^2^ and divide by \p^2^.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in \%Angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a
monochromator crystal is used, the material and the
indices of the Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarization ratio of the diffraction beam incident on the
crystal. This is the ratio of the perpendicularly polarized to
the parallel polarized component of the radiation. The
perpendicular component forms an angle of
_diffrn_radiation.polarisn_norm to the normal to the
diffraction plane of the sample (i.e. the plane containing
the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between
the normal to the polarization plane and the laboratory Y
axis as defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monochromater.
This differs from the value of
_diffrn_radiation.polarisn_norm
in that _diffrn_radiation.polarisn_norm refers to
polarization relative to the diffraction plane rather than
to the laboratory axis system.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane should be taken
as the XZ plane and the angle as 0.
See _diffrn_radiation.polarizn_source_ratio.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared)
of the electric vector in the plane of the normal to the
plane of polarization.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane is to be taken
as the XZ plane and the normal is parallel to the Y axis.
Thus, if there was complete polarization in the plane of
polarization, the value of
_diffrn_radiation.polarizn_source_ratio would be 1, and
for an unpolarized beam
_diffrn_radiation.polarizn_source_ratio would have a
value of 0.
If the X axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of 'MONOCHROMATOR' in the Denzo glossary, and values of near
1 should be expected for a bending-magnet source. However,
if the X axis were perpendicular to the polarization plane
(not a common choice), then the Denzo value would be the
negative of _diffrn_radiation.polarizn_source_ratio.
See http://www.hkl-xray.com for information on Denzo and
Otwinowski & Minor (1997).
This differs both in the choice of ratio and choice of
orientation from _diffrn_radiation.polarisn_ratio, which,
unlike _diffrn_radiation.polarizn_source_ratio, is
unbounded.
Reference: Otwinowski, Z. & Minor, W. (1997). 'Processing of
X-ray diffraction data collected in oscillation mode.' Methods
Enzymol. 276, 307-326.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly
recommended that this be given so that the
probe radiation is clearly specified.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'X-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for the probe
radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to
_diffrn_radiation_wavelength.id in the
DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.category_id diffrn_radiation
_item.mandatory_code yes
_item_type.code code
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
; This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
;
_category.id diffrn_refln
_category.mandatory_code no
_category_key.name '_diffrn_refln.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
; This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
; Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
_category_key.name '_diffrn_scan.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. In this example, three rotation axes and one translation axis
at nonzero values are specified, with one axis stepping. There is no
reason why more axes could not have been specified to step. Range
information has been specified, but note that it can be calculated from
the number of frames and the increment, so the data item
_diffrn_scan_axis.angle_range could be dropped.
Both the sweep data and the data for a single frame are specified.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
_diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
_diffrn_scan_frame.integration_time and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustments are made to
scan times and nonlinear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.angle_increment
_diffrn_scan_frame_axis.displacement
_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
; Example 2 - a more extensive example (R. M. Sweet, P. J. Ellis &
H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the goniometer.
This leads to a choice: either the axes of
the detector are defined at the origin, and then a Z setting of -240
is entered, or the axes are defined with the necessary Z offset.
In this case, the setting is used and the offset is left as zero.
This axis is called DETECTOR_Z.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm X 0.150mm, the centre of the first pixel is at (0.075,
0.075) in this coordinate system.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
; Example 3 - Example 2 revised for a spiral scan (R. M. Sweet,
P. J. Ellis & H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the
goniometer, as in Example 2 above, but in this example the
image plate is scanned in a spiral pattern from the outside edge in.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. The rotation axis is called ELEMENT_ROT and the
radial axis is called ELEMENT_RAD. A 150 micrometre radial pitch
and a 75 micrometre 'constant velocity' angular pitch are assumed.
Indexing is carried out first on the rotation axis and the radial axis
is made to be dependent on it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.angle
_array_structure_list_axis.displacement
_array_structure_list_axis.angular_pitch
_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
; The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
; The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
; Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
_diffrn_scan_frame.integration_time, even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
; The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frame_id_end
_item_description.description
; The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frames
_item_description.description
; The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
; Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
; The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.angle_start
_item_description.description
; The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
; The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
; The increment for each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_increment. The
sum of the values of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
; The increment after each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_rstrt_incr. The
sum of the values of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment
and _diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.angle for this
next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
; The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
; The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_increment.
The sum of the values of
_diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_rstrt_incr.
The sum of the values of
_diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.displacement
for this next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_angle.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_angle will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_angle (e.g.
the mean).
If not specified, the value defaults to zero.
;
_item.name '_diffrn_scan_axis.reference_angle'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_displacement.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_displacement will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_displacement (e.g.
the mean).
If not specified, the value defaults to to the value of
_diffrn_scan_axis.displacement.
;
_item.name '_diffrn_scan_axis.reference_displacement'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
; Data items in the DIFFRN_SCAN_FRAME category describe
the relationships of particular frames to scans.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
; The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame.frame_number
_item_description.description
; The value of this data item is the number of the frame
within the scan, starting with 1. It is not necessarily
the same as the value of _diffrn_scan_frame.frame_id,
but it may be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
; The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of _diffrn_scan.integration_time.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
; Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the
settings of axes for particular frames. Unspecified axes are
assumed to be at their zero points. If, for any given frame,
nonzero values apply for any of the data items in this category,
those values should be given explicitly in this category and not
simply inferred from values in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
; The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
; The increment for this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
; The increment after this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment and
_diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.angle for this next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.displacement for this next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be zero.
;
_item.name '_diffrn_scan_frame_axis.reference_angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be equal to
_diffrn_scan_frame_axis.displacement.
;
_item.name '_diffrn_scan_frame_axis.reference_displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
#######
# MAP #
#######
save_MAP
_category.description
; Data items in the MAP category record
the details of a maps. Maps record values of parameters,
such as density, that are functions of position within
a cell or are functions of orthogonal coordinates in
three space.
A map may is composed of one or more map segments
specified in the MAP_SEGMENT category.
Examples are given in the MAP_SEGMENT category.
;
_category.id map
_category.mandatory_code no
loop_
_category_key.name '_map.id'
'_map.diffrn_id'
'_map.entry_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id
_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.details
_item_description.description
; The value of _map.details should give a
description of special aspects of each map.
;
_item.name '_map.details'
_item.category_id map
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id
_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.diffrn_id
_item_description.description
; This item is a pointer to _diffrn.id in the
DIFFRN category.
;
_item.name '_map.diffrn_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.entry_id
_item_description.description
; This item is a pointer to _entry.id in the
ENTRY category.
;
_item.name '_map.entry_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.id
_item_description.description
; The value of _map.id must uniquely identify
each map for the given diffrn.id or entry.id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map.id' map yes
'_map_segment.id' map_segment yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_segment.id' '_map.id'
save_
###########################
# MAP_SEGMENT #
###########################
save_MAP_SEGMENT
_category.description
; Data items in the MAP_SEGMENT category record
the details about each segment (section or brick) of a map.
;
_category.id map_segment
_category.mandatory_code no
loop_
_category_key.name '_map_segment.id'
'_map_segment.map_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map, each consisting of one
segment, both using the same array structure
and mask.
;
;
loop_
_map.id
_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
loop_
_map_segment.map_id
_map_segment.id
_map_segment.array_id
_map_segment.binary_id
_map_segment.mask_array_id
_map_segment.mask_binary_id
rho_calc rho_calc map_structure 1 mask_structure 1
rho_obs rho_obs map_structure 2 mask_structure 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map_segment.array_id
_item_description.description
; The value of _map_segment.array_id identifies the array structure
into which the map is organized.
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.array_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code code
save_
save__map_segment.binary_id
_item_description.description
; The value of _map_segment.binary_id distinguishes the particular
set of data organized according to _map_segment.array_id in
which the data values of the map are stored.
This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.mask_array_id
_item_description.description
; The value of _map_segment.mask_array_id, if given, the array
structure into which the mask for the map is organized. If no
value is given, then all elements of the map are valid. If a
value is given, then only elements of the map for which the
corresponding element of the mask is non-zero are valid. The
value of _map_segment.mask_array_id differs from the value of
_map_segment.array_id in order to permit the mask to be given
as, say, unsigned 8-bit integers, while the map is given as
a data type with more range. However, the two array structures
must be aligned, using the same axes in the same order with the
same displacements and increments
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.mask_array_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code code
save_
save__map_segment.mask_binary_id
_item_description.description
; The value of _map_segment.mask_binary_id identifies the
particular set of data organized according to
_map_segment.mask_array_id specifying the mask for the map.
This item is a pointer to _array_data.mask_binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.mask_binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.id
_item_description.description
; The value of _map_segment.id must uniquely
identify each segment of a map.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map_segment.id'
map_segment
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_data_frame.map_segment_id'
'_map_segment.id'
save_
save__map_segment.map_id
_item_description.description
; This item is a pointer to _map.id
in the MAP category.
;
_item.name '_map_segment.map_id'
_item.category_id map_segment
_item.mandatory_code yes
_item_type.code code
save_
save__map_segment.details
_item_description.description
; The value of _map_segment.details should give a
description of special aspects of each segment of a map.
;
_item.name '_map_segment.details'
_item.category_id map_segment
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
; Example to be provided
;
;
;
save_
######################## DEPRECATED DATA ITEMS ########################
save__diffrn_detector_axis.id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_detector_axis.id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_element.center[1]
_item_description.description
; The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
Because of ambiguity about the setting used to determine this
center, use of this data item is deprecated. The data item
_diffrn_data_frame.center_fast
which is referenced to the detector coordinate system and not
directly to the laboratory coordinate system should be used
instead.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
; The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
Because of ambiguity about the setting used to determine this
center, use of this data item is deprecated. The data item
_diffrn_data_frame.center_slow
which is referenced to the detector coordinate system and not
directly to the laboratory coordinate system should be used
instead.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_measurement_axis.id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_measurement_axis.id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
######################### DEPRECATED CATEGORY #########################
#####################
# DIFFRN_FRAME_DATA #
#####################
save_DIFFRN_FRAME_DATA
_category.description
; Data items in the DIFFRN_FRAME_DATA category record
the details about each frame of data.
The items in this category are now in the
DIFFRN_DATA_FRAME category.
The items in the DIFFRN_FRAME_DATA category
are now deprecated. The items from this category
are provided as aliases in the 1.0 dictionary
or, in the case of _diffrn_frame_data.details,
in the 1.4 dictionary. THESE ITEMS SHOULD NOT
BE USED FOR NEW WORK.
The items from the old category are provided
in this dictionary for completeness
but should not be used or cited. To avoid
confusion, the example has been removed
and the redundant parent-child links to other
categories have been removed.
;
_category.id diffrn_frame_data
_category.mandatory_code no
loop_
_category_key.name '_diffrn_frame_data.id'
'_diffrn_frame_data.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
THE DIFFRN_FRAME_DATA category is deprecated and should not be used.
;
;
# EXAMPLE REMOVED #
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_frame_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.array_id'
_item.category_id diffrn_frame_data
_item.mandatory_code implicit
_item_type.code code
save_
save__diffrn_frame_data.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.binary_id'
_item.category_id diffrn_frame_data
_item.mandatory_code implicit
_item_type.code int
save_
save__diffrn_frame_data.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.detector_element_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.id
_item_description.description
; The value of _diffrn_frame_data.id must uniquely identify
each complete frame of data.
DEPRECATED -- DO NOT USE
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_frame_data.id' diffrn_frame_data yes
_item_type.code code
save_
save__diffrn_frame_data.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.details'
_item.category_id diffrn_frame_data
_item.mandatory_code no
_item_type.code text
save_
################ END DEPRECATED SECTION ###########
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive) ...
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items (case insensitive)...
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
point numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9]?[0-9]\
((T[0-2][0-9](:[0-5][0-9](:[0-5][0-9](.[0-9]+)?)?)?)?\
([+-][0-5][0-9]:[0-5][0-9]))?
;
;
Standard format for CIF date and time strings (see
http://www.iucr.org/iucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character 'T' followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
decimal fraction on the seconds of time.
Time is local time if no time-zone offset is given.
Note that this type extends the mmCIF yyyy-mm-dd type
but does not conform to the mmCIF yyyy-mm-dd:hh:mm
type that uses a ':' in place if the 'T' specified
by the IUCr standard. For reading, both forms should
be accepted, but for writing, only the IUCr form should
be used.
For maximal compatibility, the special time zone
indicator 'Z' (for 'zulu') should be accepted on
reading in place of '+00:00' for GMT.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2)^)'
'millimetres' 'millimetres (metres * 10^( -3)^)'
'nanometres' 'nanometres (metres * 10^( -9)^)'
'angstroms' '\%Angstroms (metres * 10^(-10)^)'
'picometres' 'picometres (metres * 10^(-12)^)'
'femtometres' 'femtometres (metres * 10^(-15)^)'
#
'reciprocal_metres' 'reciprocal metres (metres^(-1)^)'
'reciprocal_centimetres'
'reciprocal centimetres ((metres * 10^( -2)^)^(-1)^)'
'reciprocal_millimetres'
'reciprocal millimetres ((metres * 10^( -3)^)^(-1)^)'
'reciprocal_nanometres'
'reciprocal nanometres ((metres * 10^( -9)^)^(-1)^)'
'reciprocal_angstroms'
'reciprocal \%Angstroms ((metres * 10^(-10)^)^(-1)^)'
'reciprocal_picometres'
'reciprocal picometres ((metres * 10^(-12)^)^(-1)^)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9)^)^2^'
'angstroms_squared' '\%Angstroms squared (metres * 10^(-10)^)^2^'
'8pi2_angstroms_squared'
'8\p^2^ * \%Angstroms squared (metres * 10^(-10)^)^2^'
'picometres_squared' 'picometres squared (metres * 10^(-12)^)^2^'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9)^)^3^'
'angstroms_cubed' '\%Angstroms cubed (metres * 10^(-10)^)^3^'
'picometres_cubed' 'picometres cubed (metres * 10^(-12)^)^3^'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^( -9)^)^(-3)^)
;
'electrons_per_angstroms_cubed'
; electrons per \%Angstroms cubed (electrons/(metres * 10^(-10)^)^(-3)^)
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (electrons/(metres * 10^(-12)^)^(-3)^)
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'pixels_per_element' '(image) pixels per (array) element'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.5.3 2007-07-08
; Changes to support SLS miniCBF and suggestions
from the 24 May 07 BNL imgCIF workshop (HJB)
+ Added new data items
'_array_data.header_contents',
'_array_data.header_convention',
'_diffrn_data_frame.center_fast',
'_diffrn_data_frame.center_slow',
'_diffrn_data_frame.center_units',
'_diffrn_measurement.sample_detector_distance',
'_diffrn_measurement.sample_detector_voffset
+ Deprecated data items
'_diffrn_detector_element.center[1]',
'_diffrn_detector_element.center[2]'
+ Added comments and example on miniCBF
+ Changed all array_id data items to implicit
;
1.5.2 2007-05-06
; Further clarifications of the coordinate system. (HJB)
;
1.5.1 2007-04-26
; Improve defintion of X-axis to cover the case of no goniometer
and clean up more line folds (HJB)
;
1.5 2007-07-25
; This is a cummulative list of the changes proposed since the
imgCIF workshop in Hawaii in July 2006. It is the result
of contributions by H. J. Bernstein, A. Hammersley,
J. Wright and W. Kabsch.
2007-02-19 Consolidated changes (edited by HJB)
+ Added new data items
'_array_structure.compression_type_flag',
'_array_structure_list_axis.fract_displacement',
'_array_structure_list_axis.displacement_increment',
'_array_structure_list_axis.reference_angle',
'_array_structure_list_axis.reference_displacement',
'_axis.system',
'_diffrn_detector_element.reference_center_fast',
'_diffrn_detector_element.reference_center_slow',
'_diffrn_scan_axis.reference_angle',
'_diffrn_scan_axis.reference_displacement',
'_map.details', '_map.diffrn_id',
'_map.entry_id', '_map.id',
'_map_segment.array_id', '_map_segment.binary_id',
'_map_segment.mask_array_id', '_map_segment.mask_binary_id',
'_map_segment.id', '_map_segment.map_id',
'_map_segment.details.
+ Change type of
'_array_structure.byte_order' and
'_array_structure.compression_type'
to ucode to make these values case-insensitive
+ Add values 'packed_v2' and 'byte_offset' to enumeration of values for
'_array_structure.compression_type'
+ Add to defintions for the binary data type to handle new compression
types, maps, and a variety of new axis types.
2007-07-25 Cleanup of typos for formal release (HJB)
+ Corrected text fields for reference_ tag descriptions that
were off by one column
+ Fix typos in comments listing fract_ tags
+ Changed name of release from 1.5_DRAFT to 1.5
+ Fix unclosed text fields in various map definitions
;
1.4 2006-07-04
; This is a change to reintegrate all changes made in the course of
publication of ITVG, by the RCSB from April 2005 through
August 2008 and changes for the 2006 imgCIF workshop in
Hawaii.
2006-07-04 Consolidated changes for the 2006 imgCIF workshop (edited by HJB)
+ Correct type of '_array_structure_list.direction' from 'int' to 'code'.
+ Added new data items suggested by CN
'_diffrn_data_frame.details'
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size and
'_array_intensities.pixel_binning_method
+ Added deprecated item for completeness
'_diffrn_frame_data.details'
+ Added entry for missing item in contents list
'_array_structure_list_axis.displacement'
+ Added new MIME type X-BASE32K based on work by VL, KM, GD, HJB
+ Correct description of MIME boundary delimiter to start in
column 1.
+ General cleanup of text fields to conform to changes for ITVG
by removing empty lines at start and finish of text field.
+ Amend example for ARRAY_INTENSITIES to include binning.
+ Add local copy of type specification (as 'code') for all children
of '_diffrn.id'.
+ For consistency, change all references to 'pi' to '\p' and all
references to 'Angstroms' to '\%Angstroms'.
+ Clean up all powers to use IUCr convention of '^power^', as in
'10^3^' for '10**3'.
+ Update 'yyyy-mm-dd' type regex to allow truncation from the right
and improve comments to explain handling of related mmCIF
'yyyy-mm-dd:hh:mm' type, and use of 'Z' for GMT time zone.
2005-03-08 and
2004-08-08 fixed cases where _item_units.code used
instead of _item_type.code (JDW)
2004-04-15 fixed item ordering in
_diffrn_measurement_axis.measurement_id
added sub_category 'vector' (JDW)
;
1.3.2 2005-06-25
; 2005-06-25 ITEM_TYPE_LIST: code, ucode, line, uline regexps updated
to those of current mmCIF; float modified by allowing integers
terminated by a point as valid. The 'time' part of
yyyy-mm-dd types made optional in the regexp. (BM)
2005-06-17 Minor corrections as for proofs for IT G Chapter 4.6
(NJA)
2005-02-21 Minor corrections to spelling and punctuation
(NJA)
2005-01-08 Changes as per Nicola Ashcroft.
+ Updated example 1 for DIFFRN_MEASUREMENT to agree with mmCIF.
+ Spelled out "micrometres" for "um" and "millimetres" for "mm".
+ Removed phrase "which may be stored" from ARRAY_STRUCTURE
description.
+ Removed unused 'byte-offsets' compressions and updated
cites to ITVG for '_array_structure.compression_type'.
(HJB)
;
1.3.1 2003-08-13
;
Changes as per Frances C. Bernstein.
+ Identify initials.
+ Adopt British spelling for centre in text.
+ Set \p and \%Angstrom and powers.
+ Clean up commas and unclear wordings.
+ Clean up tenses in history.
Changes as per Gotzon Madariaga.
+ Fix the ARRAY_DATA example to align '_array_data.binary_id'
and X-Binary-ID.
+ Add a range to '_array_intensities.gain_esd'.
+ In the example of DIFFRN_DETECTOR_ELEMENT,
'_diffrn_detector_element.id' and
'_diffrn_detector_element.detector_id' interchanged.
+ Fix typos for direction, detector and axes.
+ Clarify description of polarisation.
+ Clarify axes in '_diffrn_detector_element.center[1]'
'_diffrn_detector_element.center[2]'.
+ Add local item types for items that are pointers.
(HJB)
;
1.3.0 2003-07-24
;
Changes as per Brian McMahon.
+ Consistently quote tags embedded in text.
+ Clean up introductory comments.
+ Adjust line lengths to fit in 80 character window.
+ Fix several descriptions in AXIS category which
referred to '_axis.type' instead of the current item.
+ Fix erroneous use of deprecated item
'_diffrn_detector_axis.id' in examples for
DIFFRN_SCAN_AXIS.
+ Add deprecated items '_diffrn_detector_axis.id'
and '_diffrn_measurement_axis.id'.
(HJB)
;
1.2.4 2003-07-14
;
Changes as per I. David Brown.
+ Enhance descriptions in DIFFRN_SCAN_AXIS to make them less
dependent on the descriptions in DIFFRN_SCAN_FRAME_AXIS.
+ Provide a copy of the deprecated DIFFRN_FRAME_DATA
category for completeness.
(HJB)
;
1.2.3 2003-07-03
;
Cleanup to conform to ITVG.
+ Correct sign error in ..._cubed units.
+ Correct '_diffrn_radiation.polarisn_norm' range.
(HJB)
;
1.2.2 2003-03-10
;
Correction of typos in various DIFFRN_SCAN_AXIS descriptions.
(HJB)
;
1.2.1 2003-02-22
;
Correction of ATOM_ for ARRAY_ typos in various descriptions.
(HJB)
;
1.2 2003-02-07
;
Corrections to encodings (remove extraneous hyphens) remove
extraneous underscore in '_array_structure.encoding_type'
enumeration. Correct typos in items units list. (HJB)
;
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB.
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li.
;
1.1.1 2001-02-16
;
Several typo corrections by JW.
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS. (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME.
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to
'_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source',
'_diffrn_radiation.polarizn_source_norm',
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add '_diffrn_measurement.device' to category key.
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to
allow for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up. (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes. (JW)
+ Correct spelling of diffrn_measurement_axis in '_axis.id'
+ Correct ordering of uses of '_item.mandatory_code' and
'_item_default.value'.
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown. (HJB)
+ Add further comments on '\n' and '\t'.
+ Update ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Change 'meter' to 'metre' throughout.
+ Add missing enumerations to '_array_structure.compression_type'
and make 'none' the default.
+ Remove parent-child relationship between
'_array_structure_list.index' and '_array_structure_list.precedence'.
+ Improve alphabetization.
+ Fix '_array_intensities_gain.esd' related function.
+ Improve comments in AXIS.
+ Fix DIFFRN_FRAME_DATA example.
+ Remove erroneous DIFFRN_MEASUREMENT example.
+ Add '_diffrn_measurement_axis.id' to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data. (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors. (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for '_diffrn_scan.id' definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header. (HJB)
+ Restore '_diffrn_detector.diffrn_id' to DIFFRN_DETECTOR KEY.
+ Add AXIS category.
+ Bring in complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
from cif_mm.dic for clarity.
+ Change '_array_structure.encoding_type' from type code to uline and
added X-Binary-Element-Type to MIME header.
+ Add detector beam centre '_diffrn_detector_element.center[1]' and
'_diffrn_detector_element.center[2]'.
+ Correct item name of '_diffrn_refln.frame_id'.
+ Replace reference to '_array_intensities.undefined' by
'_array_intensities.undefined_value'.
+ Replace references to '_array_intensity.scaling' with
'_array_intensities.scaling'.
+ Add DIFFRN_SCAN... categories.
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft. (HJB)
+ Reflow comment lines over 80 characters and corrected typos.
+ Update examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF. (HJB)
+ Add binary type, which is a text field containing a variant on
MIME encoded data.
+ Change type of '_array_data.data' to binary and specify internal
structure of raw binary data.
+ Add '_array_data.binary_id', and make
'_diffrn_frame_data.binary_id' and '_array_intensities.binary_id'
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft. (JW)
+ Add category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes are made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA is renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE is renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for '_diffrn_frame_data.array_id' is changed from
'_array_structure_list.array_id' to '_array_structure.id'. Item
'_diffrn_detector.array_id' is deleted.
+ Add data item '_diffrn_frame_data.binary_id' to identify data
groups within a binary section. The formal identification of the
binary section is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version is adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley
(AH).
Modifications to the CBF draft. (JW)
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories
have been generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category
ARRAY_DATA. This departs from the CBF notion of data existing
in some special comment. In this description, data are handled as an
ordinary data item encapsulated in a character data type. Although
data this manner deviates from CIF conventions, it does not violate
any DDL 2.1 rules. DDL 2.1 regular expressions can be used to define
the binary representation which will permit some level of data
validation. In this version, the placeholder type code "any" has
been used. This translates to a regular expression which will match
any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary.
It may be possible to use the DDL 2.1 ITEM_STRUCTURE and
ITEM_STRUCTURE_LIST categories to provide the information that is
carried in by the ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By
moving the array structure to the DDL level it would be possible to
define an array type as well as a regular expression defining the
data format.
+ Multiple array sections can be properly handled within a single
datablock.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
./CBFlib-0.9.2.2/doc/Imap.diffrn_id.html 0000644 0000765 0000765 00000004665 11603702115 016055 0 ustar yaya yaya
(IUCr) CIF Definition save__map.diffrn_id
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Data encoding of a single element of array data.
The type 'unsigned 1-bit integer' is used for
packed Booleans arrays for masks. Each element
of the array corresponds to a single bit
packed in unsigned 8-bit data.
In several cases, the IEEE format is referenced.
See IEEE Standard 754-1985 (IEEE, 1985).
Ref: IEEE (1985). IEEE Standard for Binary Floating-Point
Arithmetic. ANSI/IEEE Std 754-1985. New York: Institute of
Electrical and Electronics Engineers.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
_diffrn_scan_frame.integration_time, even
if all steps have the same integration time.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Beam crossfire correlation degrees^2^ between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
direction of each photon in XZ plane times the deviations
of the direction of the same photon in the YZ plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons, this value is specified in
milliradians^2^, in which case a conversion would be needed.
To go from a value in milliradians^2^ to a value in
degrees^2^, multiply by 0.180^2^ and divide by \p^2^.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
This data item is a pointer to _diffrn.id in the DIFFRN
category.
Type: code
Mandatory item: yes
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The setting of the specified axis as a decimal fraction of
the axis unit vector for the first data point of the array
index with the corresponding value of
_array_structure_list.axis_set_id.
If the index is specified as 'increasing', this will be the
centre of the pixel with index value 1. If the index is
specified as 'decreasing', this will be the centre of the
pixel with maximum index value.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _axis.id in the
AXIS category.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id.
The word 'positioner' is a general term used in
instrumentation design for devices that are used to change
the positions of portions of apparatus by linear
translation, rotation or combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Flags modifying the type of data-compression method used to
compress the arraydata.
Type: ucode
Mandatory item: no
The data value must be one of the following:
uncorrelated_sections
When applying packed or packed_v2 compression on an array with
uncorrelated sections, do not average in points from the prior
section.
flat
When applying packed or packed_v2 compression on an array with
treat the entire image as a single line set the maximum number
of bits for an offset to 65 bits.
The flag is included for compatibility with software prior to
CBFlib_0.7.7, and should not be used for new data sets.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.1.3 #
# of 2001-04-19 #
# #
# Adapted from the #
# imgCIF Workshop, BNL Oct 1997 #
# and #
# Crystallographic Binary File Format Draft Proposal #
# by Andy Hammersley #
# #
##############################################################################
# #
# First DDL 2.1 Version #
# by #
# John Westbrook #
# Nucleic Acid Database #
# Rutgers University #
# #
##############################################################################
# These revisions by: Herbert J. Bernstein, yaya@bernstein-plus-sons.com #
# Incorporating comments by I. David Brown, John Westbrook, Brian McMahon. #
# Bob Sweet, Paul Ellis, Harry Powell, Wilfred Li and others #
##############################################################################
data_cif_img.dic
_dictionary.title cif_img.dic
_dictionary.version 1.1.3
_dictionary.datablock_id cif_img.dic
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.gain
# _array_intensities.gain_esd
# _array_intensities.linearity
# _array_intensities.offset
# _array_intensities.scaling
# _array_intensities.overload
# _array_intensities.undefined_value
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.encoding_type
# _array_structure.id
#
# category ARRAY_STRUCTURE_LIST
#
# _array_structure_list.axis_set_id
# _array_structure_list.array_id
# _array_structure_list.dimension
# _array_structure_list.direction
# _array_structure_list.index
# _array_structure_list.precedence
#
# category ARRAY_STRUCTURE_LIST_AXIS
#
# _array_structure_list_axis.axis_id
# _array_structure_list_axis.axis_set_id
# _array_structure_list_axis.angle
# _array_structure_list_axis.angle_increment
# _array_structure_list_axis.displacement_increment
# _array_structure_list_axis.angular_pitch
# _array_structure_list_axis.radial_pitch
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.type
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
#
# category DIFFRN_DATA_FRAME
#
# _diffrn_data_frame.array_id
# _diffrn_data_frame.binary_id
# _diffrn_data_frame.detector_element_id
# _diffrn_data_frame.id
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.id
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.axis_id
# _diffrn_detector_axis.detector_id
#
# category DIFFRN_DETECTOR_ELEMENT
#
# _diffrn_detector_element.center[1]
# _diffrn_detector_element.center[2]
# _diffrn_detector_element.id
# _diffrn_detector_element.detector_id
#
# category DIFFRN_MEASUREMENT
#
# _diffrn_measurement.diffrn_id
# _diffrn_measurement.details
# _diffrn_measurement.device
# _diffrn_measurement.device_details
# _diffrn_measurement.device_type
# _diffrn_measurement.id
# _diffrn_measurement.method
# _diffrn_measurement.number_of_axes
# _diffrn_measurement.specimen_support
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.axis_id
# _diffrn_measurement_axis.measurement_device
# _diffrn_measurement_axis.measurement_id
#
# category DIFFRN_RADIATION
#
# _diffrn_radiation.collimation
# _diffrn_radiation.diffrn_id
# _diffrn_radiation.div_x_source
# _diffrn_radiation.div_y_source
# _diffrn_radiation.div_x_y_source
# _diffrn_radiation.filter_edge'
# _diffrn_radiation.inhomogeneity
# _diffrn_radiation.monochromator
# _diffrn_radiation.polarisn_norm
# _diffrn_radiation.polarisn_ratio
# _diffrn_radiation.polarizn_source_norm
# _diffrn_radiation.polarizn_source_ratio
# _diffrn_radiation.probe
# _diffrn_radiation.type
# _diffrn_radiation.xray_symbol
# _diffrn_radiation.wavelength_id
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.date_end
# _diffrn_scan.date_start
# _diffrn_scan.integration_time
# _diffrn_scan.frame_id_start
# _diffrn_scan.frame_id_end
# _diffrn_scan.frames
#
# category DIFFRN_SCAN_AXIS
#
# _diffrn_scan_axis.axis_id
# _diffrn_scan_axis.angle_start
# _diffrn_scan_axis.angle_range
# _diffrn_scan_axis.angle_increment
# _diffrn_scan_axis.angle_rstrt_incr
# _diffrn_scan_axis.displacement_start
# _diffrn_scan_axis.displacement_range
# _diffrn_scan_axis.displacement_increment
# _diffrn_scan_axis.displacement_rstrt_incr
# _diffrn_scan_axis.scan_id
#
# category DIFFRN_SCAN_FRAME
#
# _diffrn_scan_frame.date
# _diffrn_scan_frame.frame_id
# _diffrn_scan_frame.frame_number
# _diffrn_scan_frame.integration_time
# _diffrn_scan_frame.scan_id
#
# category DIFFRN_SCAN_FRAME_AXIS
#
# _diffrn_scan_frame_axis.axis_id
# _diffrn_scan_frame_axis.angle
# _diffrn_scan_frame_axis.angle_increment
# _diffrn_scan_frame_axis.angle_rstrt_incr
# _diffrn_scan_frame_axis.displacement
# _diffrn_scan_frame_axis.displacement_increment
# _diffrn_scan_frame_axis.displacement_rstrt_incr
# _diffrn_scan_frame_axis.frame_id
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
;
Data items in the ARRAY_DATA category are the containers for
the array data items described in category ARRAY_STRUCTURE.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and
presented as hexadecimal data. The first character "H" on the
data lines means hexadecimal. It could have been "O" for octal
or "D" for decimal. The second character on the line shows
the number of bytes in each word (in this case "4"), which then
requires 8 hexadecimal digits per word. The third character
gives the order of octets within a word, in this case "<"
for the ordering 4321 (i.e. "big-endian"). Alternatively the
character ">" could have been used for the ordering 1234
(i.e. "little-endian"). The block has a "message digest"
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id_array_data.binary_id_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 1
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-Id, these values should be equal.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
"--CIF-BINARY-FORMAT-SECTION--" (including the
required initial "--").
The Content-Type may be any of the discrete types permitted
in RFC 2045; "application/octet-stream" is recommended.
If an octet stream was compressed, the compression should
be specified by the parameter 'conversions="x-CBF_PACKED"'
or the parameter 'conversions="x-CBF_CANONICAL"'.
The Content-Transfer-Encoding may be "BASE-64",
"Quoted-Printable", "X-BASE-8", "X-BASE-10", or
"X-BASE-16" for an imgCIF or "BINARY" for a CBF. The
octal, decimal and hexadecimal transfer encodings are
for convenience in debugging, and are not recommended
for archiving and data interchange.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In a CBF, the
raw binary data begins after an empty line terminating
the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of
the message size, nor in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. And adjustment is made for
the deprecated binary formats in which 8 bytes of binary
header are used for the compression type. In that case,
the 8 bytes used for the compression type is subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is "unsigned 32-bit integer".
An MD5 message digest may, optionally, be used. The "RSA Data
Security, Inc. MD5 Message-Digest Algorithm" should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is "X-BASE-8", "X-BASE-10", or
"X-BASE-16", the data is presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ("big-
endian") or 1234... (little-endian). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as "==" for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is "H", "O", or "D" for hexadecimal, octal or
decimal, n is the number of octets per word. and d is "<"
for ">" for the "...4321" and "1234..." octet orderings
respectively. The "==" padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hex, octal and decimal formats, only, comments
beginning with "#" are permitted to improve readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three, c1, c2, c3. The resulting 24 bits
are broken into four 6-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order 4 bits of the second octet ((c1 & 3)<<4 | (c2>>4)),
then the bottom 4 bits of the second octet followed by the
high order two bits of the last octet ((c2 & 15)<<2 | (c3>>6)),
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
With short groups of octets padded on the right with one "="
if c3 is missing, and with "==" if both c2 and c3 are missing.
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32..38,
42, 48..57, 59..60, 62, 64..126 and the octet is not a ";"
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
"wrapped" with a terminating "=" (i.e. the MIME conventions
for an implicit line terminator are never used).
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
;
Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ATOM_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.index
_item_description.description
;
This item is a pointer to _array_structure_list.index in the
ATOM_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
;
The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
;
Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The actual detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
'_array_intensities.gain'. If raw, uncorrected values
are presented (e.g for calibration experiments), the
value of '_array_intensities.linearity' will be 'raw'
and '_array_intensities.gain' will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id_array_intensities.linearity_array_intensities.gain_array_intensities.overload_array_intensities.undefined_value
image_1 linear 1.2 655535 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ATOM_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
;
Detector "gain". The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
;
The estimated standard deviation in detector "gain".
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
;
The intensity linearity scaling used from raw intensity
to the stored element value:
'linear' is obvious
'offset' means that the value defined by
'_array_intensities.offset' should be added to each
element value.
'scaling' means that the value defined by
'_array_intensities.scaling' should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by '_array_intensities.scaling' is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
'logarithmic_scaled' means that the logarithm based 10 of
raw intensities multiplied by '_array_intensities.scaling'
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and calculating 10
to the power of this number.
'raw' means that the data is the raw is a set of raw values
straight from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
;
The value defined by '_array_intensities.offset' should
be added to each element value.
;
'scaling'
;
The value defined by '_array_intensities.scaling' should be
multiplied with each element value.
;
'scaling_offset'
;
The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
;
The square root of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
;
'logarithmic_scaled'
;
The logarithm based 10 of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
'_array_intensities.scaling' and calculating 10 to the
power of this number.
;
'raw'
;
The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
;
Offset value to add to array element values in the manner
described by item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.scaling
_item_description.description
;
Multiplicative scaling value to be applied to array data
in the manner described by item _array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
;
The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.undefined_value
_item_description.description
;
A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
;
Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data which may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
_category_key.name '_array_structure.id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
;
The order of bytes for integer values which require more
than 1-byte.
(IBM-PC's and compatibles, and Dec-Vaxes use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. Dec-Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
;
The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
;
The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
;
Type of data compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code code
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'none'
;
Data are stored in normal format as defined by
'_array_structure.encoding_type' and
'_array_structure.byte_order'.
;
'byte_offsets'
;
Using the compression scheme defined in CBF definition
Section 5.0.
;
'packed'
;
Using the 'packed' compression scheme, a CCP4-style packing
(CBFlib section 3.3.2)
;
'canonical'
;
Using the 'canonical' compression scheme (CBFlib section
3.3.1)
;
save_
save__array_structure.encoding_type
_item_description.description
;
Data encoding of a single element of array data.
In several cases, the IEEE format is referenced.
See "IEEE Standard for Binary Floating-Point Arithmetic",
ANSI/IEEE Std 754-1985, the Institute of Electrical and
Electronics Engineers, Inc., NY 1985.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit_integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure yes
'_array_data.array_id' array_data yes
'_array_structure_list.array_id' array_structure_list yes
'_array_intensities.array_id' array_intensities yes
'_diffrn_data_frame.array_id' diffrn_data_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
;
Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left-to-right (increasing) in
first dimension and bottom-to-top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differ
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the "poise" of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
;
The number of elements stored in the array structure in this
dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
;
Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
;
Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
;
Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
;
Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
;
Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
;
Data items in the ARRAY_STRUCTURE_LIST_AXIS category describes
the physical settings of sets axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axis, one for the angular
direction, one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
'_array_structure_list_axis.axis_set_id'
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
;
The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id .
This item is a pointer to _array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
save_
save__array_structure_list_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of '_array_structure_list.axis_set_id'. If the index is
specified as 'increasing' this will be the center of the
pixel with index value 1. If the index is specified as
'decreasing' this will be the center of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
;
The pixel-center-to-pixel-center increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified in that case.
See '_array_structure_list_axis.angular_pitch'.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
;
The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of '_array_structure_list.axis_set_id'. If the index is
specified as 'increasing' this will be the center of the
pixel with index value 1. If the index is specified as
'decreasing' this will be the center of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
;
The pixel-center-to-pixel-center increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
;
The pixel-center-to-pixel-center distance for a one step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans,
or for uncoupled angular scans at a constant radius
(cylindrical scan) and should not be specified for cases
in which the angle between pixels, rather than the distance
between pixels is uniform.
See '_array_structure_list_axis.angle_increment'.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
;
The radial distance from one "cylinder" of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of '_array_structure_list_axis.displacement_increment'.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
########
# AXIS #
########
save_AXIS
_category.description
;
Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection. The location of each
axis is specified by two vectors: the axis itself, given as a unit
vector, and an offset to the base of the unit vector. These vectors
are referenced to a right-handed laboratory coordinate system with
its origin in the sample or specimen:
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
These axes are based on the goniometer, not on the orientation of the
detector, gravity, etc. The vectors necessary to specify all other
axes are given by sets of three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to, but significantly
different from the choice in MOSFLM (Andrew G.W. Leslie, Harry Powell,
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH,UK
http://www.dl.ac.uk/CCP/CCP4/dist/x-windows/Mosflm/). In MOSFLM,
X is along the X-ray beam (our Z axis) and Z is along the rotation axis.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam center.
The location of the beam center on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected mm from the (0,0) corner
of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, we need to specify the
location of the beam center on the detector in terms of the origin of the
detector, which is, of course, not coincident with the center of the
sample.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows the axis specification of the axes of a kappa
geometry goniometer (See "X-Ray Structure Determination, A Practical
Guide", 2nd ed. by G. H. Stout, L. H. Jensen, Wiley Interscience,
1989, 453 pp, p 134.).
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X-axis. The next innermost axis, kappa,
is at a 50 degree angle to the X-axis, pointed away from the source.
The innermost axis, phi, aligns with the X-axis when omega and
phi are at their zero-points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
x' = (T-omega) (T-kappa) (T-phi) x
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
This example show the axis specification of the axes of a
detector, source and gravity. We have juggled the order as a
reminder that the ordering of presentation of tokens is not
significant. We have taken the center of rotation of the detector
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.type specifies the next outermost
axis upon which this axis depends.
This item is a pointer to axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.type specifies the type of equipment
using the axis: goniometer, detector, gravity, source
or general
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so that the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: rotation, translation (or general when the type is
not relevant, as for gravity)
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
;
Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases, but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element is
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id
;
;
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0.00
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
;
This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.id
_item_description.description
;
The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Need new example here.
;
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detectors used to measure
the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
;
The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of _diffrn_detector.diffrn_id
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
;
The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id
The word "positioner" is a general term used in instrumentation
design for devices that are used to change the positions of
portions of apparatus by linear translation, rotation, or
combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
;
Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
;
This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named '_diffrn_detector_axis.id'
which is now a deprecated name. The old name is
provided as an alias, but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
;
Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, the more detailed information provided
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
are preferable to simply providing the centre.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square. in the pattern
1 2
*
3 4
Note that the beam center is slightly off of each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4.
;
;
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id_diffrn_detector_element.center[1]_diffrn_detector_element.center[2]
d1 d1_ccd_1 201.5 -1.5
d1 d1_ccd_2 -1.8 -1.5
d1 d1_ccd_3 201.6 201.4
d1 d1_ccd_4 -1.7 201.5
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.center[1]
_item_description.description
;
The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
;
The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.id
_item_description.description
;
The value of _diffrn_detector_element.id must uniquely identify
each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
;
This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the diffraction
data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model x'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; Need new example here
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support and
orient the specimen.
If the value of _diffrn_measurement.device is not given, it is
implicitly equal to the value of _diffrn_measurement.diffrn_id
Either '_diffrn_measurement.device' or '_diffrn_measurement.id'
may be used to link to other categories. If the experimental
setup admits multiple devices, then '_diffrn_measurement.id'
is used to provide a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to measure
the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'homemade'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
;
The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of _diffrn_measurement.diffrn_id
Either '_diffrn_measurement.device' or '_diffrn_measurement.id'
may be used to link to other categories. If the experimental
setup admits multiple devices, then '_diffrn_measurement.id'
is used to provide a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
;
The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
;
Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
;
This data item is a pointer to _diffrn_measurement.device in
the DIFFRN_MEASUREMENT category.
;
_item.name '_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
;
This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named '_diffrn_measurement_axis.id'
which is now a deprecated name. The old name is
provided as an alias, but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0.00
_item.mandatory_code implicit
save_
####################
# DIFFRN_RADIATION #
####################
save_DIFFRN_RADIATION
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used in measuring diffraction intensities,
its collimation and monochromatisation before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
_category_key.name '_diffrn_radiation.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the esd of the directions of photons in the X-Z plane
around the mean source beam direction.
Note that some synchrotrons specify this value in milliradians,
in which case a conversion would be needed. To go from a
value in milliradians to a value in degrees, multiply by 0.180
and divide by Pi.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the esd of the directions of photons in the Y-Z plane
around the mean source beam direction.
Note that some synchrotrons specify this value in milliradians,
in which case a conversion would be needed. To go from a
value in milliradians to a value in degrees, multiply by 0.180
and divide by Pi.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation degrees**2 between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
directin of each photons in X-Z plane times the deviations
of the direction of the same photon in the Y-Z plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons specify this value in
milliradians**2, in which case a conversion would be needed.
To go from a value in milliradians**2 to a value in
degrees**2, multiply by 0.180**2 and divide by Pi**2.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a mono-
chromator crystal is used the material and the indices of the
Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarisation and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarisation ratio of the diffraction beam incident on the
crystal. It is the ratio of the perpendicularly polarised to the
parallel polarised component of the radiation. The perpendicular
component forms an angle of _diffrn_radiation.polarisn_norm to
the normal to the diffraction plane of the sample (i.e. the
plane containing the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
normal to the polarization plane and the laboratory Y axis as
defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monchromater.
This differs from the value of '_diffrn_radiation.polarisn_norm'
in that '_diffrn_radiation.polarisn_norm' refers to polarization
relative to the diffraction plane rather than to the laboratory
axis system.
In the case of an unpolarized beam, or a beam with true circular
polarization, in which no single plane of polarization can be
determined, the plane should be taken as the X-Z plane, and the
angle as 0.
See '_diffrn_radiation.polarizn_source_ratio'.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity (amplitude squared)
of the electric vector in the plane of polarization and In is
the intensity (amplitude squared) of the electric vector
in plane of the normal to the plane of polarization.
Thus, if we had complete polarization in the plane of
polarization, the value of
'_diffrn_radiation.polarizn_source_ratio' would
be 1, and an unpolarized beam would have a value of 0.
If the X-axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of "MONOCHROMATOR" in the Denzo glossary, and values of near
1 should be expected for a bending magnet source. However,
if the X-axis were, for some reason to be, say, perpendicular
to the polarization plane (not a common choice), then the
Denzo value would be the negative of
'_diffrn_radiation.polarizn_source_ratio'.
See http://www.hkl-xray.com for information on Denzo, and
Z. Otwinowski and W. Minor, " Processing of X-ray Diffraction
Data Collected in Oscillation Mode ", Methods in Enzymology,
Volume 276: Macromolecular Crystallography, part A, p.307-326,
1997,C.W. Carter, Jr. & R. M. Sweet, Eds., Academic Press.
This differs both in the choice of ratio and choice of
orientation from '_diffrn_radiation.polarisn_ratio', which,
unlike '_diffrn_radiation.polarizn_source_ratio', is unbounded.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly encouraged
that this field be specified so that the probe radiation
can be simply determined.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'x-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for probe radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to _diffrn_radiation_wavelength.id
in the DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.mandatory_code yes
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
;
This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
;
_category.id diffrn_refln
_category.mandatory_code no
_category_key.name '_diffrn_refln.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
;
This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
;
Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
_category_key.name '_diffrn_scan.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. We have specified three rotation axes and one translation axis
at non-zero values, with one axis stepping. There is no reason why
more axes could not have been specified to step. We have specified
range information, but note that it is redundant from the number of
frames and the increment, so we could drop the data item
_diffrn_scan_axis.angle_range .
We have specified both the sweep data and the data for a single frame.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
'_diffrn_scan.integration_time' and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
'_diffrn_scan_frame.integration_time' and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustements are made to
scan times and non-linear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.angle_increment_diffrn_scan_frame_axis.displacement_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
;
Example 2 - a more extensive example, R. M. Sweet, P. Ellis, H. Bernstein.
We place a detector 240 mm along the Z axis from the goniometer.
This presents us with a choice -- either we define the axes of
the detector at the origin, and then put a Z setting of -240 in
for the actual use, or we define the axes with the necessary Z-offset.
In this case we use the setting, and leave the offset as zero.
We call this axis DETECTOR_Z.
The axis for positioning the detector in the Y-direction depends
on the detector Z-axis. We call this axis, DETECTOR_Y.
The axis for positioning the dector in the X-direction depends
on the detector Y-axis (and therefore on the detector Z-axis).
We call this axis DETECTOR_X.
This detector may be rotated around the Y-axis. This rotation axis
depends on the three translation axies. We call it DETECTOR_PITCH.
We define a coordinate system on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm x 0.150mm, the center of the first pixel is at (0.075,
0.075) in this coordinate system.
;
;
###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.displacement_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
;
Example 3 - Example 2 revised for a spiral scan, R. M. Sweet,
P. Ellis, H. Bernstein.
We place a detector 240 mm along the Z axis from the goniometer,
as in Example 2, above, but in this example, the image plate is
scanned in a spiral pattern outside edge in.
The axis for positioning the detector in the Y-direction depends
on the detector Z-axis. We call this axis, DETECTOR_Y.
The axis for positioning the dector in the X-direction depends
on the detector Y-axis (and therefore on the detector Z-axis).
We call this axis DETECTOR_X.
This detector may be rotated around the Y-axis. This rotation axis
depends on the three translation axies. We call it DETECTOR_PITCH.
We define a coordinate system on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. Let us call rotation axis ELEMENT_ROT, and the
radial axis ELEMENT_RAD. We assume 150 um radial pitch and 75 um
'constant velocity' angular pitch.
We index first on the rotation axis and make the radial axis
dependent on
it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
;
###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id_diffrn_radiation.wavelength_id_diffrn_radiation.monochromator_diffrn_radiation.polarizn_source_ratio_diffrn_radiation.polarizn_source_norm_diffrn_radiation.div_x_source_diffrn_radiation.div_y_source_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id_diffrn_detector.id_diffrn_detector.type_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.id_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id_diffrn_data_frame.detector_element_id_diffrn_data_frame.array_id_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id_diffrn_measurement.id_diffrn_measurement.number_of_axes_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id_diffrn_scan.frame_id_start_diffrn_scan.frame_id_end_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id_diffrn_scan_axis.axis_id_diffrn_scan_axis.angle_start_diffrn_scan_axis.angle_range_diffrn_scan_axis.angle_increment_diffrn_scan_axis.displacement_start_diffrn_scan_axis.displacement_range_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id_diffrn_scan_frame.frame_number_diffrn_scan_frame.integration_time_diffrn_scan_frame.scan_id_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id_diffrn_scan_frame_axis.axis_id_diffrn_scan_frame_axis.angle_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id_axis.type_axis.equipment_axis.depends_on_axis.vector[1]_axis.vector[2]_axis.vector[3]_axis.offset[1]_axis.offset[2]_axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id_array_structure_list.index_array_structure_list.dimension_array_structure_list.precedence_array_structure_list.direction_array_structure_list.axis_set_id
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id_array_structure_list_axis.axis_id_array_structure_list_axis.angle_array_structure_list_axis.displacement_array_structure_list_axis.angular_pitch_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id_array_element_size.index_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id_array_intensities.binary_id_array_intensities.linearity_array_intensities.gain_array_intensities.gain_esd_array_intensities.overload_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id_array_structure.encoding_type_array_structure.compression_type_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id_array_data.binary_id_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
;
The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
;
The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
;
Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
'_diffrn_scan_frame.integration_time', even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
;
The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frame_id_end
_item_description.description
;
The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frames
_item_description.description
;
The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
;
The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
'_diffrn_scan.id'.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
'_diffrn_scan.id'.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.angle_start
_item_description.description
;
The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
;
The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
;
The increment for each step for the specified axis
in degrees. In general, this will agree with
'_array_structure_list_axis.angle_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
;
The increment after each step for the specified axis
in degrees. In general, this will agree with
'_array_structure_list_axis.angle_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
;
The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
;
The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
;
The increment for each step for the specified axis
in millimetres. In general, this will agree with
'_diffrn_scan_frame_axis.displacement_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
;
The increment for each step for the specified axis
in millimetres. In general, this will agree with
'_diffrn_scan_frame_axis.displacement_rstrt_incr', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
;
Data items in the DIFFRN_SCAN_FRAME category describe the settings of
axes for particular frames. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
;
The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
save__diffrn_scan_frame.frame_number
_item_description.description
;
The value of this data item is the number of the frame within
the scan, starting with 1. It is not necessarily the same as
the value of _diffrn_scan_frame.frame_id, but may
be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
;
The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of '_diffrn_scan.integration_time'.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_FRAME_AXIS category describes the settings
of axes for particular frames. Unspecified axes are assumed to be at
their zero points. If, for any given frame, non-zero values apply
for any of the data items in this category, those values should be
given explicitly in this category and not simply inferred from values
in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
;
The increment for this frame for angular setting of
the specified axis in degrees. The sum of the values
of '_diffrn_scan_frame_axis.angle' and
'_diffrn_scan_frame_axis.angle_increment' is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
;
The increment after this frame for angular setting of
the specified axis in degrees. The sum of the values
of '_diffrn_scan_frame_axis.angle' and
'_diffrn_scan_frame_axis.angle_increment' and
'_diffrn_scan_frame_axis.angle_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame, and should equal
'_diffrn_scan_frame_axis.angle' for that next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
;
The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
;
The increment for this frame for displacement setting of
the specified axis in millimetres. The sum of the values
of '_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
;
The increment for this frame for displacement setting of
the specified axis in millimetres. The sum of the values
of '_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' and
'_diffrn_scan_frame_axis.displacement_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame, and should equal
'_diffrn_scan_frame_axis.displacement' for that next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id .
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive)
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items (case insensitive)
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*}\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]\
(T[0-2][0-9]:[0-5][0-9]:[0-5][0-9](.[0-9]+)([+-][0-5][0-9]:[0-5][0-9]))
;
;
Standard format for CIF date and time strings (see
http://www.iucr.orgiucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character "T" followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
deciaml fraction on the seconds of time.
Time is local time if no time-zone offset is given.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2))'
'millimetres' 'millimetres (metres * 10^( -3))'
'nanometres' 'nanometres (metres * 10^( -9))'
'angstroms' 'angstroms (metres * 10^(-10))'
'picometres' 'picometres (metres * 10^(-12))'
'femtometres' 'femtometres (metres * 10^(-15))'
#
'reciprocal_metres' 'reciprocal metres (metres * 10^-1)'
'reciprocal_centimetres' 'reciprocal centimetres (metres * 10^( -2)^-1)'
'reciprocal_millimetres' 'reciprocal millimetres (metres * 10^( -3)^-1)'
'reciprocal_nanometres' 'reciprocal nanometres (metres * 10^( -9)^-1)'
'reciprocal_angstroms' 'reciprocal angstroms (metres * 10^(-10)^-1)'
'reciprocal_picometres' 'reciprocal picometres (metres * 10^(-12)^-1)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9))^2'
'angstroms_squared' 'angstroms squared (metres * 10^(-10))^2'
'8pi2_angstroms_squared' '8pi^2 * angstroms squared (metres * 10^(-10))^2'
'picometres_squared' 'picometres squared (metres * 10^(-12))^2'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9))^3'
'angstroms_cubed' 'angstroms cubed (metres * 10^(-10))^3'
'picometres_cubed' 'picometres cubed (metres * 10^(-12))^3'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (metres * 10^( -9))^3
;
'electrons_per_angstroms_cubed'
; electrons per angstroms cubed (metres * 10^(-10))^3
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (metres * 10^(-12))^3
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E-09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E+03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E-06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E+09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li
;
1.1.1 2001-02-16
;
Several typo corrections by JW
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to '_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source', '_diffrn_radiation.polarizn_source_norm',
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add _diffrn_measurement.device to category key
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to allow
for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes (JW)
+ Correct spelling of diffrn_measurement_axis in _axis.id
+ Correct ordering of uses of _item.mandatory_code and _item_default.value
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown (HJB)
+ Added further comments on '\n' and '\t'
+ Updated ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Changed all spelling 'meter' to 'metre' throughout.
+ Added missing enumerations to _array_structure.compression_type
and made 'none' the default.
+ Removed parent-child relationship between _array_structure_list.index
and _array_structure_list.precedence .
+ Improve alphabetization.
+ Fix _array_intensities_gain.esd related function.
+ Improved comments in AXIS.
+ Fixed DIFFRN_FRAME_DATA example.
+ Removed erroneous DIFFRN_MEASUREMENT example.
+ Added _diffrn_measurement_axis.id to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for _diffrn_scan.id definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header (HJB)
+ Restored _diffrn_detector.diffrn_id to DIFFRN_DETECTOR KEY.
+ Added AXIS category.
+ Brought complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
in from cif_mm.dic for clarity.
+ changed _array_structure.encoding_type from type code to uline and
added X-Binary-Element-Type to MIME header.
+ added detector beam center _diffrn_detector_element.center[1] and
_diffrn_detector_element.center[2]
+ corrected item name of _diffrn_refln.frame_id
+ replace reference to _array_intensities.undefined by
_array_intensities.undefined_value
+ replace references to _array_intensity.scaling with
_array_intensities.scaling
+ added DIFFRN_SCAN... categories
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft (HJB)
+ Reflowed comment lines over 80 characters and corrected typos.
+ Updated examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF (HJB)
+ Added binary type, which is a text field containing a variant on
MIME encoded data.
+ Changed type of _array_data.data to binary and specified internal
structure of raw binary data.
+ Added _array_data.binary_id, and made
_diffrn_frame_data.binary_id and _array_intensities.binary_id
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft (JW):
+ Added category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes were made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA was renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE was renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for _diffrn_frame_data.array_id was changed from
array_structure_list.array_id to array_structure.id. Item
_diffrn_detector.array_id was deleted.
+ Added data item _diffrn_frame_data.binary_id to identify data groups
within a binary section. The formal identification of the binary section
is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version was adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley (AH).
Modifications to the CBF draft (JW):
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories have been
generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category ARRAY_DATA .
This departs from the CBF notion of data existing in some special comment.
In this description, data is handled as an ordinary data item encapsulated
in a character data type. Although handling binary data this manner
deviates from CIF conventions, it does not violate any DDL 2.1 rules.
DDL 2.1 regular expressions can be used to define the binary
representation which will permit some level of data validation. In
this version, the placeholder type code "any" has been used.
This translates to a regular expression which will match any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary. It
may be possible to use the DDL 2.1 ITEM_STRUCTURE and ITEM_STRUCTURE_LIST
categories to provide the information that is carried in by the
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By moving the array
structure to the DDL level it would be possible to define an array
type as well as a regular expression defining the data format.
+ Multiple array sections can be properly handled within a single datablock.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
_array_intensities.gain. If raw, uncorrected values
are presented (e.g. for calibration experiments), the
value of _array_intensities.linearity will be 'raw'
and _array_intensities.gain will not be used.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be zero.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The value of _diffrn_data_frame.center_slow is
the slow index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_data_frame.center_units' along the slow
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement the current setting of detector
positioner given frame are used.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions
of photons in the YZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
./CBFlib-0.9.2.2/doc/mmcif_ddl_2.1.6.dic 0000644 0000765 0000765 00000314352 11603702115 015476 0 ustar yaya yaya ###########################################################################
#
# File: mmcif_ddl.dic
# Date: Mon Aug 9 02:48:08 EDT 2004
#
# Created from files in CVS module dict-mmcif_ddl.dic unless noted:
# mmcif_ddl-header.dic
# mmcif_ddl-data.dic
# mmcif_ddl-def-1.dic
# mmcif_ddl-def-2.dic
#
###########################################################################
###########################################################################
#
# File: mmcif_ddl-header.dic
#
# mmCIF DDL Core Dictionary with NDB extensions
#
# This DDL dictionary is a mirror of ddl_core.dic-org with all implicit
# data items fully expanded and with NDB extensions added.
#
# Header Section
#
#
###########################################################################
data_mmcif_ddl.dic
_datablock.id mmcif_ddl.dic
_datablock.description
;
This data block holds the core DDL.
;
_dictionary.datablock_id mmcif_ddl.dic
_dictionary.title mmcif_ddl.dic
_dictionary.version 2.1.6
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.1 1994-07-25
;
DDL 1.1 from Syd Hall et. al.
;
1.2.1 1994-09-18
;
Changes:.........etc. etc. John Westbrook
;
1.2.9 1994-10-05
;
Reflect the results of the Treaty of Brussels. JW.
;
2.0.1 1994-10-15
;
Adapted for closer mapping to DDL1.3 and clearer presentation. SRH/NS.
;
2.0.2 1994-10-16
;
Even closer................... SRH/NS.
;
2.0.3 1994-10-17
;
Coming to grips with the links and dependencies..... SRH/NS.
;
2.0.4 1994-10-20
;
Backed in changes from mm-ddl 1.2.12
Many other changes ... (JW)
;
2.0.5 1994-10-20
;
Some small adjustments..........SRH.
;
2.0.6 1994-10-20
;
More small adjustments..........JW.
;
2.0.7 1994-11-03
;
Changes: (JW)
+ Place all item and item_linked category definitions with the parent
item.
+ Fixed a number of not so trivial typos.
+ Corrected errors in the data type conversion table.
+ Corrected key item inconsistencies.
+ Added the item_aliases category.
;
2.0.8 1994-11-10
;
Miscellaneous corrections: (JW)
+ defined sub_category_group
+ corrected typo in category_examples.id definition
+ added _item_type_conditions.name in item category
+ added _item_structure.name in item category
+ corrected typo in item_aliases category definition
+ corrected typo in sub_category.method_id definition
;
2.0.9 1994-11-14
;
Changes: (JW)
+ added ITEM_UNITS, ITEM_UNITS_LIST, and UNITS_CONVERSION
categories.
+ added an additional primitive type for character type items
for which comparisons must be case insensitive.
Since it is customary to permit item names and category
identifiers to be specified in mixed case, it is necessary
to declare that case should NOT be considered in any
comparisons of these items.
;
2.0.10 1994-11-23
;
Changes: (JW)
+ Several name category changes for the sake of consistency:
enumeration -> item_enumeration
enumeration_default -> item_enumeration_default
enumeration_limit -> item_enumeration_limit
units_conversion -> item_units_conversion
+ Added _item_related.function_code alternate_exclusive
to identify mutually exclusive alternative declarations
of the same item.
+ Added structure options for real symmetric matrices.
+ Changed from zero based indices to one based indices
for compatibility with existing matrix component
definitions.
+ Add _item_linked.parent_name to the key of the item_linked
category.
+ Reorder items in the DDL so be alphabetical within
category groups.
;
2.0.11 1994-11-28
;
Changes: (JW)
+ Corrected spelling error for the data type code in
the DICTIONARY_HISTORY category.
+ Add category BLOCK to hold the data block name and data
block description. The block identifier was also added
to the key of the item category. The block identifier
can be implicitly derived from the STAR "data_" delimiter.
This identifier is required to form the key for categories
which are conceptually related to the data block as a
whole.
;
2.0.12 1994-11-30
;
Changes: (JW)
+ Added a data item _block.scope to indicate the scope of
data item names defined within included data blocks.
;
2.0.13 1994-12-12
;
Changes: (JW)
+ Deleted data item _block.scope.
+ Changed DICTIONARY category key to _dictionary.block_id
to guarantee only one dictionary definition per block.
+ Deleted data item _item.block_id as this will be replaced
by an item address syntax that will include block, save
frame, and url.
;
2.0.14 1994-12-15
;
Changes: (JW)
+ Made some terminology changes suggested by PMDF
_item_enumeration.code -> _item_enumeration.value
ITEM_ENUMERATION_DEFAULT -> ITEM_DEFAULT
ITEM_ENUMERATION_LIMIT -> ITEM_RANGE
+ Added item _item_type_list.detail
+ Version 2.0.14 is being frozen and exported.
;
2.0.15 1995-02-13
;
Changes: (JW)
+ Added '_' prefix to all data item save frame names.
References to data item names now always include
a leading underscore independent of the usage context.
+ A few miscellaneous corrections.
;
2.0.16 1995-06-18
;
Changes: (JW)
+ Revised the block level categories in the following ways:
Changed category BLOCK to DATA_BLOCK.
Added connection from _data_block.id to _category.implicit_key
in order to provide a formal means of merging the contents
of categories between data blocks.
+ Moved ennumerations for _method_list.code and
method_list.language to examples.
+ Removed symmetric matrix options from the ennumerations
for _item_structure.organization.
+ Added _item_related.function codes for 'associated_value',
'associated_esd', 'replaces' and 'replacedby'
+ Added data items _item_aliases.dictionary and
_item_aliases.dictionary_version.
+ Reorganized method categories such that multiple methods can
be applied at each level of data structure. Introduced a
consistent set of categories to hold method associations:
ITEM_METHODS, CATEGORY_METHODS, SUB_CATEGORY_METHODS, and
DATA_BLOCK_METHODS. Removed data items _category.method_id
_sub_category.method_id.
;
2.0.17 1995-06-22
;
Changes: (JW)
+ Quoted data vaules containing the leading string 'data_'.
;
2.1.0 1995-07-20
;
Changes: (JW)
Final adjustments before the first release of the mmCIF dictionary:
+ changed data_block to datablock to avoid any problems with
the STAR data_ reserved token.
+ created new category to hold item subcategory associations
and deleted the subcategory attribute from ITEM category.
+ modified regular expressions to reflect limitations observed
on several platforms.
+ expanded the ennumeration of _item_related.function_code.
+ removed default value from _item.manadatory_code.
+ removed type construct for date and changed date data type
to yyyy-mm-dd
+ added less restrictive data type for alias names.
;
2.1.1 1995-09-26
;
Changes: (JW)
+ Changed regular expressions for type code to permit
single quote.
+ Corrected regular expression syntax for type name and
type date.
+ Corrected lower bound description for item_range.minimum.
The incorrect <= condition is changed to <.
+ _item_mandatory.code has been now a mandatory item.
+ _item_aliases.dictionary and _item_aliases.dictionary_version
are added to the composite key for category ITEM_ALIASES.
+ _datablock.id data type changes to type code.
+ Shortened the name _item_aliases.dictionary_version to
_item_aliases.version
;
2.1.2 1997-01-24
;
Changes: (JW)
+ Added associated_error to the enumeration list of
_item_related.function_code.
;
2.1.3 2000-10-16
;
Changes: (JW)
+ Changed data type for regular expression in
_item_type_list.construct to type text.
;
2.1.5 2003-06-23
; Changes: (JW)
+ NDB extensions adopted into ddl_core
+ New partitioning scheme implemented
;
2.1.6 2004-04-15
; Changes: (JW)
+ Name changed to mmcif_ddl.dic
;
### EOF mmcif_ddl-header.dic ####
###########################################################################
#
# File: mmcif_ddl-data.dic
#
# mmCIF DDL Core Dictionary with NDB extensions
#
# This DDL dictionary is a mirror of ddl_core.dic-org with all implicit
# data items fully expanded and with NDB extensions added.
#
# Data Section
#
#
###########################################################################
# DATA TYPE CONVERSION TABLE
# --------------------------
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.detail
_item_type_list.construct
code char 'A single word'
'[^\t\n "]*'
char char 'A single line of text'
'[^\n]*'
text char 'Text which may span lines'
'.*'
int numb 'Unsigned integer data'
'[0-9]+'
name uchar 'A data item name (restrictive type)'
'_[_A-Za-z0-9]+[.][][_A-Za-z0-9\<\>%/-]+'
aliasname uchar 'A DDL 1.4 data item name (less restrictive type)'
'_[^\t\n "]+'
idname uchar 'A data item name component or identifier'
'[_A-Za-z0-9]+'
any char 'Any data type'
'.*'
yyyy-mm-dd char 'A date format'
'[0-9][0-9][0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]'
#
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'ddl_group' .
;
Component categories of the macromolecular DDL
;
'datablock_group' 'ddl_group'
;
Categories that describe the characteristics of data blocks.
;
'category_group' 'ddl_group'
;
Categories that describe the characteristics of categories.
;
'sub_category_group' 'ddl_group'
;
Categories that describe the characteristics of subcategories.
;
'item_group' 'ddl_group'
;
Categories that describe the characteristics of data items.
;
'dictionary_group' 'ddl_group'
;
Categories that describe the dictionary.
;
'compliance_group' 'ddl_group'
;
Categories that are retained specifically for compliance with
older versions of the DDL.
;
### EOF mmcif_ddl-data.dic
###########################################################################
#
# File: mmcif_ddl-def-1.dic
#
# mmCIF DDL Core Dictionary with NDB extensions
#
# This DDL dictionary is a mirror of ddl_core.dic-org with all implicit
# data items fully expanded and with NDB extensions added.
#
# Definition Section 1.
# (Core Definitions)
#
#
###########################################################################
# ----------------------------------------------------------------------------
save_DATABLOCK
_category.description
;
Attributes defining the characteristics of a data block.
;
_category.id datablock
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id datablock
_category_key.name '_datablock.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' datablock
'datablock_group' datablock
save_
save__datablock.id
_item_description.name '_datablock.id'
_item_description.description
;
The identity of the data block.
;
_item.name '_datablock.id'
_item.category_id datablock
_item.mandatory_code implicit
_item_type.name '_datablock.id'
_item_type.code code
loop_
_item_linked.parent_name
_item_linked.child_name
'_datablock.id' '_datablock_methods.datablock_id'
'_datablock.id' '_dictionary.datablock_id'
'_datablock.id' '_category.implicit_key'
save_
save__datablock.description
_item_description.name '_datablock.description'
_item_description.description
;
Text description of the data block.
;
_item.name '_datablock.description'
_item.category_id datablock
_item.mandatory_code yes
_item_type.name '_datablock.description'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_DATABLOCK_METHODS
_category.description
;
Attributes specifying the association between data blocks and methods.
;
_category.id datablock_methods
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
datablock_methods '_datablock_methods.method_id'
datablock_methods '_datablock_methods.datablock_id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' datablock_methods
'datablock_group' datablock_methods
save_
save__datablock_methods.datablock_id
_item_description.name '_datablock_methods.datablock_id'
_item_description.description
;
Identifier of data block.
;
_item.name '_datablock_methods.datablock_id'
_item.category_id datablock_methods
_item.mandatory_code implicit
_item_type.name '_datablock_methods.datablock_id'
_item_type.code code
save_
save__datablock_methods.method_id
_item_description.name '_datablock_methods.method_id'
_item_description.description
;
Unique method identifier associated with a data block.
;
_item.name '_datablock_methods.method_id'
_item.category_id datablock_methods
_item.mandatory_code yes
_item_type.name '_datablock_methods.method_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_CATEGORY
_category.description
;
Attributes defining the functionality for the entire category.
;
_category.id category
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id category
_category_key.name '_category.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' category
'category_group' category
save_
save__category.id
_item_description.name '_category.id'
_item_description.description
;
The identity of the data category. Data items may only be looped
with items of the same category.
;
_item.name '_category.id'
_item.category_id category
_item.mandatory_code yes
_item_type.name '_category.id'
_item_type.code idname
loop_
_item_linked.child_name
_item_linked.parent_name
'_category_examples.id' '_category.id'
'_category_group.category_id' '_category.id'
'_category_key.id' '_category.id'
'_category_methods.category_id' '_category.id'
'_item.category_id' '_category.id'
save_
save__category.description
_item_description.name '_category.description'
_item_description.description
;
Text description of a category.
;
_item.name '_category.description'
_item.category_id category
_item.mandatory_code yes
_item_type.name '_category.description'
_item_type.code text
save_
save__category.implicit_key
_item_description.name '_category.implicit_key'
_item_description.description
;
An identifier that may be used to distinguish the contents of
like categories between data blocks.
;
_item.name '_category.implicit_key'
_item.category_id category
_item.mandatory_code implicit
_item_type.name '_category.implicit_key'
_item_type.code code
save_
save__category.mandatory_code
_item_description.name '_category.mandatory_code'
_item_description.description
;
Whether the category must be specified in a dictionary.
;
_item.name '_category.mandatory_code'
_item.category_id category
_item.mandatory_code yes
_item_type.name '_category.mandatory_code'
_item_type.code code
save_
# ----------------------------------------------------------------------------
save_CATEGORY_EXAMPLES
_category.description
;
Example applications and descriptions of data items in this category.
;
_category.id category_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
category_examples '_category_examples.id'
category_examples '_category_examples.case'
save_
save__category_examples.id
_item_description.name '_category_examples.id'
_item_description.description
;
The name of category.
;
_item.name '_category_examples.id'
_item.category_id category_examples
_item.mandatory_code implicit
_item_type.name '_category_examples.id'
_item_type.code idname
save_
save__category_examples.case
_item_description.name '_category_examples.case'
_item_description.description
;
A case of examples involving items in this category.
;
_item.name '_category_examples.case'
_item.category_id category_examples
_item.mandatory_code yes
_item_type.name '_category_examples.case'
_item_type.code text
save_
save__category_examples.detail
_item_description.name '_category_examples.detail'
_item_description.description
;
A description of an example _category_examples.case
;
_item.name '_category_examples.detail'
_item.category_id category_examples
_item.mandatory_code no
_item_type.name '_category_examples.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_CATEGORY_KEY
_category.description
;
This category holds a list of the item names that uniquely
identify the elements of the category.
;
_category.id category_key
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
category_key '_category_key.name'
category_key '_category_key.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' category_key
'category_group' category_key
save_
save__category_key.name
_item_description.name '_category_key.name'
_item_description.description
;
The name of a data item that serves as a key identifier for the
category (eg. a component of the primary key).
;
_item.name '_category_key.name'
_item.category_id category_key
_item.mandatory_code yes
_item_type.name '_category_key.name'
_item_type.code name
save_
save__category_key.id
_item_description.name '_category_key.id'
_item_description.description
;
The identifier of the category (eg. a component of the primary key).
;
_item.name '_category_key.id'
_item.category_id category_key
_item.mandatory_code implicit
_item_type.name '_category_key.id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_CATEGORY_GROUP
_category.description
;
Provides a list of category groups to which the base category
belongs.
;
_category.id category_group
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
category_group '_category_group.id'
category_group '_category_group.category_id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' category_group
'category_group' category_group
save_
save__category_group.id
_item_description.name '_category_group.id'
_item_description.description
;
The name of a category group ...
;
_item.name '_category_group.id'
_item.category_id category_group
_item.mandatory_code yes
_item_type.name '_category_group.id'
_item_type.code idname
save_
save__category_group.category_id
_item_description.name '_category_group.category_id'
_item_description.description
;
The name of a category ...
;
_item.name '_category_group.category_id'
_item.category_id category_group
_item.mandatory_code implicit
_item_type.name '_category_group.category_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_CATEGORY_GROUP_LIST
_category.description
;
This category provides the definition of each category group.
A category group is a collection of related categories.
;
_category.id category_group_list
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id category_group_list
_category_key.name '_category_group_list.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' category_group_list
'category_group' category_group_list
save_
save__category_group_list.id
_item_description.name '_category_group_list.id'
_item_description.description
;
The name of a category group ...
;
_item.name '_category_group_list.id'
_item.category_id category_group_list
_item.mandatory_code yes
_item_type.name '_category_group_list.id'
_item_type.code idname
loop_
_item_linked.child_name
_item_linked.parent_name
'_category_group.id' '_category_group_list.id'
'_category_group_list.parent_id' '_category_group_list.id'
save_
save__category_group_list.description
_item_description.name '_category_group_list.description'
_item_description.description
;
Text description of a category group...
;
_item.name '_category_group_list.description'
_item.category_id category_group_list
_item.mandatory_code yes
_item_type.name '_category_group_list.description'
_item_type.code text
save_
save__category_group_list.parent_id
_item_description.name '_category_group_list.parent_id'
_item_description.description
;
The name of the optional parent category group.
;
_item.name '_category_group_list.parent_id'
_item.category_id category_group_list
_item.mandatory_code no
_item_type.name '_category_group_list.parent_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_CATEGORY_METHODS
_category.description
;
Attributes specifying the association between categories and methods.
;
_category.id category_methods
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
category_methods '_category_methods.method_id'
category_methods '_category_methods.category_id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' category_methods
'category_group' category_methods
save_
save__category_methods.category_id
_item_description.name '_category_methods.category_id'
_item_description.description
;
The name of the category
;
_item.name '_category_methods.category_id'
_item.category_id category_methods
_item.mandatory_code implicit
_item_type.name '_category_methods.category_id'
_item_type.code idname
save_
save__category_methods.method_id
_item_description.name '_category_methods.method_id'
_item_description.description
;
The name of the method
;
_item.name '_category_methods.method_id'
_item.category_id category_methods
_item.mandatory_code yes
_item_type.name '_category_methods.method_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_SUB_CATEGORY
_category.description
;
The purpose of a sub-category is to define an association between
data items within a category and optionally provide a method to
validate the collection of items. The sub-category named
'cartesian' might be applied to the data items for the coordinates
x, y, and z.
;
_category.id sub_category
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id sub_category
_category_key.name '_sub_category.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' sub_category
'sub_category_group' sub_category
save_
save__sub_category.id
_item_description.name '_sub_category.id'
_item_description.description
;
The identity of the sub-category.
;
_item.name '_sub_category.id'
_item.category_id sub_category
_item.mandatory_code yes
_item_type.name '_sub_category.id'
_item_type.code idname
loop_
_item_linked.child_name
_item_linked.parent_name
'_sub_category_examples.id' '_sub_category.id'
'_sub_category_methods.sub_category_id' '_sub_category.id'
'_item_sub_category.id' '_sub_category.id'
save_
save__sub_category.description
_item_description.name '_sub_category.description'
_item_description.description
;
Description of the sub-category.
;
_item.name '_sub_category.description'
_item.category_id sub_category
_item.mandatory_code yes
_item_type.name '_sub_category.description'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_SUB_CATEGORY_EXAMPLES
_category.description
;
Example applications and descriptions of data items in this subcategory.
;
_category.id sub_category_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
sub_category_examples '_sub_category_examples.id'
sub_category_examples '_sub_category_examples.case'
loop_
_category_group.id
_category_group.category_id
'ddl_group' sub_category_examples
'sub_category_group' sub_category_examples
save_
save__sub_category_examples.id
_item_description.name '_sub_category_examples.id'
_item_description.description
;
The name for the subcategory.
;
_item.name '_sub_category_examples.id'
_item.category_id sub_category_examples
_item.mandatory_code yes
_item_type.name '_sub_category_examples.id'
_item_type.code idname
save_
save__sub_category_examples.case
_item_description.name '_sub_category_examples.case'
_item_description.description
;
An example involving items in this subcategory.
;
_item.name '_sub_category_examples.case'
_item.category_id sub_category_examples
_item.mandatory_code yes
_item_type.name '_sub_category_examples.case'
_item_type.code text
save_
save__sub_category_examples.detail
_item_description.name '_sub_category_examples.detail'
_item_description.description
;
A description of an example _sub_category_examples.case
;
_item.name '_sub_category_examples.detail'
_item.category_id sub_category_examples
_item.mandatory_code no
_item_type.name '_sub_category_examples.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_SUB_CATEGORY_METHODS
_category.description
;
Attributes specifying the association between subcategories and methods.
;
_category.id sub_category_methods
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
sub_category_methods '_sub_category_methods.method_id'
sub_category_methods '_sub_category_methods.sub_category_id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' sub_category_methods
'sub_category_group' sub_category_methods
save_
save__sub_category_methods.sub_category_id
_item_description.name '_sub_category_methods.sub_category_id'
_item_description.description
;
The name of the subcategory
;
_item.name '_sub_category_methods.sub_category_id'
_item.category_id sub_category_methods
_item.mandatory_code yes
_item_type.name '_sub_category_methods.sub_category_id'
_item_type.code idname
save_
save__sub_category_methods.method_id
_item_description.name '_sub_category_methods.method_id'
_item_description.description
;
The name of the method
;
_item.name '_sub_category_methods.method_id'
_item.category_id sub_category_methods
_item.mandatory_code yes
_item_type.name '_sub_category_methods.method_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_ITEM
_category.description
;
Attributes which describe the characteristics of a data item.
;
_category.id item
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item
_category_key.name '_item.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item
'item_group' item
save_
save__item.name
_item_description.name '_item.name'
_item_description.description
;
Data name of the defined item.
;
_item_type.name '_item.name'
_item_type.code name
_item.name '_item.name'
_item.category_id item
_item.mandatory_code implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_category_key.name' '_item.name'
'_item_aliases.name' '_item.name'
'_item_default.name' '_item.name'
'_item_dependent.name' '_item.name'
'_item_dependent.dependent_name' '_item.name'
'_item_description.name' '_item.name'
'_item_enumeration.name' '_item.name'
'_item_examples.name' '_item.name'
'_item_linked.child_name' '_item.name'
'_item_linked.parent_name' '_item.name'
'_item_methods.name' '_item.name'
'_item_range.name' '_item.name'
'_item_related.name' '_item.name'
'_item_related.related_name' '_item.name'
'_item_type.name' '_item.name'
'_item_type_conditions.name' '_item.name'
'_item_structure.name' '_item.name'
'_item_sub_category.name' '_item.name'
'_item_units.name' '_item.name'
save_
save__item.mandatory_code
_item_description.name '_item.mandatory_code'
_item_description.description
;
Signals if the defined item is mandatory for the proper description
of its category.
;
_item.name '_item.mandatory_code'
_item.category_id item
_item.mandatory_code yes
_item_type.name '_item.mandatory_code'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item.mandatory_code'
yes 'required item in this category'
'_item.mandatory_code'
no 'optional item in this category'
'_item.mandatory_code'
implicit 'required item but may be determined from context'
save_
save__item.category_id
_item_description.name '_item.category_id'
_item_description.description
;
This is category id of the item.
;
_item.name '_item.category_id'
_item.category_id item
_item.mandatory_code implicit
_item_type.name '_item.category_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_ITEM_ALIASES
_category.description
;
This category holds a list of possible alias names or synonyms for
each data item. Each alias name is identified by the name and
version of the dictionary to which it belongs.
;
_category.id item_aliases
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_aliases '_item_aliases.alias_name'
item_aliases '_item_aliases.dictionary'
item_aliases '_item_aliases.version'
save_
save__item_aliases.name
_item_description.name '_item_aliases.name'
_item_description.description
;
Name for the data item.
;
_item.name '_item_aliases.name'
_item.category_id item_aliases
_item.mandatory_code implicit
_item_type.name '_item_aliases.name'
_item_type.code name
save_
save__item_aliases.alias_name
_item_description.name '_item_aliases.alias_name'
_item_description.description
;
Alias name for the data item.
;
_item.name '_item_aliases.alias_name'
_item.category_id item_aliases
_item.mandatory_code yes
_item_type.name '_item_aliases.alias_name'
_item_type.code aliasname
save_
save__item_aliases.dictionary
_item_description.name '_item_aliases.dictionary'
_item_description.description
;
The dictionary in which the alias name is defined.
;
_item.name '_item_aliases.dictionary'
_item.category_id item_aliases
_item.mandatory_code yes
_item_type.name '_item_aliases.dictionary'
_item_type.code char
save_
save__item_aliases.version
_item_description.name '_item_aliases.version'
_item_description.description
;
The version of the dictionary in which the alias name is defined.
;
_item.name '_item_aliases.version'
_item.category_id item_aliases
_item.mandatory_code yes
_item_type.name '_item_aliases.version'
_item_type.code char
save_
# ----------------------------------------------------------------------------
save_ITEM_DEFAULT
_category.description
;
Attributes specifying the default value for a data item.
;
_category.id item_default
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_default
_category_key.name '_item_default.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_default
'item_group' item_default
save_
save__item_default.name
_item_description.name '_item_default.name'
_item_description.description
;
The name of item for which the default value is defined
;
_item.name '_item_default.name'
_item.category_id item_default
_item.mandatory_code implicit
_item_type.name '_item_default.name'
_item_type.code name
save_
save__item_default.value
_item_description.name '_item_default.value'
_item_description.description
;
The default value for the defined item if it is not specified
explicitly. If a data value is not declared, the default is
assumed to be the most likely or natural value.
;
_item.name '_item_default.value'
_item.category_id item_default
_item.mandatory_code no
_item_type.name '_item_default.value'
_item_type.code any
save_
# ----------------------------------------------------------------------------
save_ITEM_DEPENDENT
_category.description
;
Attributes which identify other data items that must be specified
for the defined data item to be valid.
;
_category.id item_dependent
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_dependent '_item_dependent.name'
item_dependent '_item_dependent.dependent_name'
save_
save__item_dependent.name
_item_description.name '_item_dependent.name'
_item_description.description
;
Item name of a dependent item.
;
_item.name '_item_dependent.name'
_item.category_id item_dependent
_item.mandatory_code implicit
_item_type.name '_item_dependent.name'
_item_type.code name
save_
save__item_dependent.dependent_name
_item_description.name '_item_dependent.dependent_name'
_item_description.description
;
Data name of a dependent item.
;
_item.name '_item_dependent.dependent_name'
_item.category_id item_dependent
_item.mandatory_code yes
_item_type.name '_item_dependent.dependent_name'
_item_type.code name
save_
# ----------------------------------------------------------------------------
save_ITEM_DESCRIPTION
_category.description
;
This category holds the descriptions of each data item.
;
_category.id item_description
_category.mandatory_code yes
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_description '_item_description.name'
item_description '_item_description.description'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_description
'item_group' item_description
save_
save__item_description.name
_item_description.name '_item_description.name'
_item_description.description
;
Tne name of data item.
;
_item.name '_item_description.name'
_item.category_id item_description
_item.mandatory_code implicit
_item_type.name '_item_description.name'
_item_type.code name
save_
save__item_description.description
_item_description.name '_item_description.description'
_item_description.description
;
Text decription of the defined data item.
;
_item.name '_item_description.description'
_item.category_id item_description
_item.mandatory_code yes
_item_type.name '_item_description.description'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_ITEM_ENUMERATION
_category.description
;
Attributes which specify the permitted enumeration of the items.
;
_category.id item_enumeration
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_enumeration '_item_enumeration.name'
item_enumeration '_item_enumeration.value'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_enumeration
'item_group' item_enumeration
save_
save__item_enumeration.name
_item_description.name '_item_enumeration.name'
_item_description.description
;
Name of data item.
;
_item.name '_item_enumeration.name'
_item.category_id item_enumeration
_item.mandatory_code implicit
_item_type.name '_item_enumeration.name'
_item_type.code name
save_
save__item_enumeration.value
_item_description.name '_item_enumeration.value'
_item_description.description
;
A permissible value, character or number, for the defined item.
;
_item.name '_item_enumeration.value'
_item.category_id item_enumeration
_item.mandatory_code yes
_item_type.name '_item_enumeration.value'
_item_type.code any
save_
save__item_enumeration.detail
_item_description.name '_item_enumeration.detail'
_item_description.description
;
A description of a permissible value for the defined item.
;
_item.name '_item_enumeration.detail'
_item.category_id item_enumeration
_item.mandatory_code no
_item_type.name '_item_enumeration.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_ITEM_EXAMPLES
_category.description
;
Attributes for describing application examples of the data item.
;
_category.id item_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_examples '_item_examples.name'
item_examples '_item_examples.case'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_examples
'item_group' item_examples
save_
save__item_examples.name
_item_description.name '_item_examples.name'
_item_description.description
;
The name of data item for the example.
;
_item.name '_item_examples.name'
_item.category_id item_examples
_item.mandatory_code implicit
_item_type.name '_item_examples.name'
_item_type.code name
save_
save__item_examples.case
_item_description.name '_item_examples.case'
_item_description.description
;
An example application of the defined data item.
;
_item.name '_item_examples.case'
_item.category_id item_examples
_item.mandatory_code no
_item_type.name '_item_examples.case'
_item_type.code text
save_
save__item_examples.detail
_item_description.name '_item_examples.detail'
_item_description.description
;
A description of an example specified in _item_example.case
;
_item.name '_item_examples.detail'
_item.category_id item_examples
_item.mandatory_code no
_item_type.name '_item_examples.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_ITEM_LINKED
_category.description
;
Attributes which describe how equivalent data items are linked
within categories and across different categories.
;
_category.id item_linked
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_linked '_item_linked.child_name'
item_linked '_item_linked.parent_name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_linked
'item_group' item_linked
save_
save__item_linked.child_name
_item_description.name '_item_linked.child_name'
_item_description.description
;
Name of the child data item.
;
_item.name '_item_linked.child_name'
_item.category_id item_linked
_item.mandatory_code yes
_item_type.name '_item_linked.child_name'
_item_type.code name
save_
save__item_linked.parent_name
_item_description.name '_item_linked.parent_name'
_item_description.description
;
Name of the parent data item.
;
_item.name '_item_linked.parent_name'
_item.category_id item_linked
_item.mandatory_code implicit
_item_type.name '_item_linked.parent_name'
_item_type.code name
save_
# ----------------------------------------------------------------------------
save_ITEM_METHODS
_category.description
;
Attributes specifying the association between data items and methods.
;
_category.id item_methods
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_methods '_item_methods.method_id'
item_methods '_item_methods.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_methods
'item_group' item_methods
save_
save__item_methods.name
_item_description.name '_item_methods.name'
_item_description.description
;
The name of the item
;
_item.name '_item_methods.name'
_item.category_id item_methods
_item.mandatory_code implicit
_item_type.name '_item_methods.name'
_item_type.code name
save_
save__item_methods.method_id
_item_description.name '_item_methods.method_id'
_item_description.description
;
The name of itemthe method
;
_item.name '_item_methods.method_id'
_item.category_id item_methods
_item.mandatory_code yes
_item_type.name '_item_methods.method_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_ITEM_RANGE
_category.description
;
The range of permissible values of a data item. When multiple
ranges are specified they are interpreted sequentially
using a logical OR. To specify that an item value may be
equal to a boundary value, specify an item range where the
maximum and mimimum values equal the boundary value.
;
_category.id item_range
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_range '_item_range.name'
item_range '_item_range.minimum'
item_range '_item_range.maximum'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_range
'item_group' item_range
save_
save__item_range.name
_item_description.name '_item_range.name'
_item_description.description
;
Name of data item ...
;
_item.name '_item_range.name'
_item.category_id item_range
_item.mandatory_code implicit
_item_type.name '_item_range.name'
_item_type.code name
save_
save__item_range.minimum
_item_description.name '_item_range.minimum'
_item_description.description
;
Minimum permissible value of a data item or the lower bound
of a permissible range. ( minimum value < data value)
;
_item.name '_item_range.minimum'
_item.category_id item_range
_item.mandatory_code no
_item_type.name '_item_range.minimum'
_item_type.code any
save_
save__item_range.maximum
_item_description.name '_item_range.maximum'
_item_description.description
;
Maximum permissible value of a data item or the upper bound
of a permissible range. ( maximum value > data value)
;
_item.name '_item_range.maximum'
_item.category_id item_range
_item.mandatory_code no
_item_type.name '_item_range.maximum'
_item_type.code any
save_
# ----------------------------------------------------------------------------
save_ITEM_RELATED
_category.description
;
Attributes which specify recognized relationships between data items.
;
_category.id item_related
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_related '_item_related.name'
item_related '_item_related.related_name'
item_related '_item_related.function_code'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_related
'item_group' item_related
save_
save__item_related.name
_item_description.name '_item_related.name'
_item_description.description
;
Identifies a defined data item ...
;
_item.name '_item_related.name'
_item.category_id item_related
_item.mandatory_code implicit
_item_type.name '_item_related.name'
_item_type.code name
save_
save__item_related.related_name
_item_description.name '_item_related.related_name'
_item_description.description
;
Identifies a data item by name which is closely related to the
defined data item by the manner described by _item_related.function_code
;
_item.name '_item_related.related_name'
_item.category_id item_related
_item.mandatory_code yes
_item_type.name '_item_related.related_name'
_item_type.code name
save_
save__item_related.function_code
_item_description.name '_item_related.function_code'
_item_description.description
;
The code for the type of relationship of the item identified by
_item_related.name and the defined item.
ALTERNATE indicates that the item identified in
_item_related.related_name is an alternative expression in terms
of its application and attributes to the item in this definition.
ALTERNATE_EXCLUSIVE indicates that the item identified in
_item_related.related_name is an alternative expression in terms
of its application and attributes to the item in this definition.
Only one of the alternative forms may be specified.
CONVENTION indicates that the item identified in
_item_related.related_name differs from the defined item only
in terms of a convention in its expression.
CONVERSION_CONSTANT indicates that the item identified in
_item_related.related_name differs from the defined item only
by a known constant.
CONVERSION_ARBITRARY indicates that the item identified in
_item_related.related_name differs from the defined item only
by a arbitrary constant.
REPLACES indicates that the defined item replaces the item identified
in _item_related.related_name.
REPLACEDBY indicates that the defined item is replaced by the
item identified in _item_related.related_name.
ASSOCIATED_VALUE indicates that the item identified in
_item_related.related_name is meaningful when associated with the
defined item.
ASSOCIATED_ESD indicates that the item identified in
_item_related.related_name is the estimated standard deviation of
of the defined item.
;
_item.name '_item_related.function_code'
_item.category_id item_related
_item.mandatory_code yes
_item_type.name '_item_related.function_code'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item_related.function_code'
alternate 'alternate form of the item'
'_item_related.function_code'
alternate_exclusive 'mutually exclusive alternate form of the item'
'_item_related.function_code'
convention 'depends on defined convention'
'_item_related.function_code'
conversion_constant 'related by a known conversion factor'
'_item_related.function_code'
conversion_arbitrary 'related by a arbitrary conversion factor'
'_item_related.function_code'
replaces 'a replacement definition'
'_item_related.function_code'
replacedby 'an obsolete definition'
'_item_related.function_code'
associated_value 'a meaningful value when related to the item'
'_item_related.function_code'
associated_esd 'an estimated standard deviation of the item'
'_item_related.function_code'
associated_error 'an estimated error of the item'
save_
# ----------------------------------------------------------------------------
save_ITEM_STRUCTURE
_category.description
;
This category holds the association between data items and
named vector/matrix declarations.
;
_category.id item_structure
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_structure
_category_key.name '_item_structure.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_structure
'item_group' item_structure
save_
save__item_structure.name
_item_description.name '_item_structure.name'
_item_description.description
;
The name of data item
;
_item.name '_item_structure.name'
_item.category_id item_structure
_item.mandatory_code implicit
_item_type.name '_item_structure.name'
_item_type.code name
save_
save__item_structure.code
_item_description.name '_item_structure.code'
_item_description.description
;
Provides an indirect reference into the list of structure
type definition in category item_structure_list.
;
_item.name '_item_structure.code'
_item.category_id item_structure
_item.mandatory_code yes
_item_type.name '_item_structure.code'
_item_type.code code
save_
save__item_structure.organization
_item_description.name '_item_structure.organization'
_item_description.description
;
Identifies if the struct is defined in column or row major order.
Only the unique elements of symmetric matrices are specified.
;
_item.name '_item_structure.organization'
_item.category_id item_structure
_item.mandatory_code yes
_item_type.name '_item_structure.organization'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item_structure.organization' 'columnwise' 'column major order'
'_item_structure.organization' 'rowwise' 'row major order'
save_
# ----------------------------------------------------------------------------
save_ITEM_STRUCTURE_LIST
_category.description
;
This category holds a description for each structure type.
;
_category.id item_structure_list
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_structure_list '_item_structure_list.code'
item_structure_list '_item_structure_list.index'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_structure_list
'item_group' item_structure_list
save_
save__item_structure_list.code
_item_description.name '_item_structure_list.code'
_item_description.description
;
The name of the matrix/vector structure declaration.
;
_item.name '_item_structure_list.code'
_item.category_id item_structure_list
_item.mandatory_code yes
_item_linked.parent_name '_item_structure_list.code'
_item_linked.child_name '_item_structure.code'
_item_type.name '_item_structure_list.code'
_item_type.code code
save_
save__item_structure_list.index
_item_description.name '_item_structure_list.index'
_item_description.description
;
Identifies the one based index of a row/column of the structure.
;
_item.name '_item_structure_list.index'
_item.category_id item_structure_list
_item.mandatory_code yes
loop_
_item_range.name
_item_range.minimum
_item_range.maximum
'_item_structure_list.index' 1 1
'_item_structure_list.index' 1 .
_item_type.name '_item_structure_list.index'
_item_type.code int
save_
save__item_structure_list.dimension
_item_description.name '_item_structure_list.dimension'
_item_description.description
;
Identifies the length of this row/column of the structure.
;
_item.name '_item_structure_list.dimension'
_item.category_id item_structure_list
_item.mandatory_code yes
loop_
_item_range.name
_item_range.minimum
_item_range.maximum
'_item_structure_list.dimension' 1 1
'_item_structure_list.dimension' 1 .
_item_type.name '_item_structure_list.dimension'
_item_type.code int
save_
# ----------------------------------------------------------------------------
save_ITEM_SUB_CATEGORY
_category.description
;
This category assigns data items to subcategories.
;
_category.id item_sub_category
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_sub_category '_item_sub_category.id'
item_sub_category '_item_sub_category.name'
loop_
_category_group.id
_category_group.category_id
'sub_category_group' item_sub_category
'item_group' item_sub_category
save_
save__item_sub_category.name
_item_description.name '_item_sub_category.name'
_item_description.description
;
The name of data item
;
_item.name '_item_sub_category.name'
_item.category_id item_sub_category
_item.mandatory_code implicit
_item_type.name '_item_sub_category.name'
_item_type.code name
save_
save__item_sub_category.id
_item_description.name '_item_sub_category.id'
_item_description.description
;
The identifier of subcategory
;
_item.name '_item_sub_category.id'
_item.category_id item_sub_category
_item.mandatory_code yes
_item_type.name '_item_sub_category.id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_ITEM_TYPE
_category.description
;
Attributes for specifying the data type code for each data item.
;
_category.id item_type
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_type
_category_key.name '_item_type.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_type
'item_group' item_type
save_
save__item_type.name
_item_description.name '_item_type.name'
_item_description.description
;
The name of data item
;
_item.name '_item_type.name'
_item.category_id item_type
_item.mandatory_code implicit
_item_type.name '_item_type.name'
_item_type.code name
save_
save__item_type.code
_item_description.name '_item_type.code'
_item_description.description
;
Data type of defined data item
;
_item.name '_item_type.code'
_item.category_id item_type
_item.mandatory_code yes
_item_type.name '_item_type.code'
_item_type.code code
save_
# ----------------------------------------------------------------------------
save_ITEM_TYPE_CONDITIONS
_category.description
;
Attributes for specifying additional conditions associated with
the data type of the item.
;
_category.id item_type_conditions
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_type_conditions
_category_key.name '_item_type_conditions.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_type_conditions
'item_group' item_type_conditions
'compliance_group' item_type_conditions
save_
save__item_type_conditions.name
_item_description.name '_item_type_conditions.name'
_item_description.description
;
The name of data item
;
_item.name '_item_type_conditions.name'
_item.category_id item_type_conditions
_item.mandatory_code implicit
_item_type.name '_item_type_conditions.name'
_item_type.code name
save_
save__item_type_conditions.code
_item_description.name '_item_type_conditions.code'
_item_description.description
;
Codes defining conditions on the _item_type.code specification.
'esd' permits a number string to contain an appended standard
deviation number enclosed within parentheses. E.g. 4.37(5)
'seq' permits data to be declared as a sequence of values
separated by a comma <,> or a colon <:>.
* The sequence v1,v2,v3,. signals that v1, v2, v3, etc.
are alternative values or the data item.
* The sequence v1:v2 signals that v1 and v2 are the boundary
values of a continuous range of values. This mechanism
was used to specify permitted ranges of an item in
previous DDL versions.
Combinations of alternate and range sequences are permitted.
;
_item.name '_item_type_conditions.code'
_item.category_id item_type_conditions
_item.mandatory_code yes
_item_type.name '_item_type_conditions.code'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item_type_conditions.code'
none 'no extra conditions apply to this data item'
'_item_type_conditions.code'
esd 'numbers may have esd values appended within ()'
'_item_type_conditions.code'
seq 'data may be declared as a comma or colon separated sequence'
save_
# ----------------------------------------------------------------------------
save_ITEM_TYPE_LIST
_category.description
;
Attributes which define each type code.
;
_category.id item_type_list
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_type_list
_category_key.name '_item_type_list.code'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_type_list
'item_group' item_type_list
save_
save__item_type_list.code
_item_description.name '_item_type_list.code'
_item_description.description
;
The codes specifying the nature of the data value.
;
_item.name '_item_type_list.code'
_item.category_id item_type_list
_item.mandatory_code yes
_item_type.name '_item_type_list.code'
_item_type.code code
_item_linked.child_name '_item_type.code'
_item_linked.parent_name '_item_type_list.code'
save_
save__item_type_list.primitive_code
_item_description.name '_item_type_list.primitive_code'
_item_description.description
;
The codes specifying the primitive type of the data value.
;
_item.name '_item_type_list.primitive_code'
_item.category_id item_type_list
_item.mandatory_code yes
_item_type.name '_item_type_list.primitive_code'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item_type_list.primitive_code'
numb 'numerically-interpretable string'
'_item_type_list.primitive_code'
char 'character or text string (case-sensitive)'
'_item_type_list.primitive_code'
uchar 'character or text string (case-insensitive)'
'_item_type_list.primitive_code'
null 'for dictionary purposes only'
save_
save__item_type_list.construct
_item_description.name '_item_type_list.construct'
_item_description.description
;
When a data value can be defined as a pre-determined sequence of
characters, or optional characters, or data names (for which the
definition is also available), it is specified as a construction.
The rules of construction conform to the the regular expression
(REGEX) specificatiopns detailed in the IEEE document P1003.2
Draft 11.2 Sept 1991 (ftp file '/doc/POSIX/1003.2/p121-140').
Resolved data names for which _item_type_list.construct
specifications exist are replaced by these constructions,
otherwise the data name string is not replaced.
;
_item.name '_item_type_list.construct'
_item.category_id item_type_list
_item.mandatory_code no
_item_type.name '_item_type_list.construct'
_item_type.code text
_item_examples.name '_item_type_list.construct'
_item_examples.case '{_year}-{_month}-{_day}'
_item_examples.detail 'typical construction for _date'
save_
save__item_type_list.detail
_item_description.name '_item_type_list.detail'
_item_description.description
;
An optional description of the data type
;
_item.name '_item_type_list.detail'
_item.category_id item_type_list
_item.mandatory_code no
_item_type.name '_item_type_list.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_ITEM_UNITS
_category.description
;
Specifies the physical units in which data items are expressed.
;
_category.id item_units
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_units
_category_key.name '_item_units.name'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_units
'item_group' item_units
save_
save__item_units.name
_item_description.name '_item_units.name'
_item_description.description
;
The name of data item
;
_item.name '_item_units.name'
_item.category_id item_units
_item.mandatory_code implicit
_item_type.name '_item_units.name'
_item_type.code name
save_
save__item_units.code
_item_description.name '_item_units.code'
_item_description.description
;
The identifier of unit in which the data item is expressed.
;
_item.name '_item_units.code'
_item.category_id item_units
_item.mandatory_code yes
_item_type.name '_item_units.code'
_item_type.code code
save_
# ----------------------------------------------------------------------------
save_ITEM_UNITS_CONVERSION
_category.description
;
Conversion factors between the various units of measure defined
in the ITEM_UNITS_LIST category.
;
_category.id item_units_conversion
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
item_units_conversion '_item_units_conversion.from_code'
item_units_conversion '_item_units_conversion.to_code'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_units_conversion
'item_group' item_units_conversion
save_
save__item_units_conversion.from_code
_item_description.name '_item_units_conversion.from_code'
_item_description.description
;
The unit system on which the conversion operation is applied
to produce the unit system specified in _item_units_conversion.to_code.
=
;
_item.name '_item_units_conversion.from_code'
_item.category_id item_units_conversion
_item.mandatory_code yes
_item_type.name '_item_units_conversion.from_code'
_item_type.code code
save_
save__item_units_conversion.to_code
_item_description.name '_item_units_conversion.to_code'
_item_description.description
;
The unit system produced after an operation is applied to the unit
system specified by _item_units_conversion.from_code.
=
;
_item.name '_item_units_conversion.to_code'
_item.category_id item_units_conversion
_item.mandatory_code yes
_item_type.name '_item_units_conversion.to_code'
_item_type.code code
save_
save__item_units_conversion.operator
_item_description.name '_item_units_conversion.operator'
_item_description.description
;
The arithmetic operator required to convert between the
unit systems:
=
;
_item.name '_item_units_conversion.operator'
_item.category_id item_units_conversion
_item.mandatory_code yes
_item_type.name '_item_units_conversion.operator'
_item_type.code code
loop_
_item_enumeration.name
_item_enumeration.value
_item_enumeration.detail
'_item_units_conversion.operator' '+' 'addition'
'_item_units_conversion.operator' '-' 'subtraction'
'_item_units_conversion.operator' '*' 'multiplication'
'_item_units_conversion.operator' '/' 'division'
save_
save__item_units_conversion.factor
_item_description.name '_item_units_conversion.factor'
_item_description.description
;
The arithmetic operation required to convert between the
unit systems:
=
;
_item.name '_item_units_conversion.factor'
_item.category_id item_units_conversion
_item.mandatory_code yes
_item_type.name '_item_units_conversion.factor'
_item_type.code any
save_
# ----------------------------------------------------------------------------
save_ITEM_UNITS_LIST
_category.description
;
Attributes which describe the physical units of measure
in which data items may be expressed.
;
_category.id item_units_list
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id item_units_list
_category_key.name '_item_units_list.code'
loop_
_category_group.id
_category_group.category_id
'ddl_group' item_units_list
'item_group' item_units_list
save_
save__item_units_list.code
_item_description.name '_item_units_list.code'
_item_description.description
;
The code specifying the name of the unit of measure.
;
_item.name '_item_units_list.code'
_item.category_id item_units_list
_item.mandatory_code yes
_item_type.name '_item_units_list.code'
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_item_units.code' '_item_units_list.code'
'_item_units_conversion.from_code' '_item_units_list.code'
'_item_units_conversion.to_code' '_item_units_list.code'
save_
save__item_units_list.detail
_item_description.name '_item_units_list.detail'
_item_description.description
;
A description of the unit of measure.
;
_item.name '_item_units_list.detail'
_item.category_id item_units_list
_item.mandatory_code no
_item_type.name '_item_units_list.detail'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_METHOD_LIST
_category.description
;
Attributes specifying the list of methods applicable to data items,
sub-categories, and categories.
;
_category.id method_list
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id method_list
_category_key.name '_method_list.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' method_list
'item_group' method_list
'category_group' method_list
save_
save__method_list.id
_item_description.name '_method_list.id'
_item_description.description
;
Identity of method in the list referenced by _method.id
;
_item.name '_method_list.id'
_item.category_id method_list
_item.mandatory_code yes
_item_type.name '_method_list.id'
_item_type.code idname
loop_
_item_linked.child_name
_item_linked.parent_name
'_item_methods.method_id' '_method_list.id'
'_category_methods.method_id' '_method_list.id'
'_sub_category_methods.method_id' '_method_list.id'
'_datablock_methods.method_id' '_method_list.id'
save_
save__method_list.detail
_item_description.name '_method_list.detail'
_item_description.description
;
Description of application method in _method_list.id
;
_item.name '_method_list.detail'
_item.category_id method_list
_item.mandatory_code no
_item_type.name '_method_list.detail'
_item_type.code text
save_
save__method_list.inline
_item_description.name '_method_list.inline'
_item_description.description
;
Inline text of a method associated with the data item.
;
_item.name '_method_list.inline'
_item.category_id method_list
_item.mandatory_code yes
_item_type.name '_method_list.inline'
_item_type.code text
save_
save__method_list.code
_item_description.name '_method_list.code'
_item_description.description
;
A code that describes the function of the method.
;
_item.name '_method_list.code'
_item.category_id method_list
_item.mandatory_code yes
_item_type.name '_method_list.code'
_item_type.code code
loop_
_item_examples.name
_item_examples.case
_item_examples.detail
'_method_list.code' calculation 'method to calculate the item '
'_method_list.code' verification 'method to verify the data item '
'_method_list.code' cast 'method to provide cast conversion '
'_method_list.code' addition 'method to define item + item '
'_method_list.code' division 'method to define item / item '
'_method_list.code' multiplication 'method to define item * item '
'_method_list.code' equivalence 'method to define item = item '
'_method_list.code' other 'miscellaneous method '
save_
save__method_list.language
_item_description.name '_method_list.language'
_item_description.description
;
Language in which the method is expressed.
;
_item.name '_method_list.language'
_item.category_id method_list
_item.mandatory_code yes
_item_type.name '_method_list.language'
_item_type.code code
loop_
_item_examples.name
_item_examples.case
_item_examples.detail
'_method_list.language' BNF ?
'_method_list.language' C ?
'_method_list.language' C++ ?
'_method_list.language' FORTRAN ?
'_method_list.language' LISP ?
'_method_list.language' PASCAL ?
'_method_list.language' PEARL ?
'_method_list.language' TCL ?
'_method_list.language' OTHER ?
save_
# ----------------------------------------------------------------------------
save_DICTIONARY
_category.description
;
Attributes for specifying the dictionary title, version and
data block identifier.
;
_category.id dictionary
_category.mandatory_code yes
_category.implicit_key mmcif_ddl.dic
_category_key.id dictionary
_category_key.name '_dictionary.datablock_id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' dictionary
'datablock_group' dictionary
'dictionary_group' dictionary
save_
save__dictionary.datablock_id
_item_description.name '_dictionary.datablock_id'
_item_description.description
;
The identifier for the data block containing the dictionary.
;
_item.name '_dictionary.datablock_id'
_item.category_id dictionary
_item.mandatory_code implicit
_item_type.name '_dictionary.datablock_id'
_item_type.code code
save_
save__dictionary.title
_item_description.name '_dictionary.title'
_item_description.description
;
Title identification of the dictionary.
;
_item.name '_dictionary.title'
_item.category_id dictionary
_item.mandatory_code yes
_item_type.name '_dictionary.title'
_item_type.code char
save_
save__dictionary.version
_item_description.name '_dictionary.version'
_item_description.description
;
A unique version identifier for the dictionary.
;
_item.name '_dictionary.version'
_item.category_id dictionary
_item.mandatory_code yes
_item_type.name '_dictionary.version'
_item_type.code char
save_
# ----------------------------------------------------------------------------
save_DICTIONARY_HISTORY
_category.description
;
Attributes for specifying the revision history of the dictionary.
;
_category.id dictionary_history
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id dictionary_history
_category_key.name '_dictionary_history.version'
loop_
_category_group.id
_category_group.category_id
'ddl_group' dictionary_history
'dictionary_group' dictionary_history
save_
save__dictionary_history.version
_item_description.name '_dictionary_history.version'
_item_description.description
;
A unique version identifier for the dictionary revision.
;
_item.name '_dictionary_history.version'
_item.category_id dictionary_history
_item.mandatory_code yes
_item_type.name '_dictionary_history.version'
_item_type.code char
_item_linked.child_name '_dictionary.version'
_item_linked.parent_name '_dictionary_history.version'
save_
save__dictionary_history.update
_item_description.name '_dictionary_history.update'
_item_description.description
;
The date that the last dictionary revision took place.
;
_item.name '_dictionary_history.update'
_item.category_id dictionary_history
_item.mandatory_code yes
_item_type.name '_dictionary_history.update'
_item_type.code yyyy-mm-dd
save_
save__dictionary_history.revision
_item_description.name '_dictionary_history.revision'
_item_description.description
;
Text description of the dictionary revision.
;
_item.name '_dictionary_history.revision'
_item.category_id dictionary_history
_item.mandatory_code yes
_item_type.name '_dictionary_history.revision'
_item_type.code text
save_
### EOF mmcif_ddl-def-1.dic
###########################################################################
#
# File: mmcif_ddl-def-1.dic
#
# mmCIF DDL Core Dictionary with NDB extensions
#
# This DDL dictionary is a mirror of ddl_core.dic-org with all implicit
# data items fully expanded and with NDB extensions added.
#
# Definition Section 2.
# (NDB Extension Definitions)
#
#
###########################################################################
save_NDB_CATEGORY_DESCRIPTION
_category.description
;
NDB description of data items in this category.
;
_category.id ndb_category_description
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
ndb_category_description '_ndb_category_description.id'
ndb_category_description '_ndb_category_description.description'
save_
save__ndb_category_description.id
_item.name '_ndb_category_description.id'
_item.category_id ndb_category_description
_item.mandatory_code implicit
_item_type.name '_ndb_category_description.id'
_item_type.code idname
_item_linked.child_name '_ndb_category_description.id'
_item_linked.parent_name '_category.id'
save_
save__ndb_category_description.description
_item_description.name '_ndb_category_description.description'
_item_description.description
;
NDB text description of a category.
;
_item.name '_ndb_category_description.description'
_item.category_id ndb_category_description
_item.mandatory_code yes
_item_type.name '_ndb_category_description.description'
_item_type.code text
save_
# --------------------------------------------------------------------------
save_NDB_CATEGORY_EXAMPLES
_category.description
;
NDB example applications and descriptions of data items in this
category.
;
_category.id ndb_category_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
ndb_category_examples '_ndb_category_examples.id'
ndb_category_examples '_ndb_category_examples.case'
save_
save__ndb_category_examples.id
_item.name '_ndb_category_examples.id'
_item.category_id ndb_category_examples
_item.mandatory_code implicit
_item_type.name '_ndb_category_examples.id'
_item_type.code idname
_item_linked.child_name '_ndb_category_examples.id'
_item_linked.parent_name '_category.id'
save_
save__ndb_category_examples.case
_item_description.name '_ndb_category_examples.case'
_item_description.description
;
NDB case of examples involving items in this category.
;
_item.name '_ndb_category_examples.case'
_item.category_id ndb_category_examples
_item.mandatory_code yes
_item_type.name '_ndb_category_examples.case'
_item_type.code text
save_
save__ndb_category_examples.detail
_item_description.name '_ndb_category_examples.detail'
_item_description.description
;
NDB description of an example _category_examples.case
;
_item.name '_ndb_category_examples.detail'
_item.category_id ndb_category_examples
_item.mandatory_code no
_item_type.name '_ndb_category_examples.detail'
_item_type.code text
save_
#--------------------------------------------------------------------------
save_NDB_ITEM_DESCRIPTION
_category.description
;
This category holds the NDB descriptions of each data item.
;
_category.id ndb_item_description
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
ndb_item_description '_ndb_item_description.name'
ndb_item_description '_ndb_item_description.description'
loop_
_category_group.id
_category_group.category_id
'ddl_group' ndb_item_description
'item_group' ndb_item_description
save_
save__ndb_item_description.name
_item_description.name '_ndb_item_description.name'
_item_description.description
;
Data name of the defined item.
;
_item.name '_ndb_item_description.name'
_item.category_id ndb_item_description
_item.mandatory_code implicit
_item_type.name '_ndb_item_description.name'
_item_type.code name
_item_linked.child_name '_ndb_item_description.name'
_item_linked.parent_name '_item.name'
save_
save__ndb_item_description.description
_item_description.name '_ndb_item_description.description'
_item_description.description
;
NDB text description of the defined data item.
;
_item.name '_ndb_item_description.description'
_item.category_id ndb_item_description
_item.mandatory_code yes
_item_type.name '_ndb_item_description.description'
_item_type.code text
save_
# --------------------------------------------------------------------------
save_NDB_ITEM_ENUMERATION
_category.description
;
Attributes which specify the permitted enumeration of the items.
;
_category.id ndb_item_enumeration
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
ndb_item_enumeration '_ndb_item_enumeration.name'
ndb_item_enumeration '_ndb_item_enumeration.value'
loop_
_category_group.category_id
_category_group.id
ndb_item_enumeration 'ddl_group'
ndb_item_enumeration 'item_group'
save_
save__ndb_item_enumeration.name
_item.name '_ndb_item_enumeration.name'
_item.category_id ndb_item_enumeration
_item.mandatory_code implicit
_item_type.name '_ndb_item_enumeration.name'
_item_type.code name
_item_linked.child_name '_ndb_item_enumeration.name'
_item_linked.parent_name '_item.name'
save_
save__ndb_item_enumeration.value
_item_description.name '_ndb_item_enumeration.value'
_item_description.description
;
A permissible value, character or number, for the defined item.
;
_item.name '_ndb_item_enumeration.value'
_item.category_id ndb_item_enumeration
_item.mandatory_code yes
_item_type.name '_ndb_item_enumeration.value'
_item_type.code any
save_
save__ndb_item_enumeration.detail
_item_description.name '_ndb_item_enumeration.detail'
_item_description.description
;
A description of a permissible value for the defined item.
;
_item.name '_ndb_item_enumeration.detail'
_item.category_id ndb_item_enumeration
_item.mandatory_code no
_item_type.name '_ndb_item_enumeration.detail'
_item_type.code text
save_
# --------------------------------------------------------------------------
save_NDB_ITEM_EXAMPLES
_category.description
;
Attributes for describing application examples of the data item.
;
_category.id ndb_item_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
ndb_item_examples '_ndb_item_examples.name'
ndb_item_examples '_ndb_item_examples.case'
loop_
_category_group.id
_category_group.category_id
'ddl_group' ndb_item_examples
'item_group' ndb_item_examples
save_
save__ndb_item_examples.case
_item_description.name '_ndb_item_examples.case'
_item_description.description
;
NDB example application of the defined data item.
;
_item.name '_ndb_item_examples.case'
_item.category_id ndb_item_examples
_item.mandatory_code yes
_item_type.name '_ndb_item_examples.case'
_item_type.code text
save_
save__ndb_item_examples.detail
_item_description.name '_ndb_item_examples.detail'
_item_description.description
;
NDB description of an example specified in _ndb_item_example.case
;
_item.name '_ndb_item_examples.detail'
_item.category_id ndb_item_examples
_item.mandatory_code yes
_item_type.name '_ndb_item_examples.detail'
_item_type.code text
save_
save__ndb_item_examples.name
_item.name '_ndb_item_examples.name'
_item.category_id ndb_item_examples
_item.mandatory_code implicit
_item_type.name '_ndb_item_examples.name'
_item_type.code name
_item_linked.child_name '_ndb_item_examples.name'
_item_linked.parent_name '_item.name'
save_
#### EOF mmcif_ddl-def-2.dic
./CBFlib-0.9.2.2/doc/Idiffrn_scan_axis.scan_id.html 0000644 0000765 0000765 00000005572 11603702115 020252 0 ustar yaya yaya
(IUCr) CIF Definition save__diffrn_scan_axis.scan_id
The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The [1] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of _diffrn_scan.integration_time.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
(Ip-In)/(Ip+In), where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared)
of the electric vector in the plane of the normal to the
plane of polarization.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane is to be taken
as the XZ plane and the normal is parallel to the Y axis.
Thus, if there was complete polarization in the plane of
polarization, the value of
_diffrn_radiation.polarizn_source_ratio would be 1, and
for an unpolarized beam
_diffrn_radiation.polarizn_source_ratio would have a
value of 0.
If the X axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of 'MONOCHROMATOR' in the Denzo glossary, and values of near
1 should be expected for a bending-magnet source. However,
if the X axis were perpendicular to the polarization plane
(not a common choice), then the Denzo value would be the
negative of _diffrn_radiation.polarizn_source_ratio.
See http://www.hkl-xray.com for information on Denzo and
Otwinowski & Minor (1997).
This differs both in the choice of ratio and choice of
orientation from _diffrn_radiation.polarisn_ratio, which,
unlike _diffrn_radiation.polarizn_source_ratio, is
unbounded.
Reference: Otwinowski, Z. & Minor, W. (1997). 'Processing of
X-ray diffraction data collected in oscillation mode.' Methods
Enzymol. 276, 307-326.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
./CBFlib-0.9.2.2/doc/cif_img_1.1.3.dic 0000644 0000765 0000765 00000517542 11603702115 015157 0 ustar yaya yaya ##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.1.3 #
# of 2001-04-19 #
# #
# Adapted from the #
# imgCIF Workshop, BNL Oct 1997 #
# and #
# Crystallographic Binary File Format Draft Proposal #
# by Andy Hammersley #
# #
##############################################################################
# #
# First DDL 2.1 Version #
# by #
# John Westbrook #
# Nucleic Acid Database #
# Rutgers University #
# #
##############################################################################
# These revisions by: Herbert J. Bernstein, yaya@bernstein-plus-sons.com #
# Incorporating comments by I. David Brown, John Westbrook, Brian McMahon. #
# Bob Sweet, Paul Ellis, Harry Powell, Wilfred Li and others #
##############################################################################
data_cif_img.dic
_dictionary.title cif_img.dic
_dictionary.version 1.1.3
_dictionary.datablock_id cif_img.dic
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.gain
# _array_intensities.gain_esd
# _array_intensities.linearity
# _array_intensities.offset
# _array_intensities.scaling
# _array_intensities.overload
# _array_intensities.undefined_value
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.encoding_type
# _array_structure.id
#
# category ARRAY_STRUCTURE_LIST
#
# _array_structure_list.axis_set_id
# _array_structure_list.array_id
# _array_structure_list.dimension
# _array_structure_list.direction
# _array_structure_list.index
# _array_structure_list.precedence
#
# category ARRAY_STRUCTURE_LIST_AXIS
#
# _array_structure_list_axis.axis_id
# _array_structure_list_axis.axis_set_id
# _array_structure_list_axis.angle
# _array_structure_list_axis.angle_increment
# _array_structure_list_axis.displacement_increment
# _array_structure_list_axis.angular_pitch
# _array_structure_list_axis.radial_pitch
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.type
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
#
# category DIFFRN_DATA_FRAME
#
# _diffrn_data_frame.array_id
# _diffrn_data_frame.binary_id
# _diffrn_data_frame.detector_element_id
# _diffrn_data_frame.id
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.id
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.axis_id
# _diffrn_detector_axis.detector_id
#
# category DIFFRN_DETECTOR_ELEMENT
#
# _diffrn_detector_element.center[1]
# _diffrn_detector_element.center[2]
# _diffrn_detector_element.id
# _diffrn_detector_element.detector_id
#
# category DIFFRN_MEASUREMENT
#
# _diffrn_measurement.diffrn_id
# _diffrn_measurement.details
# _diffrn_measurement.device
# _diffrn_measurement.device_details
# _diffrn_measurement.device_type
# _diffrn_measurement.id
# _diffrn_measurement.method
# _diffrn_measurement.number_of_axes
# _diffrn_measurement.specimen_support
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.axis_id
# _diffrn_measurement_axis.measurement_device
# _diffrn_measurement_axis.measurement_id
#
# category DIFFRN_RADIATION
#
# _diffrn_radiation.collimation
# _diffrn_radiation.diffrn_id
# _diffrn_radiation.div_x_source
# _diffrn_radiation.div_y_source
# _diffrn_radiation.div_x_y_source
# _diffrn_radiation.filter_edge'
# _diffrn_radiation.inhomogeneity
# _diffrn_radiation.monochromator
# _diffrn_radiation.polarisn_norm
# _diffrn_radiation.polarisn_ratio
# _diffrn_radiation.polarizn_source_norm
# _diffrn_radiation.polarizn_source_ratio
# _diffrn_radiation.probe
# _diffrn_radiation.type
# _diffrn_radiation.xray_symbol
# _diffrn_radiation.wavelength_id
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.date_end
# _diffrn_scan.date_start
# _diffrn_scan.integration_time
# _diffrn_scan.frame_id_start
# _diffrn_scan.frame_id_end
# _diffrn_scan.frames
#
# category DIFFRN_SCAN_AXIS
#
# _diffrn_scan_axis.axis_id
# _diffrn_scan_axis.angle_start
# _diffrn_scan_axis.angle_range
# _diffrn_scan_axis.angle_increment
# _diffrn_scan_axis.angle_rstrt_incr
# _diffrn_scan_axis.displacement_start
# _diffrn_scan_axis.displacement_range
# _diffrn_scan_axis.displacement_increment
# _diffrn_scan_axis.displacement_rstrt_incr
# _diffrn_scan_axis.scan_id
#
# category DIFFRN_SCAN_FRAME
#
# _diffrn_scan_frame.date
# _diffrn_scan_frame.frame_id
# _diffrn_scan_frame.frame_number
# _diffrn_scan_frame.integration_time
# _diffrn_scan_frame.scan_id
#
# category DIFFRN_SCAN_FRAME_AXIS
#
# _diffrn_scan_frame_axis.axis_id
# _diffrn_scan_frame_axis.angle
# _diffrn_scan_frame_axis.angle_increment
# _diffrn_scan_frame_axis.angle_rstrt_incr
# _diffrn_scan_frame_axis.displacement
# _diffrn_scan_frame_axis.displacement_increment
# _diffrn_scan_frame_axis.displacement_rstrt_incr
# _diffrn_scan_frame_axis.frame_id
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
;
Data items in the ARRAY_DATA category are the containers for
the array data items described in category ARRAY_STRUCTURE.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and
presented as hexadecimal data. The first character "H" on the
data lines means hexadecimal. It could have been "O" for octal
or "D" for decimal. The second character on the line shows
the number of bytes in each word (in this case "4"), which then
requires 8 hexadecimal digits per word. The third character
gives the order of octets within a word, in this case "<"
for the ordering 4321 (i.e. "big-endian"). Alternatively the
character ">" could have been used for the ordering 1234
(i.e. "little-endian"). The block has a "message digest"
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 1
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-Id, these values should be equal.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
"--CIF-BINARY-FORMAT-SECTION--" (including the
required initial "--").
The Content-Type may be any of the discrete types permitted
in RFC 2045; "application/octet-stream" is recommended.
If an octet stream was compressed, the compression should
be specified by the parameter 'conversions="x-CBF_PACKED"'
or the parameter 'conversions="x-CBF_CANONICAL"'.
The Content-Transfer-Encoding may be "BASE-64",
"Quoted-Printable", "X-BASE-8", "X-BASE-10", or
"X-BASE-16" for an imgCIF or "BINARY" for a CBF. The
octal, decimal and hexadecimal transfer encodings are
for convenience in debugging, and are not recommended
for archiving and data interchange.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In a CBF, the
raw binary data begins after an empty line terminating
the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of
the message size, nor in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. And adjustment is made for
the deprecated binary formats in which 8 bytes of binary
header are used for the compression type. In that case,
the 8 bytes used for the compression type is subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is "unsigned 32-bit integer".
An MD5 message digest may, optionally, be used. The "RSA Data
Security, Inc. MD5 Message-Digest Algorithm" should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is "X-BASE-8", "X-BASE-10", or
"X-BASE-16", the data is presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ("big-
endian") or 1234... (little-endian). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as "==" for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is "H", "O", or "D" for hexadecimal, octal or
decimal, n is the number of octets per word. and d is "<"
for ">" for the "...4321" and "1234..." octet orderings
respectively. The "==" padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hex, octal and decimal formats, only, comments
beginning with "#" are permitted to improve readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three, c1, c2, c3. The resulting 24 bits
are broken into four 6-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order 4 bits of the second octet ((c1 & 3)<<4 | (c2>>4)),
then the bottom 4 bits of the second octet followed by the
high order two bits of the last octet ((c2 & 15)<<2 | (c3>>6)),
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
With short groups of octets padded on the right with one "="
if c3 is missing, and with "==" if both c2 and c3 are missing.
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32..38,
42, 48..57, 59..60, 62, 64..126 and the octet is not a ";"
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
"wrapped" with a terminating "=" (i.e. the MIME conventions
for an implicit line terminator are never used).
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
;
Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ATOM_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.index
_item_description.description
;
This item is a pointer to _array_structure_list.index in the
ATOM_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
;
The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
;
Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The actual detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
'_array_intensities.gain'. If raw, uncorrected values
are presented (e.g for calibration experiments), the
value of '_array_intensities.linearity' will be 'raw'
and '_array_intensities.gain' will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.overload
_array_intensities.undefined_value
image_1 linear 1.2 655535 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ATOM_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
;
Detector "gain". The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
;
The estimated standard deviation in detector "gain".
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
;
The intensity linearity scaling used from raw intensity
to the stored element value:
'linear' is obvious
'offset' means that the value defined by
'_array_intensities.offset' should be added to each
element value.
'scaling' means that the value defined by
'_array_intensities.scaling' should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by '_array_intensities.scaling' is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
'logarithmic_scaled' means that the logarithm based 10 of
raw intensities multiplied by '_array_intensities.scaling'
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and calculating 10
to the power of this number.
'raw' means that the data is the raw is a set of raw values
straight from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
;
The value defined by '_array_intensities.offset' should
be added to each element value.
;
'scaling'
;
The value defined by '_array_intensities.scaling' should be
multiplied with each element value.
;
'scaling_offset'
;
The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
;
The square root of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
;
'logarithmic_scaled'
;
The logarithm based 10 of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
'_array_intensities.scaling' and calculating 10 to the
power of this number.
;
'raw'
;
The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
;
Offset value to add to array element values in the manner
described by item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.scaling
_item_description.description
;
Multiplicative scaling value to be applied to array data
in the manner described by item _array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
;
The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.undefined_value
_item_description.description
;
A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
;
Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data which may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
_category_key.name '_array_structure.id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
;
The order of bytes for integer values which require more
than 1-byte.
(IBM-PC's and compatibles, and Dec-Vaxes use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. Dec-Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
;
The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
;
The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
;
Type of data compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code code
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'none'
;
Data are stored in normal format as defined by
'_array_structure.encoding_type' and
'_array_structure.byte_order'.
;
'byte_offsets'
;
Using the compression scheme defined in CBF definition
Section 5.0.
;
'packed'
;
Using the 'packed' compression scheme, a CCP4-style packing
(CBFlib section 3.3.2)
;
'canonical'
;
Using the 'canonical' compression scheme (CBFlib section
3.3.1)
;
save_
save__array_structure.encoding_type
_item_description.description
;
Data encoding of a single element of array data.
In several cases, the IEEE format is referenced.
See "IEEE Standard for Binary Floating-Point Arithmetic",
ANSI/IEEE Std 754-1985, the Institute of Electrical and
Electronics Engineers, Inc., NY 1985.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit_integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure yes
'_array_data.array_id' array_data yes
'_array_structure_list.array_id' array_structure_list yes
'_array_intensities.array_id' array_intensities yes
'_diffrn_data_frame.array_id' diffrn_data_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
;
Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left-to-right (increasing) in
first dimension and bottom-to-top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differ
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the "poise" of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
;
The number of elements stored in the array structure in this
dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
;
Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
;
Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
;
Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
;
Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
;
Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
;
Data items in the ARRAY_STRUCTURE_LIST_AXIS category describes
the physical settings of sets axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axis, one for the angular
direction, one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
'_array_structure_list_axis.axis_set_id'
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
;
The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id .
This item is a pointer to _array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
save_
save__array_structure_list_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of '_array_structure_list.axis_set_id'. If the index is
specified as 'increasing' this will be the center of the
pixel with index value 1. If the index is specified as
'decreasing' this will be the center of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
;
The pixel-center-to-pixel-center increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified in that case.
See '_array_structure_list_axis.angular_pitch'.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
;
The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of '_array_structure_list.axis_set_id'. If the index is
specified as 'increasing' this will be the center of the
pixel with index value 1. If the index is specified as
'decreasing' this will be the center of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
;
The pixel-center-to-pixel-center increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
;
The pixel-center-to-pixel-center distance for a one step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans,
or for uncoupled angular scans at a constant radius
(cylindrical scan) and should not be specified for cases
in which the angle between pixels, rather than the distance
between pixels is uniform.
See '_array_structure_list_axis.angle_increment'.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
;
The radial distance from one "cylinder" of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of '_array_structure_list_axis.displacement_increment'.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
########
# AXIS #
########
save_AXIS
_category.description
;
Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection. The location of each
axis is specified by two vectors: the axis itself, given as a unit
vector, and an offset to the base of the unit vector. These vectors
are referenced to a right-handed laboratory coordinate system with
its origin in the sample or specimen:
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
These axes are based on the goniometer, not on the orientation of the
detector, gravity, etc. The vectors necessary to specify all other
axes are given by sets of three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to, but significantly
different from the choice in MOSFLM (Andrew G.W. Leslie, Harry Powell,
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH,UK
http://www.dl.ac.uk/CCP/CCP4/dist/x-windows/Mosflm/). In MOSFLM,
X is along the X-ray beam (our Z axis) and Z is along the rotation axis.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam center.
The location of the beam center on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected mm from the (0,0) corner
of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, we need to specify the
location of the beam center on the detector in terms of the origin of the
detector, which is, of course, not coincident with the center of the
sample.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows the axis specification of the axes of a kappa
geometry goniometer (See "X-Ray Structure Determination, A Practical
Guide", 2nd ed. by G. H. Stout, L. H. Jensen, Wiley Interscience,
1989, 453 pp, p 134.).
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X-axis. The next innermost axis, kappa,
is at a 50 degree angle to the X-axis, pointed away from the source.
The innermost axis, phi, aligns with the X-axis when omega and
phi are at their zero-points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
x' = (T-omega) (T-kappa) (T-phi) x
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
This example show the axis specification of the axes of a
detector, source and gravity. We have juggled the order as a
reminder that the ordering of presentation of tokens is not
significant. We have taken the center of rotation of the detector
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.type specifies the next outermost
axis upon which this axis depends.
This item is a pointer to axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.type specifies the type of equipment
using the axis: goniometer, detector, gravity, source
or general
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so that the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: rotation, translation (or general when the type is
not relevant, as for gravity)
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
;
Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases, but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element is
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id
;
;
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0.00
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
;
This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.id
_item_description.description
;
The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Need new example here.
;
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detectors used to measure
the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
;
The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of _diffrn_detector.diffrn_id
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
;
The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id
The word "positioner" is a general term used in instrumentation
design for devices that are used to change the positions of
portions of apparatus by linear translation, rotation, or
combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
;
Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
;
This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named '_diffrn_detector_axis.id'
which is now a deprecated name. The old name is
provided as an alias, but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
;
Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, the more detailed information provided
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
are preferable to simply providing the centre.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square. in the pattern
1 2
*
3 4
Note that the beam center is slightly off of each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4.
;
;
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
_diffrn_detector_element.center[1]
_diffrn_detector_element.center[2]
d1 d1_ccd_1 201.5 -1.5
d1 d1_ccd_2 -1.8 -1.5
d1 d1_ccd_3 201.6 201.4
d1 d1_ccd_4 -1.7 201.5
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.center[1]
_item_description.description
;
The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
;
The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.id
_item_description.description
;
The value of _diffrn_detector_element.id must uniquely identify
each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
;
This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the diffraction
data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model x'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; Need new example here
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support and
orient the specimen.
If the value of _diffrn_measurement.device is not given, it is
implicitly equal to the value of _diffrn_measurement.diffrn_id
Either '_diffrn_measurement.device' or '_diffrn_measurement.id'
may be used to link to other categories. If the experimental
setup admits multiple devices, then '_diffrn_measurement.id'
is used to provide a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to measure
the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'homemade'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
;
The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of _diffrn_measurement.diffrn_id
Either '_diffrn_measurement.device' or '_diffrn_measurement.id'
may be used to link to other categories. If the experimental
setup admits multiple devices, then '_diffrn_measurement.id'
is used to provide a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
;
The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
;
Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
;
This data item is a pointer to _diffrn_measurement.device in
the DIFFRN_MEASUREMENT category.
;
_item.name '_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
;
This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named '_diffrn_measurement_axis.id'
which is now a deprecated name. The old name is
provided as an alias, but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0.00
_item.mandatory_code implicit
save_
####################
# DIFFRN_RADIATION #
####################
save_DIFFRN_RADIATION
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used in measuring diffraction intensities,
its collimation and monochromatisation before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
_category_key.name '_diffrn_radiation.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the esd of the directions of photons in the X-Z plane
around the mean source beam direction.
Note that some synchrotrons specify this value in milliradians,
in which case a conversion would be needed. To go from a
value in milliradians to a value in degrees, multiply by 0.180
and divide by Pi.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the esd of the directions of photons in the Y-Z plane
around the mean source beam direction.
Note that some synchrotrons specify this value in milliradians,
in which case a conversion would be needed. To go from a
value in milliradians to a value in degrees, multiply by 0.180
and divide by Pi.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation degrees**2 between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
directin of each photons in X-Z plane times the deviations
of the direction of the same photon in the Y-Z plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons specify this value in
milliradians**2, in which case a conversion would be needed.
To go from a value in milliradians**2 to a value in
degrees**2, multiply by 0.180**2 and divide by Pi**2.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a mono-
chromator crystal is used the material and the indices of the
Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarisation and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarisation ratio of the diffraction beam incident on the
crystal. It is the ratio of the perpendicularly polarised to the
parallel polarised component of the radiation. The perpendicular
component forms an angle of _diffrn_radiation.polarisn_norm to
the normal to the diffraction plane of the sample (i.e. the
plane containing the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
normal to the polarization plane and the laboratory Y axis as
defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monchromater.
This differs from the value of '_diffrn_radiation.polarisn_norm'
in that '_diffrn_radiation.polarisn_norm' refers to polarization
relative to the diffraction plane rather than to the laboratory
axis system.
In the case of an unpolarized beam, or a beam with true circular
polarization, in which no single plane of polarization can be
determined, the plane should be taken as the X-Z plane, and the
angle as 0.
See '_diffrn_radiation.polarizn_source_ratio'.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity (amplitude squared)
of the electric vector in the plane of polarization and In is
the intensity (amplitude squared) of the electric vector
in plane of the normal to the plane of polarization.
Thus, if we had complete polarization in the plane of
polarization, the value of
'_diffrn_radiation.polarizn_source_ratio' would
be 1, and an unpolarized beam would have a value of 0.
If the X-axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of "MONOCHROMATOR" in the Denzo glossary, and values of near
1 should be expected for a bending magnet source. However,
if the X-axis were, for some reason to be, say, perpendicular
to the polarization plane (not a common choice), then the
Denzo value would be the negative of
'_diffrn_radiation.polarizn_source_ratio'.
See http://www.hkl-xray.com for information on Denzo, and
Z. Otwinowski and W. Minor, " Processing of X-ray Diffraction
Data Collected in Oscillation Mode ", Methods in Enzymology,
Volume 276: Macromolecular Crystallography, part A, p.307-326,
1997,C.W. Carter, Jr. & R. M. Sweet, Eds., Academic Press.
This differs both in the choice of ratio and choice of
orientation from '_diffrn_radiation.polarisn_ratio', which,
unlike '_diffrn_radiation.polarizn_source_ratio', is unbounded.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly encouraged
that this field be specified so that the probe radiation
can be simply determined.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'x-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for probe radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to _diffrn_radiation_wavelength.id
in the DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.mandatory_code yes
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
;
This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
;
_category.id diffrn_refln
_category.mandatory_code no
_category_key.name '_diffrn_refln.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
;
This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
;
Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
_category_key.name '_diffrn_scan.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. We have specified three rotation axes and one translation axis
at non-zero values, with one axis stepping. There is no reason why
more axes could not have been specified to step. We have specified
range information, but note that it is redundant from the number of
frames and the increment, so we could drop the data item
_diffrn_scan_axis.angle_range .
We have specified both the sweep data and the data for a single frame.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
'_diffrn_scan.integration_time' and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
'_diffrn_scan_frame.integration_time' and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustements are made to
scan times and non-linear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.angle_increment
_diffrn_scan_frame_axis.displacement
_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
;
Example 2 - a more extensive example, R. M. Sweet, P. Ellis, H. Bernstein.
We place a detector 240 mm along the Z axis from the goniometer.
This presents us with a choice -- either we define the axes of
the detector at the origin, and then put a Z setting of -240 in
for the actual use, or we define the axes with the necessary Z-offset.
In this case we use the setting, and leave the offset as zero.
We call this axis DETECTOR_Z.
The axis for positioning the detector in the Y-direction depends
on the detector Z-axis. We call this axis, DETECTOR_Y.
The axis for positioning the dector in the X-direction depends
on the detector Y-axis (and therefore on the detector Z-axis).
We call this axis DETECTOR_X.
This detector may be rotated around the Y-axis. This rotation axis
depends on the three translation axies. We call it DETECTOR_PITCH.
We define a coordinate system on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm x 0.150mm, the center of the first pixel is at (0.075,
0.075) in this coordinate system.
;
;
###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
;
Example 3 - Example 2 revised for a spiral scan, R. M. Sweet,
P. Ellis, H. Bernstein.
We place a detector 240 mm along the Z axis from the goniometer,
as in Example 2, above, but in this example, the image plate is
scanned in a spiral pattern outside edge in.
The axis for positioning the detector in the Y-direction depends
on the detector Z-axis. We call this axis, DETECTOR_Y.
The axis for positioning the dector in the X-direction depends
on the detector Y-axis (and therefore on the detector Z-axis).
We call this axis DETECTOR_X.
This detector may be rotated around the Y-axis. This rotation axis
depends on the three translation axies. We call it DETECTOR_PITCH.
We define a coordinate system on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. Let us call rotation axis ELEMENT_ROT, and the
radial axis ELEMENT_RAD. We assume 150 um radial pitch and 75 um
'constant velocity' angular pitch.
We index first on the rotation axis and make the radial axis
dependent on
it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
;
###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.angle
_array_structure_list_axis.displacement
_array_structure_list_axis.angular_pitch
_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
;
The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
;
The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
;
Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
'_diffrn_scan_frame.integration_time', even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
;
The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frame_id_end
_item_description.description
;
The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frames
_item_description.description
;
The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
;
The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
'_diffrn_scan.id'.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
'_diffrn_scan.id'.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.angle_start
_item_description.description
;
The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
;
The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
;
The increment for each step for the specified axis
in degrees. In general, this will agree with
'_array_structure_list_axis.angle_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
;
The increment after each step for the specified axis
in degrees. In general, this will agree with
'_array_structure_list_axis.angle_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
;
The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
;
The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
;
The increment for each step for the specified axis
in millimetres. In general, this will agree with
'_diffrn_scan_frame_axis.displacement_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
;
The increment for each step for the specified axis
in millimetres. In general, this will agree with
'_diffrn_scan_frame_axis.displacement_rstrt_incr', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
;
Data items in the DIFFRN_SCAN_FRAME category describe the settings of
axes for particular frames. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
;
The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
save__diffrn_scan_frame.frame_number
_item_description.description
;
The value of this data item is the number of the frame within
the scan, starting with 1. It is not necessarily the same as
the value of _diffrn_scan_frame.frame_id, but may
be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
;
The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of '_diffrn_scan.integration_time'.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_FRAME_AXIS category describes the settings
of axes for particular frames. Unspecified axes are assumed to be at
their zero points. If, for any given frame, non-zero values apply
for any of the data items in this category, those values should be
given explicitly in this category and not simply inferred from values
in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
;
The increment for this frame for angular setting of
the specified axis in degrees. The sum of the values
of '_diffrn_scan_frame_axis.angle' and
'_diffrn_scan_frame_axis.angle_increment' is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
;
The increment after this frame for angular setting of
the specified axis in degrees. The sum of the values
of '_diffrn_scan_frame_axis.angle' and
'_diffrn_scan_frame_axis.angle_increment' and
'_diffrn_scan_frame_axis.angle_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame, and should equal
'_diffrn_scan_frame_axis.angle' for that next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
;
The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
;
The increment for this frame for displacement setting of
the specified axis in millimetres. The sum of the values
of '_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
;
The increment for this frame for displacement setting of
the specified axis in millimetres. The sum of the values
of '_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' and
'_diffrn_scan_frame_axis.displacement_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame, and should equal
'_diffrn_scan_frame_axis.displacement' for that next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id .
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive)
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items (case insensitive)
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*}\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]\
(T[0-2][0-9]:[0-5][0-9]:[0-5][0-9](.[0-9]+)([+-][0-5][0-9]:[0-5][0-9]))
;
;
Standard format for CIF date and time strings (see
http://www.iucr.orgiucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character "T" followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
deciaml fraction on the seconds of time.
Time is local time if no time-zone offset is given.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2))'
'millimetres' 'millimetres (metres * 10^( -3))'
'nanometres' 'nanometres (metres * 10^( -9))'
'angstroms' 'angstroms (metres * 10^(-10))'
'picometres' 'picometres (metres * 10^(-12))'
'femtometres' 'femtometres (metres * 10^(-15))'
#
'reciprocal_metres' 'reciprocal metres (metres * 10^-1)'
'reciprocal_centimetres' 'reciprocal centimetres (metres * 10^( -2)^-1)'
'reciprocal_millimetres' 'reciprocal millimetres (metres * 10^( -3)^-1)'
'reciprocal_nanometres' 'reciprocal nanometres (metres * 10^( -9)^-1)'
'reciprocal_angstroms' 'reciprocal angstroms (metres * 10^(-10)^-1)'
'reciprocal_picometres' 'reciprocal picometres (metres * 10^(-12)^-1)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9))^2'
'angstroms_squared' 'angstroms squared (metres * 10^(-10))^2'
'8pi2_angstroms_squared' '8pi^2 * angstroms squared (metres * 10^(-10))^2'
'picometres_squared' 'picometres squared (metres * 10^(-12))^2'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9))^3'
'angstroms_cubed' 'angstroms cubed (metres * 10^(-10))^3'
'picometres_cubed' 'picometres cubed (metres * 10^(-12))^3'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (metres * 10^( -9))^3
;
'electrons_per_angstroms_cubed'
; electrons per angstroms cubed (metres * 10^(-10))^3
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (metres * 10^(-12))^3
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E-09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E+03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E-06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E+09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li
;
1.1.1 2001-02-16
;
Several typo corrections by JW
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to '_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source', '_diffrn_radiation.polarizn_source_norm'
,
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add _diffrn_measurement.device to category key
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to al
low
for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes (JW)
+ Correct spelling of diffrn_measurement_axis in _axis.id
+ Correct ordering of uses of _item.mandatory_code and _item_default.value
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown (HJB)
+ Added further comments on '\n' and '\t'
+ Updated ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Changed all spelling 'meter' to 'metre' throughout.
+ Added missing enumerations to _array_structure.compression_type
and made 'none' the default.
+ Removed parent-child relationship between _array_structure_list.index
and _array_structure_list.precedence .
+ Improve alphabetization.
+ Fix _array_intensities_gain.esd related function.
+ Improved comments in AXIS.
+ Fixed DIFFRN_FRAME_DATA example.
+ Removed erroneous DIFFRN_MEASUREMENT example.
+ Added _diffrn_measurement_axis.id to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for _diffrn_scan.id definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header (HJB)
+ Restored _diffrn_detector.diffrn_id to DIFFRN_DETECTOR KEY.
+ Added AXIS category.
+ Brought complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
in from cif_mm.dic for clarity.
+ changed _array_structure.encoding_type from type code to uline and
added X-Binary-Element-Type to MIME header.
+ added detector beam center _diffrn_detector_element.center[1] and
_diffrn_detector_element.center[2]
+ corrected item name of _diffrn_refln.frame_id
+ replace reference to _array_intensities.undefined by
_array_intensities.undefined_value
+ replace references to _array_intensity.scaling with
_array_intensities.scaling
+ added DIFFRN_SCAN... categories
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft (HJB)
+ Reflowed comment lines over 80 characters and corrected typos.
+ Updated examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF (HJB)
+ Added binary type, which is a text field containing a variant on
MIME encoded data.
+ Changed type of _array_data.data to binary and specified internal
structure of raw binary data.
+ Added _array_data.binary_id, and made
_diffrn_frame_data.binary_id and _array_intensities.binary_id
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft (JW):
+ Added category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes were made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA was renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE was renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for _diffrn_frame_data.array_id was changed from
array_structure_list.array_id to array_structure.id. Item
_diffrn_detector.array_id was deleted.
+ Added data item _diffrn_frame_data.binary_id to identify data groups
within a binary section. The formal identification of the binary section
is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version was adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley (AH).
Modifications to the CBF draft (JW):
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories have been
generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category ARRAY_DATA
.
This departs from the CBF notion of data existing in some special comment.
In this description, data is handled as an ordinary data item encapsulated
in a character data type. Although handling binary data this manner
deviates from CIF conventions, it does not violate any DDL 2.1 rules.
DDL 2.1 regular expressions can be used to define the binary
representation which will permit some level of data validation. In
this version, the placeholder type code "any" has been used.
This translates to a regular expression which will match any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary. It
may be possible to use the DDL 2.1 ITEM_STRUCTURE and ITEM_STRUCTURE_LIST
categories to provide the information that is carried in by the
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By moving the array
structure to the DDL level it would be possible to define an array
type as well as a regular expression defining the data format.
+ Multiple array sections can be properly handled within a single datablock.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
./CBFlib-0.9.2.2/doc/cif_img_1.1.3.txt 0000644 0000765 0000765 00000517542 11603702115 015237 0 ustar yaya yaya ##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.1.3 #
# of 2001-04-19 #
# #
# Adapted from the #
# imgCIF Workshop, BNL Oct 1997 #
# and #
# Crystallographic Binary File Format Draft Proposal #
# by Andy Hammersley #
# #
##############################################################################
# #
# First DDL 2.1 Version #
# by #
# John Westbrook #
# Nucleic Acid Database #
# Rutgers University #
# #
##############################################################################
# These revisions by: Herbert J. Bernstein, yaya@bernstein-plus-sons.com #
# Incorporating comments by I. David Brown, John Westbrook, Brian McMahon. #
# Bob Sweet, Paul Ellis, Harry Powell, Wilfred Li and others #
##############################################################################
data_cif_img.dic
_dictionary.title cif_img.dic
_dictionary.version 1.1.3
_dictionary.datablock_id cif_img.dic
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.gain
# _array_intensities.gain_esd
# _array_intensities.linearity
# _array_intensities.offset
# _array_intensities.scaling
# _array_intensities.overload
# _array_intensities.undefined_value
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.encoding_type
# _array_structure.id
#
# category ARRAY_STRUCTURE_LIST
#
# _array_structure_list.axis_set_id
# _array_structure_list.array_id
# _array_structure_list.dimension
# _array_structure_list.direction
# _array_structure_list.index
# _array_structure_list.precedence
#
# category ARRAY_STRUCTURE_LIST_AXIS
#
# _array_structure_list_axis.axis_id
# _array_structure_list_axis.axis_set_id
# _array_structure_list_axis.angle
# _array_structure_list_axis.angle_increment
# _array_structure_list_axis.displacement_increment
# _array_structure_list_axis.angular_pitch
# _array_structure_list_axis.radial_pitch
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.type
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
#
# category DIFFRN_DATA_FRAME
#
# _diffrn_data_frame.array_id
# _diffrn_data_frame.binary_id
# _diffrn_data_frame.detector_element_id
# _diffrn_data_frame.id
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.id
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.axis_id
# _diffrn_detector_axis.detector_id
#
# category DIFFRN_DETECTOR_ELEMENT
#
# _diffrn_detector_element.center[1]
# _diffrn_detector_element.center[2]
# _diffrn_detector_element.id
# _diffrn_detector_element.detector_id
#
# category DIFFRN_MEASUREMENT
#
# _diffrn_measurement.diffrn_id
# _diffrn_measurement.details
# _diffrn_measurement.device
# _diffrn_measurement.device_details
# _diffrn_measurement.device_type
# _diffrn_measurement.id
# _diffrn_measurement.method
# _diffrn_measurement.number_of_axes
# _diffrn_measurement.specimen_support
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.axis_id
# _diffrn_measurement_axis.measurement_device
# _diffrn_measurement_axis.measurement_id
#
# category DIFFRN_RADIATION
#
# _diffrn_radiation.collimation
# _diffrn_radiation.diffrn_id
# _diffrn_radiation.div_x_source
# _diffrn_radiation.div_y_source
# _diffrn_radiation.div_x_y_source
# _diffrn_radiation.filter_edge'
# _diffrn_radiation.inhomogeneity
# _diffrn_radiation.monochromator
# _diffrn_radiation.polarisn_norm
# _diffrn_radiation.polarisn_ratio
# _diffrn_radiation.polarizn_source_norm
# _diffrn_radiation.polarizn_source_ratio
# _diffrn_radiation.probe
# _diffrn_radiation.type
# _diffrn_radiation.xray_symbol
# _diffrn_radiation.wavelength_id
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.date_end
# _diffrn_scan.date_start
# _diffrn_scan.integration_time
# _diffrn_scan.frame_id_start
# _diffrn_scan.frame_id_end
# _diffrn_scan.frames
#
# category DIFFRN_SCAN_AXIS
#
# _diffrn_scan_axis.axis_id
# _diffrn_scan_axis.angle_start
# _diffrn_scan_axis.angle_range
# _diffrn_scan_axis.angle_increment
# _diffrn_scan_axis.angle_rstrt_incr
# _diffrn_scan_axis.displacement_start
# _diffrn_scan_axis.displacement_range
# _diffrn_scan_axis.displacement_increment
# _diffrn_scan_axis.displacement_rstrt_incr
# _diffrn_scan_axis.scan_id
#
# category DIFFRN_SCAN_FRAME
#
# _diffrn_scan_frame.date
# _diffrn_scan_frame.frame_id
# _diffrn_scan_frame.frame_number
# _diffrn_scan_frame.integration_time
# _diffrn_scan_frame.scan_id
#
# category DIFFRN_SCAN_FRAME_AXIS
#
# _diffrn_scan_frame_axis.axis_id
# _diffrn_scan_frame_axis.angle
# _diffrn_scan_frame_axis.angle_increment
# _diffrn_scan_frame_axis.angle_rstrt_incr
# _diffrn_scan_frame_axis.displacement
# _diffrn_scan_frame_axis.displacement_increment
# _diffrn_scan_frame_axis.displacement_rstrt_incr
# _diffrn_scan_frame_axis.frame_id
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
;
Data items in the ARRAY_DATA category are the containers for
the array data items described in category ARRAY_STRUCTURE.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and
presented as hexadecimal data. The first character "H" on the
data lines means hexadecimal. It could have been "O" for octal
or "D" for decimal. The second character on the line shows
the number of bytes in each word (in this case "4"), which then
requires 8 hexadecimal digits per word. The third character
gives the order of octets within a word, in this case "<"
for the ordering 4321 (i.e. "big-endian"). Alternatively the
character ">" could have been used for the ordering 1234
(i.e. "little-endian"). The block has a "message digest"
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 1
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-Id, these values should be equal.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; The value of _array_data.data contains the array data
encapsulated in a STAR string.
The representation used is a variant on the
Multipurpose Internet Mail Extensions (MIME) specified
in RFC 2045-2049 by N. Freed et al. The boundary
delimiter used in writing an imgCIF or CBF is
"--CIF-BINARY-FORMAT-SECTION--" (including the
required initial "--").
The Content-Type may be any of the discrete types permitted
in RFC 2045; "application/octet-stream" is recommended.
If an octet stream was compressed, the compression should
be specified by the parameter 'conversions="x-CBF_PACKED"'
or the parameter 'conversions="x-CBF_CANONICAL"'.
The Content-Transfer-Encoding may be "BASE-64",
"Quoted-Printable", "X-BASE-8", "X-BASE-10", or
"X-BASE-16" for an imgCIF or "BINARY" for a CBF. The
octal, decimal and hexadecimal transfer encodings are
for convenience in debugging, and are not recommended
for archiving and data interchange.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In a CBF, the
raw binary data begins after an empty line terminating
the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of
the message size, nor in the calculation of the
message digest.
The X-Binary-Size header specifies the size of the
equivalent binary data in octets. If compression was
used, this size is the size after compression, including
any book-keeping fields. And adjustment is made for
the deprecated binary formats in which 8 bytes of binary
header are used for the compression type. In that case,
the 8 bytes used for the compression type is subtracted
from the size, so that the same size will be reported
if the compression type is supplied in the MIME header.
Use of the MIME header is the recommended way to
supply the compression type. In general, no portion of
the binary header is included in the calculation of the size.
The X-Binary-Element-Type header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is "unsigned 32-bit integer".
An MD5 message digest may, optionally, be used. The "RSA Data
Security, Inc. MD5 Message-Digest Algorithm" should be used.
No portion of the header is included in the calculation of the
message digest.
If the Transfer Encoding is "X-BASE-8", "X-BASE-10", or
"X-BASE-16", the data is presented as octal, decimal or
hexadecimal data organized into lines or words. Each word
is created by composing octets of data in fixed groups of
2, 3, 4, 6 or 8 octets, either in the order ...4321 ("big-
endian") or 1234... (little-endian). If there are fewer
than the specified number of octets to fill the last word,
then the missing octets are presented as "==" for each
missing octet. Exactly two equal signs are used for each
missing octet even for octal and decimal encoding.
The format of lines is:
rnd xxxxxx xxxxxx xxxxxx
where r is "H", "O", or "D" for hexadecimal, octal or
decimal, n is the number of octets per word. and d is "<"
for ">" for the "...4321" and "1234..." octet orderings
respectively. The "==" padding for the last word should
be on the appropriate side to correspond to the missing
octets, e.g.
H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000
or
H3> FF0700 00====
For these hex, octal and decimal formats, only, comments
beginning with "#" are permitted to improve readability.
BASE64 encoding follows MIME conventions. Octets are
in groups of three, c1, c2, c3. The resulting 24 bits
are broken into four 6-bit quantities, starting with
the high-order six bits (c1 >> 2) of the first octet, then
the low-order two bits of the first octet followed by the
high-order 4 bits of the second octet ((c1 & 3)<<4 | (c2>>4)),
then the bottom 4 bits of the second octet followed by the
high order two bits of the last octet ((c2 & 15)<<2 | (c3>>6)),
then the bottom six bits of the last octet (c3 & 63). Each
of these four quantities is translated into an ASCII character
using the mapping:
1 2 3 4 5 6
0123456789012345678901234567890123456789012345678901234567890123
| | | | | | |
ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/
With short groups of octets padded on the right with one "="
if c3 is missing, and with "==" if both c2 and c3 are missing.
QUOTED-PRINTABLE encoding also follows MIME conventions, copying
octets without translation if their ASCII values are 32..38,
42, 48..57, 59..60, 62, 64..126 and the octet is not a ";"
in column 1. All other characters are translated to =nn, where
nn is the hexadecimal encoding of the octet. All lines are
"wrapped" with a terminating "=" (i.e. the MIME conventions
for an implicit line terminator are never used).
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
;
Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ATOM_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.index
_item_description.description
;
This item is a pointer to _array_structure_list.index in the
ATOM_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
;
The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
;
Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The actual detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
'_array_intensities.gain'. If raw, uncorrected values
are presented (e.g for calibration experiments), the
value of '_array_intensities.linearity' will be 'raw'
and '_array_intensities.gain' will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.overload
_array_intensities.undefined_value
image_1 linear 1.2 655535 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ATOM_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
;
Detector "gain". The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
;
The estimated standard deviation in detector "gain".
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
;
The intensity linearity scaling used from raw intensity
to the stored element value:
'linear' is obvious
'offset' means that the value defined by
'_array_intensities.offset' should be added to each
element value.
'scaling' means that the value defined by
'_array_intensities.scaling' should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by '_array_intensities.scaling' is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
'logarithmic_scaled' means that the logarithm based 10 of
raw intensities multiplied by '_array_intensities.scaling'
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by '_array_intensities.scaling' and calculating 10
to the power of this number.
'raw' means that the data is the raw is a set of raw values
straight from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
;
The value defined by '_array_intensities.offset' should
be added to each element value.
;
'scaling'
;
The value defined by '_array_intensities.scaling' should be
multiplied with each element value.
;
'scaling_offset'
;
The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
;
The square root of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by '_array_intensities.scaling' and squaring the
result.
;
'logarithmic_scaled'
;
The logarithm based 10 of raw intensities multiplied by
'_array_intensities.scaling' is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
'_array_intensities.scaling' and calculating 10 to the
power of this number.
;
'raw'
;
The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
;
Offset value to add to array element values in the manner
described by item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.scaling
_item_description.description
;
Multiplicative scaling value to be applied to array data
in the manner described by item _array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
;
The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.undefined_value
_item_description.description
;
A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
;
Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data which may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
_category_key.name '_array_structure.id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
;
The order of bytes for integer values which require more
than 1-byte.
(IBM-PC's and compatibles, and Dec-Vaxes use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. Dec-Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
;
The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
;
The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
;
Type of data compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code code
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'none'
;
Data are stored in normal format as defined by
'_array_structure.encoding_type' and
'_array_structure.byte_order'.
;
'byte_offsets'
;
Using the compression scheme defined in CBF definition
Section 5.0.
;
'packed'
;
Using the 'packed' compression scheme, a CCP4-style packing
(CBFlib section 3.3.2)
;
'canonical'
;
Using the 'canonical' compression scheme (CBFlib section
3.3.1)
;
save_
save__array_structure.encoding_type
_item_description.description
;
Data encoding of a single element of array data.
In several cases, the IEEE format is referenced.
See "IEEE Standard for Binary Floating-Point Arithmetic",
ANSI/IEEE Std 754-1985, the Institute of Electrical and
Electronics Engineers, Inc., NY 1985.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit_integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure yes
'_array_data.array_id' array_data yes
'_array_structure_list.array_id' array_structure_list yes
'_array_intensities.array_id' array_intensities yes
'_diffrn_data_frame.array_id' diffrn_data_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
;
Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left-to-right (increasing) in
first dimension and bottom-to-top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differ
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the "poise" of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
;
The number of elements stored in the array structure in this
dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
;
Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
;
Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
;
Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
;
Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
;
Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
;
Data items in the ARRAY_STRUCTURE_LIST_AXIS category describes
the physical settings of sets axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axis, one for the angular
direction, one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
'_array_structure_list_axis.axis_set_id'
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
;
The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id .
This item is a pointer to _array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
save_
save__array_structure_list_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of '_array_structure_list.axis_set_id'. If the index is
specified as 'increasing' this will be the center of the
pixel with index value 1. If the index is specified as
'decreasing' this will be the center of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
;
The pixel-center-to-pixel-center increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified in that case.
See '_array_structure_list_axis.angular_pitch'.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
;
The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of '_array_structure_list.axis_set_id'. If the index is
specified as 'increasing' this will be the center of the
pixel with index value 1. If the index is specified as
'decreasing' this will be the center of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
;
The pixel-center-to-pixel-center increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
;
The pixel-center-to-pixel-center distance for a one step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans,
or for uncoupled angular scans at a constant radius
(cylindrical scan) and should not be specified for cases
in which the angle between pixels, rather than the distance
between pixels is uniform.
See '_array_structure_list_axis.angle_increment'.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
;
The radial distance from one "cylinder" of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of '_array_structure_list_axis.displacement_increment'.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
########
# AXIS #
########
save_AXIS
_category.description
;
Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection. The location of each
axis is specified by two vectors: the axis itself, given as a unit
vector, and an offset to the base of the unit vector. These vectors
are referenced to a right-handed laboratory coordinate system with
its origin in the sample or specimen:
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
These axes are based on the goniometer, not on the orientation of the
detector, gravity, etc. The vectors necessary to specify all other
axes are given by sets of three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to, but significantly
different from the choice in MOSFLM (Andrew G.W. Leslie, Harry Powell,
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH,UK
http://www.dl.ac.uk/CCP/CCP4/dist/x-windows/Mosflm/). In MOSFLM,
X is along the X-ray beam (our Z axis) and Z is along the rotation axis.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam center.
The location of the beam center on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected mm from the (0,0) corner
of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, we need to specify the
location of the beam center on the detector in terms of the origin of the
detector, which is, of course, not coincident with the center of the
sample.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows the axis specification of the axes of a kappa
geometry goniometer (See "X-Ray Structure Determination, A Practical
Guide", 2nd ed. by G. H. Stout, L. H. Jensen, Wiley Interscience,
1989, 453 pp, p 134.).
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X-axis. The next innermost axis, kappa,
is at a 50 degree angle to the X-axis, pointed away from the source.
The innermost axis, phi, aligns with the X-axis when omega and
phi are at their zero-points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
x' = (T-omega) (T-kappa) (T-phi) x
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
This example show the axis specification of the axes of a
detector, source and gravity. We have juggled the order as a
reminder that the ordering of presentation of tokens is not
significant. We have taken the center of rotation of the detector
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.type specifies the next outermost
axis upon which this axis depends.
This item is a pointer to axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.type specifies the type of equipment
using the axis: goniometer, detector, gravity, source
or general
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so that the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: rotation, translation (or general when the type is
not relevant, as for gravity)
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the 3-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector, and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
;
Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases, but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element is
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id
;
;
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0.00
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
;
This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.id
_item_description.description
;
The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_DIFFRN_DETECTOR
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; Need new example here.
;
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detectors used to measure
the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
;
The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of _diffrn_detector.diffrn_id
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.number_of_axes
_item_description.description
;
The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id
The word "positioner" is a general term used in instrumentation
design for devices that are used to change the positions of
portions of apparatus by linear translation, rotation, or
combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_DIFFRN_DETECTOR_AXIS
_category.description
;
Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
;
This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named '_diffrn_detector_axis.id'
which is now a deprecated name. The old name is
provided as an alias, but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_DIFFRN_DETECTOR_ELEMENT
_category.description
;
Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, the more detailed information provided
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
are preferable to simply providing the centre.
;
_category.id diffrn_detector_element
_category.mandatory_code no
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square. in the pattern
1 2
*
3 4
Note that the beam center is slightly off of each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4.
;
;
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
_diffrn_detector_element.center[1]
_diffrn_detector_element.center[2]
d1 d1_ccd_1 201.5 -1.5
d1 d1_ccd_2 -1.8 -1.5
d1 d1_ccd_3 201.6 201.4
d1 d1_ccd_4 -1.7 201.5
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.center[1]
_item_description.description
;
The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
;
The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam-center in mm from the
(0, 0) (lower left) corner of the detector element viewed from
the sample side.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.id
_item_description.description
;
The value of _diffrn_detector_element.id must uniquely identify
each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
;
This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_DIFFRN_MEASUREMENT
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the diffraction
data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model x'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; Need new example here
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support and
orient the specimen.
If the value of _diffrn_measurement.device is not given, it is
implicitly equal to the value of _diffrn_measurement.diffrn_id
Either '_diffrn_measurement.device' or '_diffrn_measurement.id'
may be used to link to other categories. If the experimental
setup admits multiple devices, then '_diffrn_measurement.id'
is used to provide a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to measure
the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'homemade'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
;
The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of _diffrn_measurement.diffrn_id
Either '_diffrn_measurement.device' or '_diffrn_measurement.id'
may be used to link to other categories. If the experimental
setup admits multiple devices, then '_diffrn_measurement.id'
is used to provide a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
;
The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_DIFFRN_MEASUREMENT_AXIS
_category.description
;
Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
loop_
_category_key.name '_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
;
This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
;
This data item is a pointer to _diffrn_measurement.device in
the DIFFRN_MEASUREMENT category.
;
_item.name '_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
;
This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named '_diffrn_measurement_axis.id'
which is now a deprecated name. The old name is
provided as an alias, but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0.00
_item.mandatory_code implicit
save_
####################
# DIFFRN_RADIATION #
####################
save_DIFFRN_RADIATION
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used in measuring diffraction intensities,
its collimation and monochromatisation before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
_category_key.name '_diffrn_radiation.diffrn_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991).
Acta Cryst. C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.mandatory_code yes
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the esd of the directions of photons in the X-Z plane
around the mean source beam direction.
Note that some synchrotrons specify this value in milliradians,
in which case a conversion would be needed. To go from a
value in milliradians to a value in degrees, multiply by 0.180
and divide by Pi.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the esd of the directions of photons in the Y-Z plane
around the mean source beam direction.
Note that some synchrotrons specify this value in milliradians,
in which case a conversion would be needed. To go from a
value in milliradians to a value in degrees, multiply by 0.180
and divide by Pi.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation degrees**2 between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the xray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
directin of each photons in X-Z plane times the deviations
of the direction of the same photon in the Y-Z plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons specify this value in
milliradians**2, in which case a conversion would be needed.
To go from a value in milliradians**2 to a value in
degrees**2, multiply by 0.180**2 and divide by Pi**2.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a mono-
chromator crystal is used the material and the indices of the
Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarisation and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarisation ratio of the diffraction beam incident on the
crystal. It is the ratio of the perpendicularly polarised to the
parallel polarised component of the radiation. The perpendicular
component forms an angle of _diffrn_radiation.polarisn_norm to
the normal to the diffraction plane of the sample (i.e. the
plane containing the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
normal to the polarization plane and the laboratory Y axis as
defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monchromater.
This differs from the value of '_diffrn_radiation.polarisn_norm'
in that '_diffrn_radiation.polarisn_norm' refers to polarization
relative to the diffraction plane rather than to the laboratory
axis system.
In the case of an unpolarized beam, or a beam with true circular
polarization, in which no single plane of polarization can be
determined, the plane should be taken as the X-Z plane, and the
angle as 0.
See '_diffrn_radiation.polarizn_source_ratio'.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity (amplitude squared)
of the electric vector in the plane of polarization and In is
the intensity (amplitude squared) of the electric vector
in plane of the normal to the plane of polarization.
Thus, if we had complete polarization in the plane of
polarization, the value of
'_diffrn_radiation.polarizn_source_ratio' would
be 1, and an unpolarized beam would have a value of 0.
If the X-axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of "MONOCHROMATOR" in the Denzo glossary, and values of near
1 should be expected for a bending magnet source. However,
if the X-axis were, for some reason to be, say, perpendicular
to the polarization plane (not a common choice), then the
Denzo value would be the negative of
'_diffrn_radiation.polarizn_source_ratio'.
See http://www.hkl-xray.com for information on Denzo, and
Z. Otwinowski and W. Minor, " Processing of X-ray Diffraction
Data Collected in Oscillation Mode ", Methods in Enzymology,
Volume 276: Macromolecular Crystallography, part A, p.307-326,
1997,C.W. Carter, Jr. & R. M. Sweet, Eds., Academic Press.
This differs both in the choice of ratio and choice of
orientation from '_diffrn_radiation.polarisn_ratio', which,
unlike '_diffrn_radiation.polarizn_source_ratio', is unbounded.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly encouraged
that this field be specified so that the probe radiation
can be simply determined.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'x-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for probe radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to _diffrn_radiation_wavelength.id
in the DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.mandatory_code yes
save_
################
# DIFFRN_REFLN #
################
save_DIFFRN_REFLN
_category.description
;
This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
;
_category.id diffrn_refln
_category.mandatory_code no
_category_key.name '_diffrn_refln.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
;
This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_DIFFRN_SCAN
_category.description
;
Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
_category_key.name '_diffrn_scan.id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. We have specified three rotation axes and one translation axis
at non-zero values, with one axis stepping. There is no reason why
more axes could not have been specified to step. We have specified
range information, but note that it is redundant from the number of
frames and the increment, so we could drop the data item
_diffrn_scan_axis.angle_range .
We have specified both the sweep data and the data for a single frame.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
'_diffrn_scan.integration_time' and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
'_diffrn_scan_frame.integration_time' and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustements are made to
scan times and non-linear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.angle_increment
_diffrn_scan_frame_axis.displacement
_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
;
Example 2 - a more extensive example, R. M. Sweet, P. Ellis, H. Bernstein.
We place a detector 240 mm along the Z axis from the goniometer.
This presents us with a choice -- either we define the axes of
the detector at the origin, and then put a Z setting of -240 in
for the actual use, or we define the axes with the necessary Z-offset.
In this case we use the setting, and leave the offset as zero.
We call this axis DETECTOR_Z.
The axis for positioning the detector in the Y-direction depends
on the detector Z-axis. We call this axis, DETECTOR_Y.
The axis for positioning the dector in the X-direction depends
on the detector Y-axis (and therefore on the detector Z-axis).
We call this axis DETECTOR_X.
This detector may be rotated around the Y-axis. This rotation axis
depends on the three translation axies. We call it DETECTOR_PITCH.
We define a coordinate system on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm x 0.150mm, the center of the first pixel is at (0.075,
0.075) in this coordinate system.
;
;
###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
;
Example 3 - Example 2 revised for a spiral scan, R. M. Sweet,
P. Ellis, H. Bernstein.
We place a detector 240 mm along the Z axis from the goniometer,
as in Example 2, above, but in this example, the image plate is
scanned in a spiral pattern outside edge in.
The axis for positioning the detector in the Y-direction depends
on the detector Z-axis. We call this axis, DETECTOR_Y.
The axis for positioning the dector in the X-direction depends
on the detector Y-axis (and therefore on the detector Z-axis).
We call this axis DETECTOR_X.
This detector may be rotated around the Y-axis. This rotation axis
depends on the three translation axies. We call it DETECTOR_PITCH.
We define a coordinate system on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. Let us call rotation axis ELEMENT_ROT, and the
radial axis ELEMENT_RAD. We assume 150 um radial pitch and 75 um
'constant velocity' angular pitch.
We index first on the rotation axis and make the radial axis
dependent on
it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
;
###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.angle
_array_structure_list_axis.displacement
_array_structure_list_axis.angular_pitch
_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
;
The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
;
The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
;
Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
'_diffrn_scan_frame.integration_time', even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
;
The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frame_id_end
_item_description.description
;
The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
save_
save__diffrn_scan.frames
_item_description.description
;
The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_DIFFRN_SCAN_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
;
The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
'_diffrn_scan.id'.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
'_diffrn_scan.id'.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
save_
save__diffrn_scan_axis.angle_start
_item_description.description
;
The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
;
The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
;
The increment for each step for the specified axis
in degrees. In general, this will agree with
'_array_structure_list_axis.angle_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
;
The increment after each step for the specified axis
in degrees. In general, this will agree with
'_array_structure_list_axis.angle_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
;
The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
;
The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
;
The increment for each step for the specified axis
in millimetres. In general, this will agree with
'_diffrn_scan_frame_axis.displacement_increment', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
;
The increment for each step for the specified axis
in millimetres. In general, this will agree with
'_diffrn_scan_frame_axis.displacement_rstrt_incr', which
see for a precise description.
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_DIFFRN_SCAN_FRAME
_category.description
;
Data items in the DIFFRN_SCAN_FRAME category describe the settings of
axes for particular frames. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
;
The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
save__diffrn_scan_frame.frame_number
_item_description.description
;
The value of this data item is the number of the frame within
the scan, starting with 1. It is not necessarily the same as
the value of _diffrn_scan_frame.frame_id, but may
be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
;
The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of '_diffrn_scan.integration_time'.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_DIFFRN_SCAN_FRAME_AXIS
_category.description
;
Data items in the DIFFRN_SCAN_FRAME_AXIS category describes the settings
of axes for particular frames. Unspecified axes are assumed to be at
their zero points. If, for any given frame, non-zero values apply
for any of the data items in this category, those values should be
given explicitly in this category and not simply inferred from values
in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
;
The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
;
The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
;
The increment for this frame for angular setting of
the specified axis in degrees. The sum of the values
of '_diffrn_scan_frame_axis.angle' and
'_diffrn_scan_frame_axis.angle_increment' is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
;
The increment after this frame for angular setting of
the specified axis in degrees. The sum of the values
of '_diffrn_scan_frame_axis.angle' and
'_diffrn_scan_frame_axis.angle_increment' and
'_diffrn_scan_frame_axis.angle_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame, and should equal
'_diffrn_scan_frame_axis.angle' for that next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
;
The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
;
The increment for this frame for displacement setting of
the specified axis in millimetres. The sum of the values
of '_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
;
The increment for this frame for displacement setting of
the specified axis in millimetres. The sum of the values
of '_diffrn_scan_frame_axis.displacement' and
'_diffrn_scan_frame_axis.displacement_increment' and
'_diffrn_scan_frame_axis.displacement_rstrt_incr' is the
angular setting of the axis at the start of the integration
time for the next frame, and should equal
'_diffrn_scan_frame_axis.displacement' for that next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
;
The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id .
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
save_
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive)
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types / multi-word items (case insensitive)
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*}\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]\
(T[0-2][0-9]:[0-5][0-9]:[0-5][0-9](.[0-9]+)([+-][0-5][0-9]:[0-5][0-9]))
;
;
Standard format for CIF date and time strings (see
http://www.iucr.orgiucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character "T" followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
deciaml fraction on the seconds of time.
Time is local time if no time-zone offset is given.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2))'
'millimetres' 'millimetres (metres * 10^( -3))'
'nanometres' 'nanometres (metres * 10^( -9))'
'angstroms' 'angstroms (metres * 10^(-10))'
'picometres' 'picometres (metres * 10^(-12))'
'femtometres' 'femtometres (metres * 10^(-15))'
#
'reciprocal_metres' 'reciprocal metres (metres * 10^-1)'
'reciprocal_centimetres' 'reciprocal centimetres (metres * 10^( -2)^-1)'
'reciprocal_millimetres' 'reciprocal millimetres (metres * 10^( -3)^-1)'
'reciprocal_nanometres' 'reciprocal nanometres (metres * 10^( -9)^-1)'
'reciprocal_angstroms' 'reciprocal angstroms (metres * 10^(-10)^-1)'
'reciprocal_picometres' 'reciprocal picometres (metres * 10^(-12)^-1)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9))^2'
'angstroms_squared' 'angstroms squared (metres * 10^(-10))^2'
'8pi2_angstroms_squared' '8pi^2 * angstroms squared (metres * 10^(-10))^2'
'picometres_squared' 'picometres squared (metres * 10^(-12))^2'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9))^3'
'angstroms_cubed' 'angstroms cubed (metres * 10^(-10))^3'
'picometres_cubed' 'picometres cubed (metres * 10^(-12))^3'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (metres * 10^( -9))^3
;
'electrons_per_angstroms_cubed'
; electrons per angstroms cubed (metres * 10^(-10))^3
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (metres * 10^(-12))^3
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E-09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E+03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E-06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E+09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li
;
1.1.1 2001-02-16
;
Several typo corrections by JW
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to '_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source', '_diffrn_radiation.polarizn_source_norm'
,
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add _diffrn_measurement.device to category key
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to al
low
for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes (JW)
+ Correct spelling of diffrn_measurement_axis in _axis.id
+ Correct ordering of uses of _item.mandatory_code and _item_default.value
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown (HJB)
+ Added further comments on '\n' and '\t'
+ Updated ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Changed all spelling 'meter' to 'metre' throughout.
+ Added missing enumerations to _array_structure.compression_type
and made 'none' the default.
+ Removed parent-child relationship between _array_structure_list.index
and _array_structure_list.precedence .
+ Improve alphabetization.
+ Fix _array_intensities_gain.esd related function.
+ Improved comments in AXIS.
+ Fixed DIFFRN_FRAME_DATA example.
+ Removed erroneous DIFFRN_MEASUREMENT example.
+ Added _diffrn_measurement_axis.id to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for _diffrn_scan.id definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header (HJB)
+ Restored _diffrn_detector.diffrn_id to DIFFRN_DETECTOR KEY.
+ Added AXIS category.
+ Brought complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
in from cif_mm.dic for clarity.
+ changed _array_structure.encoding_type from type code to uline and
added X-Binary-Element-Type to MIME header.
+ added detector beam center _diffrn_detector_element.center[1] and
_diffrn_detector_element.center[2]
+ corrected item name of _diffrn_refln.frame_id
+ replace reference to _array_intensities.undefined by
_array_intensities.undefined_value
+ replace references to _array_intensity.scaling with
_array_intensities.scaling
+ added DIFFRN_SCAN... categories
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft (HJB)
+ Reflowed comment lines over 80 characters and corrected typos.
+ Updated examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF (HJB)
+ Added binary type, which is a text field containing a variant on
MIME encoded data.
+ Changed type of _array_data.data to binary and specified internal
structure of raw binary data.
+ Added _array_data.binary_id, and made
_diffrn_frame_data.binary_id and _array_intensities.binary_id
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft (JW):
+ Added category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes were made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA was renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE was renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for _diffrn_frame_data.array_id was changed from
array_structure_list.array_id to array_structure.id. Item
_diffrn_detector.array_id was deleted.
+ Added data item _diffrn_frame_data.binary_id to identify data groups
within a binary section. The formal identification of the binary section
is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version was adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley (AH).
Modifications to the CBF draft (JW):
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories have been
generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category ARRAY_DATA
.
This departs from the CBF notion of data existing in some special comment.
In this description, data is handled as an ordinary data item encapsulated
in a character data type. Although handling binary data this manner
deviates from CIF conventions, it does not violate any DDL 2.1 rules.
DDL 2.1 regular expressions can be used to define the binary
representation which will permit some level of data validation. In
this version, the placeholder type code "any" has been used.
This translates to a regular expression which will match any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary. It
may be possible to use the DDL 2.1 ITEM_STRUCTURE and ITEM_STRUCTURE_LIST
categories to provide the information that is carried in by the
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By moving the array
structure to the DDL level it would be possible to define an array
type as well as a regular expression defining the data format.
+ Multiple array sections can be properly handled within a single datablock.
;
#-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof-eof
./CBFlib-0.9.2.2/doc/Carray_structure_list.html 0000644 0000765 0000765 00000007074 11603702115 017635 0 ustar yaya yaya
(IUCr) CIF Definition save_array_structure_list
Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
Example:
Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left to right (increasing) in the
first dimension and bottom to top (decreasing) in
the second dimension.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL.
ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS
OF THE LGPL.
Before using this software, please read the
for important disclaimers and the IUCr Policy
on the Use of the Crystallographic Information File (CIF) and for other important
information.
Work on imgCIF and CBFlib supported in part by the U. S. Department of
Energy (DOE) under grants ER63601-1021466-0009501 and
ER64212-1027708-0011962, by the U. S. National Science Foundation (NSF)
under grants DBI-0610407, DBI-0315281 and EF-0312612, the U. S.
National Institutes of Health (NIH) under grants 1R15GM078077 from
NIGMS and 1R13RR023192 from NCRR and funding from the International
Union for Crystallographyn (IUCr). The content is solely the
responsibility of the authors and does not necessarily represent the
official views of DOE, NSF, NIH, NIGMS, NCRR or IUCr.
Version History
Version
Date
By
Description
0.1
Apr. 1998
PJE
This was the
first CBFlib release. It
supported binary CBF files using binary strings.
This release
added ascii imgCIF support using MIME-encoded binary sections, added
the option of MIME headers for the binary strings was well. MIME code
adapted from mpack 1.5. Added hooks needed for DDL1-style names without
categories.
This release
merged much of the message digest code into the general file reading and
writing to reduce the number of passes. More consistency checking between
the MIME header and the binary header was introduced. The size in the
MIME header was adjusted to agree with the version 0.2 documentation.
This release
removed the redundant information (binary id, size, compression id)
from a binary header when there is a MIME header, removed the unused
repeat argument, and made the memory allocation for buffering and
tables with many rows sensitive to the current memory allocation already used.
This release
modified cbf_simple.c to reorder image data on read so that the
indices are always increasing in memory (this behavior was
undefined previously).
This release cleans up some
compiler warnings, corrects a parse error on quoted strings with
a leading blank as adds the new routines for support of
aliases, dictionaries and real arrays, higher level routines
to get and set pixel sizes, do cell computations, and to set beam centers,
improves support for conversion of images, picking up more data from
headers.
This release reorganizes the kit
into two pieces: CBFlib_0.7.6_Data_Files and CBFlib_0.7.6. An optional local copy
of getopt is added. The 1.4 draft dictionary has been added. cif2cbf
updated to support vcif2 validation. convert_image and cif2cbf updated
to report text of error messages. convert_image updated to support
tag and category aliases, default to adxv images. convert_image and
img updated to support row-major images. Support added for binning.
API Support added for validation, wide files and line folding.
Logic changed for beam center reporting. Added new routines:
cbf_validate,
cbf_get_bin_sizes,
cbf_set_bin_sizes,
cbf_find_last_typed_child,
cbf_compose_itemname,
cbf_set_cbf_logfile,
cbf_make_widefile,
cbf_read_anyfile,
cbf_read_widefile,
cbf_write_local_file,
cbf_write_widefile,
cbf_column_number,
cbf_blockitem_number,
cbf_log,
cbf_check_category_tags,
cbf_set_beam_center
This release reflects changes
for base 32K support developed by G. Darakev, and changes
for support of reals, 3d arrays, byte_offset compression and
J. P. Abrahams packed compression
made in consultation with (in alphabetic order) E. Eikenberry,
A. Hammerley, W. Kabsch, M. Kobas, J. Wright and others at PSI
and ESRF in January 2007, as well accumulated changes fixing
problems in release 0.7.6.
This release is a patch
to 0.7.7 to change the treatment of the byteorder parameter from
strcpy semantics to return of a pointer to a string constant.
Our thanks to E. Eikenberry for pointing out the problem.
This release is a patch
to 0.7.7.3 to add f90 support for reading of CBF byte-offset and
packed compression, to fix problems with gcc 4.4.1 and to correct
errors in multidimensional packed compression.
New default release with updated pycbf, tiff support, removal of
default use of PyCifRW to avoid Fedora license issue.
Known Problems
The example program tiff2cbf needs the enviroment variable LD_LIBRARY_PATH
set to the location of the lib directory in CBFlib_0.9.2, unless
a system install of tiff-3.9.4-rev-6Feb11 has been done.
Due to license issues, PyCifRW is not included with default releases
of CBFlib. Users can download PyCifRW separately.
There are some issues with Peter Chang's lastest java wrapper under
the CBFlib 0.9.2 release. Until
they are resolved, the CBFlib 0.8.1 release should be used
for Java applications.
This version does not have support for predictor compression.
If your system has the program wget, you only need the source code. The download of the other tar balls will be
handled automatically.
Be careful about space. A full build and test can use 350 MB or more. If space is tight, be sure to read the
instructions below on using only the signatures of the test files.
Uncompress and unpack :
gunzip < CBFlib_0.9.2.tar.gz | tar xvf -
To run the test programs, you will also need
Paul Ellis's sample MAR345 image,
example.mar2300,
Chris Nielsen's sample ADSC Quantum 315 image,
mb_LP_1_001.img, and Eric Eikenberry's SLS sample Pilatus 6m image,
insulin_pilatus6m, as sample data. In addition there are
is a PDB mmCIF file, 9ins.cif, and 3 special test files
testflatin.cbf, testflatpackedin.cbf and testrealin.cbf.
All these files will be
dowloaded and extracted by the Makefile from CBFlib_0.9.2_Data_Files_Input. Do
not download copies into the top level directory.
Thare are various sample Makefiles for common
configurations. The Makefile_OSX
samples is for systems with gfortran from prior to
the release of gcc 4.2. For the most recent gfortran,
use Makefile_OSX_gcc42. All
the Makefiles are generated from m4/Makefile.m4.
The Makefiles use GNU make constructs, such as ifeq
and ifneq. If you need to use a different version of
make, you will need to edit out the conditionals
The operation of the Makefiles is sensitive to the
following environment variables:
CBFLIB_USE_PYCIFRW If you define this environment variable,
you may rebuild the Makefiles to include James Hester's PyCifRW. The
process under bash is:
export CBFLIB_USE_PYCIFRW=yes
cd CBFlib_0.9.2
touch m4/Makefile.m4
make Makefiles
CBF_DONT_USE_LONG_LONG If you define this environment variable,
use of the long long data type in CBFlib is replaced by
use of a struct. The Makefiles do not need to be rebuilt. Makefile_MINGW
does not use the long long data type even without defining
this variable.
NOFORTRAN If you define this environment variable,
use of the fortran compiler is suppressed.
If necessary, adjust the definition of CC and C++ and
other defintions in
Makefile to point to your compilers.
Set the definition of CFLAGS to an appropriate value
for your C and C++ compilers,
the definition of F90C to point to your
Fortan-90/95 compiler, and the definitions of
F90FLAGS and F90LDFLAGS to approriate values
for your Fortan-90/95 compilers, and then
make all make tests
or, if space is at a premium:
make all make tests_sigs_only
If you do not have a fortran compiler, you will need
edit the Makefile or to define the variable NOFORTRAN, either in the Makefile
or in the environment
CBFlib 0.9.2 includes a program, tiff2cbf, to convert from tiff files
to CBF files, that requires an augmented version of tiff-3.9.4 called
tiff-3.9.4-rev-6Feb11, that installs into the CBFlib_0.9.2 directory.
If a system copy is desired, download and install
http://downloads.sf.net/cbflib/tiff-3.9.4-rev-6Feb11.tar.gz
CBFlib (Crystallographic Binary File library) is a library of ANSI-C functions providing a simple mechanism for accessing
Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files.
The CBFlib API is loosely based on the
CIFPARSE API for mmCIF files. Like CIFPARSE, CBFlib does not perform any semantic
integrity checks; rather it simply provides functions to create, read, modify and write CBF binary
data files and imgCIF ASCII data files.
Starting with version 0.7.7, an envolving FCBlib (Fortran Crystallographic Binary library) has been
added. As of this release it includes code for reading byte-offset and packed compression
image files created by CBFlib.
Almost all of the CBFlib functions receive a value of type cbf_handle
(a CBF handle) as the first argument.
Several of the high-level CBFlib functions dealing with geometry
receive a value of type cbf_goniometer (a handle for a CBF goniometer object)
or cbf_detector (a handle for a CBF detector object).
All functions return an integer
equal to 0 for success or an error code for failure.
CBFlib permits a program to use multiple CBF objects simultaneously. To identify
the CBF object on which a function will operate, CBFlib uses a value of type cbf_handle.
All functions in the library except cbf_make_handle expect a value of type cbf_handle
as the first argument.
The function cbf_make_handle creates and initializes a new CBF handle.
The function cbf_free_handle destroys a handle and frees all memory associated with
the corresponding CBF object.
To represent a detector surface mounted on a positioning system, CBFlib
uses a value of type cbf_detector.
A goniometer object is created and initialized from a CBF object using
one of the functions cbf_construct_detector,
cbf_construct_reference_detector or cbf_require_reference_detector.
The function cbf_free_detector destroys a detector handle and frees
all memory associated with the corresponding object.
The current version of CBFlib only decompresses a binary section from disk when requested
by the program.
When a file containing one or more binary sections is read, CBFlib saves the file
pointer and the position of the binary section within the file and then jumps past
the binary section. When the program attempts to access the binary data, CBFlib
sets the file position back to the start of the binary section and then reads the data.
For this scheme to work:
1. The file must be a random-access file opened in binary
mode (fopen ( ," rb")).
2. The program must not
close the file. CBFlib will close the file using fclose ( ) when it is no longer
needed.
At present, this also means that a program cant read a file and then write back to
the same file. This restriction will be eliminated in a future version.
When reading an imgCIF vs a CBF, the difference is detected automatically.
When a program passes CBFlib a binary value, the data is compressed to a temporary
file. If the CBF object is subsequently written to a file, the data is simply copied
from the temporary file to the output file.
The output file can be of any type. If the program indicates to CBFlib that the file
is a random-access and readable, CBFlib will conserve disk space by closing the temporary
file and using the output file as the location at which the binary value is stored.
For this option to work:
1. The file must be a random-access file opened in binary
update mode (fopen ( , "w+b")).
2. The program must not
close the file. CBFlib will close the file using fclose ( )
when it is no longer
needed.
If this option is not used:
1. CBFlib will continue using the temporary file.
2. CBFlib will not
close the file. This is the responsibility of the main program.
1. Open disk files to read using the mode "rb".
2. If possible, open disk files to write using the mode "w+b"
and tell CBFlib that it can use the file as a buffer.
3. Do not
close any files read by CBFlib or written by CBFlib with
buffering turned on.
4. Do not attempt to read from a file, then
write to the same file.
There are two major conventions in the ordering of array indices:
fs: Fast to slow. The first array index (the one numbered "1") is the one
for which the values of that index change "fastest". That is, as we move
forward in memory, the value of this index changes more rapidly than any other.
sf: Slow to fast. The first array index (the one numbered "1") is the one
for which the values of that index change "slowest". That is as we move
forward in memory, the value of this index changes more slowly than any other.
During the development of CBFlib, both conventions have been used. In order to avoid confusion,
the functions for which array indices are used are available in three forms: a default version
which may used either one convention or the other, a form in which the name of the function
has an "_fs" suffix for the fast to slow convention and a form in which the name of the
function has a "_sf" suffix for the slow to fast convention. Designers of applications
are advised to use one of the two suffix conventions. There is no burden on performance for using
one convention or the other. The differences are resolved at compile time by use of
preprocessor macros.
cbf_make_handle creates and initializes a new internal CBF object.
All other CBFlib
functions operating on this object receive the CBF handle
as the first argument.
ARGUMENTS
handle
Pointer to a CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_read_file (cbf_handle handle, FILE *file, int flags);
int cbf_read_widefile (cbf_handle handle, FILE *file, int flags);
DESCRIPTION
cbf_read_file reads the CBF or CIF file file
into the CBF object specified by handle, using the CIF 1.0 convention of 80 character lines.
cbf_read_widefile reads the CBF or CIF file file
into the CBF object specified by handle, using the CIF 1.1 convention of 2048 character lines.
A warning is issued to stderr for ascii lines over the limit. No test is performed on binary
sections.
Validation is performed in three ways levels: during the lexical scan, during the
parse, and, if a dictionary was converted, against the value types, value
enumerations, categories and parent-child relationships specified
in the dictionary.
flags controls the interpretation of binary section headers, the parsing of
brackets constructs and the parsing of treble-quoted strings.
MSG_DIGEST:
Instructs CBFlib to check that the digest of the
binary section matches any
header digest value. If the digests do
not match, the call will return CBF_FORMAT. This evaluation and comparison
is delayed (a "lazy" evaluation) to ensure maximal processing efficiency.
If an immediately evaluation is required, see MSG_DIGESTNOW, below.
MSG_DIGESTNOW:
Instructs CBFlib to check that the digest of the
binary section matches any
header digeste value. If the digests do
not match, the call will return CBF_FORMAT. This evaluation and comparison
is performed during initial parsing of the section to ensure timely
error reporting at the expense of processing efficiency.
If a more efficient delayed ("lazy") evaluation is required, see MSG_DIGEST, above.
MSG_DIGESTWARN:
Instructs CBFlib to check that the digest of the
binary section matches any
header digeste value. If the digests do
not match, a warning message will be sent to stderr, but processing will
attempt to continue. This evaluation and comparison
is first performed during initial parsing of the section to ensure timely
error reporting at the expense of processing efficiency.
An mismatch of the message digest usually indicates a serious error, but it
is sometimes worth continuing processing to try to isolate the cause of
the error. Use this option with caution.
MSG_NODIGEST:
Do not check the digest (default).
PARSE_BRACKETS:
Accept DDLm bracket-delimited [item,item,...item] or
{item,item,...item} or (item,item,...item) constructs as
valid, stripping non-quoted embedded whitespace and comments. These constructs may span multiple lines.
PARSE_LIBERAL_BRACKETS:
Accept DDLm bracket-delimited [item,item,...item] or
{item,item,...item} or (item,item,...item) constructs as
valid, stripping embedded non-quoted, non-separating whitespace and comments. These constructs may span multiple lines. In
this case, whitespace may be used as an alternative to the comma.
PARSE_TRIPLE_QUOTES:
Accept DDLm triple-quoted """item,item,...item""" or
'''item,item,...item''' constructs as
valid, stripping embedded whitespace and comments. These constructs may span multiple lines. If this flag
is set, then ''' will not be interpreted as a quoted apoptrophe and
""" will not be interpreted as a quoted double quote mark and
PARSE_NOBRACKETS:
Do not accept DDLm bracket-delimited [item,item,...item] or
{item,item,...item} or (item,item,...item) constructs as
valid, stripping non-quoted embedded whitespace and comments. These constructs may span multiple lines.
PARSE_NOTRIPLE_QUOTES:
No not accept DDLm triple-quoted """item,item,...item""" or
'''item,item,...item''' constructs as
valid, stripping embedded whitespace and comments. These constructs may span multiple lines. If this flag
is set, then ''' will be interpreted as a quoted apostrophe and
""" will be interpreted as a quoted double quote mark.
CBFlib defers reading binary sections as long as possible. In the current version
of CBFlib, this means that:
1. The file must be a random-access file opened in binary mode
(fopen ( , "rb")).
2. The program must not
close the file. CBFlib will close the file using fclose ( ) when it is no longer
needed.
These restrictions may change in a future release.
ARGUMENTS
handle
CBF handle.
file
Pointer to a file descriptor.
headers
Controls interprestation of binary section headers.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_write_file (cbf_handle handle, FILE *file, int readable, int ciforcbf, int flags, int encoding);
int cbf_write_widefile (cbf_handle handle, FILE *file, int readable, int ciforcbf, int flags, int encoding);
DESCRIPTION
cbf_write_file writes the CBF object specified by handle
into the file file, following CIF 1.0 conventions of 80 character lines.
cbf_write_widefile writes the CBF object specified by handle
into the file file, following CIF 1.1 conventions of 2048 character lines.
A warning is issued to stderr for ascii lines over the limit, and an attempt is
made to fold lines to fit. No test is performed on binary
sections.
If a dictionary has been provided, aliases will be applied on output.
Unlike cbf_read_file, the file does not have to be random-access.
If the file is random-access and readable, readable can be set to
non-0 to indicate to CBFlib that
the file can be used as a buffer to conserve disk space.
If the file is not random-access or not
readable, readable must be 0.
If readable is non-0, CBFlib will close the file when it is
no longer required, otherwise this is
the responsibility of the program.
ciforcbf selects the format in which the binary sections are written:
CIF
Write an imgCIF file.
CBF
Write a CBF file (default).
flags selects the type of header used in CBF binary sections, selects whether message
digests are generated, and controls the style of output. The value of flags can be a logical OR of any of:
MIME_HEADERS
Use MIME-type headers (default).
MIME_NOHEADERS
Use a simple ASCII headers.
MSG_DIGEST
Generate message digests for binary data validation.
MSG_NODIGEST
Do not generate message digests (default).
PARSE_BRACKETS
Do not convert bracketed strings to text fields (default).
PARSE_LIBERAL_BRACKETS
Do not convert bracketed strings to text fields (default).
PARSE_NOBRACKETS
Convert bracketed strings to text fields (default).
PARSE_TRIPLE_QUOTES
Do not convert triple-quoted strings to text fields (default).
PARSE_NOTRIPLE_QUOTES
Convert triple-quoted strings to text fields (default).
PAD_1K
Pad binary sections with 1023 nulls.
PAD_2K
Pad binary sections with 2047 nulls.
PAD_4K
Pad binary sections with 4095 nulls.
Note that on output, the types "prns&, "brcs" and "bkts" will be
converted to "text" fields if PARSE_NOBRACKETS has been set flags,
and that the types "tsqs" and "tdqs" will
be converted to "text" fields if the flag PARSE_NOTRIPLE_QUOTES has been set in the
flags. It is an error to set PARSE_NOBRACKETS and to set either PARSE_BRACKETS or
PARSE_LIBERAL_BRACKETS. It is an error to set both PARSE_NOTRIPLE_QUOTES and PARSE_TRIPLE_QUOTES.
encoding selects the type of encoding used for binary sections and the type of line-termination in
imgCIF files. The value can be a logical OR of any of:
ENC_BASE64
Use BASE64 encoding (default).
ENC_QP
Use QUOTED-PRINTABLE encoding.
ENC_BASE8
Use BASE8 (octal) encoding.
ENC_BASE10
Use BASE10 (decimal) encoding.
ENC_BASE16
Use BASE16 (hexadecimal) encoding.
ENC_FORWARD
For BASE8, BASE10 or BASE16 encoding, map bytes to words
forward (1234) (default on little-endian machines).
ENC_BACKWARD
Map bytes to words backward (4321) (default on big-endian
machines).
ENC_CRTERM
Terminate lines with CR.
ENC_LFTERM
Terminate lines with LF (default).
ARGUMENTS
handle
CBF handle.
file
Pointer to a file descriptor.
readable
If non-0: this file is random-access
and readable and can be used as a buffer.
ciforcbf
Selects the format in which the
binary sections are written (CIF/CBF).
headers
Selects the type of header in CBF
binary sections and message digest generation.
encoding
Selects the type of encoding used
for binary sections and the type of line-termination
in imgCIF files.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_new_datablock (cbf_handle handle, const char *datablockname);
int cbf_new_saveframe (cbf_handle handle, const char *saveframename);
DESCRIPTION
cbf_new_datablock creates a new data block with name datablockname
and makes it the current data block.
cbf_new_saveframe creates a new save frame with name saveframename
within the current data block
and makes the new save frame the current save frame.
If a data block or save frame with this name already exists, the existing data block
or save frame
becomes the current data block or save frame.
ARGUMENTS
handle
CBF handle.
datablockname
The name of the new data block.
saveframename
The name of the new save frame.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_force_new_datablock (cbf_handle handle,
const char *datablockname);
int cbf_force_new_saveframe (cbf_handle handle,
const char *saveframename);
DESCRIPTION
cbf_force_new_datablock creates a new data block with name datablockname
and makes it the current data block. Duplicate data block names are allowed.
cbf_force_new_saveframe creates a new savew frame with name saveframename
and makes it the current save frame. Duplicate save frame names are allowed.
Even if a save frame with this name already exists, a new save frame
is created and becomes the current save frame.
ARGUMENTS
handle
CBF handle.
datablockname
The name of the new data block.
saveframename
The name of the new save frame.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_force_new_category (cbf_handle handle, const char *categoryname);
DESCRIPTION
cbf_force_new_category creates a new category in the current data block with name categoryname
and makes it the current category. Duplicate category names are allowed.
Even if a category with this name already exists, a new category of
the same name is created and becomes the current category. The
allows for the creation of unlooped tag/value lists drawn from
the same category.
ARGUMENTS
handle
CBF handle.
categoryname
The name of the new category.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_insert_row (cbf_handle handle, unsigned int rownumber);
DESCRIPTION
cbf_insert_row adds a new row to the current category. The new row is inserted as
row rownumber
and existing rows starting from rownumber
are moved up by 1. The new row becomes the current row.
If the category has fewer than rownumber
rows, the function returns CBF_NOTFOUND.
The row numbers start from 0.
ARGUMENTS
handle
CBF handle.
rownumber
The row number of the new row.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_delete_row (cbf_handle handle, unsigned int rownumber);
DESCRIPTION
cbf_delete_row deletes a row from the current category. Rows starting from rownumber
+1 are moved down by 1. If the current row
was higher than rownumber, or if the current row is the last row, it will also move down by 1.
The row numbers start from 0.
ARGUMENTS
handle
CBF handle.
rownumber
The number of the row to delete.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_set_datablockname (cbf_handle handle, const char *datablockname);
int cbf_set_saveframename (cbf_handle handle, const char *saveframename);
DESCRIPTION
cbf_set_datablockname changes the name of the current data block to datablockname.
cbf_set_saveframename changes the name of the current save frame to saveframename.
If a data block or save frame with this name already exists (comparison is case-insensitive), the
function returns CBF_IDENTICAL.
ARGUMENTS
handle
CBF handle.
datablockname
The new data block name.
datablockname
The new save frame name.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_rewind_category (cbf_handle handle);
int cbf_rewind_saveframe (cbf_handle handle);
int cbf_rewind_blockitem (cbf_handle handle, CBF_NODETYPE * type);
DESCRIPTION
cbf_rewind_category makes the first category in the current data block the current
category.
cbf_rewind_saveframe makes the first saveframe in the current data block the current
saveframe.
cbf_rewind_blockitem makes the first blockitem (category or saveframe) in the current data block the current
blockitem. The type of the blockitem (CBF_CATEGORY or CBF_SAVEFRAME) is returned in type.
If there are no categories, saveframes or blockitems the function returns CBF_NOTFOUND.
The current column and row become undefined.
ARGUMENTS
handle
CBF handle.
type
CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_find_nextrow (cbf_handle handle, const char *value);
DESCRIPTION
cbf_find_nextrow makes the makes the next row in the current column
with value value the current row. The search starts from the
row following the last row found with cbf_find_row or cbf_find_nextrow,
or from the current row if the current row was defined using any other
function.
The comparison is case-sensitive.
If no more matching rows exist, the function returns CBF_NOTFOUND.
The current column is not affected.
ARGUMENTS
handle
CBF handle.
value
the value to search for.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_value (cbf_handle handle, const char **value);
int cbf_require_value (cbf_handle handle, const char **value, const char *defaultvalue );
DESCRIPTION
cbf_get_value sets *value
to point to the ASCII value of the item at the current column and row.
cbf_require_value sets *value
to point to the ASCII value of the item at the current column and row,
creating the data item if necessary
and initializing it to a copy of defaultvalue.
If the value is not ASCII, the function returns CBF_BINARY.
The value will be valid as long as the item exists and has not been set to a new value.
The value must not be modified by the program in any way.
ARGUMENTS
handle
CBF handle.
value
Pointer to the destination value pointer.
defaultvalue
Default value character string.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_typeofvalue (cbf_handle handle, const char **typeofvalue);
DESCRIPTION
cbf_get_value sets *typeofvalue
to point an ASCII descriptor of the value of the item at the current column and row.
The strings that may be returned are:
"null"
for a null value indicated by a "." or a "?"
"bnry"
for a binary value
"word"
for an unquoted string
"dblq"
for a double-quoted string
"sglq"
for a single-quoted string
"text"
for a semicolon-quoted string (multiline text field)
"prns"
for a parenthesis-bracketed string (multiline text field)
"brcs"
for a brace-bracketed string (multiline text field)
"bkts"
for a square-bracket-bracketed string (multiline text field)
"tsqs"
for a treble-single-quote quoted string (multiline text field)
"tdqs"
for a treble-double-quote quoted string (multiline text field)
Not all types are valid for all type of CIF
files. In partcular the types "prns", "brcs", "bkts" were
introduced with DDLm and are not valid in DDL1 or DDL2 CIFS. The types "tsqs" and
"tdqs" are not formally part of the CIF syntax.
A field for which no value has been set sets
*typeofvalue to NULL rather than to the
string "null".
The typeofvalue must not be modified by the program in any way.
ARGUMENTS
handle
CBF handle.
typeofvalue
Pointer to the destination type-of-value string pointer.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_set_typeofvalue (cbf_handle handle, const char *typeofvalue);
DESCRIPTION
cbf_set_typeofvalue
sets the type of the item at the current column and row to the type specified by
the ASCII character string given by typeofvalue. The strings that may be used
are:
"null"
for a null value indicated by a "." or a "?"
"bnry"
for a binary value
"word"
for an unquoted string
"dblq"
for a double-quoted string
"sglq"
for a single-quoted string
"text"
for a semicolon-quoted string (multiline text field)
"prns"
for a parenthesis-bracketed string (multiline text field)
"brcs"
for a brace-bracketed string (multiline text field)
"bkts"
for a square-bracket-bracketed string (multiline text field)
"tsqs"
for a treble-single-quote quoted string (multiline text field)
"tdqs"
for a treble-double-quote quoted string (multiline text field)
Not all types may be used for all values. Not all types are valid for all type of CIF
files. In partcular the types "prns", "brcs", "bkts" were
introduced with DDLm and are not valid in DDL1 or DDL2 CIFS. The types "tsqs" and
"tdqs" are not formally part of the CIF syntax. No changes may be made to the
type of binary values. You may not set the type of a string that contains a single quote
followed by a blank or a tab or which contains multiple lines to "sglq". You may
not set the type of a string that contains a double quote followed by a
blank or a tab or which contains multiple lines to "dblq".
ARGUMENTS
handle
CBF handle.
typeofvalue
ASCII string for desired type of value.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_integervalue (cbf_handle handle, int *number);
int cbf_require_integervalue (cbf_handle handle, int *number, int defaultvalue);
DESCRIPTION
cbf_get_integervalue sets *number
to the value of the ASCII item at the current column and row interpreted as a decimal
integer.
cbf_require_integervalue sets *number
to the value of the ASCII item at the current column and row interpreted as a decimal
integer, setting it to defaultvalue if necessary.
If the value is not ASCII, the function returns CBF_BINARY.
ARGUMENTS
handle
CBF handle.
number
pointer to the number.
defaultvalue
default number value.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_doublevalue (cbf_handle handle, double *number);
int cbf_require_doublevalue (cbf_handle handle, double *number, double defaultvalue);
DESCRIPTION
cbf_get_doublevalue sets *number
to the value of the ASCII item at the current column and row interpreted as a decimal
floating-point number.
cbf_require_doublevalue sets *number
to the value of the ASCII item at the current column and row interpreted as a decimal
floating-point number, setting it to defaultvalue if necessary.
If the value is not ASCII, the function returns CBF_BINARY.
ARGUMENTS
handle
CBF handle.
number
Pointer to the destination number.
defaultvalue
default number value.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_set_doublevalue (cbf_handle handle,
const char *format, double number);
DESCRIPTION
cbf_set_doublevalue sets the item at the current column and
row to the floating-point value number
written as an ASCII string with the format specified by
format as appropriate for the printf function.
ARGUMENTS
handle
CBF handle.
format
Format for the number.
number
Floating-point value.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_integerarrayparameters (cbf_handle handle,
unsigned int *compression,
int *binary_id,
size_t *elsize,
int *elsigned, int *elunsigned,
size_t *elements,
int *minelement, int *maxelement);
int cbf_get_integerarrayparameters_wdims (cbf_handle handle,
unsigned int *compression,
int *binary_id,
size_t *elsize,
int *elsigned, int *elunsigned,
size_t *elements,
int *minelement, int *maxelement,
const char **byteorder,
size_t *dimfast,
size_t *dimmid,
size_t *dimslow,
size_t *padding);
int cbf_get_integerarrayparameters_wdims_fs (cbf_handle handle,
unsigned int *compression,
int *binary_id,
size_t *elsize,
int *elsigned, int *elunsigned,
size_t *elements,
int *minelement, int *maxelement,
const char **byteorder,
size_t *dimfast,
size_t *dimmid,
size_t *dimslow,
size_t *padding);
int cbf_get_integerarrayparameters_wdims_sf (cbf_handle handle,
unsigned int *compression,
int *binary_id,
size_t *elsize,
int *elsigned, int *elunsigned,
size_t *elements,
int *minelement, int *maxelement,
const char **byteorder,
size_t *dimslow,
size_t *dimmid,
size_t *dimfast,
size_t *padding);
int cbf_get_realarrayparameters (cbf_handle handle,
unsigned int *compression,
int *binary_id,
size_t *elsize,
size_t *elements);
int cbf_get_realarrayparameters_wdims (cbf_handle handle,
unsigned int *compression,
int *binary_id,
size_t *elsize,
size_t *elements,
const char **byteorder,
size_t *dimfast,
size_t *dimmid,
size_t *dimslow,
size_t *padding);
int cbf_get_realarrayparameters_wdims_fs (cbf_handle handle,
unsigned int *compression,
int *binary_id,
size_t *elsize,
size_t *elements,
const char **byteorder,
size_t *dimfast,
size_t *dimmid,
size_t *dimslow,
size_t *padding);
int cbf_get_realarrayparameters_wdims_sf (cbf_handle handle,
unsigned int *compression,
int *binary_id,
size_t *elsize,
size_t *elements,
const char **byteorder,
size_t *dimslow,
size_t *dimmid,
size_t *dimfast,
size_t *padding);
DESCRIPTION
cbf_get_integerarrayparameters sets *compression,
*binary_id, *elsize,
*elsigned, *elunsigned,
*elements, *minelement
and *maxelement
to values read from the binary value of the item at the
current column and row.
This provides all the arguments needed for a subsequent call to
cbf_set_integerarray,
if a copy of the array is to be made into another CIF or CBF.
cbf_get_realarrayparameters sets *compression,
*binary_id, *elsize,
*elements
to values read from the binary value of the item at the
current column and row.
This provides all the arguments needed for a subsequent call to
cbf_set_realarray,
if a copy of the arry is to be made into another CIF or CBF.
The variants cbf_get_integerarrayparameters_wdims, cbf_get_integerarrayparameters_wdims_fs, cbf_get_integerarrayparameters_wdims_sf,
cbf_get_realarrayparameters_wdims, cbf_get_realarrayparameters_wdims_fs, cbf_get_realarrayparameters_wdims_sf set **byteorder,
*dimfast,
*dimmid,
*dimslow,
and *padding as well, providing the additional parameters
needed for a subsequent call to cbf_set_integerarray_wdims
or cbf_set_realarray_wdims.
The value returned in *byteorder is a pointer either
to the string "little_endian" or to the string "big_endian".
This should be the byte order of the data, not necessarily
of the host machine.
No attempt should be made to modify this string. At this
time only "little_endian" will be returned.
The values returned in *dimfast, *dimmid and *dimslow
are the sizes of the fastest changing, second fastest
changing and third fastest changing dimensions of the
array, if specified, or zero, if not specified.
The value returned in *padding is the size of
the post-data padding, if any and if specified in the data
header. The value is given as a count of octets.
If the value is not binary, the function returns CBF_ASCII.
ARGUMENTS
handle
CBF handle.
compression
Compression method used.
elsize
Size in bytes of each array element.
binary_id
Pointer to the destination integer binary identifier.
elsigned
Pointer to an integer. Set to 1 if the elements can be read as signed integers.
elunsigned
Pointer to an integer. Set to 1 if the elements can be read as unsigned
integers.
elements
Pointer to the destination number of elements.
minelement
Pointer to the destination smallest element.
maxelement
Pointer to the destination largest element.
byteorder
Pointer to the destination byte order.
dimfast
Pointer to the destination fastest dimension.
dimmid
Pointer to the destination second fastest dimension.
dimslow
Pointer to the destination third fastest dimension.
padding
Pointer to the destination padding size.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_integerarray (cbf_handle handle,
int *binary_id,
void *array, size_t elsize, int elsigned,
size_t elements, size_t *elements_read);
int cbf_get_realarray (cbf_handle handle,
int *binary_id,
void *array, size_t elsize,
size_t elements, size_t *elements_read);
DESCRIPTION
cbf_get_integerarray reads the binary value of the item at the current
column and row into an integer array. The array consists of
elements elements of elsize bytes each, starting at
array. The elements are signed if elsigned
is non-0 and unsigned otherwise. *binary_id
is set to the binary section identifier and *elements_read
to the number of elements actually read.
cbf_get_realarray reads the binary value of the item at the current
column and row into a real array. The array consists of
elements elements of elsize bytes each, starting at
array. *binary_id
is set to the binary section identifier and *elements_read
to the number of elements actually read.
If any element in the integer binary data cant fit into the destination
element, the destination is set the nearest possible value.
If the value is not binary, the function returns CBF_ASCII.
If the requested number of elements cant be read, the function
will read as many as
it can and then return CBF_ENDOFDATA.
Currently, the destination array must consist of chars,
shorts or ints (signed or unsigned). If elsize
is not equal to sizeof (char), sizeof (short) or sizeof (int), for cbf_get_integerarray, or
sizeof(double) or sizeof(float), for cbf_get_realarray the
function returns
CBF_ARGUMENT.
An additional restriction in the current version of CBFlib is that values too large
to fit in an int are not correctly decompressed. As an example, if the machine with
32-bit ints is reading an array containing a value outside the range
0 .. 2^32-1 (unsigned) or -2^31 .. 2^31-1
(signed), the array will not be correctly decompressed. This
restriction will be removed in a future release. For cbf_get_realarray, only
IEEE format is supported. No conversion to other floating point formats
is done at this time.
ARGUMENTS
handle
CBF handle.
binary_id
Pointer to the destination
integer binary identifier.
array
Pointer to the destination array.
elsize
Size in bytes of each
destination array element.
elsigned
Set to non-0 if the
destination array elements are signed.
elements
The number of elements to read.
elements_read
Pointer to the
destination number of elements actually read.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
int cbf_set_integerarray (cbf_handle handle,
unsigned int compression,
int binary_id,
void *array, size_t elsize, int elsigned,
size_t elements);
int cbf_set_integerarray_wdims (cbf_handle handle,
unsigned int compression,
int binary_id,
void *array, size_t elsize, int elsigned,
size_t elements, const char *byteorder,
size_t dimfast, size_t dimmid,
size_t dimslow, size_t padding);
int cbf_set_integerarray_wdims_fs (cbf_handle handle,
unsigned int compression,
int binary_id,
void *array, size_t elsize, int elsigned,
size_t elements, const char *byteorder,
size_t dimfast, size_t dimmid,
size_t dimslow, size_t padding);
int cbf_set_integerarray_wdims_sf (cbf_handle handle,
unsigned int compression,
int binary_id,
void *array, size_t elsize, int elsigned,
size_t elements, const char *byteorder,
size_t dimslow, size_t dimmid,
size_t dimfast, size_t padding);
int cbf_set_realarray (cbf_handle handle,
unsigned int compression,
int binary_id,
void *array, size_t elsize,
size_t elements);
int cbf_set_realarray_wdims (cbf_handle handle,
unsigned int compression,
int binary_id,
void *array, size_t elsize,
size_t elements, const char *byteorder,
size_t dimfast, size_t dimmid,
size_t dimslow, size_t padding);
int cbf_set_realarray_wdims_fs (cbf_handle handle,
unsigned int compression,
int binary_id,
void *array, size_t elsize,
size_t elements, const char *byteorder,
size_t dimfast, size_t dimmid,
size_t dimslow, size_t padding);
int cbf_set_realarray_wdims_sf (cbf_handle handle,
unsigned int compression,
int binary_id,
void *array, size_t elsize,
size_t elements, const char *byteorder,
size_t dimslow, size_t dimmid,
size_t dimfast, size_t padding);
DESCRIPTION
cbf_set_integerarray sets the binary value of the item at the current
column and row to an integer array.
The array consists of elements
elements of elsize
bytes each, starting at array. The elements
are signed if elsigned
is non-0 and unsigned otherwise. binary_id
is the binary section identifier.
cbf_set_realarray sets the binary value of the item at the current
column and row to an integer array.
The array consists of elements
elements of elsize
bytes each, starting at array. binary_id
is the binary section identifier.
The cbf_set_integerarray_wdims, cbf_set_integerarray_wdims_fs, cbf_set_integerarray_wdims_sf,
cbf_set_realarray_wdims, cbf_set_realarray_wdims_fs and cbf_set_realarray_wdims_sf variants
allow the data header values of byteorder,
dimfast, dimmid, dimslow and padding
to be set to the data byte order, the fastest,
second fastest and third fastest array dimensions and
the size in byte of the post data padding to be used.
The array will be compressed using the compression scheme specifed
by compression. Currently, the available schemes are:
CBF_CANONICAL
Canonical-code compression (section 3.3.1)
CBF_PACKED
CCP4-style packing (section 3.3.2)
CBF_PACKED_V2
CCP4-style packing, version 2 (section 3.3.2)
CBF_BYTE_OFFSET
Simple "byte_offset" compression.
CBF_NONE
No compression. NOTE: This scheme is by
far the slowest of the four and uses much more disk space. It is
intended for routine use with small arrays only. With large arrays
(like images) it should be used only for debugging.
The values compressed are limited to 64 bits. If any element in the array is larger
than 64 bits, the value compressed is the nearest 64-bit value.
Currently, the source array must consist of chars, shorts or ints (signed or unsigned),
for cbf_set_integerarray, or IEEE doubles or floats for cbf_set_realarray.
If elsize
is not equal to sizeof (char), sizeof (short) or sizeof (int), the function returns
CBF_ARGUMENT.
ARGUMENTS
handle
CBF handle.
compression
Compression method to use.
binary_id
Integer binary identifier.
array
Pointer to the source array.
elsize
Size in bytes of each source array element.
elsigned
Set to non-0 if the source array elements are signed.
elements: The number of elements in the array.
RETURN VALUE
Returns an error code on failure or 0 for success.
cbf_failnez is a macro used for error propagation throughout CBFlib. cbf_failnez
executes the function f
and saves the returned error value. If the error value is non-0, cbf_failnez executes
a return with the error value as argument. If CBFDEBUG is defined, then a report of
the error is also printed to the standard error stream, stderr, in the form
CBFlib error f in "symbol"
where f is the decimal value of the error and symbol is the symbolic
form.
cbf_onfailnez is a macro used for error propagation throughout CBFlib.
cbf_onfailnez executes the function f
and saves the returned error value. If the error value is non-0,
cbf_failnez executes first the statement c
and then a return with the error value as argument. If CBFDEBUG is defined,
then a report of
the error is also printed to the standard error stream, stderr, in the form
CBFlib error f in "symbol"
where f is the decimal value of the error and symbol is the symbolic
form.
int cbf_require_category (cbf_handle handle,
const char *categoryname);
DESCRIPTION
cbf_rewuire_category makes the category in the current data block with
name categoryname the current category, if it exists, or creates
the catagory if it does not exist.
The comparison is case-insensitive.
The current column and row become undefined.
ARGUMENTS
handle
CBF handle.
categoryname
The name of the category to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
cbf_require_column_doublevalue
sets *value
to the ASCII item at the current row for the column given
with the name given by *columnname, or to the string
given by defaultvalue if the
item cannot be found.
ARGUMENTS
handle
CBF handle.
columnname
Name of the column containing the number.
value
pointer to the location to receive the value.
defaultvalue
Value to use if the requested
column and value cannot be found.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_require_column_integervalue (cbf_handle handle,
const char *columnname,
int *number,
const int defaultvalue);
DESCRIPTION
cbf_require_column_doublevalue
sets *number
to the value of the ASCII item at the current row for the column given
with the name given by *columnname, with the value interpreted as an
integer number, or to the number given by defaultvalue if the
item cannot be found.
ARGUMENTS
handle
CBF handle.
columnname
Name of the column containing the number.
number
pointer to the location to receive the integer value.
defaultvalue
Value to use if the requested
column and value cannot be found.
RETURN VALUE
Returns an error code on failure or 0 for success.
cbf_require_column_doublevalue
sets *number
to the value of the ASCII item at the current row for the column given
with the name given by *columnname, with the value interpreted as a decimal
floating-point number, or to the number given by defaultvalue if the
item cannot be found.
ARGUMENTS
handle
CBF handle.
columnname
Name of the column containing the number.
number
pointer to the location to receive the floating-point value.
defaultvalue
Value to use if the requested
column and value cannot be found.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_local_integer_byte_order (char ** byte_order);
int cbf_get_local_real_byte_order (char ** byte_order);
int cbf_get_local_real_format (char ** real_format );
DESCRIPTION
cbf_get_local_integer_byte_order returns the byte order of integers
on the machine on which the API is being run in the form of a character string
returned as the value pointed to by byte_order. cbf_get_local_real_byte_order
returns the byte order of reals on the machine on which the API is being run
in the form of a character string returned as the value pointed to by byte_order.
cbf_get_local_real_format returns the format of floats on the machine on which
the API is being run in the form of a character string returned as the value pointed to by
real_format. The strings returned must not be modified in any way.
The values returned in byte_order may be the strings "little_endian"
or "big-endian". The values returned in real_format may be the strings
"ieee 754-1985" or "other". Additional values may be returned
by future versions of the API.
ARGUMENTS
byte_order
pointer to the returned string
real_format
pointer to the returned string
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_dictionary (cbf_handle handle, cbf_handle * dictionary);
int cbf_set_dictionary (cbf_handle handle, cbf_handle dictionary_in);
int cbf_require_dictionary (cbf_handle handle, cbf_handle * dictionary)
DESCRIPTION
cbf_get_dictionary sets *dictionary to the handle of a CBF which has been
associated with the CBF handle by cbf_set_dictionary. cbf_set_dictionary
associates the CBF handle dictionary_in with handle as its dictionary.
cbf_require_dictionary sets *dictionary to the handle of a CBF which has been
associated with the CBF handle by cbf_set_dictionary or creates a new
empty CBF and associates it with handle, returning the new handle in
*dictionary.
ARGUMENTS
handle
CBF handle.
dictionary
Pointer to CBF handle of dictionary.
dictionary_in
CBF handle of dcitionary.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_convert_dictionary (cbf_handle handle, cbf_handle dictionary )
DESCRIPTION
cbf_convert_dictionary converts dictionary as a DDL1 or DDL2 dictionary to
a CBF dictionary of category and item properties for handle, creating
a new dictionary if none exists or layering the definitions in dictionary
onto the existing dictionary of handle if one exists.
If a CBF is read into handle after calling cbf_convert_dictionary, then
the dictionary will be used for validation of the CBF as it is read.
ARGUMENTS
handle
CBF handle.
dictionary
CBF handle of dictionary.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_find_tag (cbf_handle handle, const char *tag)
int cbf_find_local_tag (cbf_handle handle, const char *tag)
DESCRIPTION
cbf_find_tag searches all of the CBF handle for the CIF tag given
by the string tag and makes it the current tag. The search does
not include the dictionary, but does include save frames as well as
categories.
The string tag is the complete tag in either DDL1 or DDL2 format,
starting with the leading underscore, not just a category or column.
ARGUMENTS
handle
CBF handle.
tag
CIF tag.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_find_category_root (cbf_handle handle, const char* categoryname,
const char** categoryroot);
int cbf_set_category_root (cbf_handle handle, const char* categoryname_in,
const char*categoryroot);
int cbf_require_category_root (cbf_handle handle, const char* categoryname,
const char** categoryroot);
DESCRIPTION
cbf_find_category_root sets *categoryroot to the root category
of which categoryname is an alias. cbf_set_category_root
sets categoryname_in as an alias of categoryroot in the
dictionary associated with handle, creating the dictionary
if necessary. cbf_require_category_root sets *categoryroot
to the root category of which categoryname is an alias, if
there is one, or to the value of categoryname, if
categoryname is not an alias.
A returned categoryroot string must not be modified in any way.
ARGUMENTS
handle
CBF handle.
categoryname
category name which may be an alias.
categoryroot
pointer to a returned category root name.
categoryroot_in
input category root name.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_find_tag_root (cbf_handle handle, const char* tagname,
const char** tagroot);
int cbf_set_tag_root (cbf_handle handle, const char* tagname,
const char*tagroot_in);
int cbf_require_tag_root (cbf_handle handle, const char* tagname,
const char** tagroot);
DESCRIPTION
cbf_find_tag_root sets *tagroot to the root tag
of which tagname is an alias. cbf_set_tag_root
sets tagname as an alias of tagroot_in in the
dictionary associated with handle, creating the dictionary
if necessary. cbf_require_tag_root sets *tagroot
to the root tag of which tagname is an alias, if
there is one, or to the value of tagname, if
tagname is not an alias.
A returned tagroot string must not be modified in any way.
ARGUMENTS
handle
CBF handle.
tagname
tag name which may be an alias.
tagroot
pointer to a returned tag root name.
tagroot_in
input tag root name.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_find_tag_category (cbf_handle handle, const char* tagname,
const char** categoryname);
int cbf_set_tag_category (cbf_handle handle, const char* tagname,
const char* categoryname_in);
DESCRIPTION
cbf_find_tag_category sets categoryname to the category associated
with tagname in the dictionary associated with handle.
cbf_set_tag_category upddates the dictionary associated with handle
to indicated that tagname is in category categoryname_in.
ARGUMENTS
handle
CBF handle.
tagname
tag name.
categoryname
pointer to a returned category name.
categoryname_in
input category name.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_diffrn_id (cbf_handle handle, const char **diffrn_id);
int cbf_require_diffrn_id (cbf_handle handle, const char **diffrn_id, const char *default_id)
DESCRIPTION
cbf_get_diffrn_id sets *diffrn_id to point to the ASCII value of the
"diffrn.id" entry.
cbf_require_diffrn_id also sets *diffrn_id to point to the ASCII value of the
"diffrn.id" entry, but, if the "diffrn.id" entry does not exist,
it sets the value in the CBF and in*diffrn_id to the character string given by
default_id, creating the category and column is necessary.
The diffrn_id will be valid as long as the item exists and has not been set to a new value.
The diffrn_id must not be modified by the program in any way.
ARGUMENTS
handle
CBF handle.
diffrn_id
Pointer to the destination value pointer.
default_id
Character string default value.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_set_diffrn_id (cbf_handle handle, const char *diffrn_id);
DESCRIPTION
cbf_set_diffrn_id sets the "diffrn.id" entry of the current datablock to the ASCII value diffrn_id.
This function also changes corresponding "diffrn_id" entries in the "diffrn_source", "diffrn_radiation", "diffrn_detector" and "diffrn_measurement" categories.
ARGUMENTS
handle
CBF handle.
diffrn_id
ASCII value.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_element_id (cbf_handle handle, unsigned int element_number, const char **element_id);
DESCRIPTION
cbf_get_element_id sets *element_id to point to the ASCII value of the element_number'th "diffrn_data_frame.detector_element_id" entry, counting from 0.
If the detector element does not exist, the function returns CBF_NOTFOUND.
The element_id will be valid as long as the item exists and has not been set to a new value.
The element_id must not be modified by the program in any way.
ARGUMENTS
handle
CBF handle.
element_number
The number of the detector element counting from 0 by order of appearance in the "diffrn_data_frame" category.
element_id
Pointer to the destination.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_set_integration_time (cbf_handle handle, unsigned int reserved, double time);
DESCRIPTION
cbf_set_integration_time sets the integration time in seconds to the value specified by time. The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle
CBF handle.
reserved
Unused. Any value other than 0 is invalid.
time Integration
time in seconds.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_timestamp (cbf_handle handle, unsigned int reserved, double *time, int *timezone);
DESCRIPTION
cbf_get_timestamp sets *time to the collection timestamp in seconds since January 1 1970. *timezone is set to timezone difference from UTC in minutes. The parameter reserved is presently unused and should be set to 0.
Either of the destination pointers may be NULL.
ARGUMENTS
handle
CBF handle.
reserved
Unused. Any value other than 0 is invalid.
time
Pointer to the destination collection timestamp.
timezone
Pointer to the destination timezone difference.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_set_timestamp (cbf_handle handle, unsigned int reserved, double time, int timezone,
double precision);
DESCRIPTION
cbf_set_timestamp sets the collection timestamp in seconds since January 1 1970 to the value specified by time. The timezone difference from UTC in minutes is set to timezone. If no timezone is desired, timezone should be CBF_NOTIM
EZONE. The parameter reserved is presently unused and should be set to 0.
The precision of the new timestamp is specified by the value precision in seconds. If precision is 0, the saved timestamp is assumed accurate to 1 second.
ARGUMENTS
handle
CBF handle.
reserved
Unused. Any value other than 0 is invalid.
time
Timestamp in seconds since January 1 1970.
timezone
Timezone difference from UTC in minutes or CBF_NOTIMEZONE.
precision
Timestamp precision in seconds.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_datestamp (cbf_handle handle, unsigned int reserved, int *year, int *month, int *day,
int *hour, int *minute, double *second, int *timezone);
DESCRIPTION
cbf_get_datestamp sets *year, *month, *day, *hour, *minute and *second to the corresponding values of the collection timestamp. *timezone is set to timezone difference from UTC in minutes. The parameter <
i>reserved
is presently unused and should be set to 0.
Any of the destination pointers may be NULL.
ARGUMENTS
handle
CBF handle.
reserved
Unused. Any value other than 0 is invalid.
year
Pointer to the destination timestamp year.
month
Pointer to the destination timestamp month (1-12).
day
Pointer to the destination timestamp day (1-31).
hour
Pointer to the destination timestamp hour (0-23).
minute
Pointer to the destination timestamp minute (0-59).
second
Pointer to the destination timestamp second (0-60.0).
timezone
Pointer to the destination timezone difference from UTC in minutes.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_set_datestamp (cbf_handle handle, unsigned int reserved, int year, int month, int day, int hour,
int minute, double second, int timezone, double precision);
DESCRIPTION
cbf_set_datestamp sets the collection timestamp in seconds since January 1 1970 to the value specified by time. The timezone difference from UTC in minutes is set to timezone. If no timezone is desired, timezone should be CBF_NOTIM
EZONE. The parameter reserved is presently unused and should be set to 0.
The precision of the new timestamp is specified by the value precision in seconds. If precision is 0, the saved timestamp is assumed accurate to 1 second.
ARGUMENTS
handle
CBF handle.
reserved
Unused. Any value other than 0 is invalid.
time
Timestamp in seconds since January 1 1970.
timezone
Timezone difference from UTC in minutes or CBF_NOTIMEZONE.
precision
Timestamp precision in seconds.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_set_current_timestamp (cbf_handle handle, unsigned int reserved, int timezone);
DESCRIPTION
cbf_set_current_timestamp sets the collection timestamp to the current time. The timezone difference from UTC in minutes is set to timezone. If no timezone is desired, timezone should be CBF_NOTIMEZONE. If no timezone is used, the timest
amp will be UTC. The parameter reserved is presently unused and should be set to 0.
The new timestamp will have a precision of 1 second.
ARGUMENTS
handle
CBF handle.
reserved
Unused. Any value other than 0 is invalid.
timezone
Timezone difference from UTC in minutes or CBF_NOTIMEZONE.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_image_size (cbf_handle handle, unsigned int reserved, unsigned int element_number,
size_t *ndimslow, size_t *ndimfast);
int cbf_get_image_size_fs (cbf_handle handle, unsigned int reserved, unsigned int element_number,
size_t *ndimfast, size_t *ndimslow);
int cbf_get_image_size_sf (cbf_handle handle, unsigned int reserved, unsigned int element_number,
size_t *ndimslow, size_t *ndimfast);
int cbf_get_3d_image_size (cbf_handle handle, unsigned int reserved, unsigned int element_number,
size_t *ndimslow, size_t *ndimmid, size_t *ndimfast);
int cbf_get_3d_image_size_fs (cbf_handle handle, unsigned int reserved, unsigned int element_number,
size_t *ndimfast, size_t *ndimmid, size_t *ndimslow);
int cbf_get_3d_image_size_sf (cbf_handle handle, unsigned int reserved, unsigned int element_number,
size_t *ndimslow, size_t *ndimmid, size_t *ndimfast);
DESCRIPTION
cbf_get_image_size, cbf_get_image_size_fs and cbf_get_image_size_sf set *ndimslow and *ndimfast to the slow and fast dimensions of the image array
for element number element_number. If the array is 1-dimensional, *ndimslow will be set
to the array size and *ndimfast will be set to 1. If the array is 3-dimensional an error code
will be returned.
cbf_get_3d_image_size, cbf_get_3d_image_size_fs and cbf_get_3d_image_size_sf set
*ndimslow, *ndimmid and *ndimfast to the slowest, next fastest and
fastest dimensions, respectively, of the 3D image array for element number element_number. If the
array is 1-dimensional, *ndimslow will be set to the array size and *ndimmid and *ndimfast
will be set to 1. If the array is 2-dimensional *ndimslow and *ndimmid will be set as for
a call to cbf_get_image_size and *ndimfast will be set to 1.
The _fs calls give the dimensions in a fast-to-slow order. The calls with no suffix and the
calls _sf calls give the dimensions in slow-to-fast order
Note that the ordering of dimensions is specified by values of the tag _array_structure_list.precedence
with a precedence of 1 for the fastest dimension, 2 for the next slower, etc., which is opposite to the
ordering of the dimension arguments for these functions, except for the ones with the _fs suffix..
Any of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle
CBF handle.
reserved
Unused. Any value other than 0 is invalid.
element_number
The number of the detector element counting from 0 by order of appearance in the "diffrn_data_frame" category.
ndimslow
Pointer to the destination slowest dimension.
ndimmid
Pointer to the destination next faster dimension.
ndimfast
Pointer to the destination fastest dimension.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, int elsign, size_t ndimslow, size_t ndimfast);
int cbf_get_image_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, int elsign, size_t ndimfast, size_t ndimslow);
int cbf_get_image_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, int elsign, size_t ndimslow, size_t ndimfast);
int cbf_get_real_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, size_t ndimslow, size_t ndimfast);
int cbf_get_real_image_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, size_t ndimfast, size_t ndimslow);
int cbf_get_real_image_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, size_t ndimslow, size_t ndimfast);
int cbf_get_3d_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, int elsign, size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_get_3d_image_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, int elsign, size_t ndimfast, size_t ndimmid, size_t ndimslow);
int cbf_get_3d_image_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, int elsign, size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_get_real_3d_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_get_real_3d_image_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, size_t ndimfast, size_t ndimmid, size_t ndimslow);
int cbf_get_real_3d_image_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array,
size_t elsize, size_t ndimslow, size_t ndimmid, size_t ndimfast);
DESCRIPTION
cbf_get_image, cbf_get_image_fs and cbf_get_image_sf read the image array for element number element_number into an array.
The array consists of ndimslow×ndimfast elements of elsize bytes each, starting at array.
The elements are signed if elsign is non-0 and unsigned otherwise. cbf_get_real_image,
cbf_get_real_image_fs and cbf_get_real_image_sf
read the image array of IEEE doubles or floats for element number element_number
into an array. A real array is always signed.
cbf_get_3d_image, cbf_get_3d_image_fs and cbf_get_3d_image_sf read the 3D image array for element number element_number into an array.
The array consists of ndimslow×ndimmid×ndimfast elements of elsize bytes each,
starting at array.
The elements are signed if elsign is non-0 and unsigned otherwise. cbf_get_real_3d_image, cbf_get_real_3d_image_fs, cbf_get_real_3d_image_sf
reads the 3D image array of IEEE doubles or floats for element number element_number
into an array. A real array is always signed.
The _fs calls give the dimensions in a fast-to-slow order. The calls with no suffix and the
calls _sf calls give the dimensions in slow-to-fast order
The structure of the array as a 1-, 2- or 3-dimensional array should agree with the
structure of the array given in the ARRAY_STRUCTURE_LIST category.
If the array is 1-dimensional, ndimslow should be the array size and ndimfast and, for
the 3D calls, ndimmid, should be set to 1 both in the call and in the imgCIF
data being processed. If the array is 2-dimensional and a 3D call
is used, ndimslow and ndimmid should be the array dimensions and ndimfast
should be set to 1 both in the call and in the imgCIF
data being processed.
If any element in the binary data canÕt fit into the destination element, the
destination is set the nearest possible value.
If the value is not binary, the function returns CBF_ASCII.
If the requested number of elements canÕt be read, the function will read as many as it
can and then return CBF_ENDOFDATA.
Currently, the destination array must consist of chars, shorts or ints (signed or unsigned)
for cbf_get_image, or IEEE doubles or floats for cbf_get_real_image.
If elsize is not equal to sizeof (char), sizeof (short), sizeof (int), sizeof(double)
or sizeof(float), the function returns CBF_ARGUMENT.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle
CBF handle.
reserved
Unused. Any value other than 0 is invalid.
element_number
The number of the detector element counting from 0 by order of appearance in the "diffrn_data_frame" category.
array
Pointer to the destination array.
elsize
Size in bytes of each destination array element.
elsigned
Set to non-0 if the destination array elements are signed.
ndimslow
Slowest array dimension.
ndimmid
Next faster array dimension.
ndimfast
Fastest array dimension.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_set_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array, size_t elsize,
int elsign, size_t ndimslow, size_t ndimfast);
int cbf_set_image_fs(cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array, size_t elsize,
int elsign, size_t ndimfast, size_t ndimslow);
int cbf_set_image_sf(cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array, size_t elsize,
int elsign, size_t ndimslow, size_t ndimfast);
int cbf_set_real_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array,size_t elsize,
size_t ndimslow, size_t ndimfast);
int cbf_set_real_image_fs(cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array,size_t elsize,
size_t ndimfast, size_t ndimslow);
int cbf_set_real_image_sf(cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array,size_t elsize,
size_t ndimslow, size_t ndimfast);
int cbf_set_3d_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array, size_t elsize,
int elsign, size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_set_3d_image_fs(cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array, size_t elsize,
int elsign, size_t ndimfast, size_t ndimmid, size_t ndimslow);
int cbf_set_3d_image_sf(cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array, size_t elsize,
int elsign, size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_set_real_3d_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array,size_t elsize,
size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_set_real_3d_image_fs(cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array,size_t elsize,
size_t ndimfast, size_t ndimmid, size_t ndimslow);
int cbf_set_real_3d_image_sf(cbf_handle handle, unsigned int reserved,
unsigned int element_number,
unsigned int compression, void *array,size_t elsize,
size_t ndimslow, size_t ndimmid, size_t ndimfast);
DESCRIPTION
cbf_set_image, cbf_set_image_fs and cbf_set_image_sf write the image array for element number
element_number. The array
consists of ndimfast×ndimslow elements of elsize bytes each, starting
at array. The elements are signed if elsign is non-zero
and unsigned otherwise. cbf_set_real_image, cbf_set_real_image_fs and cbf_set_real_image_sf
write the image array for element number element_number. The array
consists of ndimfast×ndimslow IEEE double or float elements of elsize
bytes each, starting at array.
cbf_set_3d_image, cbf_set_3d_image_fs and cbf_set_3d_image_sf write the 3D image array for
element number element_number. The array
consists of ndimfast×ndimmid×ndimslow elements of elsize
bytes each, starting at array. The elements are signed if elsign is non-0
and unsigned otherwise. cbf_set_real_3d_image, cbf_set_real_3d_image_fs and cbf_set_real_3d_image_sf
writes the 3D image array for element number element_number. The array
consists of ndimfast×ndimmid×ndimslow IEEE double or float elements of elsize
bytes each, starting at array.
The _fs calls give the dimensions in a fast-to-slow order. The calls with no suffix and the
calls _sf calls give the dimensions in slow-to-fast order
If the array is 1-dimensional, ndimslow should be the array size and ndimfast and,
for the 3D calls, ndimmid, should be set to 1. If the array is 2-dimensional and
the 3D calls are used, ndimslow and ndimmid should be used for the array dimensions
and ndimfast should be set to 1.
The array will be compressed using the compression scheme specifed by compression. Currently,
the available schemes are:
CBF_CANONICAL
Canonical-code compression (section 3.3.1)
CBF_PACKED
CCP4-style packing (section 3.3.2)
CBF_PACKED_V2
CCP4-style packing, version 2 (section 3.3.2)
CBF_BYTE_OFFSET
Simple "byte_offset" compression.
CBF_NONE
No compression.
The values compressed are limited to 64 bits. If any element in the array is larger than 64 bits, the
value compressed is the nearest 64-bit value.
Currently, the source array must consist of chars, shorts or ints (signed or unsigned)for
cbf_set_image, or IEEE doubles or floats for cbf_set_real_image.
If elsize is not equal to sizeof (short), sizeof (int), sizeof(double)
or sizeof(float), the function returns CBF_ARGUMENT.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle
CBF handle.
reserved
Unused. Any value other than 0 is invalid.
element_number
The number of the detector element counting from 0 by order of appearance in the "diffrn_data_frame" category.
compression
Compression type.
array
Pointer to the image array.
elsize
Size in bytes of each image array element.
elsigned
Set to non-0 if the image array elements are signed.
ndimslow
Slowest array dimension.
ndimmid
Second slowest array dimension.
ndimfast
Fastest array dimension.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_construct_goniometer (cbf_handle handle, cbf_goniometer *goniometer);
DESCRIPTION
cbf_construct_goniometer constructs a goniometer object using the description in the CBF object handle and initialises the goniometer handle *goniometer.
ARGUMENTS
handle
CBF handle.
goniometer
Pointer to the destination goniometer handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
cbf_rotate_vector sets *final1, *final2, and *final3 to the 3 components of the of the vector (initial1, initial2, initial3) after reorientation by applying the goniometer rotations. The value ratio specif
ies the goniometer setting and varies from 0.0 at the beginning of the exposure to 1.0 at the end, irrespective of the actual rotation range.
Any of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
goniometer
Goniometer handle.
reserved
Unused. Any value other than 0 is invalid.
ratio
Goniometer setting. 0 = beginning of exposure, 1 = end.
initial1
x component of the initial vector.
initial2
y component of the initial vector.
initial3
z component of the initial vector.
vector1
Pointer to the destination x component of the final vector.
vector2
Pointer to the destination y component of the final vector.
vector3
Pointer to the destination z component of the final vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
cbf_get_reciprocal sets *reciprocal1, * reciprocal2, and * reciprocal3 to the 3 components of the of the reciprocal-space vector corresponding to the real-space vector (real1, real2, real3). The reciprocal-space
vector is oriented to correspond to the goniometer setting with all axes at 0. The value wavelength is the wavlength in Å and the value ratio specifies the current goniometer setting and varies from 0.0 at the beginning of the exposur
e to 1.0 at the end, irrespective of the actual rotation range.
Any of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
goniometer
Goniometer handle.
reserved
Unused. Any value other than 0 is invalid.
ratio
Goniometer setting. 0 = beginning of exposure, 1 = end.
wavelength
Wavelength in Å.
real1
x component of the real-space vector.
real2
y component of the real-space vector.
real3
z component of the real-space vector.
reciprocal1
Pointer to the destination x component of the reciprocal-space vector.
reciprocal2
Pointer to the destination y component of the reciprocal-space vector.
reciprocal3
Pointer to the destination z component of the reciprocal-space vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_construct_detector (cbf_handle handle, cbf_detector *detector, unsigned int element_number);
int cbf_construct_reference_detector (cbf_handle handle, cbf_detector *detector, unsigned int element_number);
int cbf_require_reference_detector (cbf_handle handle, cbf_detector *detector, unsigned int element_number);
DESCRIPTION
cbf_construct_detector constructs a detector object for detector element number element_number
using the description in the CBF object handle and initialises the detector handle *detector.
cbf_construct_reference_detector constructs a detector object for detector element number element_number
using the description in the CBF object handle and initialises the detector handle *detector using the
reference settings of the axes. cbf_require_reference_detector is similar, but try to force the
creations of missing intermediate categories needed to construct a detector object.
ARGUMENTS
handle
CBF handle.
detector
Pointer to the destination detector handle.
element_number
The number of the detector element counting from 0 by order of appearance in the "diffrn_data_frame" category.
RETURN VALUE
Returns an error code on failure or 0 for success.
cbf_get_beam_center sets *centerfast and *centerslow to the displacements in mm
along the detector axes from pixel (0, 0) to the point at which the beam intersects the
detector and *indexfast and *indexslow to the corresponding indices.
cbf_set_beam_center sets the offsets in the axis category for the detector element
axis with precedence 1 to place the beam center at the position given in mm by *centerfast
and *centerslow as the displacements in mm along the detector axes from pixel (0, 0)
to the point at which the beam intersects the detector at the indices given *indexfast and
*indexslow. cbf_set_reference_beam_center sets the displacments in the array_structure_list_axis
category to place the beam center at the position given in mm by *centerfast
and *centerslow as the displacements in mm along the detector axes from pixel (0, 0)
to the point at which the beam intersects the detector at the indices given by *indexfast and
*indexslow. In order to achieve consistent results, a reference detector should be used
for detector to have all axes at their reference settings.
Note that the precedence 1 axis is the fastest axis, so that *centerfast and *indexfast
are the fast axis components of the center and *centerslow and *indexslow are the
slow axis components of the center.
The _fs calls give the displacments in a fast-to-slow order. The calls with no suffix and the
calls _sf calls give the displacements in slow-to-fast order
Any of the destination pointers may be NULL for getting the beam center. For setting the beam
axis, either the indices of the center must not be NULL.
The indices are non-negative for beam centers within the detector surface, but the center for an axis with
a negative increment will be negative for a beam center within the detector surface.
For cbf_set_beam_center if the diffrn_data_frame category exists with a row for the corresponding element id,
the values will be set for _diffrn_data_frame.center_fast and _diffrn_data_frame.center_slow
in millimetres and the value of _diffrn_data_frame.center_units will be set to 'mm'.
For cbf_set_reference_beam_center if the diffrn_detector_element category exists with a row for the corresponding element id,
the values will be set for _diffrn_detector_element.reference_center_fast and _diffrn_detector_element.reference_center_slow
in millimetres and the value of _diffrn_detector_element.reference_units will be set to 'mm'.
ARGUMENTS
detector
Detector handle.
indexfast
Pointer to the destination fast index.
indexslow
Pointer to the destination slow index.
centerfast
Pointer to the destination displacement along the fast axis.
centerslow
Pointer to the destination displacement along the slow axis.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_detector_normal (cbf_detector detector, double *normal1, double *normal2,
double *normal3);
DESCRIPTION
cbf_get_detector_normal sets *normal1, *normal2, and *normal3 to the 3 components of the of the normal vector to the detector plane. The vector is normalized.
Any of the destination pointers may be NULL.
ARGUMENTS
detector
Detector handle.
normal1
Pointer to the destination x component of the normal vector.
normal2
Pointer to the destination y component of the normal vector.
normal3
Pointer to the destination z component of the normal vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
cbf_get_detector_axis_slow sets *slowaxis1, *slowaxis2, and *slowaxis3 to the 3 components of
the slow axis of the specified detector at the current settings of all axes.
cbf_get_detector_axis_slow sets *fastaxis1, *fastaxis2, and *fastaxis3 to the 3 components of
the fast axis of the specified detector at the current settings of all axes.
cbf_get_detector_axes, cbf_get_detector_axes_fs and int cbf_get_detector_axes_sf set
*slowaxis1, *slowaxis2, and *slowaxis3 to the 3 components of
the slow axis and *fastaxis1, *fastaxis2, and *fastaxis3 to the 3 components of
the fast axis of the specified detector at the current settings of all axes.
Any of the destination pointers may be NULL.
ARGUMENTS
detector
Detector handle.
slowaxis1
Pointer to the destination x component of the slow axis vector.
slowaxis2
Pointer to the destination y component of the slow axis vector.
slowaxis3
Pointer to the destination z component of the slow axis vector.
fastaxis1
Pointer to the destination x component of the fast axis vector.
fastaxis2
Pointer to the destination y component of the fast axis vector.
fastaxis3
Pointer to the destination z component of the fast axis vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
cbf_get_pixel_coordinates, cbf_get_pixel_coordinates_fs and cbf_get_pixel_coordinates_sf ses *coordinate1, *coordinate2, and *coordinate3
to the vector position of pixel (indexfast, indexslow) on the detector surface. If
indexslow and indexfast are integers then the coordinates
correspond to the center of a pixel.
Any of the destination pointers may be NULL.
ARGUMENTS
detector
Detector handle.
indexslow
Slow index.
indexfast
Fast index.
coordinate1
Pointer to the destination x component.
coordinate2
Pointer to the destination y component.
coordinate3
Pointer to the destination z component.
RETURN VALUE
Returns an error code on failure or 0 for success.
cbf_get_detector_normal, cbf_get_pixel_normal_fs and cbf_get_pixel_normal_sf set
*normal1, *normal2, and *normal3 to the 3 components of the of the normal vector
to the pixel at (indexfast, indexslow). The vector is normalized.
Any of the destination pointers may be NULL.
ARGUMENTS
detector
Detector handle.
indexslow
Slow index.
indexfast
Fast index.
normal1
Pointer to the destination x component of the normal vector.
normal2
Pointer to the destination y component of the normal vector.
normal3
Pointer to the destination z component of the normal vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
cbf_get_pixel_area, cbf_get_pixel_area_fs and cbf_get_pixel_area_sf set *area to the area of the pixel at (indexfast, indexslow)
on the detector surface and *projected_area to the apparent area of the pixel as viewed
from the sample position, with indexslow being the slow axis and indexfast being the fast axis.
Either of the destination pointers may be NULL.
ARGUMENTS
detector
Detector handle.
indexfast
Fast index.
indexslow
Slow index.
area
Pointer to the destination area in mm2.
projected_area
Pointer to the destination apparent area in mm2.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_pixel_size (cbf_handle handle, unsigned int element_number,
int axis_number, double *psize);
int cbf_get_pixel_size_fs(cbf_handle handle, unsigned int element_number,
int axis_number, double *psize);
int cbf_get_pixel_size_sf(cbf_handle handle, unsigned int element_number,
int axis_number, double *psize);
DESCRIPTION
cbf_get_pixel_size and cbf_get_pixel_size_sf set *psize to point to the double value in millimeters of the
axis axis_number of the detector element element_number. The axis_number
is numbered from 1, starting with the slowest axis. cbf_get_pixel_size_fs sets *psize to point to
the double value in millimeters of the axis axis_number of the detector element element_number.
The axis_number
is numbered from 1, starting with the fastest axis.
If a negative axis number is given, the order of axes is reversed, so that -1
specifies the slowest axis for cbf_get_pixel_size_fs and the fastest axis for
cbf_get_pixel_size_sf.
If the pixel size is not given explcitly in the "array_element_size" category,
the function returns CBF_NOTFOUND.
ARGUMENTS
handle
CBF handle.
element_number
The number of the detector element counting from 0 by order of appearance in the "diffrn_data_frame" category.
axis_number
The number of the axis, starting from 1 for the fastest for
cbf_get_pixel_size and cbf_get_pixel_size_fs and the slowest for cbf_get_pixel_size_sf.
psize
Pointer to the destination pixel size.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_set_pixel_size (cbf_handle handle, unsigned int element_number,
int axis_number, double psize);
int cbf_set_pixel_size_fs(cbf_handle handle, unsigned int element_number,
int axis_number, double psize);
int cbf_set_pixel_size_sf(cbf_handle handle, unsigned int element_number,
int axis_number, double psize);
DESCRIPTION
cbf_set_pixel_size and cbf_set_pixel_size_sf set the item in the "e;size"e; column of the "array_structure_list"
category at the row which matches axis axis_number of the detector element element_number
converting the double pixel size psize from meters to millimeters in storing it in the "size"
column for the axis axis_number of the detector element element_number. The axis_number
is numbered from 1, starting with the slowest axis.
cbf_set_pixel_size_fs sets the item in the "e;size"e; column of the "array_structure_list"
category at the row which matches axis axis_number of the detector element element_number
converting the double pixel size psize from meters to millimeters in storing it in the "size"
column for the axis axis_number of the detector element element_number. The axis_number
is numbered from 1, starting with the fastest axis.
If a negative axis number is given, the order of axes is reversed, so that -1
specifies the slowest axis for cbf_get_pixel_size_fs and the fastest axis for
cbf_get_pixel_size_sf.
If the "array_structure_list" category does not already exist, it is created.
If the appropriate row in the "array_structure_list" catgeory does not already exist, it is created.
If the pixel size is not given explcitly in the "array_element_size category", the function returns CBF_NOTFOUND.
ARGUMENTS
handle
CBF handle.
element_number
The number of the detector element counting from 0 by order of appearance in the "diffrn_data_frame" category.
axis_number
The number of the axis, fastest first, starting from 1.
psize
The pixel size in millimeters.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_inferred_pixel_size (cbf_detector detector,
int axis_number,
double *psize);
int cbf_get_inferred_pixel_size_fs(cbf_detector detector,
int axis_number,
double *psize);
int cbf_get_inferred_pixel_size_sf(cbf_detector detector,
int axis_number,
double *psize);
DESCRIPTION
cbf_get_inferred_pixel_size, cbf_get_inferred_pixel_size_sf set *psize to point to
the double value in millimeters of the
pixel size for the axis axis_number value. The slow index is treated as axis 1 and the next faster index is treated
as axis 2. cbf_get_inferred_pixel_size_fs sets *psize to point to the double value in
millimeters of the
pixel size for the axis axis_number value. The fast index is treated as axis 1 and the next slower index is treated
as axis 2.
If the axis number is negative, the axes are used in the reverse order so that an axis_number
of -1 indicates the fast axes in a call to cbf_get_inferred_pixel_size or cbf_get_inferred_pixel_size_sf
and indicates the fast axis in a call to cbf_get_inferred_pixel_size_fs.
ARGUMENTS
detector
Detector handle.
axis_number
The number of the axis.
area
Pointer to the destination pizel size in mm.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_unit_cell (cbf_handle handle,
double cell[6], double cell_esd[6] );
DESCRIPTION
cbf_get_unit_cell sets cell[0:2] to the double values of the cell edge
lengths a, b and c in Ångstroms, cell[3:5] to the double values
of the cell angles α, β and γ in degrees, cell_esd[0:2] to the double values of
the estimated strandard deviations of the cell edge lengths a, b and c in
Ångstroms, cell_esd[3:5] to the double values of the estimated
standard deviations of the the cell angles α, β and γ in degrees.
The values returned are retrieved from the first row of the "cell"
category. The value of "_cell.entry_id" is ignored.
cell or cell_esd may be NULL.
If cell is NULL, the cell parameters are not retrieved.
If cell_esd is NULL, the cell parameter esds are not retrieved.
If the "cell" category is present, but some of the values
are missing, zeros are returned for the missing values.
ARGUMENTS
handle
CBF handle.
cell
Pointer to the destination array
of 6 doubles for the cell parameters.
cell_esd
Pointer to the destination
array of 6 doubles for the cell parameter esds.
RETURN VALUE
Returns an error code on failure or 0 for success. No errors is returned for
missing values if the "cell" category exists.
int cbf_set_unit_cell (cbf_handle handle,
double cell[6], double cell_esd[6] );
DESCRIPTION
cbf_set_unit_cell sets the cell parameters to the double values given in cell[0:2]
for the cell edge
lengths a, b and c in Ångstroms, the double values given in cell[3:5]
for the cell angles α, β and γ in degrees, the double values given in cell_esd[0:2] for
the estimated strandard deviations of the cell edge lengths a, b and c in
Ångstroms, and the double values given in cell_esd[3:5] for the estimated
standard deviations of the the cell angles α, β and γ in degrees.
The values are placed in the first row of the "cell"
category. If no value has been given for "_cell.entry_id", it is set to
the value of the "diffrn.id" entry of the current data block.
cell or cell_esd may be NULL.
If cell is NULL, the cell parameters are not set.
If cell_esd is NULL, the cell parameter esds are not set.
If the "cell" category is not present, it is created.
If any of the necessary columns are not present, they are created.
ARGUMENTS
handle
CBF handle.
cell
Pointer to the array
of 6 doubles for the cell parameters.
cell_esd
Pointer to the
array of 6 doubles for the cell parameter esds.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_reciprocal_cell (cbf_handle handle,
double cell[6], double cell_esd[6] );
DESCRIPTION
cbf_get_reciprocal_cell sets cell[0:2] to the double values of the
reciprocal cell edge
lengths a*, b* and c* in Ångstroms-1, cell[3:5] to the double values
of the reciprocal cell angles α*, β* and γ* in degrees, cell_esd[0:2] to the double values of
the estimated strandard deviations of the reciprocal cell edge lengths a*,
b* and c* in
Ångstroms-1, cell_esd[3:5] to the double values of the estimated
standard deviations of the the reciprocal cell angles α*, β* and γ* in degrees.
The values returned are retrieved from the first row of the "cell"
category. The value of "_cell.entry_id" is ignored.
cell or cell_esd may be NULL.
If cell is NULL, the reciprocal cell parameters are not retrieved.
If cell_esd is NULL, the reciprocal cell parameter esds are not retrieved.
If the "cell" category is present, but some of the values
are missing, zeros are returned for the missing values.
ARGUMENTS
handle
CBF handle.
cell
Pointer to the destination array
of 6 doubles for the reciprocal cell parameters.
cell_esd
Pointer to the destination
array of 6 doubles for the reciprocal cell parameter esds.
RETURN VALUE
Returns an error code on failure or 0 for success. No errors is returned for
missing values if the "cell" category exists.
int cbf_set_reciprocal_cell (cbf_handle handle,
double cell[6], double cell_esd[6] );
DESCRIPTION
cbf_set_reciprocal_cell sets the reciprocal cell parameters to the
double values given in cell[0:2] for the reciprocal cell edge
lengths a*, b* and c*
in Ångstroms-1, the double values given in cell[3:5]
for the reciprocal cell angles
α*, β* and γ*
in degrees, the double values given in cell_esd[0:2] for
the estimated strandard deviations of the reciprocal cell edge lengths
a*, b* and c* in
Ångstroms, and the double values given in cell_esd[3:5] for the estimated
standard deviations of the reciprocal cell angles
α*, β* and γ*
in degrees.
The values are placed in the first row of the "cell"
category. If no value has been given for "_cell.entry_id", it is set to
the value of the "diffrn.id" entry of the current data block.
cell or cell_esd may be NULL.
If cell is NULL, the reciprocal cell parameters are not set.
If cell_esd is NULL, the reciprocal cell parameter esds are not set.
If the "cell" category is not present, it is created.
If any of the necessary columns are not present, they are created.
ARGUMENTS
handle
CBF handle.
cell
Pointer to the array
of 6 doubles for the reciprocal cell parameters.
cell_esd
Pointer to the
array of 6 doubles for the reciprocal cell parameter esds.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_compute_cell_volume ( double cell[6], double *volume );
DESCRIPTION
cbf_compute_cell_volume sets *volume to point to the volume of the unit cell
computed from the double values in cell[0:2]
for the cell edge lengths a, b and c in Ångstroms and
the double values given in cell[3:5]
for the cell angles α, β and γ in degrees.
ARGUMENTS
cell
Pointer to the array
of 6 doubles giving the cell parameters.
volume
Pointer to the
doubles for cell volume.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_compute_reciprocal_cell ( double cell[6], double rcell[6] );
DESCRIPTION
cbf_compute_reciprocal_cell sets rcell to point to the array of reciprocal cell
parameters computed from the double values cell[0:2] giving the cell edge
lengths a, b and c in Ångstroms, and the double values cell[3:5]
giving the cell angles α, β and γ in degrees. The double values
rcell[0:2] will be set to the reciprocal cell
lengths a*, b* and c* in Ångstroms-1
and the double values rcell[3:5] will be set to the reciprocal cell
angles α*, β* and γ* in degrees.
ARGUMENTS
cell
Pointer to the array
of 6 doubles giving the cell parameters.
rcell
Pointer to the destination array
of 6 doubles giving the reciprocal cell parameters.
volume
Pointer to the
doubles for cell volume.
RETURN VALUE
Returns an error code on failure or 0 for success.
int cbf_get_bin_sizes(cbf_handle handle, unsigned int element_number, double * slowbinsize,
double * fastbinsize);
int cbf_set_bin_sizes(cbf_handle handle, unsigned int element_number, double slowbinsize_in,double fastbinsize_in);
DESCRIPTION
cbf_get_bin_sizes sets slowbinsize to point to the value of the
number of pixels composing one array element in the dimension that changes at
the second-fastest rate and fastbinsize to point to the value of the
number of pixels composing one array element in the dimension that changes at
the fastest rate for the dectector element with the ordinal element_number.
cbf_set_bin_sizes sets the the pixel bin sizes in the
"array_intensities" category to the values of
slowbinsize_in for the
number of pixels composing one array element in the dimension that changes at
the second-fastest rate and fastbinsize_in for the
number of pixels composing one array element in the dimension that changes at
the fastest rate for the dectector element with the ordinal element_number.
In order to allow for software binning involving fractions of pixels,
the bin sizes are doubles rather than ints.
ARGUMENTS
handle
CBF handle.
element_number
The number of the detector element counting from 0 by order of appearance in the "diffrn_data_frame" category.
slowbinsize
Pointer to the returned number of pixels composing one array element in the dimension that changes at
the second-fastest rate.
fastbinsize
Pointer to the returned number of pixels composing one array element in the dimension that changes at
the fastest rate.
slowbinsize_in
The number of pixels composing one array element in the dimension that changes at
the second-fastest rate.
fastbinsize_in
The number of pixels composing one array element in the dimension that changes at
the fastest rate.
RETURN VALUE
Returns an error code on failure or 0 for success.
At the suggestion of W. Kabsch, Fortran 90/95 routines have been added
to CBFlib. As of this writing code has been written to allow the reading
of CBF_BYTE_OFFSET, CBF_PACKED and CBF_PACKED_V2 binary images. This code
has been gather into FCBlib (Fortran Crystallographic Binary library) as
lib/libfcb.
In general, most of the FCBlib functions return 0 for normal completion and a non-zero
value in case of an error. In a few cases, such as FCB_ATOL_WCNT and FCB_NBLEN_ARRAY
in order to conform to the conventions for commonly used C-equivalent functions,
the function return is the value being computed.
For each function, an interface is given to be included in the declarations of your
Fortran 90/95 code. Some functions in FCBlIB are not intended for external
use and are subject to change: FCB_UPDATE_JPA_POINTERS_I2,
FCB_UPDATE_JPA_POINTERS_I4, FCB_UPDATE_JPA_POINTERS_3D_I2,
FCB_UPDATE_JPA_POINTERS_3D_I4 and CNT2PIX. These
names should not be used for user routines.
The functions involving reading of a CBF have been done strictly in Fortran
without the use of C code. This has required some compromises and the use
of direct access I/O. Rather than
putting the buffer and its control variables into COMMON these are passed
as local arguments to make the routines inherently 'threadsafe' in a parallel
programming environment. Note also, that a reading error could occur for the
last record if it does not fill a full block. The code is written to
recover from end-of-record and end-of-file errors, if possible. On
many modern system, no special action is required, but
on some systems it may be necessary to make use of the padding
between the end of binary data and the terminal MIME boundary marker
in binary sections. To ensure maximum portability of CBF files,
a padding of 4095 bytes is recommended. Existing files without
padding can be converted to files with padding by use of the new
-p4 option for cif2cbf.
INTERFACE
INTEGER(8) FUNCTION FCB_ATOL_WCNT(ARRAY, N, CNT)
INTEGER(1),INTENT(IN):: ARRAY(N)
INTEGER, INTENT(IN):: N
INTEGER, INTENT(OUT):: CNT
END FUNCTION
END INTERFACE
FCB_ATOL_WCNT converts INTEGER(1) bytes in ARRAY of N bytes
to an INTEGER(8) value returned as the function value. The number of
bytes of ARRAY actually used before encountering a character
not used to form the number is returned in CNT.
The scan stops at the first byte in ARRAY that cannot be properly parsed as
part of the integer result.
ARGUMENTS
ARRAY
The array of INTEGER(1) bytes to be scanned
N
The INTEGER size of ARRAY
CNT
The INTEGER size of the portion of ARRAY scanned.
RETURN VALUE
Returns the INTEGER(8) value derived from the characters ARRAY(1:CNT) scanned.
INTERFACE
INTEGER FUNCTION FCB_CI_STRNCMPARR(STRING>, ARRAY, N, LIMIT)
CHARACTER(LEN=*),INTENT(IN):: STRING>
INTEGER, INTENT(IN):: N, LIMIT
INTEGER(1), INTENT(IN):: ARRAY(N)
END FUNCTION
END INTERFACE
The function FCB_CI_STRNCMPARR compares up to LIMIT characters of
character string STRING and INTEGER(1) byte array ARRAY of
dimension N in a case-insensitive manner, returning 0 for a match.
ARGUMENTS
STRING
A character string
ARRAY
The array of INTEGER(1) bytes to be scanned
N
The INTEGER size of ARRAY
N
The INTEGER limit on the number of characters to consider in the comparison
RETURN VALUE
Returns 0 if the string and array match, a non-zero value otherwise.
INTERFACE
INTEGER FUNCTION FCB_EXIT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
PADDING )
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER(FCB_BYTES_IN_REC)
INTEGER(8),INTENT(IN) :: PADDING
END FUNCTION
END INTERFACE
The function FCB_EXIT_BINARY is used to skip from the end of a binary section
past any padding to the end of the text section that encloses the binary
section. The values of the arguments must be consistent with those in the last call
to FCB_NEXT_BINARY
ARGUMENTS
TAPIN
The INTEGER Fortran
device unit number assigned to image file.
LAST_CHAR
The last character
(as an INTEGER(1) byte) read.
FCB_BYTES_IN_REC
The INTEGER
number of bytes in a record.
BYTE_IN_FILE
The INTEGER byte
(counting from 1) of the byte to read.
REC_IN_FILE
The INTEGER record
number (counting from 1) of next record to read.
BUFFER
The INTEGER(1) array of
length FCB_BYTES_IN_REC to hold the appropriate record from TAPIN
PADDING
The INTEGER(8) number of bytes
of padding after the binary data and before the closing MIME boundary.
RETURN VALUE
Returns 0 if the function is successful. Returns whatever non-zero error value is reported by
FCB_READ_LINE if a necessary next line cannot be read.
INTERFACE
INTEGER FUNCTION FCB_NBLEN_ARRAY(ARRAY, ARRAYLEN)
INTEGER, INTENT(IN):: ARRAYLEN
INTEGER(1), INTENT(IN):: ARRAY(ARRAYLEN)
END FUNCTION
END INTERFACE
The function FCB_NBLEN_ARRAY returns the trimmed length of the INTEGER(1)
byte array ARRAY of dimension ARRAYLEN after removal of
trailing ASCII blanks, horizontal tabs (Z'09'), newlines (Z'0A') and
carriage returns (Z'0D'). The resulting length may be zero.
The INTEGER trimmed length is returned as the function value.
ARGUMENTS
ARRAY
The array of bytes
for which the trimmed length is required.
ARRAYLEN
The dimension
of the array of bytes to be scanned.
The function FCB_NEXT_BINARY skips to the start of the next binary
section in the image file on unit TAPIN leaving the file
positioned for a subsequent read of the image data. The skip may
prior to the text field that contains the binary section. When
the text filed is reached, it will be scanned for a MIME boundary
marker, and, if it is found the subsequence MIME headers will
be used to populate the arguments ENCODING, SIZE,
ID, DIGEST, COMPRESSION, BITS,
VORZEICHEN,REELL, BYTEORDER, DIMOVER,
DIM1, DIM2,DIM3, PADDING.
The value returned in ENCODING is taken from the
MIME header Content-Transfer-Encoding as an INTEGER. It is returned
as 0 if not specified. The reported value is one
of the integer values ENC_NONE (Z'0001') for BINARY encoding,
ENC_BASE64 (Z'0002') for BASE64 encoding,
ENC_BASE32K (Z'0004') for X-BASE32K encoding,
ENC_QP (Z'0008') for QUOTED-PRINTABLE encoding,
ENC_BASE10 (Z'0010') for BASE10 encoding,
ENC_BASE16 (Z'0020') for BASE16 encoding or
ENC_BASE8 (Z'0040') for BASE8 encoding.
At this time FCBlib only supports
ENC_NONE BINARY encoding.
The value returned in SIZE is taken from the
MIME header X-Binary-Size as an INTEGER. It is returned
as 0 if not specified.
The value returned in ID is taken from the MIME header
X-Binary-ID as an INTEGER. It is returned as 0 if not
specified.
The value returned in DIGEST is taken from the
MIME header Content-MD5. It is returned
as a character string. If no digest is given, an empty
string is returned.
The value returned in COMPRESSION is taken from the
MIME header Content-Type in the conversions parameter. The
reported value is one of the INTEGER values CBF_CANONICAL (Z'0050'),
CBF_PACKED (Z'0060'), CBF_PACKED_V2 (Z'0090'), CBF_BYTE_OFFSET (Z'0070'),
CBF_PREDICTOR (Z'0080'), CBF_NONE (Z'0040'). Two flags may be
combined with CBF_PACKED or CBF_PACKED_V2: CBF_UNCORRELATED_SECTIONS (Z'0100')
or CBF_FLAT_IMAGE (Z'0200'). At this time FCBlib does not support
CBF_PREDICTOR or CBF_NONE compression.
The values returned in BITS, VORZEICHEN and REELL
are the parameters of the data types of the elements. These values are
taken from the MIME header X-Binary-Element-Type, which has
values of the form "signed BITS-bit integer",
"unsigned BITS-bit integer", "signed BITS-bit real IEEE"
or "signed BITS-bit complex IEEE". If no value is given,
REELL is reported as -1. If the value in one of the integer
types, REELL is reported as 0. If the value is one
of the real or complex types, REELL is reported as 1.
In the current release of FCBlib only the integer types for
BITS equal to 16 or 32 are supported.
The value returned in BYTEORDER is the byte order
of the data in the image file as reported in the MIME header.
The value, if specified, will be either the character string "LITTLE_ENDIAN"
or the character string "BIG_ENDIAN". If no byte order is
specified, "LITTLE_ENDIAN" is reported. This value is taken from
the MIME header X-Binary-Element-Byte-Order. As of this writing,
CBFlib will not generate "BIG_ENDIAN" byte-order files. However,
both CBFlib and FCBlib read "LITTLE_ENDIAN" byte-order files, even
on big-endian machines.
The value returned in DIMOVER is the overall number
of elements in the image array, if specified, or zero, if not
specified. This value is taken from the MIME header
X-Binary-Number-of-Elements.
The values returned in DIM1, DIM2 and DIM3
are the sizes of the fastest changing, second fastest
changing and third fastest changing dimensions of the
array, if specified, or zero, if not specified. These
values are taken from the MIME header X-Binary-Size-Fastest-Dimension,
X-Binary-Size-Second-Dimension and X-Binary-Size-Third-Dimension
respectively.
The value returned in PADDING is the size of
the post-data padding, if any, if specified or zero,
if not specified. The value is given as a count of octets.
This value is taken from the MIME header X-Binary-Size-Padding.
ARGUMENTS
TAPIN
The INTEGER Fortran
device unit number assigned to image file.
LAST_CHAR
The last character
(as an INTEGER(1) byte) read.
FCB_BYTES_IN_REC
The INTEGER
number of bytes in a record.
BYTE_IN_FILE
The INTEGER byte
(counting from 1) of the byte to read.
REC_IN_FILE
The INTEGER record
number (counting from 1) of next record to read.
BUFFER
The INTEGER(1) array of
length FCB_BYTES_IN_REC to hold the appropriate record from TAPIN
ENCODING
INTEGER type of encoding for the binary section as reported in the MIME header.
ID
INTEGER binary identifier as reported in the MIME header.
SIZE
INTEGER size of compressed binary section as reported in the MIME header.
DIGEST
The MD5 message digest as reported in the MIME header.
COMPRESSION
INTEGER compression method as reported in the MIME header.
BITS
INTEGER number of bits in each element as reported in the MIME header.
VORZEICHEN
INTEGER flag for signed or
unsigned elements as reported in the MIME header. Set to 1 if the elements can be read as signed values,
0 otherwise.
REELL
INTEGER flag for real elements as reported in the MIME header. Set to 1 if the elements can be read as REAL
BYTEORDER
The byte order as reported in the MIME header.
DIM1
Pointer to the destination fastest dimension.
DIM2
Pointer to the destination second fastest dimension.
DIM3
Pointer to the destination third fastest dimension.
INTERFACE
INTEGER FUNCTION FCB_OPEN_CIFIN(FILNAM,TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER)
CHARACTER(len=*),INTENT(IN) :: FILNAM
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER(1), INTENT(OUT):: LAST_CHAR
INTEGER, INTENT(OUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1), INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER FCB_RECORD_SIZE
END FUNCTION
END INTERFACE
The function FCB_OPEN_CIFIN opens the CBF image file given by
the file name in the character string FILNAM on the
logical unit TAPIN. The calling routine must provide
an INTEGER(1) byte buffer BUFFER of some appropriate
INTEGER size FCB_BYTES_IN_REC. The size must be
chosen to suit the machine, but in most cases, 4096 will
work. The values returned in LAST_CHAR, BYTE_IN_FILE,
and REC_IN_FILE are for use in subsequent FCBlib
I/O routines.
The image file will be checked for the initial characters "###CBF: ". If
there is no match the error value CBF_FILEREAD is returned.
ARGUMENTS
FILNAM
The
character string name of the image file to be opened.
TAPIN
The INTEGER Fortran
device unit number assigned to image file.
LAST_CHAR
The last character
(as an INTEGER(1) byte) read.
FCB_BYTES_IN_REC
The INTEGER
number of bytes in a record.
BYTE_IN_FILE
The INTEGER byte
(counting from 1) of the byte to read.
REC_IN_FILE
The INTEGER record
number (counting from 1) of next record to read.
BUFFER
The INTEGER(1) array of
length FCB_BYTES_IN_REC to hold the appropriate record from TAPIN
The functions FCB_DECOMPRESS_PACKED_I2, FCB_DECOMPRESS_PACKED_I4,
FCB_DECOMPRESS_PACKED_3D_I2 and FCB_DECOMPRESS_PACKED_3D_I4, decompress
images compress according the the CBF_PACKED or CBF_PACKED_V2
compression described in section 3.3.2 on
J. P. Abrahams CCP4 packed compression.
The relevant function should be called immediately after
a call to FCB_NEXT_BINARY, using the values
returned by FCB_NEXT_BINARY to select
the appropriate version of the function.
ARGUMENTS
ARRAY
The array to receive the image
NELEM
The INTEGER(8) number of elements to be read
NELEM_READ
The INTEGER(8) returned value of the number of elements actually read
ELSIGN
The INTEGER value of the flag for signed (1) OR unsigned (0) data
COMPRESSION
The compression of the image
DIM1
The INTEGER(8) value of the fastest dimension of ARRAY
DIM2
The INTEGER(8) value of the second fastest dimension
DIM3
The INTEGER(8) value of the third fastest dimension
TAPIN
The INTEGER Fortran
device unit number assigned to image file.
FCB_BYTES_IN_REC
The INTEGER
number of bytes in a record.
BYTE_IN_FILE
The INTEGER byte
(counting from 1) of the byte to read.
REC_IN_FILE
The INTEGER record
number (counting from 1) of next record to read.
BUFFER
The INTEGER(1) array of
length FCB_BYTES_IN_REC to hold the appropriate record from TAPIN
INTERFACE
INTEGER FUNCTION FCB_READ_BITS(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
BITCOUNT,IINT,LINT)
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER, INTENT(INOUT):: BCOUNT
INTEGER(1),INTENT(INOUT):: BBYTE
INTEGER, INTENT(IN):: BITCOUNT
INTEGER, INTENT(IN):: LINT
INTEGER(4), INTENT(OUT):: IINT(LINT)
END FUNCTION
END INTERFACE
The function FCB_READ_BITS gets the integer value starting at
BYTE_IN_FILE from file TAPIN continuing through BITCOUNT bits,
with sign extension. BYTE_IN_FILE is left at the entry value
and not incremented. The resulting, sign-extended integer value
is stored in the INTEGER(4) array IINT of dimension LINT
with the least significant portion in IINT(1).
ARGUMENTS
TAPIN
The INTEGER Fortran
device unit number assigned to image file.
FCB_BYTES_IN_REC
The INTEGER
number of bytes in a record.
BUFFER
The INTEGER(1) array of
length FCB_BYTES_IN_REC to hold the appropriate record from TAPIN
REC_IN_FILE
The INTEGER record
number (counting from 1) of next record to read.
BYTE_IN_FILE
The INTEGER byte
(counting from 1) of the byte to read.
BCOUNT
The INTEGER count of
bits remaining unused from the last call to FCB_READ_BITS.
BBYTE
The INTEGER(1) byte
containing the unused bits from the last call to FCB_READ_BITS.
BITCOUNT
The INTEGER count of
the number of bits to be extracted from the image file.
IINT
The INTEGER(4) array
into which to store the value extracted from the image file.
LINT
The INTEGER length
of the array IINT.
RETURN VALUE
Returns 0 if the function is successful. Because of the use of direct access I/O in blocks of
size FCB_BYTES_IN_REC the precise location of the end of file may not be detected.
INTERFACE
INTEGER FUNCTION FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,IBYTE)
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER(1), INTENT(OUT):: IBYTE
END FUNCTION
END INTERFACE
The function FCB_READ_BYTE reads the byte at the position BYTE_IN_FILE
in the image file TAPIN. The first byte in the file is at
BYTE_IN_FILE = 1. BYTE_IN_FILE should be set to the
desired value before the call to the function and is not incremented within the
function.
The function attempts to suppress the error caused by a read
of a short last record, and in most systems cannot determine
the exact location of the end of the image file, returning
zero bytes until the equivalent of a full final record has been
read.
ARGUMENTS
TAPIN
The INTEGER Fortran
device unit number assigned to image file.
FCB_BYTES_IN_REC
The INTEGER
number of bytes in a record.
BUFFER
The INTEGER(1) array of
length FCB_BYTES_IN_REC to hold the appropriate record from TAPIN
REC_IN_FILE
The INTEGER record
number (counting from 1) of next record to read.
BYTE_IN_FILE
The INTEGER byte
(counting from 1) of the byte to read.
IBYTE
The INTEGER(1) byte
found in the image file at the byte position BYTE_IN_FILE.
RETURN VALUE
Returns 0 if the function is successful. Because of the use of direct access I/O in blocks of
size FCB_BYTES_IN_REC the precise location of the end of file may not be detected.
The function FCB_READ_IMAGE_I2 reads a 16-bit twos complement
INTEGER(2) 2D image. The function FCB_READ_IMAGE_I4 read
a 32-bit twos complement INTEGER(4) 2D image. The function
FCB_READ_IMAGE_3D_I2 reads a 16-bit twos complement
INTEGER(2) 3D image. The function
FCB_READ_IMAGE_3D_I4 reads a 32-bit twos complement
INTEGER(4) 3D image. In each case the image is compressed
either by a BYTE_OFFSET algorithm by W. Kabsch based on a proposal
by A. Hammersley or by a PACKED algorithm by J. P. Abrahams as
used in CCP4, with modifications by P. Ellis and H. J. Bernstein.
The relevant function automatically first calls
FCB_NEXT_BINARY to skip to the
next binary section and then starts to read. An error return
will result if the parameters of this call are inconsistent
with the values in MIME header.
ARGUMENTS
ARRAY
The array to receive the image
NELEM
The INTEGER(8) number of elements to be read
NELEM_READ
The INTEGER(8) returned value of the number of elements actually read
ELSIGN
The INTEGER value of the flag for signed (1) OR unsigned (0) data
COMPRESSION
The actual compression of the image
DIM1
The INTEGER(8) value of the fastest dimension of ARRAY
DIM2
The INTEGER(8) value of the second fastest dimension
DIM3
The INTEGER(8) value of the third fastest dimension
TAPIN
The INTEGER Fortran
device unit number assigned to image file.
FCB_BYTES_IN_REC
The INTEGER
number of bytes in a record.
BYTE_IN_FILE
The INTEGER byte
(counting from 1) of the byte to read.
REC_IN_FILE
The INTEGER record
number (counting from 1) of next record to read.
BUFFER
The INTEGER(1) array of
length FCB_BYTES_IN_REC to hold the appropriate record from TAPIN
INTERFACE
INTEGER FUNCTION FCB_READ_LINE(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC, &
BYTE_IN_FILE,REC_IN_FILE,BUFFER,LINE,N,LINELEN)
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC,N
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER, INTENT(OUT):: LINELEN
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER,(FCB_BYTES_IN_REC)
INTEGER(1), INTENT(OUT):: LINE(N)
END FUNCTION
END INTERFACE
The function FCB_READ_LINE reads successive bytes into the INTEGER(1) byte array LINE of
dimension N), stopping at N bytes or the first error or the first
CR (Z'0D') or LF (Z'0A'), whichever comes first. It discards an LF after a CR.
The variable LAST_CHAR is checked for the last character from the
previous line to make this determination.
The actual number of bytes read into the line, not including any terminal
CR or LF is stored in LINELEN.
ARGUMENTS
TAPIN
The INTEGER Fortran
device unit number assigned to image file.
LAST_CHAR
The INTEGER(1)
byte holding the ASCII value of the last character read for each line read.
FCB_BYTES_IN_REC
The INTEGER
number of bytes in a record.
BYTE_IN_FILE
The INTEGER byte
(counting from 1) of the byte to read.
REC_IN_FILE
The INTEGER record
number (counting from 1) of next record to read.
BUFFER
The INTEGER(1) array of
length FCB_BYTES_IN_REC to hold the appropriate record from TAPIN.
LINE
The INTEGER(1) array of
length N to hold the line to be read from TAPIN.
INTERFACE
INTEGER FUNCTION FCB_READ_XDS_I2(FILNAM,TAPIN,NX,NY,IFRAME,JFRAME)
CHARACTER(len=*),INTENT(IN) :: FILNAM
INTEGER, INTENT(IN) :: TAPIN,NX,NY
INTEGER(2), INTENT(OUT):: IFRAME(NX*NY)
INTEGER(4), INTENT(OUT):: JFRAME(NX,NY)
END FUNCTION
END INTERFACE
The function FCB_READ_XDS_I2 read a 32-bit integer twos complement
image into a 16-bit INTEGER(2) XDS image using the CBF_BYTE_OFFSET,
CBF_PACKED or CBF_PACKED_V2 compressions for the 32-bit data. The
BYTE_OFFSET algorithm is a variant of the September 2006 version by
W. Kabsch which was based on a suggestion by A. Hammersley and which
was further modified by H. Bernstein.
The file named FILNAM is opened on the logical unit TAPIN
and FCB_NEXT_BINARY is used to skip to the next
binary image. The binary image is then decompressed to produce an
XDS 16-bit integer image array IFRAME which is NX by NY.
The dimensions must agree with the dimensions specified in MIME header.
The conversion from a 32-bit integer I32 to 16-bit XDS pixel I16 is
done as per W. Kabsch as follows: The value I32 is limited to the range
-1023 ≤ I32 ≤ 1048576. If I32 is outside that range it is truncated
to the closer boundary. The generate I16, the 16-bit result, if I32 >
32767, it is divided by 32 (producing a number between 1024 and 32768),
and then negated (producing a number between -1024 and -32768).
For CBF_BYTE_OFFSET this conversion can be done on the fly directly
into the target array IFRAME, but
for the CBF_PACKED or CBF_PACKED_V2, the full 32 bit precision is
needed during the decompression, forcing the use of an intermediate
INTEGER(4) array JFRAME to hold the 32-bit image in that case.
The image file is closed after reading one image.
ARGUMENTS
FILNAM
The
character string name of the image file to be opened.
TAPIN
The INTEGER Fortran
device unit number assigned to image file.
NX
The INTEGER fast
dimension of the image array.
NY
The INTEGER slow
dimension of the image array.
IFRAME
The INTEGER(2)
XDS image array.
JFRAME
The INTEGER(4)
32-bit image scratch array needed for CBF_PACKED or CBF_PACKED_V2 images.
RETURN VALUE
Returns 0 if the function is successful, CBF_FORMAT (=1) if it cannot handle
this CBF format (not implemented), -1 if it cannot determine endian architecture
of this machine, -2: if it cannot open the image file, -3: if it finds the wrong image
format and -4 if it cannot read the image.
The function FCB_SKIP_WHITESPACE skips forward on the current INTEGER(1) byte array
LINE of size N with valid data in LINE(1:LINELEN) from
the current position ICUR moving over MIME header whitespace and comments,
reading new lines into LINE if needed. The flag FRESH_LINE indicates that a fresh line
should be read on entry.
ARGUMENTS
TAPIN
The INTEGER Fortran
device unit number assigned to image file.
LAST_CHAR
The INTEGER(1)
byte holding the ASCII value of the last character read for each line read.
FCB_BYTES_IN_REC
The INTEGER
number of bytes in a record.
BYTE_IN_FILE
The INTEGER byte
(counting from 1) of the byte to read.
REC_IN_FILE
The INTEGER record
number (counting from 1) of next record to read.
BUFFER
The INTEGER(1) array of
length FCB_BYTES_IN_REC to hold the appropriate record from TAPIN.
LINE
The INTEGER(1) array of
length N to hold the line to be read from TAPIN.
With the exception of the binary sections, a CBF file is an
mmCIF-format ASCII file, so a CBF file with no binary sections is a CIF
file. An imgCIF file has any binary sections encoded as CIF-format
ASCII strings and is a CIF file whether or not it contains binary
sections. In most cases, CBFlib can also be used to access normal
CIF files as well as CBF and imgCIF files.
Before getting to the binary data itself, there are some preliminaries
to allow a smooth transition from the conventions of CIF to those of
raw or encoded streams of "octets" (8-bit bytes). The binary data is
given as the essential part of a specially formatted semicolon-delimited
CIF multi-line text string. This text string is the value associated
with the tag "_array_data.data".
The specific format of the binary sections differs between an
imgCIF and a CBF file.
Each binary section is encoded as a semicolon-delimited string.
Within the text string, the conventions
developed for transmitting email messages
including binary attachments are followed. There is
secondary ASCII header information, formatted as
Multipurpose Internet Mail Extensions
(MIME) headers (see RFCs 2045-49 by Freed, et al.).
The boundary marker for the beginning of
all this is the special string
--CIF-BINARY-FORMAT-SECTION--
at the beginning of a line. The initial "--" says that
this is a MIME boundary. We cannot put
"###" in front of it and conform to MIME conventions.
Immediately after the boundary marker
are MIME headers, describing some useful information we
will need to process the binary
section. MIME headers can appear in different orders,
and can be very confusing (look at the raw
contents of a email message with attachments),
but there is only one header which is has to be
understood to process an imgCIF: "Content-Transfer-Encoding".
If the value given on this
header is "BINARY", this is a CBF and the
data will be presented as raw binary, containing a
count (in the header described in
3.2.2 Format of CBF binary sections)
so that we'll know when to
start looking for more information.
If the value given for "Content-Transfer-Encoding"
is one of the real encodings: "BASE64",
"QUOTED-PRINTABLE", "X-BASE8",
"X-BASE10" or "X-BASE16", the file is an imgCIF,
and we'll need some other headers to
process the encoded binary data properly. It is a
good practice to give headers in all cases. The meanings of
various encodings is given in the
CBF extensions dictionary, cif_img_1.5.4.dic,
as one html file, or as separate pages for each defintion.
For certain compressions (e.g. CBF_PACKED) MIME headers are
essential to determine the parameters of the compression.
The full list of MIME headers recognized by and generated by CBFlib is:
Content-Type:
Content-Transfer-Encoding:
Content-MD5:
X-Binary-Size:
X-Binary-ID:
X-Binary-Element-Type:
X-Binary-Element-Byte-Order:
X-Binary-Number-of-Elements:
X-Binary-Size-Fastest-Dimension:
X-Binary-Size-Second-Dimension:
X-Binary-Size-Third-Dimension:
X-Binary-Size-Padding:
Content-Type:
The "Content-Type" header tells us what
sort of data we have (currently always
"application/octet-stream" for a miscellaneous
stream of binary data) and, optionally, the
conversions that were applied to the original data.
The default is to compress the data with
the "CBF-PACKED" algorithm.
The Content-Type may be any of the discrete types permitted
in RFC 2045; 'application/octet-stream' is recommended.
If an octet stream was compressed, the compression should
be specified by the parameter
'conversions="X-CBF_PACKED"'
or the parameter
'conversions="X-CBF_PACKED_V2"'
or the parameter
'conversions="X-CBF_CANONICAL"'
or the parameter
'conversions="X-CBF_BYTE_OFFSET"'
If the parameter
'conversions="X-CBF_PACKED"'
or
'conversions="X-CBF_PACKED_V2"'
is given it may be further modified with the parameters
'"uncorrelated_sections"'
or
'"flat"'
If the '"uncorrelated_sections"' parameter is
given, each section will be compressed without using
the prior section for averaging.
If the '"flat"' parameter is given, each the
image will be treated as one long row.
Content-Transfer-Encoding:
The "Content-Transfer-Encoding" may be 'BASE64',
'Quoted-Printable', 'X-BASE8', 'X-BASE10',
'X-BASE16' or 'X-BASE32K', for an imgCIF or 'BINARY'
for a CBF. The octal, decimal and hexadecimal transfer
encodings are provided for convenience in debugging and
are not recommended for archiving and data interchange.
In a CIF, one of the parameters 'charset=us-ascii',
'charset=utf-8' or 'charset=utf-16' may be used on the
Content-Transfer-Encoding to specify the character set
used for the external presentation of the encoded data.
If no charset parameter is given, the character set of
the enclosing CIF is assumed. In any case, if a BOM
flag is detected (FE FF for big-endian UTF-16, FF FE for
little-endian UTF-16 or EF BB BF for UTF-8) is detected,
the indicated charset will be assumed until the end of the
encoded data or the detection of a different BOM. The
charset of the Content-Transfer-Encoding is not the character
set of the encoded data, only the character set of the
presentation of the encoded data and should be respecified
for each distinct STAR string.
In an imgCIF file, the encoded binary data begins after
the empty line terminating the header. In an imgCIF file,
the encoded binary data ends with the terminating boundary
delimiter '\n--CIF-BINARY-FORMAT-SECTION----'
in the currently effective charset or with the '\n; '
that terminates the STAR string.
In a CBF, the raw binary data begins after an empty line
terminating the header and after the sequence:
None of these octets are included in the calculation of
the message size or in the calculation of the
message digest.
Content-MD5:
An MD5 message digest may, optionally, be used. The 'RSA Data
Security, Inc. MD5 Message-Digest Algorithm' should be used.
No portion of the header is included in the calculation of the
message digest. The optional "Content-MD5" header provides a much
more sophisticated check on the integrity
of the binary data than size checks alone can provide.
X-Binary-Size:
The "X-Binary-Size" header specifies the size of the
equivalent binary data in octets.
This is the size after any
compressions, but before any ascii encodings.
This is useful in making a simple check for a
missing portion of this file. The 8 bytes for the
Compression type (see below)
are not counted in this field,
so the value of "X-Binary-Size" is 8 less than
the quantity in bytes 12-19 of the raw binary data (
3.2.2 Format of CBF binary sections).
X-Binary-ID:
The "X-Binary-ID" header should contain the
same value as was given for "_array_data.binary_id".
X-Binary-Element-Type:
The "X-Binary-Element-Type" header specifies the type of
binary data in the octets, using the same descriptive
phrases as in _array_structure.encoding_type. The default
value is 'unsigned 32-bit integer'.
X-Binary-Element-Byte-Order:
The "X-Binary-Element-Byte-Order" can specify either
'"BIG_ENDIAN"' or '"LITTLE_ENDIAN"' byte order
of the image data. CBFlib only writes '"LITTLE_ENDIAN"',
and in general can only process LITTLE_ENDIAN
even on machines that are BIG_ENDIAN.
X-Binary-Number-of-Elements:
The "X-Binary-Number-of-Elements" specifies the
number of elements (not the number of octets) in the decompressed, decoded image.
X-Binary-Size-Fastest-Dimension:
The optional "X-Binary-Size-Fastest-Dimension" specifies
the number of elements (not the number of octets) in one row
of the fastest changing dimension of the binary data array.
This information must be in the MIME header for proper
operation of some of the decompression algorithms.
X-Binary-Size-Second-Dimension:
The optional "X-Binary-Size-Second-Dimension" specifies
the number of elements (not the number of octets) in one column
of the second-fastest changing dimension of the binary data array.
This information must be in the MIME header for proper
operation of some of the decompression algorithms.
X-Binary-Size-Third-Dimension:
The optional "X-Binary-Size-Third-Dimension" specifies
the number of sections
for the third-fastest changing dimension of the binary data array.
X-Binary-Size-Padding:
The optional "X-Binary-Size-Padding" specifies the size
in octets of an optional padding
after the binary array data and before the closing flags for
a binary section. CBFlib always writes this padding as zeros,
but this information should be in the MIME header for a binary
section that uses padding, especially if non-zero padding is
used.
A blank line separator immediately precedes the start of the
encoded binary data. Blank spaces
may be added prior to the preceding "line separator"
if desired (e.g. to force word or block
alignment).
Because CBFLIB may jump forward in the file from the MIME header,
the length of encoded
data cannot be greater than the value defined
by "X-Binary-Size" (except when "X-Binary-Size"
is zero, which means that the size is unknown), unless
"X-Binary-Size-Padding" is specified to
allow for the padding.
At exactly the byte following the full binary section
as defined by the length and padding values is the end of
binary section identifier. This consists of the
line-termination sequence followed by:
--CIF-BINARY-FORMAT-SECTION----
;
with each of these lines followed by a line-termination sequence.
This brings us back into a
normal CIF environment. This identifier is, in a sense,
redundant because the binary data length
value tells the a program how many bytes to jump over to
the end of the binary data. This
redundancy has been deliberately added for error checking,
and for possible file recovery in the
case of a corrupted file and this identifier must be
present at the end of every block of binary data.
In a CBF file, each binary section is encoded as a ;-delimited string,
starting with an
arbitrary number of pure-ASCII characters.
Note: For historical reasons, CIFlib has the option of writing simple
header and footer sections: "START OF BINARY SECTION" at
the start of a binary section and
"END OF BINARY SECTION" at the end of a binary section,
or writing MIME-type header
and footer sections (3.2.1
Format of imgCIF binary sections).
If the simple header is used, the actual ASCII text is ignored when the
binary section is read. Use of the simple binary header is deprecated.
The MIME header is
recommended.
Between the ASCII header and the actual CBF binary data is a series of
bytes ("octets") to try to stop the listing of the header,
bytes which define the binary identifier which should match the
"binary_id" defined in the header, and bytes which define the
length of the binary section.
Octet
Hex
Decimal
Purpose
1
0C
12
(ctrl-L) End of Page
2
1A
26
(ctrl-Z) Stop listings in MS-DOS
3
04
04
(Ctrl-D) Stop listings in UNIX
4
D5
213
Binary section begins
5..5+n-1
Binary data (n octets)
NOTE: When a MIME header is used, only bytes 5 through 5+n-1 are considered in
computing the size and the message digest, and only these bytes are
encoded for the equivalent imgCIF file using the indicated
Content-Transfer-Encoding.
If no MIME header has been requested (a deprecated use), then bytes 5 through 28 are
used for three
8-byte words to hold the binary_id, the size and the compression type:
5..12
Binary Section Identifier
(See _array_data.binary_id)
64-bit, little endian
13..20
The size (n) of the
binary section in octets
(i.e. the offset from octet
29 to the first byte following
the data)
21..28
Compression type:
CBF_NONE
0x0040 (64)
CBF_CANONICAL
0x0050 (80)
CBF_PACKED
0x0060 (96)
CBF_BYTE_OFFSET
0x0070 (112)
CBF_PREDICTOR
0x0080 (128)
...
The binary data then follows in bytes 29 through 29+n-1.
The binary characters serve specific purposes:
The Control-L (from-feed) will terminate printing of the current page
on most operating systems.
The Control-Z will stop the listing of the file on MS-DOS
type operating systems.
The Control-D will stop the listing of the file on Unix
type operating systems.
The unsigned byte value 213 (decimal) is binary 11010101.
(Octal 325, and hexadecimal D5).
This has the eighth bit set so can be used for error checking
on 7-bit transmission. It is also asymmetric, but with the first
bit also set in the case that the bit order could be reversed
(which is not a known concern).
(The carriage return, line-feed pair before the START_OF_BIN
and other lines can also be used to check that the file has not
been corrupted e.g. by being sent by ftp in ASCII mode.)
At present four compression schemes are implemented
are defined: CBF_NONE (for no compression), CBF_CANONICAL (for
and entropy-coding scheme based on the canonical-code algorithm
described by Moffat, et al. (International
Journal of High Speed Electronics and Systems, Vol 8, No 1 (1997)
179-231)), CBF_PACKED or CBF_PACKED_V2 for J. P. Abrahams CCP4-style
packing schemes and CBF_BYTE_OFFSET
for a simple byte_offset compression scheme.. Other
compression schemes will be added to
this list in the future.
For historical reasons, CBFlib can read or write a binary
string without a MIME header. The structure of a binary string with simple
headers is:
Byte
ASCII symbol
Decimal value
Description
1
;
59
Initial ; delimiter
2
carriage-return
13
3
line-feed
10
The CBF new-line code is carriage-return, line-feed
4
S
83
5
T
84
6
A
65
7
R
83
8
T
84
9
32
10
O
79
11
F
70
12
32
13
B
66
14
I
73
15
N
78
16
A
65
17
R
83
18
Y
89
19
32
20
S
83
21
E
69
22
C
67
23
T
84
24
I
73
25
O
79
26
N
78
27
carriage-return
13
28
line-feed
10
29
form-feed
12
30
substitute
26
Stop the listing of the file in MS-DOS
31
end-of-transmission
4
Stop the listing of the file in unix
32
213
First non-ASCII value
33 .. 40
Binary section identifier (64-bit little-endien)
41 .. 48
Offset from byte 57 to the first ASCII character following the binary data
Two schemes for lossless compression of integer arrays (such as images) have been
implemented in this version of CBFlib:
1. An entropy-encoding scheme using canonical coding
2. A CCP4-style packing scheme.
Both encode the difference (or error) between the current element in the array and
the prior element. Parameters required for more sophisticated predictors have been
included in the compression functions and will be used in a future version of the
library.
The canonical-code compression scheme encodes errors in two ways: directly or indirectly.
Errors are coded directly using a symbol corresponding to the error value. Errors
are coded indirectly using a symbol for the number of bits in the (signed) error,
followed by the error iteslf.
At the start of the compression, CBFlib constructs a table containing a set of symbols,
one for each of the 2^n
direct codes from -2^(n-1)
.. 2^(n-1)-1,
one for a stop code, and one for each of the maxbits
-n
indirect codes, where n
is chosen at compress time and maxbits
is the maximum number of bits in an error. CBFlib then assigns to each symbol a
bit-code, using a shorter bit code for the more common symbols and a longer bit code
for the less common symbols. The bit-code lengths are calculated using a Huffman-type
algorithm, and the actual bit-codes are constructed using the canonical-code algorithm
described by Moffat, et al. (International
Journal of High Speed Electronics and Systems, Vol 8, No 1 (1997) 179-231).
Starting with CBFlib 0.7.7, CBFlib supports three variations on CCP4-style
compression: the "flat" version supported in versions of
CBFlib prior to release 0.7.7, as well as both version 1 and version 2
of J. P. Abrahams "pack_c" compression.
The CBF_PACKED and CBF_PACKED_V2 compression and decompression code
incorporated in CBFlib is derived in large part from the J. P. Abrahams
pack_c.c compression code in CCP4. This code is incorporated in
CBFlib under the GPL and the LGPL with both the permission
Jan Pieter Abrahams, the original author of pack_c.c (email from Jan Pieter
Abrahams of 15 January 2007) and of the CCP4 project (email from Martyn
Winn on 12 January 2007). The cooperation of J. P. Abrahams and
of the CCP4 project is gratefully acknowledged.
The basis for all three versions is a scheme to pack offsets (differences from a
base value) into a small-endian bit stream. The stream is organized
into blocks. Each block begins with a header of 6 bits in the flat
packed version and version 1 of J. P. Abrahams compression, and 7 bits
in version 2 of J. P. Abrahams compression. The header gives the
number of offsets that follow and the number of bits in each offset.
Each offset is a signed, 2's complement integer.
The first 3 bits in the header gives the logarithm base 2 of
the numer of offsets that follow the header. For example, if
a header has a zero in bits, only one offset follows the header.
If those same bits contain the number n, the number of offsets
in the block is 2n.
The following 3 bits (flat and version 1) or 4 bits (version 2)
contains a number giving an index into a table of bit-lengths
for the offsets. All offsets in a given block are of the same
length.
Bits 3 .. 5 (flat and version 1) or bits 3 .. 6 (version 2)
encode the number of bits in each offset as follows:
Value in bits 3 .. 5
Number of bits in each V1 offset
Number of bits in each V2 offset
0
0
0
1
4
3
2
5
4
3
6
5
4
7
6
5
8
7
6
16
8
7
max
9
8
10
9
11
10
12
11
13
12
14
13
15
14
16
15
max
The value "max" is determined by the compression version and the
element size. If the compression used is "flat", then "max" is 65.
If the compression is version 1 or version 2 of the JPA compression, then
"max" is the number of bits in each element, i.e. 8, 16, 32 or 64
bits.
The major difference between the three variants of packed compression is the
choice of the base value from which the offset is measured. In all cases
the first offset is measured from zero, i.e. the first offset is the value
of the first pixel of the image. If "flat"
is chosen or if the dimensions of the data array are not given, then the
remaining offset are measure against the prior value, making it similar
in approach to the "byte offset" compression described in
section 3.3.3 Byte offset compression, but with a
more efficient representation of the offsets.
In version 1 and version 2 of the J. P. Abrahams compression, the
offsets are measured against an average of earlier pixels. If there
is only one row only the prior pxiel is used, starting with the same
offsets for that row as for "flat". After the first row,
three pixels from the prior row are used in addition to using the
immediately prior pixel. If there are multiple sections,
and the sections are marked as correlated, after the first section,
4 pixels from the prior section are included in the average.
The CBFlib code differs from the pack_c code in the handling
of the beginnings and ends of rows and sections. The pack_c
code will use pixels from the other side of the image in doing the
averaging. The CBFlib code drops pixels from the other side of
the image from the pool. The details follow.
After dealing with the special case of the first pixel,
The algorithm uses an array of pointers, trail_char_data.
The assignment of pixels to the pool to be averaged begins
with trail_char_data[0] points to the pixel immediately prior
to the next pixel to be processed, either in the same row
(fastest index) or, at the end of the prior row if the next
data element to be processed is at the end of a row. The
location of the pixel pointed to by trail_char_data[0]
is used to compute the locations of the other pixels
in the pool. It will be dropped from the pool before
averaging if it is on the opposite side of the image.
The pool will consist of 1, 2, 4 or 8 pixels.
Assume ndim1, ndim2, ndim3 are the indices of the same
pixel as trail_char_data[0] points to. These indices
are incremented to be the indices of the next pixel
to be processed before populating trail_char_data.
On exit, trail_char_data[0 .. 7] will have been populated with
pointers to the pixels to be used in forming the average.
Pixels that will not be used will be set to NULL. Note
that trail_char_data[0] may be set to NULL.
If we mark the next element to be processed with a "*"
and the entries in trail_char_data with their array indices
0 .. 7, the possible patterns of settings in the general case are:
If there is no prior section (i.e. ndim3 is 0, or
the CBF_UNCORRELATED_SECTIONS flag is set
to indicate discontinuous sections), the values
for trail_char_data[4 .. 7] will all be NULL. When
there is a prior section, trail_char_data[5..7] are
pointers to the pixels immediately below the
elements pointed to by trail_char_data[1..3], except
trail_char_data[4] is one element further along
its row to be directly below the next element to
be processed.
The first element of the first row of the first section
is a special case, with no averaging.
In the first row of the first section (ndim2 == 0,
and ndim3 == 0), after the first element (ndim1 > 0),
only trail_char_data[0] is used
current section:
- - - - 0 * - - - -
For subsequent rows of the first section (ndim2 > 0,
and ndim3 == 0), for the first element (ndim1 == 0),
two elements from the prior row are used:
For sections after the first section, provided the
CBF_UNCORRELATED_SECTIONS flag is not set in the compression,
for each non-NULL entry in trail_char_data [0..3] an entry
is made in trail_char_data [4..7], except for the
first element of the first row of a section. In that
case an entry is made in trail_char_data[4].
Starting with CBFlib 0.7.7, CBFlib supports a simple and efficient "byte_offset"
algorithm originally proposed by Andy Hammerley and modified by Wolgang Kabsch and
Herbert Bernstein. The original proposal was called "byte_offsets". We
distinguish this variant by calling it "byte_offset". The major differences
are that the "byte_offsets" algorithm started with explicit storage
of the first element of the array as a 4-byte signed two's integer, and checked
for image edges to changes the selection of prior pixel. The CBFlib
"byte_offset" alogorithm starts with an assumed zero before the
first pixel and represents the value of the first pixel as an offset
of whatever number of size is needed to hold the value, and for speed, treats the
entire image as a simple linear array, allowing use of the last
pixel of one row as the base against which to compute the offset for
the first element of the next row.
The algorithm is simple and easily implemented.
This algorithm can never achieve better than a factor of two compression
relative to 16-bit raw data or 4 relative to 32-bit raw data, but for
most diffraction data the compression will indeed be very close to
these ideal values. It also has the advantage that
integer values up to 32 bits (or 31 bits and sign) may be stored efficiently
without the need for special over-load tables. It is a fixed algorithm
which does not need to calculate any image statistics, so is fast.
The algorithm works because of the following property of almost all
diffraction data and much other image data: The value of one element
tends to be close to the value of the adjacent elements, and the vast
majority of the differences use little of the full dynamic range.
However, noise in experimental data means that run-length encoding is
not useful (unless the image is separated into different bit-planes). If
a variable length code is used to store the differences, with the number
of bits used being inversely proportional to the probability of
occurrence, then compression ratios of 2.5 to 3.0 may be achieved.
However, the optimum encoding becomes dependent of the exact properties
of the image, and in particular on the noise. Here a lower compression
ratio is achieved, but the resulting algorithm is much simpler and more
robust.
The "byte_offset" compression algorithm is the following:
Start with a base pixel value of 0.
Compute the difference delta between the next pixel value
and the base pixel value.
If -127 ≤ delta ≤ 127, output delta as one byte,
make the current pixel value the base pixel value and return to step 2.
Otherwise output -128 (80 hex).
We still have to output delta. If -32767 ≤ delta ≤ 32767,
output delta as a little_endian 16-bit quantity,
make the current pixel value the base pixel value and return to step 2.
Otherwise output -32768 (8000 hex, little_endian, i.e. 00 then
80)
We still have to output delta. If -2147483647 ≤ delta ≤ 2147483647,
output delta as a little_endian 32 bit quantity,
make the current pixel value the base pixel value and return to step 2.
Otherwise output -2147483648 (80000000 hex, little_endian, i.e.
00, then 00, then 00, then 80) and then output the pixel value
as a little-endian 64 bit quantity,
make the current pixel value the base pixel value and return to step 2.
The "byte_offset" decompression algorithm is the following:
Start with a base pixel value of 0.
Read the next byte as delta
If -127 ≤ delta ≤ 127, add delta to the base pixel value,
make that the new base pixel value, place it on the
output array and return to step 2.
If delta is 80 hex, read the next two bytes as a little_endian
16-bit number and make that delta.
If -32767 ≤ delta ≤ 32767, add delta to the base pixel value,
make that the new base pixel value, place it on the
output array and return to step 2.
If delta is 8000 hex, read the next 4 bytes as a little_endian
32-bit number and make that delta
If -2147483647 ≤ delta ≤ 2147483647, add delta to the base pixel value,
make that the new base pixel value, place it on the
output array and return to step 2.
If delta is 80000000 hex, read the next 8 bytes as a little_endian
64-bit number and make that delta, add delta to the base pixel value,
make that the new base pixel value, place it on the
output array and return to step 2.
Let us look at an example, of two 1000 x 1000 flat field
images presented as a mimimal imgCIF file. The first image
uses 32-bit unsigned integers and the second image uses
16-bit unsigned integers.
The imgCIF file begins with some identifying comments (magic
numbers) to track the version of the dictionary and library:
###CBF: VERSION 1.5
# CBF file written by CBFlib v0.7.7
This is followed by the necessary syntax to start a CIF
data block and by whatever tags and values are appropriate
to describe the experiment. The minimum is something like
data_testflat
eventually we come to the actual binary data, which begins
the loop header for the array_data category
loop_
_array_data.data
with any additional tags needed, and then the data itself,
which starts with the mini-header:
followed by an empty line and then the sequence of characters:
^L^Z^D<D5>
followed immediately by the compressed data.
The binary data begins with the hex byte 80 to flag
the need for a value that will not fit in one byte.
That is followed by the small_endian hex value 3E8
saying that the first delta is 1000. Then 999,999
bytes of zero follow, since this is a flat field,
with all values equal to zero. That gives us our
entire 1000x1000 compressed flat field. However,
because we asked for 4095 bytes of padding, there
is an additional 4095 bytes of zero that are not
part of the compressed field. They are just pad
and can be ignored. Finally, after the pad, the
CIF text field that began with
;
--CIF-BINARY-FORMAT-SECTION--
is completed with
--CIF-BINARY-FORMAT-SECTION----
;
notice the extra --
The second flat field then follows, with a very
similar mini-header:
The only difference is that we have declared this
array to be 16-bit and have chosen a different
binary id (2 instead of 1). Even the checksum is the same.
CBFlib should be built on a disk with at least 200 megabytes of free space.
CBFlib.tar.gz is a "gzipped" tar of
the code as it now stands. Place the gzipped tar in the directory
that is intended to contain a new directory, named
CBFlib_0.7.5 (the "top-level" directory)
and uncompress it with gunzip and unpack it with tar:
gunzip CBFlib.tar.gz
tar xvf CBFLIB.tar
As with prior releases, to run the test programs, you will also need
Paul Ellis's sample MAR345 image,
example.mar2300, and
Chris Nielsen's sample ADSC Quantum 315 image,
mb_LP_1_001.img as sample data. Both these files will be
extracted by the Makefile from CBFlib_0.7.7_Data_Files. Do
not download copies into the top level directory.
After unpacking the archive, the top-level directory should contain
a makefile:
Makefile
Makefile for unix
and the subdirectories:
src/
CBFLIB source files
include/
CBFLIB header files
m4/
CBFLIB m4 macro files (used to build .f90 files)
examples/
Example program source files
doc/
Documentation
lib/
Compiled CBFLIB library
bin/
Executable example programs
html_images/
JPEG images used in rendering the HTML files
For instructions on compiling and testing the library, go to
the top-level directory and type:
make
The CBFLIB source and header files are in the "src" and "include" subdirectories.
The FCBLIB source and m4 files are in the "src" and "m4" subdirectories.
The files are:
src/
include/
m4/
Description
cbf.c
cbf.h
CBFLIB API functions
cbf_alloc.c
cbf_alloc.h
Memory allocation functions
cbf_ascii.c
cbf_ascii.h
Function for writing ASCII values
cbf_binary.c
cbf_binary.h
Functions for binary values
cbf_byte_offset.c
cbf_byte_offset.h
Byte-offset compression
cbf_canonical.c
cbf_canonical.h
Canonical-code compression
cbf_codes.c
cbf_codes.h
Encoding and message digest functions
cbf_compress.c
cbf_compress.h
General compression routines
cbf_context.c
cbf_context.h
Control of temporary files
cbf_file.c
cbf_file.h
File in/out functions
cbf_lex.c
cbf_lex.h
Lexical analyser
cbf_packed.c
cbf_packed.h
CCP4-style packing compression
cbf_predictor.c
cbf_predictor.h
Predictor-Huffman compression (not implemented)
cbf_read_binary.c
cbf_read_binary.h
Read binary headers
cbf_read_mime.c
cbf_read_mime.h
Read MIME-encoded binary sections
cbf_simple.c
cbf_simple.h
Higher-level CBFlib functions
cbf_string.c
cbf_string.h
Case-insensitive string comparisons
cbf_stx.c
cbf_stx.h
Parser (generated from cbf.stx.y)
cbf_tree.c
cbf_tree.h
CBF tree-structure functions
cbf_uncompressed.c
cbf_uncompressed.h
Uncompressed binary sections
cbf_write.c
cbf_write.h
Functions for writing
cbf_write_binary.c
cbf_write_binary.h
Write binary sections
cbf.stx.y
bison grammar to define cbf_stx.c (see WARNING)
md5c.c
md5.h
RSA message digest software from mpack
global.h
fcb_atol_wcnt.f90
Function to convert a string to an integer
fcb_ci_strncmparr.f90
Function to do a case-insensitive comparison of a string to
a byte array
fcb_nblen_array.f90
Function to determine the non-blank length of a byte array
fcb_read_byte.f90
Function to read a single byte
fcb_read_line.f90
Function to read a line into a byte array
fcb_skip_whitespace.f90
Function to skip whitespace and comments in a MIME header
fcb_exit_binary.m4
Function to skip past the end of the current binary text field
fcb_next_binary.m4
Function to skip to the next binary
fcb_open_cifin.m4
Function to open a CBF file for reading
fcb_packed.m4
Functions to read a JPA CCP4 compressed image
fcb_read_bits.m4
Functions to read nay number of bits as an integer
fcb_read_image.m4
Functions to read the next image in I2, I4, 3D_I2 and 3D_I4 format
fcb_read_xds_i2.m4
Function to read a single xds image.
fcblib_defines.m4
General m4 macro file for FCBLIB routines.
In the "examples" subdirectory, there are 2 additional files
used by the example programs (section 5) for reading MAR300,
MAR345 or ADSC CCD images:
img.c
img.h
Simple image library
and the example programs themselves:
makecbf.c
Make a CBF file from an image
img2cif.c
Make an imgCIF or CBF from an image
cif2cbf.c
Copy a CIF/CBF to a CIF/CBF
convert_image.c
Convert an image file to a cbf using a template file
cif2c.c
Convert a template cbf file into a function to produce the same template in an
internal cbf data structure
testcell.C
Exercise the cell functions
as well as three template files: template_adscquantum4_2304x2304.cbf,
template_mar345_2300x2300.cbf, and template_adscquantum315_3072x3072.cbf.
Two additional examples (test_fcb_read_image.f90 and test_xds_binary.f90) are created from two files
(test_fcb_read_image.m4 and test_xds_binary.m4) in the m4 directory.
The documentation files are in the "doc" subdirectory:
The example programs makecbf.c, img2cif.c and convert_image.c read an image file
from a MAR300, MAR345 or ADSC CCD detector and then uses CBFlib to
convert it to CBF format (makecbf) or either imgCIF or CBF format (img2cif).
makecbf writes the CBF-format image to disk, reads it in again, and
then compares it to the original. img2cif just writes
the desired file. makecbf works only from stated files on disk, so that
random I/O can be used. img2cif includes code to process files
from stdin and to stdout. convert_image reads a template as well
as the image file and produces a complete CBF. The program
convert_minicbf reads a minimal CBF file with just and image
and some lines of text specifying the parameters of the
data collection as done at SLS and combines the result with
a template to produce a full CBF. The program cif2cbf can
be used to convert among carious compression and encoding
schemes. The program sauter_test.C is a C++ test program
contributed by Nick Sauter to help in resolving a memory
leak he found.
The programs adscimg2cbf and cbf2adscimg are a "jiffies" contributed
by Chris Nielsen of ADSC to convert ADSC images to imgCIF/CBF format and
vice versa.
makecbf.c is a good example of how many of the CBFlib functions can be
used.
To compile makecbf and the other example programs use the Makefile in the top-level
directory:
make all
This will place the programs in the bin directory.
makecbf
To run makecbf with the example image, type:
./bin/makecbf example.mar2300 test.cbf
The program img2cif has the following command line interface:
img2cif [-i input_image] \
[-o output_cif] \
[-c {p[acked]|c[annonical]|[n[one]}] \
[-m {h[eaders]|n[oheaders]}] \
[-d {d[igest]|n[odigest]}] \
[-e {b[ase64]|q[uoted-printable]| \
d[ecimal]|h[exadecimal]|o[ctal]|n[one]}] \
[-b {f[orward]|b[ackwards]}] \
[input_image] [output_cif]
the options are:
-i input_image (default: stdin)
the input_image file in MAR300, MAR345 or ADSC CCD detector
format is given. If no input_image file is specified or is
given as "-", an image is copied from stdin to a temporary file.
-o output_cif (default: stdout)
the output cif (if base64 or quoted-printable encoding is used)
or cbf (if no encoding is used). if no output_cif is specified
or is given as "-", the output is written to stdout
-c compression_scheme (packed, canonical or none, default packed)
-m [no]headers (default headers for cifs, noheaders for cbfs)
selects MIME (N. Freed, N. Borenstein, RFC 2045, November 1996)
headers within binary data value text fields.
-d [no]digest (default md5 digest [R. Rivest, RFC 1321, April
1992 using"RSA Data Security, Inc. MD5 Message-Digest
Algorithm"] when MIME headers are selected)
-e encoding (base64, quoted-printable, decimal, hexadecimal,
octal or none, default: base64) specifies one of the standard
MIME encodings (base64 or quoted-printable) or a non-standard
decimal, hexamdecimal or octal encoding for an ascii cif
or "none" for a binary cbf
-b direction (forward or backwards, default: backwards)
specifies the direction of mapping of bytes into words
for decimal, hexadecimal or octal output, marked by '>' for
forward or '<' for backwards as the second character of each
line of output, and in '#' comment lines.
cif2cbf
The test program cif2cbf uses many of the same command line options as img2cif, but
accepts either a CIF or a CBF as input instead of an image file:
cif2cbf [-i input_cif] [-o output_cbf] \
[-u update_cif] \
[-c {p[acked]|c[annonical]|{b[yte_offset]}|\
{v[2packed}|{f[latpacked}[n[one]}] \
[-C highclipvalue] \
[-D ] \
[-I {0|2|4|8}] \
[-R {0|4|8}] \
[-L {0|4|8}] \
[-m {h[eaders]|noh[eaders]}] \
[-m {d[imensions]|nod[imensions}] \
[-d {d[igest]|n[odigest]|w[arndigest]}] \
[-B {read|liberal|noread}] [-B {write|nowrite}] \
[-S {read|noread}] [-S {write|nowrite}] \
[-T {read|noread}] [-T {write|nowrite}] \
[-e {b[ase64]|q[uoted-printable]|\
d[ecimal]|h[examdecimal|o[ctal]|n[one]}] \
[-b {f[orward]|b[ackwards]}\
[-p {1|2|4}\
[-v dictionary]* [-w] [-W]\
[input_cif] [output_cbf]
the options are:
-i input_cif (default: stdin)
the input file in CIF or CBF format. If input_cif is not
specified or is given as "-", it is copied from stdin to a
temporary file.
-o output_cbf (default: stdout)
the output cif (if base64 or quoted-printable encoding is used)
or cbf (if no encoding is used). if no output_cif is specified
or is given as "-", the output is written to stdout
if the output_cbf is /dev/null, no output is written.
-u update_cif (no default)
and optional second input file in CIF or CBF format containing
data blocks to be merged with data blocks from the primary
input CIF or CBF
The remaining options specify the characteristics of the
output cbf. Most of the characteristics of the input cif are
derived from context, except when modified by the -B, -S, -T, -v
and -w flags.
-b byte_order (forward or backwards, default forward (1234) on
little-endian machines, backwards (4321) on big-endian machines
-B [no]read or liberal (default noread)
read to enable reading of DDLm style brackets
liberal to accept whitespace for commas
-B [no]write (default write)
write to enable writing of DDLm style brackets
-c compression_scheme (packed, canonical, byte_offset,
v2packed, flatpacked or none,
default packed)
-C highclipvalue
specifies a double precision value to which to clip the data
-d [no]digest or warndigest (default md5 digest [R. Rivest,
RFC 1321, April 1992 using"RSA Data Security, Inc. MD5
Message-Digest Algorithm"] when MIME headers are selected)
-D test cbf_construct_detector
-e encoding (base64, k, quoted-printable or none, default base64)
specifies one of the standard MIME encodings for an ascii cif
or "none" for a binary cbf
-I 0 or integer element size
specifies integer conversion of the data, 0 to use the input
number of bytes, 2, 4 or 8 for short, long or long long
output integers
-L lowclipvalue
specifies a double precision value to cut off the data from
below
-m [no]headers (default headers)
selects MIME (N. Freed, N. Borenstein, RFC 2045, November 1996)
headers within binary data value text fields.
-m [nod]imensions (default dimensions)
selects detailed recovery of dimensions from the input CIF
for use in the MIME header of the output CIF
-p K_of_padding (0, 1, 2, 4) for no padding after binary data
1023, 2047 or 4095 bytes of padding after binary data
-R 0 or integer element size
specifies real conversion of the data, 0 to use the input
number of bytes, 4 or 8 for float or double output reals
-S [no]read or (default noread)
read to enable reading of whitespace and comments
-S [no]write (default write)
write to enable writing of whitespace and comments
-T [no]read or (default noread)
read to enable reading of DDLm style triple quotes
-T [no]write (default write)
write to enable writing of DDLm style triple quotes
-v dictionary specifies a dictionary to be used to validate
the input cif and to apply aliases to the output cif.
This option may be specified multiple times, with dictionaries
layered in the order given.
-w process wide (2048 character) lines
-W write wide (2048 character) lines
convert_image
The program convert_image requires two arguments: imagefile and cbffile.
Those are the primary input and output. The detector type is extracted from the
image file or from the command line, converted to lower case and used to construct the name of a template
cbf file to use for the copy. The template file name is of the form
template_name_columnsxrows. The full set of options is:
convert_image [-i input_img] [-o output_cbf] [-p template_cbf]\
[-d detector name] -m [x|y|x=y] [-z distance] \
[-c category_alias=category_root]* \
[-t tag_alias=tag_root]* [-F] [-R] \
[input_img] [output_cbf]
the options are:
-i input_img (default: stdin)
the input file as an image in smv, mar300, or mar345 format.
If input_img is not specified or is given as "-", it is copied
from stdin to a temporary file.
-p template_cbf
the template for the final cbf to be produced. If template_cbf
is not specified the name is constructed from the first token
of the detector name and the image size as
template_<type>_<columns>x<rows>.cbf
-o output_cbf (default: stdout )
the output cbf combining the image and the template. If the
output_cbf is not specified or is given as "-", it is written
to stdout.
-d detectorname
a detector name to be used if none is provided in the image
header.
-F
when writing packed compression, treat the entire image as
one line with no averaging
-m [x|y|x=y] (default x=y, square arrays only)
mirror the array in the x-axis (y -> -y)
in the y-axis (x -> -x)
or in x=y ( x -> y, y-> x)
-r n
rotate the array n times 90 degrees counter clockwise
x -> y, y -> -x for each rotation, n = 1, 2 or 3
-R
if setting a beam center, set reference values of
axis settings as well as standard settings
-z distance
detector distance along Z-axis
-c category_alias=category_root
-t tag_alias=tagroot
map the given alias to the given root, so that instead
of outputting the alias, the root will be presented in the
output cbf instead. These options may be repeated as many
times as needed.
convert_minicbf
The program convert_minicbf requires two arguments: minicbf and cbffile.
Those are the primary input and output. The detector type is extracted from the
image file or from the command line, converted to lower case and used to construct the name of a template
cbf file to use for the copy. The template file name is of the form
template_name_columnsxrows. The full set of options is:
convert_minicbf [-i input_cbf] [-o output_cbf] [-p template_cbf]\
[-q] [-C convention] \
[-d detector name] -m [x|y|x=y] [-z distance] \
[-c category_alias=category_root]* \
[-t tag_alias=tag_root]* [-F] [-R] \
[input_cbf] [output_cbf]
the options are:
-i input_cbf (default: stdin)
the input file as a CBF with at least an image.
-p template_cbf
the template for the final cbf to be produced. If template_cbf
is not specified the name is constructed from the first token
of the detector name and the image size as
template_<type>_<columns>x<rows>.cbf
-o output_cbf (default: stdout )
the output cbf combining the image and the template. If the
output_cbf is not specified or is given as "-", it is written
to stdout.
-q
exit quickly with just the miniheader expanded
after the data. No template is used.
-Q
exit quickly with just the miniheader unexpanded
before the data. No template is used.
-C convention
convert the comment form of miniheader into the
_array_data.header_convention convention
_array_data.header_contents
overriding any existing values
-d detectorname
a detector name to be used if none is provided in the image
header.
-F
when writing packed compression, treat the entire image as
one line with no averaging
-m [x|y|x=y] (default x=y, square arrays only)
mirror the array in the x-axis (y -> -y)
in the y-axis (x -> -x)
or in x=y ( x -> y, y-> x)
-r n
rotate the array n times 90 degrees counter clockwise
x -> y, y -> -x for each rotation, n = 1, 2 or 3
-R
if setting a beam center, set reference values of
axis settings as well as standard settings
-z distance
detector distance along Z-axis
-c category_alias=category_root
-t tag_alias=tagroot
map the given alias to the given root, so that instead
of outputting the alias, the root will be presented in the
output cbf instead. These options may be repeated as many
times as needed.
testreals, testflat and testflatpacked
The example programs testreals, testflat and testflatpacked exercise
the handling of reals, byte_offset compression and packed compression.
Each is run without any arguments. testreals will read real images
from the data file testrealin.cbf and write a file with real images
in testrealout.cbf, which should be identical to testrealin.cbf.
testflat and testflatpacked read 4 1000x1000 2D images and one 50x60x70
3D image and produce an output file that should be identical to the
input. testflat reads testflatin.cbf and produces testflatout.cbf using
CBF_BYTE_OFFSET compression. testflatpacked reads testflatpackedin.cbf
and produces testflatpackedout.cbf. The images are:
A 1000 x 1000 array of 32-bit integers forming a flat field with all
pixels set to 1000.
A 1000 x 1000 array of 16-bit integers forming a flat field with all
pixels set to 1000.
A 1000 x 1000 array of 32-bit integers forming a flat field with all
pixels set to 1000, except for -3 along the main diagonal and its transpose.
A 1000 x 1000 array of 16-bit integers forming a flat field with all
pixels set to 1000, except for -3 along the main diagonal and its transpose.
A 50 x 60 x 70 array of 32-bit integers in a flat field of 1000, except for
-3 along the main diagonal and the values i+j+k (counting from zero)
every 1000th pixel
test_fcb_read_image, test_xds_binary
The example programs test_fcb_read_image and test_xds_binary are designed
read the output of testflat and testflatpacked using the FCBlib routines
in lib/libfcb. test_xds_binary reads only the first image and closes
the file immediately. test_fcb_read_image reads all 5 images from the
input file. The name of the input file should be provided on stdin,
as in:
In order to compile these programs correctly for the G95 compiler
it is important to set the record size for reading to be no larger
than the padding after binary images. This in controlled in
Makefile by the line
M4FLAGS = -Dfcb_bytes_in_rec=131072
which provides good performance for gfortran. For g95, this
line must be changed to
M4FLAGS = -Dfcb_bytes_in_rec=4096
sauter_test
The program sauter_test.C is a C++ test program
contributed by Nick Sauter to help in resolving a memory
leak he found. The program is run as bin/sauter_test
and should run long enough to allow a check with
top to ensure that it has constant memory demands.
In addition, starting with release 0.7.8.1, the
addition of -DCBFLIB_MEM_DEBUG to the compiler
flags will cause detailed reports on memory use
to stderr to be reported.
adscimg2cbf
The example program adscimg2cbf accepts any number of raw or compressed ADSC images with
.img, .img.gz, .img.bz2 or .img.Z extensions and converts each of them to an imgCIF/CBF
file with a .cbf extension.
adscimg2cbf [--flag[,modifier]] file1.img ... filen.img (creates file1.cbf ... filen.cbf)
Image files may also be compressed (.gz, .bz2, .Z)
Flags:
--cbf_byte_offset Use BYTE_OFFSET compression (DEFAULT)
--cbf_packed Use CCP4 packing (JPA) compression.
--cbf_packed_v2 Use CCP4 packing version 2 (JPA) compression.
--no_compression No compression.
The following two modifiers can be appended to the flags (syntax: --flag,modifier):
flat Flat (linear) images.
uncorrelated Uncorrelated sections.
adscimg2cbf
The example program cbf2adscimg accepts any number of cbfs of ADSC images created by
adscimg1cbf or convert_image and produces raw or compressed adsc image files with
.img, .img.gz or .img.bz2 extensions.
cbf2adscimg [--flag] file1.cbf ... filen.cbf (creates file1.img ... filen.img)
Image files may be compressed on output: (.gz, .bz2) by using the flags below.\n");
Flags:
--gz Output a .gz file (e.g., filen.img.gz).
--bz2 Output a .bz2 file (e.g., filen.img.bz2).
tiff2cbf
The test program tiff2cbf converts a tiff data file to a cbf data file. The program
converts the tiff data samples directly into a minicbf with the tiff header
stored at the value of _array_data.header_contents. This conversion is
supported for the sample formats SAMPLEFORMAT_UINT (unsigned integer data),
SAMPLEFORMAT_INT (unsigned integer data), SAMPLEFORMAT_INT (signed integer data),
SAMPLEFORMAT_IEEEFP (IEEE floating point data), SAMPLEFORMAT_COMPLEXINT
(complex signed int) and SAMPLEFORMAT_COMPLEXIEEEFP (complex ieee floating).
Conversions from these formats to other CBF formats can be handled by cif2cbf.
If you wish to convert and xxx.tif written with IEEE floating point samples
into a CBF with integer values compressed by byte-offset compression
for use by XDS, creating an xxx_view.cbf with values clipped between 0 and 100,
and an xxx_xds.cbf with unclipped values for processing:
tiff2cbf xxx.tif xxx.cbf
cif2cbf -I 4 -C 100. -L 0. -e n -c b -i xxx.cbf -o xxx_view.cbf
cif2cbf -I 4 -e n -c b -i xxx.cbf -o xxx_xds.cbf
========================================================================
Version 1.5.4 (2007-07-28)
------------------------------------------------------------------------
Typographics corrections (HJB)
+ Corrected embedded degree characters to \%
+ Corrected embedded Aring to \%A
+ Added trailing ^ for a power
+ Removed 2 cases of a space after an underscore
in tag name.
========================================================================
Version 1.5.3 (2007-07-08)
------------------------------------------------------------------------
Changes to support SLS miniCBF and suggestions
from the 24 May 07 BNL imgCIF workshop (HJB)
+ Added new data items
'_array_data.header_contents',
'_array_data.header_convention',
'_diffrn_data_frame.center_fast',
'_diffrn_data_frame.center_slow',
'_diffrn_data_frame.center_units',
'_diffrn_measurement.sample_detector_distance',
'_diffrn_measurement.sample_detector_voffset
+ Deprecated data items
'_diffrn_detector_element.center[1]',
'_diffrn_detector_element.center[2]'
+ Added comments and example on miniCBF
+ Changed all array_id data items to implicit
========================================================================
Version 1.5.2 (2007-05-06)
------------------------------------------------------------------------
Further clarifications of the coordinate system. (HJB)
========================================================================
Version 1.5.1 (2007-04-26)
------------------------------------------------------------------------
Improve defintion of X-axis to cover the case of no goniometer
and clean up more line folds (HJB)
========================================================================
Version 1.5 (2007-07-25)
------------------------------------------------------------------------
This is a cummulative list of the changes proposed since the
imgCIF workshop in Hawaii in July 2006. It is the result
of contributions by H. J. Bernstein, A. Hammersley,
J. Wright and W. Kabsch.
2007-02-19 Consolidated changes (edited by HJB)
+ Added new data items
'_array_structure.compression_type_flag',
'_array_structure_list_axis.fract_displacement',
'_array_structure_list_axis.displacement_increment',
'_array_structure_list_axis.reference_angle',
'_array_structure_list_axis.reference_displacement',
'_axis.system',
'_diffrn_detector_element.reference_center_fast',
'_diffrn_detector_element.reference_center_slow',
'_diffrn_scan_axis.reference_angle',
'_diffrn_scan_axis.reference_displacement',
'_map.details', '_map.diffrn_id',
'_map.entry_id', '_map.id',
'_map_segment.array_id', '_map_segment.binary_id',
'_map_segment.mask_array_id', '_map_segment.mask_binary_id',
'_map_segment.id', '_map_segment.map_id',
'_map_segment.details.
+ Change type of
'_array_structure.byte_order' and
'_array_structure.compression_type'
to ucode to make these values case-insensitive
+ Add values 'packed_v2' and 'byte_offset' to enumeration of values for
'_array_structure.compression_type'
+ Add to definitions for the binary data type to handle new compression
types, maps, and a variety of new axis types.
2007-07-25 Cleanup of typos for formal release (HJB)
+ Corrected text fields for reference_ tag descriptions that
were off by one column
+ Fix typos in comments listing fract_ tags
+ Changed name of release from 1.5_DRAFT to 1.5
+ Fix unclosed text fields in various map definitions
========================================================================
Version 1.4 (2006-07-04)
------------------------------------------------------------------------
This is a change to reintegrate all changes made in the course of
publication of ITVG, by the RCSB from April 2005 through
August 2008 and changes for the 2006 imgCIF workshop in
Hawaii.
2006-07-04 Consolidated changes for the 2006 imgCIF workshop (edited by HJB)
+ Correct type of '_array_structure_list.direction' from 'int' to 'code'.
+ Added new data items suggested by CN
'_diffrn_data_frame.details'
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size and
'_array_intensities.pixel_binning_method
+ Added deprecated item for completeness
'_diffrn_frame_data.details'
+ Added entry for missing item in contents list
'_array_structure_list_axis.displacement'
+ Added new MIME type X-BASE32K based on work by VL, KM, GD, HJB
+ Correct description of MIME boundary delimiter to start in
column 1.
+ General cleanup of text fields to conform to changes for ITVG
by removing empty lines at start and finish of text field.
+ Amend example for ARRAY_INTENSITIES to include binning.
+ Add local copy of type specification (as 'code') for all children
of '_diffrn.id'.
+ For consistency, change all references to 'pi' to '\p' and all
references to 'Angstroms' to '\%Angstroms'.
+ Clean up all powers to use IUCr convention of '^power^', as in
'10^3^' for '10**3'.
+ Update 'yyyy-mm-dd' type regex to allow truncation from the right
and improve comments to explain handling of related mmCIF
'yyyy-mm-dd:hh:mm' type, and use of 'Z' for GMT time zone.
2005-03-08 and
2004-08-08 fixed cases where _item_units.code used
instead of _item_type.code (JDW)
2004-04-15 fixed item ordering in
_diffrn_measurement_axis.measurement_id
added sub_category 'vector' (JDW)
========================================================================
Version 1.3.2 (2005-06-25)
------------------------------------------------------------------------
2005-06-25 ITEM_TYPE_LIST: code, ucode, line, uline regexps updated
to those of current mmCIF; float modified by allowing integers
terminated by a point as valid. The 'time' part of
yyyy-mm-dd types made optional in the regexp. (BM)
2005-06-17 Minor corrections as for proofs for IT G Chapter 4.6
(NJA)
2005-02-21 Minor corrections to spelling and punctuation
(NJA)
2005-01-08 Changes as per Nicola Ashcroft.
+ Updated example 1 for DIFFRN_MEASUREMENT to agree with mmCIF.
+ Spelled out "micrometres" for "um" and "millimetres" for "mm".
+ Removed phrase "which may be stored" from ARRAY_STRUCTURE
description.
+ Removed unused 'byte-offsets' compressions and updated
cites to ITVG for '_array_structure.compression_type'.
(HJB)
========================================================================
Version 1.3.1 (2003-08-13)
------------------------------------------------------------------------
Changes as per Frances C. Bernstein.
+ Identify initials.
+ Adopt British spelling for centre in text.
+ Set \p and \%Angstrom and powers.
+ Clean up commas and unclear wordings.
+ Clean up tenses in history.
Changes as per Gotzon Madariaga.
+ Fix the ARRAY_DATA example to align '_array_data.binary_id'
and X-Binary-ID.
+ Add a range to '_array_intensities.gain_esd'.
+ In the example of DIFFRN_DETECTOR_ELEMENT,
'_diffrn_detector_element.id' and
'_diffrn_detector_element.detector_id' interchanged.
+ Fix typos for direction, detector and axes.
+ Clarify description of polarisation.
+ Clarify axes in '_diffrn_detector_element.center[1]'
'_diffrn_detector_element.center[2]'.
+ Add local item types for items that are pointers.
(HJB)
========================================================================
Version 1.3.0 (2003-07-24)
------------------------------------------------------------------------
Changes as per Brian McMahon.
+ Consistently quote tags embedded in text.
+ Clean up introductory comments.
+ Adjust line lengths to fit in 80 character window.
+ Fix several descriptions in AXIS category which
referred to '_axis.type' instead of the current item.
+ Fix erroneous use of deprecated item
'_diffrn_detector_axis.id' in examples for
DIFFRN_SCAN_AXIS.
+ Add deprecated items '_diffrn_detector_axis.id'
and '_diffrn_measurement_axis.id'.
(HJB)
========================================================================
Version 1.2.4 (2003-07-14)
------------------------------------------------------------------------
Changes as per I. David Brown.
+ Enhance descriptions in DIFFRN_SCAN_AXIS to make them less
dependent on the descriptions in DIFFRN_SCAN_FRAME_AXIS.
+ Provide a copy of the deprecated DIFFRN_FRAME_DATA
category for completeness.
(HJB)
========================================================================
Version 1.2.3 (2003-07-03)
------------------------------------------------------------------------
Cleanup to conform to ITVG.
+ Correct sign error in ..._cubed units.
+ Correct '_diffrn_radiation.polarisn_norm' range.
(HJB)
========================================================================
Version 1.2.2 (2003-03-10)
------------------------------------------------------------------------
Correction of typos in various DIFFRN_SCAN_AXIS descriptions.
(HJB)
========================================================================
Version 1.2.1 (2003-02-22)
------------------------------------------------------------------------
Correction of ATOM_ for ARRAY_ typos in various descriptions.
(HJB)
========================================================================
Version 1.2 (2003-02-07)
------------------------------------------------------------------------
Corrections to encodings (remove extraneous hyphens) remove
extraneous underscore in '_array_structure.encoding_type'
enumeration. Correct typos in items units list. (HJB)
========================================================================
Version 1.1.3 (2001-04-19)
------------------------------------------------------------------------
Another typo corrections by Wilfred Li, and cleanup by HJB.
========================================================================
Version 1.1.2 (2001-03-06)
------------------------------------------------------------------------
Several typo corrections by Wilfred Li.
========================================================================
Version 1.1.1 (2001-02-16)
------------------------------------------------------------------------
Several typo corrections by JW.
========================================================================
Version 1.1 (2001-02-06)
------------------------------------------------------------------------
Draft resulting from discussions on header for use at NSLS. (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME.
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to
'_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source',
'_diffrn_radiation.polarizn_source_norm',
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add '_diffrn_measurement.device' to category key.
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to
allow for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
========================================================================
Version 1.0 (2000-12-21)
------------------------------------------------------------------------
Release version - few typos and tidying up. (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
========================================================================
Version 0.7.1 (2000-09-29)
------------------------------------------------------------------------
Cleanup fixes. (JW)
+ Correct spelling of diffrn_measurement_axis in '_axis.id'
+ Correct ordering of uses of '_item.mandatory_code' and
'_item_default.value'.
========================================================================
Version 0.7.0 (2000-09-09)
------------------------------------------------------------------------
Respond to comments by I. David Brown. (HJB)
+ Add further comments on '\n' and '\t'.
+ Update ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Change 'meter' to 'metre' throughout.
+ Add missing enumerations to '_array_structure.compression_type'
and make 'none' the default.
+ Remove parent-child relationship between
'_array_structure_list.index' and '_array_structure_list.precedence'.
+ Improve alphabetization.
+ Fix '_array_intensities_gain.esd' related function.
+ Improve comments in AXIS.
+ Fix DIFFRN_FRAME_DATA example.
+ Remove erroneous DIFFRN_MEASUREMENT example.
+ Add '_diffrn_measurement_axis.id' to the category key.
========================================================================
Version 0.6.0 (1999-01-14)
------------------------------------------------------------------------
Remove redundant information for ENC_NONE data. (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
========================================================================
Version 0.5.1 (1999-01-03)
------------------------------------------------------------------------
Cleanup of typos and syntax errors. (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for '_diffrn_scan.id' definition.
========================================================================
Version 0.5 (1999-01-01)
------------------------------------------------------------------------
Modifications for axis definitions and reduction of binary header. (HJB)
+ Restore '_diffrn_detector.diffrn_id' to DIFFRN_DETECTOR KEY.
+ Add AXIS category.
+ Bring in complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
from cif_mm.dic for clarity.
+ Change '_array_structure.encoding_type' from type code to uline and
added X-Binary-Element-Type to MIME header.
+ Add detector beam centre '_diffrn_detector_element.center[1]' and
'_diffrn_detector_element.center[2]'.
+ Correct item name of '_diffrn_refln.frame_id'.
+ Replace reference to '_array_intensities.undefined' by
'_array_intensities.undefined_value'.
+ Replace references to '_array_intensity.scaling' with
'_array_intensities.scaling'.
+ Add DIFFRN_SCAN... categories.
========================================================================
Version 0.4 (1998-08-11)
------------------------------------------------------------------------
Modifications to the 0.3 imgCIF draft. (HJB)
+ Reflow comment lines over 80 characters and corrected typos.
+ Update examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
========================================================================
Version 0.3 (1998-07-04)
------------------------------------------------------------------------
Modifications for imgCIF. (HJB)
+ Add binary type, which is a text field containing a variant on
MIME encoded data.
+ Change type of '_array_data.data' to binary and specify internal
structure of raw binary data.
+ Add '_array_data.binary_id', and make
'_diffrn_frame_data.binary_id' and '_array_intensities.binary_id'
into pointers to this item.
========================================================================
Version 0.2 (1997-12-02)
------------------------------------------------------------------------
Modifications to the CBF draft. (JW)
+ Add category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes are made in implementing the workshop draft. Category
DIFFRN_ARRAY_DATA is renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE is renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for '_diffrn_frame_data.array_id' is changed from
'_array_structure_list.array_id' to '_array_structure.id'. Item
'_diffrn_detector.array_id' is deleted.
+ Add data item '_diffrn_frame_data.binary_id' to identify data
groups within a binary section. The formal identification of the
binary section is still fuzzy.
========================================================================
Version 0.1 (1997-01-24)
------------------------------------------------------------------------
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version is adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley
(AH).
Modifications to the CBF draft. (JW)
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories
have been generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category
ARRAY_DATA. This departs from the CBF notion of data existing
in some special comment. In this description, data are handled as an
ordinary data item encapsulated in a character data type. Although
data this manner deviates from CIF conventions, it does not violate
any DDL 2.1 rules. DDL 2.1 regular expressions can be used to define
the binary representation which will permit some level of data
validation. In this version, the placeholder type code "any" has
been used. This translates to a regular expression which will match
any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary.
It may be possible to use the DDL 2.1 ITEM_STRUCTURE and
ITEM_STRUCTURE_LIST categories to provide the information that is
carried in by the ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By
moving the array structure to the DDL level it would be possible to
define an array type as well as a regular expression defining the
data format.
+ Multiple array sections can be properly handled within a single
datablock.
========================================================================
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to
_array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
./CBFlib-0.9.2.2/doc/.undosymlinks 0000755 0000765 0000765 00000010535 11603747624 015130 0 ustar yaya yaya #!/bin/sh
######################################################################
# #
# .undosymlinks for CBFlib/doc directory #
# #
# #
# Version 0.7.8.2 25 Jun 2007 #
# #
# Paul Ellis and #
# Herbert J. Bernstein (yaya@bernstein-plus-sons.com) #
# #
# (C) Copyright 2006 - 2007 Herbert J. Bernstein #
# #
######################################################################
######################################################################
# #
# YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL #
# #
# ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS #
# OF THE LGPL #
# #
######################################################################
########################### GPL NOTICES ##############################
# #
# This program is free software; you can redistribute it and/or #
# modify it under the terms of the GNU General Public License as #
# published by the Free Software Foundation; either version 2 of #
# (the License, or (at your option) any later version. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program; if not, write to the Free Software #
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA #
# 02111-1307 USA #
# #
######################################################################
######################### LGPL NOTICES ###############################
# #
# This library is free software; you can redistribute it and/or #
# modify it under the terms of the GNU Lesser General Public #
# License as published by the Free Software Foundation; either #
# version 2.1 of the License, or (at your option) any later version. #
# #
# This library is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU #
# Lesser General Public License for more details. #
# #
# You should have received a copy of the GNU Lesser General Public #
# License along with this library; if not, write to the Free #
# Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, #
# MA 02110-1301 USA #
# #
######################################################################
# Usage ./.undosymlinks
for file in cif_img.dic cif_img.html cif_img_1_3_2.html \
cif_img_1.5.dic cif_img_1.5.html cif_img_1.5.4.html \
cif_img_1.6.dic cif_img_1.6.html cif_img_1.6.4.dic cif_img_1.6.4.html
do
rm -rf $file
done
for file in *
do
if [ -d "$file" ] ; then
if [ -e "$file/.undosymlinks" ] ; then
(cd "$file"; sh -c "./.undosymlinks")
fi
fi
done
./CBFlib-0.9.2.2/doc/Idiffrn_data_frame.array_id.html 0000644 0000765 0000765 00000005440 11603702115 020551 0 ustar yaya yaya
(IUCr) CIF Definition save__diffrn_data_frame.array_id
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
This item is an integer identifier which, along with
_array_data.array_id, should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-ID, the value of _array_data.binary_id
should be equal to the value given for X-Binary-ID.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
electrons per nanometres cubed (electrons/(metres * 10^( -9)^)^(-3)^)
electrons_per_angstroms_cubed
electrons per \%Angstroms cubed (electrons/(metres * 10^(-10)^)^(-3)^)
electrons_per_picometres_cubed
electrons per picometres cubed (electrons/(metres * 10^(-12)^)^(-3)^)
kilowatts
kilowatts
milliamperes
milliamperes
kilovolts
kilovolts
pixels_per_element
(image) pixels per (array) element
arbitrary
arbitrary system of units.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
The value of _array_intensities.pixel_fast_bin_size specifies
the number of pixels that compose one element in the direction
of the most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
Examples:
Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. In this example, three rotation axes and one translation axis
at nonzero values are specified, with one axis stepping. There is no
reason why more axes could not have been specified to step. Range
information has been specified, but note that it can be calculated from
the number of frames and the increment, so the data item
_diffrn_scan_axis.angle_range could be dropped.
Both the sweep data and the data for a single frame are specified.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
_diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
_diffrn_scan_frame.integration_time and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustments are made to
scan times and nonlinear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
Example 2 - a more extensive example (R. M. Sweet, P. J. Ellis &
H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the goniometer.
This leads to a choice: either the axes of
the detector are defined at the origin, and then a Z setting of -240
is entered, or the axes are defined with the necessary Z offset.
In this case, the setting is used and the offset is left as zero.
This axis is called DETECTOR_Z.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm X 0.150mm, the centre of the first pixel is at (0.075,
0.075) in this coordinate system.
Example 3 - Example 2 revised for a spiral scan (R. M. Sweet,
P. J. Ellis & H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the
goniometer, as in Example 2 above, but in this example the
image plate is scanned in a spiral pattern from the outside edge in.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. The rotation axis is called ELEMENT_ROT and the
radial axis is called ELEMENT_RAD. A 150 micrometre radial pitch
and a 75 micrometre 'constant velocity' angular pitch are assumed.
Indexing is carried out first on the rotation axis and the radial axis
is made to be dependent on it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon
from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:
YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL.
ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS
OF THE LGPL.
Before using this software, please read the
for important disclaimers and the IUCr Policy
on the Use of the Crystallographic Information File (CIF) and for other important
information.
Work on imgCIF and CBFlib supported in part by the U. S. Department of
Energy (DOE) under grants ER63601-1021466-0009501 and
ER64212-1027708-0011962, by the U. S. National Science Foundation (NSF)
under grants DBI-0610407, DBI-0315281 and EF-0312612, the U. S.
National Institutes of Health (NIH) under grants 1R15GM078077 from
NIGMS and 1R13RR023192 from NCRR and funding from the International
Union for Crystallographyn (IUCr). The content is solely the
responsibility of the authors and does not necessarily represent the
official views of DOE, NSF, NIH, NIGMS, NCRR or IUCr.
Version History
Version
Date
By
Description
0.1
Apr. 1998
PJE
This was the
first CBFlib release. It
supported binary CBF files using binary strings.
This release
added ascii imgCIF support using MIME-encoded binary sections, added
the option of MIME headers for the binary strings was well. MIME code
adapted from mpack 1.5. Added hooks needed for DDL1-style names without
categories.
This release
merged much of the message digest code into the general file reading and
writing to reduce the number of passes. More consistency checking between
the MIME header and the binary header was introduced. The size in the
MIME header was adjusted to agree with the version 0.2 documentation.
This release
removed the redundant information (binary id, size, compression id)
from a binary header when there is a MIME header, removed the unused
repeat argument, and made the memory allocation for buffering and
tables with many rows sensitive to the current memory allocation already used.
This release
modified cbf_simple.c to reorder image data on read so that the
indices are always increasing in memory (this behavior was
undefined previously).
This release cleans up some
compiler warnings, corrects a parse error on quoted strings with
a leading blank as adds the new routines for support of
aliases, dictionaries and real arrays, higher level routines
to get and set pixel sizes, do cell computations, and to set beam centers,
improves support for conversion of images, picking up more data from
headers.
This release reorganizes the kit
into two pieces: CBFlib_0.7.6_Data_Files and CBFlib_0.7.6. An optional local copy
of getopt is added. The 1.4 draft dictionary has been added. cif2cbf
updated to support vcif2 validation. convert_image and cif2cbf updated
to report text of error messages. convert_image updated to support
tag and category aliases, default to adxv images. convert_image and
img updated to support row-major images. Support added for binning.
API Support added for validation, wide files and line folding.
Logic changed for beam center reporting. Added new routines:
cbf_validate,
cbf_get_bin_sizes,
cbf_set_bin_sizes,
cbf_find_last_typed_child,
cbf_compose_itemname,
cbf_set_cbf_logfile,
cbf_make_widefile,
cbf_read_anyfile,
cbf_read_widefile,
cbf_write_local_file,
cbf_write_widefile,
cbf_column_number,
cbf_blockitem_number,
cbf_log,
cbf_check_category_tags,
cbf_set_beam_center
This release reflects changes
for base 32K support developed by G. Darakev, and changes
for support of reals, 3d arrays, byte_offset compression and
J. P. Abrahams packed compression
made in consultation with (in alphabetic order) E. Eikenberry,
A. Hammerley, W. Kabsch, M. Kobas, J. Wright and others at PSI
and ESRF in January 2007, as well accumulated changes fixing
problems in release 0.7.6.
This release is a patch
to 0.7.7 to change the treatment of the byteorder parameter from
strcpy semantics to return of a pointer to a string constant.
Our thanks to E. Eikenberry for pointing out the problem.
This release is a patch
to 0.7.7.3 to add f90 support for reading of CBF byte-offset and
packed compression, to fix problems with gcc 4.4.1 and to correct
errors in multidimensional packed compression.
New default release with updated pycbf, tiff support, removal of
default use of PyCifRW to avoid Fedora license issue.
Release 0.9.2, Herbert J. Bernstein, 12 February 2011
Source File
Change
Makefile.m4, Makefiles
Changes for libtiff and tiff2cbf. Create a separate
setup.py for MINGW. Allow CBF_DONT_USE_LONG_LONG variable to control
Makefiles. Disable default use of PyCifRW because of Fedora concerns
about PyCifRW license issues. Force use of long long for SWIG.
Update Makefiles to run changtestcompression. Update pycbf build.
cbf_template_t.c
Don't use /tmp for dectris template code.
Add EE's change for DLS signs
cbf_copy.c
Fix cbf_copy.c to handle not using long long correctly
Implement P. Chang's fast byte-offset decompress, but with
hooks to run on machines without long long support.
Fix bad mask, fix sign extension for MINGW and other
systems in which long long is not used.
Fix error in mpint_shift logic causing erroneous sign
Add changes in the compression infrastructure by P. Chang
to make the compressed size available on decompression.
Extend cbf_canonical to support long long and
double. Correct cbf_packed for elsize 8 data.
As per request by J. Lewis Muir, direct all warning messages
through cbf_log or new cbf_flog, so such messages can all
be suppressed by setting the logfile to NULL
cbf_byte_offset.c, cbf_file.c
Fix to byte-offset compression for 16 bit data with a delta that looks
like a flag. Fix to setting/getting file position when there is no stream.
Fix incorrect sign extension test as per N. Sauter.
convert_minicbf.c
Allow for changes in miniheader and report unrecognized lines but
continue. Also allow S/N instead of SN
Add a libtool build directory for future use of shared libraries.
cif2cbf.c
Add test for construct_detector to cif2cbf.
Fix getopt option string.
cif_tree.h
Add DDLm bracket types for nodes
adscimg2cbf.c, adscimg2cbf_sub.c
Apply mods to adscimg2cbf by C. Nielsen:
Add new command line options:
--beam_center_from_header,
Figure out beam center from ADSC header information (default);
--beam_center_mosflm,
Beam center in ADSC header: MOSFLM coordinates;
--beam_center_ulhc,
Beam center in ADSC header:
origin: upper left hand corner of image.(HKL mm);
--beam_center_llhc,
Beam center in ADSC header:
origin: lower left hand corner of image.(adxv mm)
cbff.h, cbff.c
Add src/cbff.c and include/cbff.h as start of full f95 wrapper for C code
Release 0.8.0, G. Todorov, Herbert J. Bernstein, 21 July 2008
Source File
Change
adscimg2cbf_sub.c, adscimg2cbf_sub.c
Patch to deal with gcc 4 optimization error in get_bo
Replaced with call to cbf_get_local_integer_byte_order.
Clean up spacing; trim trailing blanks in text fields; validate DDLm types.
Add MSG_DIGESTWARN.
Update spacing.
Fix includes for regex use.
Fixes on achar and anchar and element.
Added cbf_check_type_contents function that will verify ddlm types based on regular expressions.
Fix handling for bracketed unquoted words and handle more DDLm tags.
Fix scan of DDLm bracketed constructs with embedded quotes. Pick
up item names in DDLm save frames. Fix cif2cbf handling of bracketed
constructs in dictionaries.
Updates to bracketed construct parse and output logic.
Update write logic for bracketed constructs with folding.
cbf_set_tag_category() code fixed.
Change internal routine cbf_read_anyfile and add new user
routine cbf_read_buffered_file to support pre-read of input files
and memory-only files.
Add new routines cbf_io_buffersize and cbf_reset_in_bits and
change read logic to allow buffered reads.
Release 0.7.9.1, Chris Nielsen, Herbert J. Bernstein, 24 January 2008
Source File
Change
cbf2adscimg.c cbf2adscimg_sub.c
Last minutes fixes on release: Put missing byte swap in
cbf2adscimg.c for when byte orders differ. Bypass problems with gcc
optimization, and handle case then array header is there but invalid.
.symlinks .undosymlinks
Update version to 0.7.9
Makefile.m4 Makefile, Makefile_AIX ...
Update for CN's jiffies, and testing with MD5
signatures only
cbf2adscimg.c cbf2adscimg_sub.c
New inverse jiffie by Chris Nielsen of ADSC to convert
CBF files created by convert_image or adscimg2cbf to ADSC detector images.
This version depends on the header extract planted by convert_image
or adscimg2cbf.
cbf_byte_offset.c
Fix handling of byte offset compression when the data
does not compress.
cbf_codes.c
Fix 32K encoding big-endian test as per Ladislav Michnovic
.
cbf_packed.c
Correct mishandling of 64 bit data.
cbf_uncompressed.c
Remove redundant initialization of unsigned_char_data.
cbf_write.c.c
Fix conflicting uses of variable column by introducing
separate variable xcol.
README.html README
Update to version 0.7.9 directory structure and programs.
cbf.c
Fix local sensitivity of cbf_get_doublevalue
and cbf_set_doublevalue so "." will be accepted and written as the decimal point in
locales that use ",".
Release 0.7.9, Chris Nielsen, Herbert J. Bernstein, 30 December 2007
Source File
Change
Makefiles and test data
Change test cases to avoid deprecated features.
Release 0.7.8.2, Chris Nielsen, Herbert J. Bernstein, 25 December 2007
Source File
Change
adscimg2cbf.c adscimg2cbf_sub.c
New jiffie by Chris Nielsen of ADSC to convert
ADSC detector images to CBF.
Change dim1, dim2, dim3 to dimfast, dimmid, dimslow,
ndim1, ndim2 to ndimslow, ndimfast.
machines that do not provide swab.
cif2c.c
Make declaration of xciftmp conditional to avoid compiler warnings.
convert_image.c
Add code to check variations on pixel_size functions.
convert_minicbf.c
Add second quick exit option (-Q). Improve error reporting.
Update for most recent SLS miniheader.
getopt.c
Fix some compiler warnings.
Makefile.m4
add adscimg2cbf support
template_pilatus6m_2463x2527.cbf
Update pilatus6m template for correct detector axis definitions,
better comments and to list all categories used by SLS.
template_adscquantum315_3072x3072_rev.cbf
New, corrected ADSC Quantum 315 template.
Release 0.7.8.1, Chris Nielsen, Herbert J. Bernstein, 28 July 2007
Source File
Change
cbf.c
Rework cbf_free_handle to ensure release
of memory from root, not current position. Rework
cbf_read_anyfile to ensure close of file stream
on all exit cases. Fix save frame code in
cbf_validate to restart counts on each save frame.
Add name, idname and aliasname types from
latest DDL2 dictionary.
cbf_alloc.c, cbf_alloc.h
Add cbf_free_text to avoid type punning warnings
from gcc 4. Add memory debug based on adding -DCBFLIB_MEM_DEBUG
to CFLAGS.
cbf_simple.c
Add code to ensure against memory leaks
when working with a detector or positioner object.
cbf.stx.y, cbf_stx.c
Add calls to cbf_undo_links and cbf_free_text
to clean up memory leaks in parser. Add validation calls
to mark end of save frames.
cbf_tree.c, cbf_tree.h
Add cbf_undo_links to recover memory from
links used to rotate among columns of a table. Rework
cbf_free_node to avoid memory leaks.
cbf_uncompressed.c
Add #define __USE_XOPEN to avoid
a warning on use of swab on some systems.
sauter_test.C Makefile.m4
Add sauter_test to stress test for memory leaks.
On make install, place cbf.h and cbf_simple.h into include
directory.
Update handling of both beam center and
reference beam center to allow for units and new dictionary.
convert_minicbf.c
Add code to handle data in _array_data.header-contents.
Clean up error handling, map all SLS tags. Add -Q option to
convert old SLS comment format to new text field format.
Add M4FLAGS variable to control m4 expansion of
f90 test programs with different record lengths. For g95, the
record length must not be larger than the padding.
Change prototypes for all functions that return
byteorder from char * byteorder to const char ** byteorder.
Change prototypes of all functions that set byteorder from
char * byteorder to const char * byteorder
Change signatures for all functions that return
byteorder from char * byteorder to const char ** byteorder.
Change prototypes of all functions that set byteorder from
char * byteorder to const char * byteorder, and make the matching changes
in all calls.
Release 0.7.7, Herbert J. Bernstein, 19 February 2007
Source File
Change
cif2cbf.c
Add support for byte offset, packed version 2
and flat compression, and binary section padding. Add support
for base-32K encoding. Allow command line compression to
override compression_type in the file and to set
compression_type_flag.
convert_image.c
Add support for new -R and -F flags, for
use of reference beam center and flat packed compression
respectively.
cbf.h
Add constants CBF_PACKED_V2
for packed version 2 compression,
CBF_UNCORRELATED_SECTIONS for uncorrelated
sections in packed compression,
CBF_FLAT_IMAGE for original CBFlib
packed compression, PAD_1K, PAD_2K and
PAD_4K for trailing pad on binary sections,
ENC_BASE32K for base 32K encoding. Fix bad
code in DEBUG mode for failnez macros.
Add prototypes for cbf_get_arrayparameters_wdims,
cbf_get_integerarrayparameters_wdims,
cbf_get_realarrayparameters_wdims,
cbf_set_integerarray_wdims,
cbf_set_realarray_wdims,
cbf_mpint_load_acc,
cbf_mpint_store_acc,
cbf_mpint_clear_acc,
cbf_mpint_increment_acc,
cbf_mpint_decrement_acc,
cbf_mpint_negate_acc,
cbf_mpint_add_acc,
cbf_mpint_rightshift_acc,
cbf_mpint_leftshift_acc.
cbf_binary.h
Update prototypes
for cbf_get_bintext, cbf_set_bintext,
cbf_set_binary, cbf_binary_parameters,
cbf_get_binary to carry byteorder,
dimensions and padding.
cbf_byte_offset.h
Update prototypes
for cbf_compress_byte_offset,
cbf_decompress_byte_offset to carry byteorder,
dimensions and padding.
cbf_canonical.h
Update prototypes
for cbf_compress_canonical,
cbf_decompress_canonical to carry byteorder,
dimensions and padding.
cbf_codes.h
Add prototypes for base 32K
encoding: cbf_tobase32k, cbf_encode32k_bit_op,
cbf_isBigEndian, cbf_endianFix,
cbf_frombase32k, cbf_decode32k_bit_op.
cbf_compress.h
Update prototypes
for cbf_compress, cbf_decompress
to carry byteorder,
dimensions and padding.
cbf_packed.h
Update prototypes
for cbf_compress_packed,
cbf_decompress_packed to carry byteorder,
dimensions and padding.
cbf_predictor.h
Update prototypes
for cbf_compress_predictor,
cbf_decompress_predictor to carry byteorder,
dimensions and padding.
cbf_read_mime.h
Update prototype
for cbf_parse_mimeheader to carry byteorder,
dimensions and padding.
Update prototypes
for cbf_compress_none,
cbf_decompress_none to carry byteorder,
dimensions and padding.
Makefile
Update version and tests
to work against data files in
CBFlib_0.7.7_Data_Files.
cbf.c
Remove compiler warnings on signedness
and type punned pointers.
Fix bug in detection of local real format.
Add base32K support.
Fix inverted test in value range checking.
Add new routines cbf_get_arrayparameters_wdims,
cbf_get_integerarrayparameters_wdims,
cbf_get_realarrayparameters_wdims,
cbf_set_integerarray_wdims,
cbf_set_realarray_wdims,
cbf_mpint_load_acc,
cbf_mpint_store_acc,
cbf_mpint_clear_acc,
cbf_mpint_increment_acc,
cbf_mpint_decrement_acc,
cbf_mpint_negate_acc,
cbf_mpint_add_acc,
cbf_mpint_rightshift_acc,
cbf_mpint_leftshift_acc.
cbf.stx.y
Temporarily change to
use of YYSTYPE argument type to
remove an error when compiling under
on MS Windows. A better solution is
needed./
cbf_binary.c
Update cbf_get_bintext, cbf_set_bintext,
cbf_set_binary, cbf_binary_parameters,
cbf_get_binary to carry byteorder,
dimensions and padding.
cbf_byte_offset.c
Implement byte_offset
compression and decompression as
designed by A. Hammersley and
modified by W. Kabsch.
cbf_canonical.c
Fix warnings from gcc 4
on punned pointers. Update cbf_compress_canonical,
cbf_decompress_canonical to carry byteorder,
dimensions and padding.
cbf_codes.c
Add support forr base 32K
encoding: cbf_tobase32k, cbf_encode32k_bit_op,
cbf_isBigEndian, cbf_endianFix,
cbf_frombase32k, cbf_decode32k_bit_op.
cbf_compress.c
Update
cbf_compress, cbf_decompress
carry byteorder,
dimensions and padding.
cbf_file.c
Fix warnings from gcc 4
on punned pointers.
cbf_lex.c
Add support for
byteorder, dimensions and padding
and base 32K encoding.
cbf_packed.c
Update cbf_compress_packed,
cbf_decompress_packed to carry byteorder,
dimensions and padding. Add support
for J. P. Abrahams packed compression,
versions 1 and 2, while preserving
support for original CBFlib flat packed
compression. Add support for 64 bit
elements.
cbf_predictor.c
Update cbf_compress_predictor,
cbf_decompress_predictor to carry byteorder,
dimensions and padding.
cbf_simple.c
Change logic of most
image handling routines to work as special
cases of 3d routines. Add new routines
cbf_get_detector_id,
cbf_get_real_map_segment,
cbf_get_real_map_segment_mask,
cbf_set_map_segment,
cbf_set_map_segment_mask,
cbf_set_real_map_segment,
cbf_set_real_map_segment_mask,
cbf_get_3d_array_size,
cbf_get_3d_array,
cbf_set_3d_array,
cbf_get_axis_reference_setting,
cbf_set_axis_reference_setting,
cbf_construct_reference_detector,
cbf_require_reference_detector,
cbf_set_reference_beam_center.
cbf_read_mime.c
Update cbf_parse_mimeheader to read
MIME headers for new compression types and
flags and byteorder, dimensions and padding.
Add support for base 32K encoding.
cbf_tree.c
Fix warnings from gcc 4
on punned pointers.
cbf_uncompressed.c
Fix handling of 64-bit
reads and writes.
cbf_write_binary.c
Add code to write out
base-32K encoded sections, to write
byte order, dimensions and padding. Add code
to write out MIME headers for
packed compressions or packed version 2
compression with flags for uncorrelated
sections and for flat packed images.
Add include of stdio.h; change CBF_LINELENGTH
into CBF_LINELENGTH_10 and CBF_LINELENGTH_11; add new symbols
CBF_CASE_INSENSITIVE, CBF_CASE_SENSITIVE, CBF_LOGERROR,
CBF_LOGWARNING, CBF_LOGWOLINE, CBF_LOGWOCOLUMN, CBF_LOGSTARTLOC,
CBF_LOGCURRENTLOC; add information on input file and
log file to cbf handle struct; and prototypes for
cbf_read_widefile, cbf_write_local_file, cbf_write_widefile,
cbf_column_number, cbf_blockitem_number, cbf_warning,
cbf_error, cbf_log, cbf_increment_column, cbf_reset_column,
cbf_reset_refcounts, cbf_validate; added valuerow argument
to cbf_set_hashedvalue
and caseinsensitive to cbf_find_hashedvalue.
cbf.c
In cbf_make_handle, added include of cbf_ascii.h,
initialized handle->logfile, handle->warnings, handle->errors,
handle->startline, handle->startcolumn; added new routine
cbf_set_logfile; in cbf_free_handle removed gcc4 warning;
broke up cbf_read_file into cbf_read_anyfile, cbf_read_file,
added two more entries to parse array, one for the cbf handle
and one to carry an auxillary node, such as a parent
category; in cbf_write_file, reset reference counts; added
new routine cbf_write_local_file to allow writing of a local
portion of a cbf instead of the whole thing; added new routines
cbf_column_number and cbf_blockitem_number; added new
routine cbf_log to report parse errors with line numbers;
fixed cbf_require_category when dealing with null datablocks;
fixed cbf_require_column to preserve current row number;
fixed inverted logic in cbf_require_dictionary; rewrote
cbf_set_hashed_value to deal with insertions correctly;
revised cbf_find_hashedvalue to survive commong errors;
revised cbf_convert_dictionary_definition to recover
category information properly and top deal with more
complex loop-singleton interactions; added new routines
cbf_increment_column, cbf_reset_column, cbf_reset_refcounts;
updated cbf_convert_dictionary to align database with changes
in cbf_convert_dictionary_definition and to distribute
unspecified items from parents to children; fixed
cbf_find_local_tag for DDL1 names and categories;
updated cbf_find_category_root and cbf_require_category_root
to allow for DDL1 categories drawn from dictionaries;
changed cbf_find_tag_root and cbf_set_tag_root to use
cbf_find_hashedvalue and cbf_set_hashedvalue; added routines
cbf_check_category_tags, cbf_validate.
cbf.stx.y
To facilitate validation, changed save frame
logic to append partial save frame to the base cif from the
beginning instead of waiting for the end of the save frame;
added cbf_validate calls at all levels and provided detailed
parse form common errors with reports via cbf_log
cbf_ascii.h
Add prototype for cbf_foldtextline.
cbf_ascii.c
Added new routine cbf_foldtextline; in
cbf_write_ascii changed logic to no longer backslash-quote
individual embedded semicolons in text fields and to
use full line-folding spec;
cbf_canonical.c
fixed gcc4 warning.
cbf_cantext.c
fixed gcc4 warnings.
cbf_file.h
Add columnlimit to strcut; add
prototype for cbf_make_widefile.
cbf_file.c
In cbf_make_file added intialization of line
length; added new routine cbf_make_widefile; in
cbf_read_character do not increment column number at EOF;
in cbf_read_line report lines over the limit
cbf_lex.c
Added lexical validation for line length,
illegal characters, long data block names, long save frame
names, failure to provide whitespace after loop_, unterminated
quoted strings.
cbf_packed.c
Fix gcc4 warnings
cbf_read_mime.c
Pick up corrections to parse of types from
work by GD for X-BASE32K.
cbf_simple.h
Add prototypes for cbf_get_bin_sizes,
cbf_set_bin_sizes
cbf_simple.c
Changed cbf_read_template to use cbf_read_widefile;
added new routines cbf_get_bin_sizes and cbf_set_bin_sizes;
changed cbf_set_gain, cbf_set_overload, cbf_set_integration_time,
cbf_set_datestamp, cbf_set_axis_setting to force in intervening
categories and columns; in cbf_free_positioner, cbf_free_detector,
fixed gcc4 warnings; revised cbf_set_beam_center to adjust the
displacement rather than the offset.
cbf_tree.h
Add symbol for CBF_VALUE as a node type to
use for validation; add prototype for cbf_find_last_typed_child.
cbf_tree.c
In cbf_free_node fixed gcc4 warning; added
new routine cbf_find_last_typed_child; changed cbf_make_child
to use cbf_find_last_typed_child instead of cbf_fid_last_child
to avoid confusion between categories and save frames when
the same name is used for both; changed cbf_compute_hashcode
to return values between 0 and 255.
cbf_write.d
Add prototype for cbf_compose_itemname.
cbf_write.c
In cbf_set_value fold text fields that contain
the text field terminator; add new routine cbf_compose_itemname,
int cbf_write_itemname catch names that are too long;
cif2cbf.c
Add "-v dictionary" command line argument
and suppress output to /dev/null and "-w" to process a
wide file; add hooks (based on symbol GNUGETOPT) to use
a local copy of getopt; add text for error exits; add code
to load layered dictionaries.
convert_image.c
Add text for error exits; add logic for
binning; alias support with command line arguments
"-c category_alias=category_root" and "-t tag_alias=tag_root",
change from _diffrn_detector.sample_detector_distance
to _diffrn_measurement.sample_detector_distance; change
to support row-major images to agree with adxv; remove
most advisory messages to stdout.
img.h
Added rowmajor to struct; redefined img_pixel
to be conditional on rowmajor; added img_pixelptr to get
the pointers to the image.
img.c
Added recognition of ADSC QUANTUM315;
added row major support
Revised header for open source licenses; added
support for aliases, dictionaries and real arrays; added
convenience routines to do searches with default creation
of what is being searched for; added reference count and
dictionary link for cbf handles; added cbf_new_saveframe,
cbf_force_new_saveframe, cbf_set_saveframename,
cbf_reset_saveframe, cbf_remove_saveframe, cbf_rewind_saveframe,
cbf_rewind_blockitem, cbf_next_saveframe, cbf_next_blockitem,
cbf_select_saveframe, cbf_select_blockitem, cbf_find_saveframe,
cbf_require_row, cbf_require_nextrow, cbf_count_saveframes,
cbf_count_blockitems, cbf_saveframe_name, cbf_require_value,
cbf_require_integervalue, cbf_require_doublevalue,
cbf_get_realarrayparameters, cbf_get_realarray, cbf_set_realarray,
cbf_require_datablock, cbf_require_category, cbf_require_column,
cbf_require_column_value, cbf_require_column_integervalue,
cbf_require_column_doublevalue, cbf_get_local_integer_byte_order,
cbf_get_local_real_byte_order, cbf_get_local_real_format,
cbf_get_dictionary, cbf_set_dictionary, cbf_require_dictionary,
cbf_set_hashedvalue, cbf_find_hashedvalue,
cbf_convert_dictionary_definition, cbf_convert_dictionary,
cbf_find_tag, cbf_find_local_tag, cbf_srch_tag,
cbf_find_category_root, cbf_require_category_root,
cbf_set_category_root, cbf_find_tag_root, cbf_require_tag_root,
cbf_set_tag_root, cbf_find_tag_category, cbf_set_tag_category.
cbf.h
Revised header for open source licenses;
added definitions of CBF_API_VERSION and CBF_DIC_VERSION;
changed the debug versions of cbf_failnez and cbf_onfailnez
to stringfy the argument; added dictionary and reference
count to cbf_handle definition; added prototypes for
cbf_new_saveframe, cbf_force_new_saveframe, cbf_set_saveframename,
cbf_remove_saveframe, cbf_rewind_saveframe, cbf_rewind_blockitem,
cbf_next_saveframe, cbf_next_blockitem, cbf_saveframe_name,
cbf_select_saveframe, cbf_select_blockitem, cbf_find_saveframe,
cbf_require_row, cbf_require_nextrow, cbf_count_saveframes,
cbf_count_blockitems, cbf_require_value,
cbf_require_integervalue, cbf_require_doublevalue,
cbf_get_realarrayparameters, cbf_get_realarray, cbf_set_realarray,
cbf_require_datablock, cbf_require_category, cbf_require_column,
cbf_require_column_value, cbf_require_column_integervalue,
cbf_require_column_doublevalue, cbf_get_local_integer_byte_order,
cbf_get_local_real_byte_order, cbf_get_local_real_format,
cbf_get_dictionary, cbf_set_dictionary, cbf_require_dictionary,
cbf_set_hashedvalue, cbf_find_hashedvalue,
cbf_convert_dictionary_definition, cbf_convert_dictionary,
cbf_find_tag, cbf_find_local_tag, cbf_srch_tag,
cbf_find_category_root, cbf_require_category_root,
cbf_set_category_root, cbf_find_tag_root, cbf_require_tag_root,
cbf_set_tag_root, cbf_find_tag_category, cbf_set_tag_category,
cbf_alloc.c
Revised header for open source licenses.
cbf_alloc.h
Revised header for open source licenses.
cbf_ascii.c
Revised header for open source licenses.
cbf_ascii.h
Revised header for open source licenses.
cbf_binary.c
Revised header for open source licenses;
added support of real arrays.
cbf_binary.h
Revised header for open source licenses;
added support of real arrays.
cbf_byte_offset.c
Revised header for open source licenses;
changed signature for support of real arrays; no actual
changes to the code.
cbf_byte_offset.h
Revised header for open source licenses;
changed signature for support of real arrays; no actual
changes to the code.
cbf_canonical.c
Revised header for open source licenses;
changed signatures for support of real arrays; no actual
changes to the code.
cbf_canonical.h
Revised header for open source licenses;
changed signatures for support of real arrays; no actual
changes to the code.
cbf_codes.c
Revised header for open source licenses.
cbf_codes.h
Revised header for open source licenses.
cbf_compress.c
Revised header for open source licenses;
added support of real arrays.
cbf_compress.h
Revised header for open source licenses;
added support of real arrays.
cbf_context.c
Revised header for open source licenses.
cbf_context.h
Revised header for open source licenses.
cbf_file.c
Revised header for open source licenses;
added support of real arrays, making extensive changes
to the handling of integers to get past 32 bit limits.
cbf_file.h
Revised header for open source licenses..
cbf_lex.c
Revised header for open source licenses;
added save frame support; required whitespace before a
comment; changed WORD to CBFWORD; corrected quoted string
parse to allow for a blank immediately after the opening
quote mark.
cbf_lex.h
Revised header for open source licenses.
cbf_packed.c
Revised header for open source licenses;
changed signatures for support of real arrays; no actual
changes to the code.
cbf_packed.h
Revised header for open source licenses;
changed signatures for support of real arrays; no actual
changes to the code.
cbf_predictor.c
Revised header for open source licenses;
changed signatures for support of real arrays; no actual
changes to the code.
cbf_predictor.h
Revised header for open source licenses;
changed signatures for support of real arrays; no actual
changes to the code.
cbf_read_binary.c
Revised header for open source licenses.
cbf_read_binary.h
Revised header for open source licenses.
cbf_read_mime.c
Revised header for open source licenses;
added support for real arrays.
cbf_read_mime.h
Revised header for open source licenses;
added support for real arrays.
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