garlic-1.6/0000755000000000000000000000000010430074716012561 5ustar rootroot00000000000000garlic-1.6/data/0000755000000000000000000000000010403105234013460 5ustar rootroot00000000000000garlic-1.6/data/favicon.ico0000644000000000000000000000047607302167720015624 0ustar rootroot00000000000000(( garlic-1.6/data/index.html0000644000000000000000000001213310361666005015470 0ustar rootroot00000000000000 Molecular Structures

Molecular Structures

PDB files, proteins, nucleic acids, vitamins, sugars, lipids, small organic compounds, flavors, garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This page contains the list of sites with molecular structures. This list contains only the sites which contain data in PDB format. Note that links are subject to changes. If this happens, use Google or some other search engine to find the site. Use the words (or even entire titles) from the middle column as search terms.

DATA LINK REFERENCE
Proteins and
Nucleic Acids 		The Protein Data Bank,
http://www.rcsb.org/pdb/ 		H.M.Berman, J.Westbrook, Z.Feng,
G.Gilliland, T.N.Bhat, H.Weissig,
I.N.Shindyalov, P.E.Bourne,
The Protein Data Bank,
Nucleic Acids Research 28,
pp. 235-242 (2000).
Hetero
Compounds 		Hetero-compound Information
Centre - Uppsala,
http://xray.bmc.uu.se/hicup/ 		Kleywegt, G.J. and Jones, T.A. (1998).
Databases in protein crystallography.
Acta Cryst D54,
1119-1131 (CCP4 Proceedings).
Many Small
Molecules 		Molecular Models from Chemistry
at Okanagan University College,
http://people.ouc.bc.ca/woodcock/molecule/molecule.html 		Prepared by Dr. Dave Woodcock.
Smells
Database 		Smells Database, ChemConnections Project,
College of Chemistry, University of California, Berkeley,
http://mc2.cchem.berkeley.edu/Smells/index.html 		ChemConnections Project.
Pedagogical
PDB's,
Vitamins 		Computer Based Resources
for Chemistry and Biochemistry Students,
Department of Chemistry, Georgia State University,
http://chemistry.gsu.edu/glactone/ 		Glactone Project,
University System of Georgia.
Small
Organic
Compounds 		Klotho: Biochemical Compounds Declarative Database,
biocheminfo.org,
http://www.biocheminfo.org/klotho
Compound List:
http://www.biocheminfo.org/klotho/compound_list.html 		Klotho: Biochemical Compounds
Declarative Database,
Brian H. Dunford-Shore,
Waheeda Sulaman, Brian Feng,
Francis Fabrizio, Jason Holcomb,
William Wise and Toni Kazic.
Vitamins PDB Files of the Vitamins and Their Cofactor Derivatives,
Glactone's CD-ROM of PDB Files,
Department of Chemistry, Georgia State University,
http://chemistry.gsu.edu/cwcs/MM-CD/workshop02/docs/vitamins.htm 		Glactone's CD-ROM of PDB Files.
Sugars PDB Files of Some Sugars,
Glactone's CD-ROM of PDB Files,
Department of Chemistry, Georgia State University,
http://chemistry.gsu.edu/cwcs/MM-CD/workshop02/docs/sugars.htm 		Glactone's CD-ROM of PDB Files.
Lipids PDB Files of Some Lipids,
Glactone's CD-ROM of PDB Files,
Department of Chemistry, Georgia State University,
http://chemistry.gsu.edu/cwcs/MM-CD/workshop02/docs/lipids.htm 		Glactone's CD-ROM of PDB Files.
Flavors PDB Files of Some Flavors,
Glactone's CD-ROM of PDB Files,
Department of Chemistry, Georgia State University,
http://chemistry.gsu.edu/cwcs/MM-CD/workshop02/docs/flavors.htm 		Glactone's CD-ROM of PDB Files.
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_\!& Garlic - Precompiled Packages

Garlic - Precompiled Packages

garlic, precompiled packages, Debian, Mandriva, SuSE, Linux MLD, Linspire, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
Precompiled garlic packages are available for a number of systems. Be sure to check the program version. It is very easy to download and compile the latest source code!
Linux distributions with precompiled garlic:
[ Debian ] [ Mandriva ] [ SuSE ] [ Linux MLD (Japanese) ] [ Linspire ]

VigyaanCD (bioinformatics, computational biology and computational chemistry for Linux):
http://www.vigyaancd.org/

FreeBSD port:
http://www.freebsd.org/ports/biology.html

HPUX:
http://hpux.cs.utah.edu/hppd/hpux/Physics/garlic-1.4/

AIX:
http://aixpdslib.seas.ucla.edu/packages/garlic.html
garlic-1.6/precompiled_packages/garlic.gif0000755000000000000000000000465010140406144020652 0ustar rootroot00000000000000GIF87aFFɲ̻ոտĻ®ȹ@]^\ @ @P @@x((]VVP(PdVd dd\?).]@vP]dD(r?V @, @()$V@@]\ @lVi(rV@@l,( ]V) @@H]@\]@HiH(\VL @(PVd @X(,Vdd*[H\L( Vh𤝂pDPD]HxM x @(IVd( Vddx(/VrP d^ @F FR<_Pd?.@2_<  @F Fn(VGR (@,FF @PÇ#Jl8  %jܸ1A$

_\!& Garlic Reference Card

Garlic Reference Card, Version 1.6

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
Garlic reference card contains the list of commands and keywords, with short description of commands. Print this page and keep it at hand during your garlic sessions. Garlic reference card is not a learning tool, it is just a reminder. Newbies should start with garlic tutorial.
html version Make sure that your browser is properly configured for printing.
garlic-1.6/refcard/garlic.gif0000644000000000000000000000465007061671123016125 0ustar rootroot00000000000000GIF87aFFɲ̻ոտĻ®ȹ@]^\ @ @P @@x((]VVP(PdVd dd\?).]@vP]dD(r?V @, @()$V@@]\ @lVi(rV@@l,( ]V) @@H]@\]@HiH(\VL @(PVd @X(,Vdd*[H\L( Vh𤝂pDPD]HxM x @(IVd( Vddx(/VrP d^ @F FR<_Pd?.@2_<  @F Fn(VGR (@,FF @PÇ#Jl8  %jܸ1A$

_\!& Garlic Reference Card, Version 1.6
COM. ARGUMENTS APPLIES TO DESCRIPTION
ADD the same as for SEL selection Add to selection
ANG angle (degrees) helical wheel,
hydrophob. mom. 		Angle for helical wheel
and hydrophobic moment
calculation
ATO 0, 1, 2, 3, 4, 5, 6, 7, BAL, BA2, SMA,
SM2, COV, CO2, SPA, SP2, BIG, BI2 		selection Set drawing style for atoms
BAC 0, 1, 2, 3, 4, 5, OFF selection Draw backbone
BAL radius (angstroms) structure Set ball radius
BG color_specification main window Change background color
BLU width height, OFF main window Blur (soften) image
BON 0, 1, 2, 3, 4, 5, NICE,
REFRESH 		selection Set bond style or
refresh (reset) bonds
CAT structure_identifier structure Catch structure
CEN none structure, selection Redefine system origin
COL detailed_color_specification,
red, green, blue, yellow, cyan,
magenta, white, yellow-green,
cyan-green, cyan-blue, magenta-blue,
magenta-red, orange, cold (default),
hot, monochrome, cpk, size, zebra,
chain, hyphob, weighted 		selection Assign color;
do not abbreviate
color scheme name!
COM none, OFF,
minimal_score segment_width,
CORNER serial1 serial2,
ZOOM zoom_factor 		both sequence
buffers 		Compare two sequences
CRE none main seq. buffer,
main struct. buffer 		Create new structure
DIS structure_identifier
*, all 		structure Discard structure
DOC identifier_1 identifier_2
OFF 		Two structures Prepare two structures
for docking
DUM AVE filename,
HYD filename,
F1 ... F7 (with filename) 		Hydrophobicity functions Dump numeric values for
selected hydrophob. f.
EDI OFF, ATO, BON atom1 atom2, CLI,
DIM, MAI, OME, PHI, PSI, SID 		structure Edit structure
EXE file_name script file Execute script
EXI none garlic session Quit garlic session
FAD FRO shift, BAC shift, OFF, PLA,
SPH, CYL, HALF-SPH, HALF-CYL 		structure Change color fading
FG color_specification main window Change text color
FON font_name all windows Change font
GRO id1 id2 ... idN,
ALL, SAV filename, SSC filename 		structure(s) Group structures
HID none selection Hide atoms and bonds
HYB none, OFF structure Generate hydrogen bonds
LAB none, OFF selection Show labels
LOA file_name structure_file Load structure (file)
LOG file_name, OFF commands Log garlic commands
MEM none, OFF, BET, RAD radius,
THI thickness, TRA transparency 		membrane Show or hide membrane,
set properties
MON none main window Switch to mono mode
MOV ALL, MEM, PLA, STR struct., memb., plane Attach controls to object
NEI none, VER, OFF main window Show or hide
sequence neighborhood
PAT = res_name_list1 / * / res_name_list2 ...
TOL number_allowed_errors 		pattern buffer define sequence pattern
or set pattern tolerance
PAU none garlic script Pause script execution
PLA none, OFF, RAD radius,
TRA transparency 		plane Show or hide plane,
set properties
PLO HYD, MOM, OFF,
HYD start_residue end_residue,
MOM_start_residue end_residue
SID start_residue end_residue
F1, F2, F3, F4, F5, F6, F7 		sequence buffer Plot average hydrophob.,
hydrophobic moment,
sided hydrophobicity
or some other function
POS x, y, z structure Move to (x, y, z)
PRO radius (angstroms) structure Set probe radius
QUI none garlic session Quit garlic session
RAD radius (angstroms) Selection sphere Change sel. sphere radius
RAM none, SEL, OFF structure Draw Ramachandran plot
REF none, OFF main window Refreshing on/off
REG none mail Register garlic
REP none structure, seq. buffer Replace selected residues
RES the same as for SEL selection Restrict selection
ROT axis angle (degrees) structure Rotate
SAV file_name
file_name SEL 		structure, selection Save atomic data to file
(SEL = selection only)
SCA EIS, KD, INT, IN2, OCT, DIF hydrophobicity scale Choose hydrophob. scale:
Eisenberg, Kyte-Doolittle,
interface, octanol
SEL chains/res_nums/res_names/atom_names,
residue_numbers,
residue_names,
*, ALL, ABO, ACI, ALI, ALT, BAD, BAS,
BEL, CHA, CIS, COM, HET, PHO, MAI,
MOD model_number, NEG, PAT, POL, POS,
SEQ, SID, SMA, SPH, TIN, TM, TRA, TRI,
2C3, 2CZ3, 2NZ3, 3C4, 3CZ4, 3NZ4, 3C5,
3CZ5, 3NZ5, 4C5, 4CZ5, 4NZ5, 3C6, 3CZ6,
3NZ6, 4C6, 4CZ6, 4NZ6, 5C6, 5CZ6, 5NZ6,
4C7, 4CZ7, 4NZ7, 5C7, 5CZ7, 5NZ7, 5P7,
6P7, 4C9, 4CZ9, 4NZ9, 5C9, 5CZ9, 5NZ9 		structure,
selection 		Define new selection
(overwrite previous);
C = charged,
Z = zwitterionic,
N = negative,
P = polar
SEQ = three_letters_code, LOAD filename,
FROM structure_identifier, COPY,
SAVE filename, SWN filename, RESET 		sequence buffer,
reference seq. buffer 		Manipulate sequence
buffer
SET PHI, PSI, OME, CHI1, CHI2, CHI3,
CHI4, CHI5 (angle required, degrees) 		structure Set dihedral angle
SHO none selection Show atoms and bonds
SLA FRO shift, BAC shift, OFF, PLA,
SPH, CYL, HALF-SPH, HALF-CYL 		structure Change slab
SSB 0, 1, 2, 3, 4, 5, NICE disulfide bonds Style for disulf. bonds
STE none, OFF main window Switch to stereo mode
STI radius (angstroms) structure Set stick radius
STR = one_letter_code, LOAD filename,
FROM structure_identifier, COPY,
SAVE filename, RESET 		sec. struct. buffer,
ref. sec. struct. buffer 		Manipulate secondary
structure buffer
TAG "string", OFF structure Assign or remove tag
TBG color_specification input and output win. Change text background
TFG color_specification input and output win. Change text color
TIT identifier x y "string"
identifier x y
identifier OFF 		main window Add, move or
remove title
TRA axis shift structure Translate
VEN none, OFF,
start_residue end_residue 		sequence buffer Draw Venn diagram with
statistics
WHE none, OFF, CLOCKWISE,
start_index end_index,
start_index end_index CLOCKWISE 		sequence buffer Draw helical wheel
WIN number_of_residues sliding window Set sliding window width
garlic-1.6/techinfo/0000755000000000000000000000000010403105234014346 5ustar rootroot00000000000000garlic-1.6/techinfo/favicon.ico0000644000000000000000000000047607063422011016501 0ustar rootroot00000000000000(( garlic-1.6/techinfo/index.html0000644000000000000000000000655010361665130016362 0ustar rootroot00000000000000 Technical Requirements

Technical Requirements

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
Garlic tends to be POSIX compliant. It is also ANSI C compliant, to the maximum possible extent. Xlib functions are the only non-ANSI functions used by this program.
OPERATING SYSTEM
Unix or Unix clone and the X window system. Linux and XFree86 recommended.

SUPPORTED HARDWARE PLATFORMS
Desktop PC, laptop, notebook, Unix workstation equipped with a color monitor with a color depth of at least 8 bits per pixel. Garlic may also be used on Apple MacIntosh running Xtools from Tenon . Click here for instructions if you have such system. No dials are required. Some X servers do not support TrueColor visual at 8 bits per pixel: try to switch to higher color depth (12, 15, 24, ...)! If you have the SGI Octane workstation, you might be interested to read this text. If you have IBM RS6000 with AIX, read this hint.

CPU
Intel, Digital Alpha, HP, SUN MIPS, SGI and some others. This program has no special hardware requirements.

GRAPHICS INTERFACE
Garlic requires the X window system. The recommended version is X11R6, but older versions may work too.
THE X SERVER SHOULD BE CAPABLE TO SUPPORT THE TrueColor VISUAL!
Some older servers may be unable to support the TrueColor visual; if you have such X server, garlic will refuse to work. Some modern X servers do not support the TrueColor visual at 8 bits per pixel, but these are usually running on a hardware which may offer 12 or more bits per pixel.

COMPILER
GNU C compiler is recommended, but other compilers compliant with ANSI C standard should work too.

REQUIRED LIBRARIES
The only required libraries are libc (C), libm (mathematical) and libX11 (the standard X11 library).

KEYBOARD
The standard PC 101/102 keyboard should work fine. The laptop keyboard may be used too. If you have some kind of Unix workstation with terminal keyboard, this may work too.

MOUSE
Any mouse should serve well.

THE LIST OF COMPATIBLE SYSTEMS
Up to now, it is confirmed that garlic may be compiled and used on these systems:
Intel and compatible processors;
Digital Alpha;
Sun Solaris;
SGI (Silicon Graphics);
HPUX (Hewlett-Packard);
MacOSX (Apple).

Please inform me ( zucic@mefos.hr ) if you successfully compiled and used garlic on a system which is not listed here.
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Mouse Usage

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
MOUSE USAGE IN DEFAULT MODE
Move the mouse pointer over the structure and you will see the textual information about the atom covered by the pointer. This information will be visible in the output window (the bottom right corner of the main window).

If viewing some large structure (like protein or DNA), the sequence neighborhood of the residue covered by the mouse pointer will be visible in the top portion of the main window (see the example below).

The structure drawing mode is not the only mode where this trick may be used: try also Ramachandran plot, hydrophobicity plots and sequence comparison. The examples below show the content of the output window for all four cases:

Structure
display 		Ramachandran
plot 		Averaged
hydrophobicity 		Sequence
comparison

The image below is an example of the sequence neighborhood. Read the text about the command NEIGHBORHOOD for more information about sequence neighborhood.



USING MOUSE INSTEAD OF KEYBOARD CONTROLS
Mouse clicks may be used for rotations, translations, and for slab and color adjustment. If you want to rotate or translate the structure, or to change slab and color fading, click on a selected button in the control window (the top right corner of the main window). Shift, alt and control play the same role as if keyboard is used for the same job.

Some desktop environments (like KDE and Gnome) use function keys to launch pop-up menus or for some other purpose. This means that function keys F1, F2, F3 and F4 will not work properly with garlic. You can use mouse to click on dummy buttons in a control window. Another approach will be to change the desktop environment settings.

MOUSE USAGE IN EDITING MODE
After executing the EDIT CLICK command, the mouse may be used to pick a single bond for editing. Read the page about the command EDIT to learn how to pick a single bond.

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Download garlic

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
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HTTP DOWNLOAD

Croatia: http://garlic.mefos.hr/sources/garlic-1.6

DEBIAN PACKAGES

Program: http://packages.debian.org/stable/science/garlic.html
Documentation: http://packages.debian.org/stable/doc/garlic-doc.html

RPM PACKAGES

The RPM package may be found at at.rpmfind.net . Use the search engine (at this site) to find the appropriate RPM package.

At least two RPM-based Linux distributions contain garlic:

[ Mandriva ] [ SuSE ] garlic-1.6/download/garlic.gif0000644000000000000000000000465007061730072016325 0ustar rootroot00000000000000GIF87aFFɲ̻ոտĻ®ȹ@]^\ @ @P @@x((]VVP(PdVd dd\?).]@vP]dD(r?V @, @()$V@@]\ @lVi(rV@@l,( ]V) @@H]@\]@HiH(\VL @(PVd @X(,Vdd*[H\L( Vh𤝂pDPD]HxM x @(IVd( Vddx(/VrP d^ @F FR<_Pd?.@2_<  @F Fn(VGR (@,FF @PÇ#Jl8  %jܸ1A$

_\!& _\!& GNU GENERAL PUBLIC LICENSE

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.

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the software is modified by someone else and passed on, we want its
recipients to know that what they have is not the original, so that any
problems introduced by others will not reflect on the original authors'
reputations.

Finally, any free program is threatened constantly by software patents. We
wish to avoid the danger that redistributors of a free program will
individually obtain patent licenses, in effect making the program
proprietary. To prevent this, we have made it clear that any patent must be
licensed for everyone's free use or not licensed at all.

The precise terms and conditions for copying, distribution and modification
follow.

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" means either the Program
or any derivative work under copyright law: 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 covered
by this License; they are outside its scope. The act of running the Program
is not restricted, and the output from the Program is covered only if its
contents constitute a work based on the Program (independent of having been
made by running the Program). 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 conspicuously and
appropriately publish on each copy an appropriate copyright notice and
disclaimer of warranty; keep intact all the 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 along with the Program.

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.

2. You may modify your copy or copies of the Program or any portion of it,
thus forming a work based on the Program, and copy and distribute such
modifications or work under the terms of Section 1 above, provided that you
also meet all of these conditions:

   * a) You must cause the modified files to carry prominent notices stating
     that you changed the files and the date of any change.

   * b) You must cause any work that you distribute or publish, that in
     whole or in part contains or is derived from the Program or any part
     thereof, to be licensed as a whole at no charge to all third parties
     under the terms of this License.

   * c) If the modified program normally reads commands interactively when
     run, you must cause it, when started running for such interactive use
     in the most ordinary way, to print or display an announcement including
     an appropriate copyright notice and a notice that there is no warranty
     (or else, saying that you provide a warranty) and that users may
     redistribute the program under these conditions, and telling the user
     how to view a copy of this License. (Exception: if the Program itself
     is interactive but does not normally print such an announcement, your
     work based on 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, and can be
reasonably considered independent and separate works in themselves, then
this License, and its terms, do not apply to those sections when you
distribute them as separate works. But when you distribute the same sections
as part of a whole which is a work based on the Program, the distribution of
the whole must be on the terms of this License, whose permissions for other
licensees extend to the 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 your
rights to work written entirely by you; rather, the intent is to exercise
the right to control the distribution of derivative or collective works
based on the Program.

In addition, mere aggregation of another work not based on the Program with
the Program (or with a work based on the Program) on a volume of a storage
or distribution medium does not bring the other work under the scope of this
License.

3. You may copy and distribute the Program (or a work based on it, under
Section 2) in object code or executable form under the terms of Sections 1
and 2 above provided that you also do one of the following:

   * a) Accompany it with the complete corresponding machine-readable source
     code, which must be distributed under the terms of Sections 1 and 2
     above on a medium customarily used for software interchange; or,

   * b) Accompany it with a written offer, valid for at least three years,
     to give any third party, for a charge no more than your cost of
     physically performing source distribution, a complete machine-readable
     copy of the corresponding source code, to be distributed under the
     terms of Sections 1 and 2 above on a medium customarily used for
     software interchange; or,

   * c) Accompany it with the information you received as to the offer to
     distribute corresponding source code. (This alternative is allowed only
     for noncommercial distribution and only if you received the program in
     object code or executable form with such an offer, in accord with
     Subsection b above.)

The source code for a work means the preferred form of the work for making
modifications to it. For an executable work, complete source code means all
the source code for all modules it contains, plus any associated interface
definition files, plus the scripts used to control compilation and
installation of the executable. However, as a special exception, the source
code distributed need not include anything that is normally distributed (in
either source or binary form) with the major components (compiler, kernel,
and so on) of the operating system on which the executable runs, unless that
component itself accompanies the executable.

If distribution of executable or object code is made by offering access to
copy from a designated place, then offering equivalent access to copy the
source code from the same place counts as distribution of the source code,
even though third parties are not compelled to copy the source along with
the object code.

4. You may not copy, modify, sublicense, or distribute the Program except as
expressly provided under this License. Any attempt otherwise to copy,
modify, sublicense or distribute the Program is void, and will automatically
terminate your rights under this License. However, parties who have received
copies, or rights, from you under this License will not have their licenses
terminated so long as such parties remain in full compliance.

5. You are not required to accept this License, since you have not signed
it. However, nothing else grants you permission to modify or distribute the
Program or its derivative works. These actions are prohibited by law if you
do not accept this License. Therefore, by modifying or distributing the
Program (or any work based on the Program), you indicate your acceptance of
this License to do so, and all its terms and conditions for copying,
distributing or modifying the Program or works based on it.

6. Each time you redistribute the Program (or any work based on the
Program), the recipient automatically receives a license from the original
licensor to copy, distribute or modify the Program subject to these terms
and conditions. You may not impose any further restrictions on the
recipients' exercise of the rights granted herein. You are not responsible
for enforcing compliance by third parties to this License.

7. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot distribute so
as to satisfy simultaneously your obligations under this License and any
other pertinent obligations, then as a consequence you may not distribute
the Program at all. For example, if a patent license would not permit
royalty-free redistribution of the Program by all those who receive copies
directly or indirectly through you, then the only way you could satisfy both
it and this License would be to refrain entirely from distribution of the
Program.

If any portion of this section is held invalid or unenforceable under any
particular circumstance, the balance of the section is intended to apply and
the section as a whole is intended to apply in other circumstances.

It is not the purpose of this section to induce you to infringe any patents
or other property right claims or to contest validity of any such claims;
this section has the sole purpose of protecting the integrity of the free
software distribution system, which is implemented by public license
practices. Many people have made generous contributions to the wide range of
software distributed through that system in reliance on consistent
application of that system; it is up to the author/donor to decide if he or
she is willing to distribute software through any other system and a
licensee cannot impose that choice.

This section is intended to make thoroughly clear what is believed to be a
consequence of the rest of this License.

8. If the distribution and/or use of the Program is restricted in certain
countries either by patents or by copyrighted interfaces, the original
copyright holder who places the Program under this License may add an
explicit geographical distribution limitation excluding those countries, so
that distribution is permitted only in or among countries not thus excluded.
In such case, this License incorporates the limitation as if written in the
body of this License.

9. The Free Software Foundation may publish revised and/or new versions of
the General Public License from time to time. Such new versions will be
similar in spirit to the present version, but may differ in detail to
address new problems or concerns.

Each version is given a distinguishing version number. If the Program
specifies a version number of this License which applies to it and "any
later version", you have the option of following the terms and conditions
either of that version or of any later version published by the Free
Software Foundation. If the Program does not specify a version number of
this License, you may choose any version ever published by the Free Software
Foundation.

10. If you wish to incorporate parts of the Program into other free programs
whose distribution conditions are different, write to the author to ask for
permission. For software which is copyrighted by the Free Software
Foundation, write to the Free Software Foundation; we sometimes make
exceptions for this. Our decision will be guided by the two goals of
preserving the free status of all derivatives of our free software and of
promoting the sharing and reuse of software generally.

NO WARRANTY

11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR
THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO
THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM
PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR
CORRECTION.

12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO
LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR
THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.

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.

one line to give the program's name and an idea of what it does.
Copyright (C) yyyy  name of author

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.

signature of Ty Coon, 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.
  ------------------------------------------------------------------------
Return to GNU's home page.

FSF & GNU inquiries & questions to gnu@gnu.org. Other ways to contact the
FSF.

Comments on these web pages to webmasters@www.gnu.org, send other questions
to gnu@gnu.org.

Copyright notice above.
Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
02111, USA

Updated: 3 Jan 2000 rms
  ------------------------------------------------------------------------
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_\!& Garlic Documentation

Garlic Documentation

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
Copyright (C) 2004-2006 Damir Zucic. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A local copy of the license is included here .
Garlic documentation is written in html format. The sections are listed below, with a brief description. Newbies are recommended to read at least parts of each section. The most important (and the most extensive) section is the one with garlic commands.
Garlic Features An overview of garlic features.
Controls Reserved keys: rotations, translations, slab and color.
Commands Detailed descriptions of garlic commands.
Mouse Usage Mouse tricks specific for garlic.
Reference Card A quick reminder, both for newbies and experienced users.
Tutorial A collection of lessons and demonstration scripts.
Options Command line options.
Configuration File Configuration file for garlic, called .garlicrc (for experts).
Environment Variables Environment variables recognized by garlic.
Molecular Structures Proteins, nucleic acids and hetero compounds.
garlic-1.6/index.html0000644000000000000000000000724310430074716014564 0ustar rootroot00000000000000 Garlic Home Page - Version 1.6

Garlic - Version 1.6

Free Molecular Viewer and Editor

Keywords: garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This is the home of garlic - free, open source molecular viewer and editor. Garlic is the most portable molecular viewer in the Unix world. Follow the links below to find more about garlic. Don't forget to visit the screenshot gallery !

Release date: This version is under development. All versions are listed here .
.
What is garlic? Screenshot gallery Documentation
Download garlic Precompiled packages Installation guide
Similar programs License (GNU GPL) Author
Journal references:
(1) Damir Zucic and Davor Juretic, Precise Annotation of Transmembrane Segments with Garlic - a Free Molecular Visualization Program, Croatica Chemica Acta Vol. 77, No. 1-2, pp. 397-401 (2004).
Download free PDF file.
(2) D. Zucic: Annotation of Transmembrane Segments of Experimentally Solved Bacterial Porins and Adhesins, Croatica Chemica Acta Vol. 78, No. 2, pp. 151-158 (2005).
Download free PDF file.
If you are using garlic for scientific work, please read and cite (if appropriate) these references!
Garlic home: [ http://garlic.mefos.hr/garlic/ ]
Garlic alternative home (development version only): [ http://www.zucic.org/garlic/ ]

Questions, Bug Reports, Comments and Suggestions

Send an e-mail message to Damir Zucic (zucic@mefos.hr) .

Garlic News

2006/01/21: Version 1.6 initiated.
garlic-1.6/bold_statement.html0000644000000000000000000000332610361656252016463 0ustar rootroot00000000000000 Garlic - The Most Portable Molecular Viewer and Editor in Unix World

Garlic

The Most Portable Molecular Viewer and Editor in Unix World

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
The statement that garlic is the most portable molecular viewer/editor in unix world might look quite bold at the first sight, but it is based on serious arguments. Garlic requires only three libraries to run: the standard C library (libc), the standard math library (libm), and the standard X11 library (libX11). These libraries are available on every serious unix or unix compatible system. All other programs, (except one: mdxvu ) require some additional binary libraries.

Compiling and/or installing a program which requires numerous libraries may turn into nightmare. Not only that all these libraries must be present on your system: a version number is important too! And if you manage to compile and/or install the program, it may behave strange when you try to use it: there is a chance that one or more libraries were not tested enough before shipping, causing core dumps and other runtime problems.

Check the list of freely available molecular visualization programs for unix and unix clones. This page lists also the libraries required to run each of these programs.
garlic-1.6/gallery/0000755000000000000000000000000010424436302014214 5ustar rootroot00000000000000garlic-1.6/gallery/favicon.ico0000644000000000000000000000047607063421766016361 0ustar rootroot00000000000000(( garlic-1.6/gallery/index.html0000644000000000000000000000421610364510704016216 0ustar rootroot00000000000000 Garlic Screenshot Gallery

Garlic Screenshot Gallery

Version 1.6

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This page contains twelve garlic screenshots reduced to a size suitable for fast downloading. Click the selected image to load the full-sized version. All images are stored in PNG format. The true-color display is recommended for viewing this page.

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Garlic Configuration File - Version 1.6

.garlicrc

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This page contains the sample configuration file for garlic. When started, garlic will try to find the configuration file called .garlicrc (or garlicrc, in one case!) in up to seven directories, in the following order:

(1) in the current working directory (file .garlicrc);
(2) in user's home directory ($HOME/.garlicrc);
(3) in garlic subdirectory of user's home directory ($HOME/garlic/.garlicrc);
(4) in /usr/share/garlic directory; recommended as the system-wide configuration directory;
(5) in /etc directory (Debian GNU/Linux style, /etc/garlicrc, without dot!);
(6) in /usr/local/lib/garlic directory (file /usr/local/lib/garlic/.garlicrc);
(7) in /usr/lib/garlic directory (file /usr/lib/garlic/.garlicrc).

The recommended pathnames:

/usr/share/garlic/.garlicrc (system-wide configuration file),
$HOME/.garlicrc (private configuration file).

THE PACKAGE MAINTAINERS (FRIENDLY HACKERS, WHICH ARE PREPARING PACKAGES FOR LINUX DISTRIBUTIONS) SOMETIMES FORGET TO PREPARE THE SYSTEM-WIDE CONFIGURATION FILE AND THE FILE WITH TEMPLATE RESIDUES, CALLED residues.pdb .
Many users can't use the commands create and replace, because they don't have the file residues.pdb, or they can't customize the program because they don't know where to find the configuration file (.garlicrc).
Read this text , please, for more details!
There is a chance that files .garlicrc and residues.pdb are already installed on your system. Use the command locate to check this:
man locate (to learn something about the command locate);
locate .garlicrc
locate residues.pdb

If all attempts fail, the hard-coded defaults will be used. The configuration file .garlicrc should be included in the original garlic package. Most parameters are explained below (read the comments). Anyway, if you have some questions, send an e-mail to me:
zucic@mefos.hr 
# Personal initialization file for garlic, free molecular viewer and editor.
# Version 1.6.
# Last modification: January 21, 2006.


# Geometry of the main window. Use the keyword default, or specify the
# geometry string (for example 780x560+10+10).

main window geometry: default


# Margins; used only if geometry string is not given. Geometry string may be
# given through command line arguments.

main window left margin: 50 pixels
main window right margin: 50 pixels
main window top margin: 50 pixels
main window bottom margin: 70 pixels


# Main font:

main font: 10x20


# Main window cursor. If you don't like default cursor, replace it; read
# the file /usr/include/X11/cursorfont.h ; remove the XC_ prefix to obtain
# the cursor name.

main window cursor: default


# A small coordinate system may be displayed in the top left corner (yes/no):

show coordinate system: yes


# Control window (top right corner) may be visible or hidden (yes/no):

show control window: yes


# Sequence neighborhood of the residue under the pointer may be hidden,
# visible and short or visible and verbose (no/yes/verbose):

show sequence neighborhood: verbose


# Stereo flag (yes/no):

display stereo image: no


# Parameters for stereo image:

stereo internal margin (screen units): 10 pixels
stereo angle: 5.0 degrees


# Light source theta and phi angle (theta is defined with respect to z axis,
# phi with respect to x axis:

light source theta angle: 150 degrees
light source phi angle:   225 degrees


# Default slab mode (possible modes are off, planar, sphere, half-sphere,
# cylinder and half-cylinder):

default slab mode: planar


# Default color fading mode (off, planar, sphere, half-sphere, cylinder and
# half-cylinder): 

default color fading mode: planar


# Default drawing style for atoms (0, 1, 2, 3, 4, 5, 6 or 7):

default atom drawing style: 2


# Default drawing style for bonds (0, 1, 2, 3, 4 or 5):

default bond drawing style: 3


# Default drawing style for backbone:

default backbone drawing style: 5


# Window colors:

main window background color: black
main window foreground color: white
text background color: black
text foreground color: white


# The number of color fading surfaces:

number of color fading surfaces: 3


# Default colors for atoms and bonds. For each fading surface, three colors
# should be specified. The surface index is a small integer following the
# word color. The largest surface index is equal to:
# (number of color fading surfaces) - 1,
# which is in this case 2. Color may be changed at runtime, of course.
# This choice of colors is equivalent to the color scheme COLD.

left   color 0: RGB:DDDD/FFFF/FFFF
middle color 0: RGB:0000/FFFF/FFFF
right  color 0: RGB:0000/8888/FFFF

left   color 1: RGB:0000/8888/FFFF
middle color 1: RGB:0000/0000/FFFF
right  color 1: RGB:0000/0000/8888

left   color 2: RGB:0000/0000/8888
middle color 2: RGB:0000/0000/4444
right  color 2: RGB:0000/0000/2222


# Default color schemes for molecular surfaces. Choose from this list:
# red, green, blue, cyan, magenta, yellow, white, orange,
# cyan-blue, cyan-green, yellow-green, magenta-blue, magenta-red,
# orange-yellow, orange-red. Do not use the following color schemes:
# hot, cold, monochrome, cpk, zebra, chain, hyphob and model.

surface outer color scheme: magenta
surface inner color scheme: blue


# Rotation steps. Normal steps is used if numeric key is pressed without
# any modifier. Large step is selected by holding [shift] while pressing
# the key, and very large step is selected by using both [alt] and [shift].
# Small step is selected by holding [control] while pressing the key, and
# very small step by using both [alt] and [control].

rotations steps: 0.2 1.0 5.0 30.0 90.0


# Five translation steps (very small, small, normal, large and very large).
# Use angstrom units.

translation steps: 0.2 1.0 5.0 25.0 100.0


# Five slab steps (very small, small, normal, large and very large).
# Use angstrom units.

slab steps: 0.2 1.0 5.0 20.0 80.0


# Five fading steps (very small, small, normal, large and very large).
# Use angstrom units.

fading steps: 0.2 1.0 5.0 20.0 80.0


# Window size limits: used only if screen width and/or height are larger
# than values specified here. By default, screen width and height are used.

maximal main window width: 3000 pixels
maximal main window height: 2500 pixels


# The nearest line (bond) thickness; used only if drawing bonds as lines
# and line thickness is used for perspective.

the nearest line thickness: 5 pixels


# Screen dimensions and position of garlic user in real world. Use realistic
# values. Do not change units (mm). Strange values may cause image distortions.

screen width in real world: 270 millimeters
screen height in real world: 195 millimeters
distance between user and screen in real world: 500 millimeters


# Scaling information: used to scale user and screen down to atomic scale.
# Only screen width is required, in angstrom units.

screen width in atomic world: 1.0 angstroms


# User z coordinate in atomic coordinate system. It must be negative
# and absolute value should be quite large. The x axis points to the right,
# y axis downward and z axis in direction opposite to observers direction.

user position in atomic coordinate system: -150.0 angstroms


# Maximal bond length is used to check which atoms and bonds are invisible.
# It is assumed that there are no atoms with radius larger than this length.

maximal bond length: 2.3 angstroms


# Crude limits for bond lengths. No distinction between N-CA and C-N is made.
# Use angstrom units. Be tolerant, there are many bad structures around.
# Generic bond length is used for atomic pairs which are not recognized.

approximate C-C bond length: from 1.3 to 1.8 angstroms
approximate C-N bond length: from 1.0 to 1.7 angstroms
approximate C-O bond length: from 1.0 to 1.7 angstroms
approximate C-S bond length: from 1.4 to 2.1 angstroms
approximate C-H bond length: from 0.8 to 1.2 angstroms
approximate N-O bond length: from 1.2 to 1.7 angstroms
approximate N-H bond length: from 0.9 to 1.3 angstroms
approximate O-H bond length: from 0.7 to 1.3 angstroms
approximate S-H bond length: from 0.9 to 1.6 angstroms
approximate O-P bond length: from 1.2 to 1.8 angstroms
approximate S-S bond length: from 1.8 to 2.3 angstroms
generic bond length:         from 0.8 to 2.0 angstroms
hydrogen bond length:        from 2.0 to 5.0 angstroms


# Hydrogen bond C-O...N angle range (obsolete since version 1.3!):

hydrogen bond C-O...N angle: from 125 to 180 degrees


# The upper limit for CA-CA distance for neighbouring residues. Used to
# draw backbone, connection neighbouring CA atoms.

maximal CA-CA distance: 4.1 angstroms


# Atomic radii, used for spacefill style. 70% of van der Waals radius may be
# a good choice.

hydrogen radius:   0.70 angstroms
carbon radius:     1.20 angstroms
nitrogen radius:   1.05 angstroms
oxygen radius:     1.00 angstroms
sulfur radius:     1.25 angstroms
phosphorus radius: 1.25 angstroms
generic radius:    1.40 angstroms


# Covalent atomic radii, used for covalent style.

hydrogen covalent radius:   0.30 angstroms
carbon covalent radius:     0.77 angstroms
nitrogen covalent radius:   0.70 angstroms
oxygen covalent radius:     0.66 angstroms
sulfur covalent radius:     1.04 angstroms
phosphorus covalent radius: 1.10 angstroms
generic covalent radius:    1.20 angstroms


# Small atomic radii. 70% of covalent radius may be a good choice.

hydrogen small radius:   0.21 angstroms
carbon small radius:     0.54 angstroms
nitrogen small radius:   0.49 angstroms
oxygen small radius:     0.46 angstroms
sulfur small radius:     0.73 angstroms
phosphorus small radius: 0.77 angstroms
generic small radius:    0.84 angstroms


# Van der Waals radii.

hydrogen van der Waals radius:   1.00 angstroms
carbon van der Waals radius:     1.70 angstroms
nitrogen van der Waals radius:   1.50 angstroms
oxygen van der Waals radius:     1.40 angstroms
sulfur van der Waals radius:     1.80 angstroms
phosphorus van der Waals radius: 1.80 angstroms
generic van der Waals radius:    2.00 angstroms


# Default ball radius (used to draw atoms as balls of equal size):

default ball radius: 0.40 angstroms


# Default bond probe radius, used to draw nice bonds with curved surfaces:

default bond probe radius: 0.80 angstroms


# Default stick radius, used to draw bonds as sticks:

default stick radius: 0.15 angstroms


# For a given atom, the chemical bonds are identified by inspecting
# distances to the neighboring atoms. The array with atomic data should
# be scanned in forward and backward direction (with respect to the given atom)
# to find which atoms are bound to the given atom. The following parameters
# define how many neighboring atoms should be checked in each direction.

number of bond candidates: 50 before and 50 after the given atom


# Blur rectangle width and height (default values). Bluring is used to reduce
# the contrast. The color of the pixel in the center of the rectangle is
# calculated by averaging the colors of all pixels in the rectangle. Both
# values should be positive integers.

blur rectangle width:  3
blur rectangle height: 3
garlic-1.6/config/important_files.html0000644000000000000000000000707410361663573020133 0ustar rootroot00000000000000 .garlicrc and residues.pdb

.garlicrc and residues.pdb

Garlic configuration file and template residues

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic. 
GARLIC CONFIGURATION FILE AND TEMPLATE RESIDUES

Garlic will try to open two ASCII files at startup, in the given order:

============================================================================
(1) CONFIGURATION FILE:
Up to  seven attempts to open the configuration file will be made.  Only the
first available file is used. If all seven attempts fail, default parameters
will be used.  Default parameters are hard-coded in the file  read_config.c.

File name:         .garlicrc (or garlicrc, but only for one directory!).
C source file:     open_config_file.c
----------------------------------------------------------------------------
 (1.1) ./.garlicrc                     (the current working directory)
 (1.2) $HOME/.garlicrc                 (the home directory, $HOME or $home)
 (1.3) $HOME/garlic/.garlicrc
 (1.4) /usr/share/garlic/.garlicrc     (recommended as system-wide default!)
 (1.5) /etc/garlicrc                   (note that file name is garlicrc !)
 (1.6) /usr/local/lib/garlic/.garlicrc
 (1.7) /usr/lib/garlic/.garlicrc
============================================================================

============================================================================
(2) TEMPLATE RESIDUES (building blocks for proteins etc.):
Up to six (6) attempts to open the file with template residues will be made.
Only the first available file is used. If not available at all, the template
residues will not be available.  The commands  CREATE  and  REPLACE  will be
useless, but the program will work (with limited capabilities).

File name:         residues.pdb
C source file:     open_template_file.c
----------------------------------------------------------------------------
 (1.1) ./residues.pdb                  (the current working directory)
 (1.2) $HOME/residues.pdb              (the home directory, $HOME or $home)
 (1.3) $HOME/garlic/residues.pdb
 (1.4) /usr/share/garlic/residues.pdb  (recommended as system-wide default!)
 (1.5) /usr/local/lib/garlic/residues.pdb
 (1.6) /usr/lib/garlic/residues.pdb
============================================================================

============================================================================
RESUME:
The suggested pathnames (see below) should be useful for most Linux and Unix
distributions. If you accept these paths and pathnames, please note that the
configuration file should be called  .garlicrc and not garlicrc!  Both files
(.garlicrc  and  residues.pdb)  may be found in the original source package.
If you don't like  the suggestions,  please edit  open_config_file.c  and/or
open_template_file.c !
----------------------------------------------------------------------------
System-wide configuration file:        /usr/share/garlic/.garlicrc
Template residues:                     /usr/share/garlic/residues.pdb
Garlic documentation directory:        /usr/share/doc/garlic/   or
                                       /var/www/html/garlic/    or
                                       some_other_html_directory !
============================================================================
garlic-1.6/config/garlic.gif0000644000000000000000000000465007064163703015767 0ustar rootroot00000000000000GIF87aFFɲ̻ոտĻ®ȹ@]^\ @ @P @@x((]VVP(PdVd dd\?).]@vP]dD(r?V @, @()$V@@]\ @lVi(rV@@l,( ]V) @@H]@\]@HiH(\VL @(PVd @X(,Vdd*[H\L( Vh𤝂pDPD]HxM x @(IVd( Vddx(/VrP d^ @F FR<_Pd?.@2_<  @F Fn(VGR (@,FF @PÇ#Jl8  %jܸ1A$

_\!& Support Garlic!

Support Garlic!

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
You can support garlic development in different ways. Some options are listed here, sorted by complexity (the simplest one is the first). Though garlic is a free software, someone has to pay for it. The author will need strong arguments to ensure support for a program which makes no money. If you like garlic, support it!
REGISTER GARLIC

The fact that you use garlic doesn't help much if I don't know that there is one more user. The easiest way to register is to execute the command:
reg
at garlic prompt. This requires that your machine is connected to the Internet. A short message will be send to zucic@garlic.mefos.hr; the only content of this message will be the word 'Hi!'. I will use the header of this message to extract your address. The address will be added to the list. Your address will not be abused, it will be kept secret and used only to count garlic users.

You can also send a more verbose message to zucic@mefos.hr with comments and suggestions.

There is one more way to register garlic: at your shell (terminal) prompt, type:
garlic -r
(if connected to the Internet, of course).

SEND A POSTCARD

You can also register by sending a postcard. I like stamps!
Here is the address:

Damir Zucic
ETF Osijek
Kneza Trpimira 2B
31000 Osijek
Croatia
Europe

INFORM OTHERS

Inform your colleagues and friends about garlic. Many potential users do not read Usenet news, so it is difficult to reach all those who might be interested to use garlic. I don't like spam and other aggressive forms of communication so I wouldn't use such methods to attract users.

ADD LINK TO YOUR WEB PAGES

Add link to your personal web page(s), pointing to garlic.

MIRROR GARLIC

If you like garlic and you can set aside few megabytes of disk space, you can establish a mirror site with garlic sources and related material. This should not be very complicated - there is only one source package and few dozens of web pages. The national academic network (CARNet) here in Croatia is pretty good, but communication lines to some countries (like U.K. and Germany) are overcrowded most of the time.

USE IT FOR LECTURES AND PRESENTATIONS

An experienced user may use garlic for lectures and presentations. There is a command pau (pause) which makes it easy to control script execution.

MAKE A DONATION

Donations are welcome, of course. Contact the author for technical details ( zucic@mefos.hr ).

garlic-1.6/support/garlic.gif0000644000000000000000000000465007066125454016241 0ustar rootroot00000000000000GIF87aFFɲ̻ոտĻ®ȹ@]^\ @ @P @@x((]VVP(PdVd dd\?).]@vP]dD(r?V @, @()$V@@]\ @lVi(rV@@l,( ]V) @@H]@\]@HiH(\VL @(PVd @X(,Vdd*[H\L( Vh𤝂pDPD]HxM x @(IVd( Vddx(/VrP d^ @F FR<_Pd?.@2_<  @F Fn(VGR (@,FF @PÇ#Jl8  %jܸ1A$

_\!& FAD, FADING

FAD, FADING

NAME
FAD, FADING - change the color dependence on a distance from the observer.

SYNOPSIS
FAD keyword
FAD FRONT shift
FAD BACK shift
FADING keyword
FADING FRONT shift
FADING BACK shift

DESCRIPTION
Change the way color depends on distance. Distance is measured from the atom to the observer. This command comes in three versions:

(1) FADING FRONT shift ----> move the front color surface;
(2) FADING BACK shift ----> move the back color surface;
(3) FADING keyword ----> switch fading off or change the type of the surfaces.

FADING FRONT shift
This command moves the front fading surface. It is recommended to use this command in scripts - in interactive mode, use controls (keys F1 and F2). The shift value should be given in angstroms. Positive shift moves the front color surface away from the observer. With most color schemes, the front (closer) portion of the structure will be brighter after the positive shift. FRONT may be abbreviated to FRO.

FADING BACK shift
This command moves the back fading surface. It is recommended to use this command in scripts - in interactive mode, use controls (keys F3 and F4). The shift value should be given in angstroms. Positive shift moves the back color surface away from the observer. With most color schemes, the contrast will be reduced after the positive shift. Negative shift results in better contrast, i.e. distant atoms will become darker. BACK may be abbreviated to BAC.

FADING keyword
Some keywords may be used to change the type of color surfaces and to switch color fading off. Here is the list of keywords:

SHORT FORM LONG FORM DESCRIPTION
OFF OFF Switch fading off:
colors should become distance independent
PLA PLANE Use planes as color surfaces
SPH SPHERE Use spheres as color surfaces
CYL CYLINDER Use cylinders as color surfaces
HALF-SPH HALF-SPHERE Use spheres as color surfaces, but apply
only to the front half of the structure.
HALF-CYL HALF-CYLINDER Use cylinders as color surfaces, but apply
only to the front half of the structure.

For most structures, the planar fading is the best choice. Spherical and semi-spherical fading may be useful when working with large globular proteins, while cylindrical and semi-cylindrical fading is useful when working with beta-barrel proteins (like porins). The cylinder axis is parallel to y axis (vertical from user's standpoint).

EXAMPLES
COMMAND DESCRIPTION
fading off Switch color fading off
fading front 4.5 Move the front color surface 4.5 angstroms
away from the observer
fading back -2.8 Move the back color surface 2.8 angstroms
closer to the observer
fading half-sph Change fading to semi-spherical

RELATED COMMANDS
color defines the color for selected atoms.

garlic-1.6/commands/rep.html0000644000000000000000000001030510364510434016033 0ustar rootroot00000000000000 REP, REPLACE

REP, REPLACE

NAME
REP, REPLACE - replace selected residues

SYNOPSIS
REP
REPLACE

DESCRIPTION
Replace the selected residues, using the sequence from the main sequence buffer. At present (version 1.6), garlic is capable to replace protein residues only. Do not use this command to replace nucleic bases or hetero residues. After the replacement, the structure will need some refinement.

A residue is treated as selected if the first atom which belongs to this residue is selected. For proteins, this is typically N (nitrogen).

The main sequence buffer has to be initialized before issuing the command REPLACE. The number of residues in the main sequence buffer should be equal to the number of selected residues.

SINGLE RESIDUE REPLACEMENT
To replace a single residue, use the following commands:
select residue_sequence_number
sequence = new_residue_name
replace

Example:
sel 29
seq = ser
rep

REPLACING THE ENTIRE SEQUENCE
The command REPLACE may be used to prepare the model of some protein using the experimentally solved structure of the related protein. To replace the entire protein sequence follow these general instructions:
(1) Prepare the file with the sequence of the unsolved protein (use FASTA format).
(2) Find the related, experimentally solved protein structure.
(3) Fix insertions and deletions in the sequence of the unsolved protein.
(4) Start garlic and load the known structure.
(5) Exclude hetero residues from selection (first SEL HET, than SEL COM).
(6) If there is more than one chain restrict selection (RES chain_id/*/*/*).
(7) Load the new sequence (use the command SEQ LOAD).
(8) Replace the old sequence.

Don't forget that the number of selected residues should match the number of residues in the sequence of the unsolved protein.

TEMPLATE RESIDUES
The selected residues will be replaced with the residues from the template file. Default template file contains 20 standard residues. This file should be named residues.pdb and stored to at least one of the following directories (listed in the search order):
(1) The current working directory.
(2) $HOME (user's home directory).
(3) $HOME/garlic (garlic subdirectory of the user's home directory).
(4) /usr/share/garlic (location for the system-wide file).
(5) /usr/local/lib/garlic (alternative location for the system-wide file).
(6) /usr/lib/garlic (another alternative location for the system-wide file).

If you want to add some extra residues (like modified amino-acids) to the template file, make your own copy of the file residues.pdb and keep it either in $HOME/garlic subdirectory or in your favorite working directory. It is very easy to add residues to the template file: just copy and paste the chosen exotic residue from the PDB file where you have it to the end of garlic template file. Be sure to include hydrogen atoms! There is one more thing: be sure that your residue does not have the same residue serial number as the preceding residue. You don't have to worry about the position and the orientation of your residue.

If you don't have the file residues.pdb, click here for html version. It is very easy to convert this version to the plain PDB, just save it as the plain text.

NOTES
(1) The command REPLACE resets the editing mode to default (no editing).

RELATED COMMANDS
Use the command SELECT to define the residues which should be replaced and SEQUENCE to define the residues which will be used as replacement. BONDS REFRESH may be used to fix bad bonds, which may sometimes be generated after executing the command REPLACE.

garlic-1.6/commands/favicon.ico0000644000000000000000000000047607063421753016517 0ustar rootroot00000000000000(( garlic-1.6/commands/sho.html0000644000000000000000000000117310357045410016040 0ustar rootroot00000000000000 SHO, SHOW

SHO, SHOW

NAME
SHO, SHOW - show selected atoms.

SYNOPSIS
SHO
SHOW

DESCRIPTION
Show selected atoms and associated bonds. Atoms and bonds drawn using style "0" will remain invisible, but they are formally treated as visible.

RELATED COMMANDS
HIDE hides selected atoms and associated bonds.

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RES, RESTRICT

NAME
RES, RESTRICT - restrict the current selection.

SYNOPSIS
RES chain_identifiers/residue_serials/residue_names/atom_names
RES residue_ranges
RES residue_names
RES ATO atomic_ranges
RES keyword
RES ELE chemical_symbol
RESTRICT chain_identifiers/residue_serials/residue_names/atom_names
RESTRICT residue_ranges
RESTRICT residue_names
RESTRICT ATOMS atomic_ranges
RESTRICT keyword
RESTRICT ELEMENT chemical_symbol

DESCRIPTION
Restrict the current selection. Atoms which do not satisfy the specified cryteria are excluded from selection. Four types of restriction cryteria may be used:

(1) detailed selection;
(2) restriction by residue serial numbers;
(3) restriction by residue names;
(4) restriction selection (by keyword);
(5) restriction by chemical symbol;
(6) restriction by atom serial number.

DETAILED RESTRICTION
In this case four data types are specified simultaneously: chain identifiers, residue serial numbers, residue names and atom names. It is not possible to specify atomic serial numbers. The string should contain exactly three slashes, separating different data types:

chain_identifiers/residue_serials/residue_names/atom_names.

Both uppercase and lowercase characters are accepted. Space ( ), comma (,) and semicolon (;) may be used as separators.

Chain identifiers are single alphabetic characters. Asterisk (*) may be used to specify all chains. The keyword EXC (EXCEPT) may be used to exclude one or more chains from restriction.

Residue serial numbers consist of digits. Minus may be used to specify a range of residue serial numbers. For example, 1-100 specifyes residues from 1 to 100, including these two. Asterisk (*) may be used to specify all residue serials. The keyword EXC (EXCEPT) may be used to exclude serial numbers or ranges from restriction.

Residue names are expected in three letters code. Asterisk (*) may be used to specify all residue names. The keyword EXC (EXCEPT) may be used to exclude one or more names from restriction. Non-standard names are accepted.

The names of atoms are expected as used in the input file; do not replace them with pure chemical symbols. C alpha, for example, should be specified as CA or ca (case is not important), if coordinates are read from PDB file. Asterisk (*) may be used to specify all atoms, while EXC may be used to exclude some atoms from this specification. Examples:

res a/*/*/* Leave only atoms which belong to chain A.
res * exc m/*/*/ca Leave only CA atoms which belong to chain M.
res */*/*/* exc ca,c,n,o Remove CA, C, N and O atoms from the selection.
res a/* exc 72-112/*/ca Leave only CA atoms which belong to chain A, but exclude residues 72-112.

RESTRICTION BY RESIDUE SERIAL NUMBERS
In this type of selection restriction, residue numbers, residue ranges or residue names may be specified. The restriction cryteria should contain no slashes. Keyword EXC (EXCEPT) is accepted, but asterisk (*) will be missintepreted. Minus may be used to specify residue ranges. Comma (,), semicolon (;) and space ( ) may be used as separators. Examples:

res 1-100 Leave only atoms which belong to residues from 1 to 100.
res 1-100 exc 20-40 Leave only atoms which belong to residues 1-100, but exclude 20-40.
res 1, 4, 8, 11-48 exc 20-32 Leave atoms which belong to residues 1, 4, 8, 11-48
but exclude residues 20-32.

RESTRICTION BY RESIDUE NAMES
Three letters code should be used. Asterisk (*) and keyword EXC (EXCEPT) are not accepted. Example:

res phe,tyr,trp Restrict selection to PHE, TYR and TRP.

RESTRICTION BY ATOMIC SERIAL NUMBERS
To restrict the current selection to a single atom by the atomic serial number, combine the command RES (RESTRICT) and the keyword ATO (ATOMS). For example, to restrict the selection to the atom number 102 type:

res ato 102

The same keyword may be used to restrict the current selection to a range of atoms or to two or more ranges. Examples:

res ato 1-100 Restrict the current selection to atoms which have
serial numbers in the range between 1 and 100.
res 1-20 40-50 Restrict the current selection to atoms which have
serial numbers between 1 and 20 and between 40 and 50.

Do not combine the keywords EXC (EXCLUDE) and ATO (ATOMS).

SPECIAL RESTRICTION KEYWORDS
Some special keywords may be combined with RES to specify residues or atoms according to some properties. A single keyword should be used; asterisk (*) and keyword EXC (EXCEPT) are not accepted. COM (COMPLEMENT) may be specified, but restriction to complement means that nothing will be left in the selection. Examples:

res *
res all 		Leave the selection unchanged (trivial, useless).
res abo
res above 		Restrict to atoms above the plane.
res aci
res acidic 		Leave only acidic amino-acids in the selection (GLU and ASP).
res ali
res aliphatic 		Leave only aliphatic amino acids (ILE, LEU and VAL).
res alt Restrict to atoms at alternate positions.
res bad Restrict selection to bad residues. A residue is treated as
bad if the peptide bond assigned to this residue is non-planar.
The peptide bond is non-planar if the omega angle is
different for 20 or more degrees from 0 or 180 degrees.
res bas
res basic 		Leave only basic amino acids (ARG, LYS and HIS).
res bel
res below 		Restrict to atoms below the plane.
res cha
res charged 		Leave only charged amino acids (ARG, LYS, HIS, GLU and ASP).
res cis Restrict selection to cis residues.
res com
res complement 		Leave only atoms which were not select previously.
res het
res hetero 		Leave only hetero atoms (heme groups, water etc.).
res pho
res hydrophobic 		Leave only hydrophobic amino acids
(ALA, ILE, LEU, MET, PHE, TRP, VAL, TYR, CYS, GLY and HIS).
res mai
res main_chain 		Leave only main chain atoms (CA, C, N and O).
res mod serial_number
res model serial_number 		Restrict to a model specified by serial_number.
NMR structure is a set of models. Example: res mod 1
res pat
res pattern 		Restrict to the sequence pattern. The command
PAT (PATTERN) is used to define the sequence pattern.
res neg
res negative 		Leave only negatively charged amino acids (GLU and ASP).
res pol
res polar 		Leave only polar amino acids
(ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TRP and TYR).
res seq
res sequence 		Restrict to sequence fragments which match the sequence
stored to the sequence buffer. The sequence buffer should
be initialized before executing this command.
res pos
res positive 		Leave only positively charged amino acids (ARG, LYS and HIS).
res sid
res side_chains 		Leave only atoms which belong to side chains (all except CA, C, N and O).
res sma
res small 		Leave only small amino acids
(GLY, ALA, SER, THR, CYS, VAL, PRO, ASP and ASN).
res sph
res sphere 		Restrict to the atoms inside the sphere. Use the command
RAD (RADIUS) to set the sphere radius.
res tin
res tiny 		Leave only tiny amino acids (GLY,ALA and SER).
res tm Restrict to the transmembrane part
(useful for membrane proteins).
res tra
res trans 		Restrict selection to trans residues.
res tri
res triplet 		If there are three (or more) positively charged residues in a fragment
of up to five protein residues, restrict the current set of selected
atoms to these three residues. Detailed explanation may found in the
article:
D. Juretic, L. Zoranic and D. Zucic,
Basic charge clusters and predictions of membrane protein topology,
Journal of Chemical Information and Computer Sciences 42, No. 3,
620-632 (2002).
res 2c3 If there are two (or more) charged residues in a fragment of
three residues, restrict the selection choosing only these residues.
res 2cz3 If there are two (or more) charged or zwitterionic residues in
a fragment of three residues, restrict the selection choosing only
these residues.
res 2nz3
res 3c4
res 3cz4
res 3nz4
res 3c5
res 3cz5
res 3nz5
res 3p5
res 4c5
res 4cz5
res 4nz5
res 3c6
res 3cz6
res 3nz6
res 4c6
res 4cz6
res 4nz6
res 5c6
res 5cz6
res 5nz6
res 4c7
res 4cz7
res 4nz7
res 5c7
res 5cz7
res 5nz7
res 5p7
res 6p7
res 4c9
res 4cz9
res 4nz9
res 5c9
res 5cz9
res 5nz9 		Analogous to res 2c3 and res 2cz3, where c stands for charged ,
cz for charged or zwitterionic , nz for negative or zwitterionic
and p for polar . The same selection criteria may be defined
using patterns, but these short keywords are more practical.
res 3p5 If there are three or more polar residues in a fragment of five residues,
restrict the selection choosing only these residues. The following
residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN,
SER, THR, TYR and TRP.
res 5p7 If there are five or more polar residues in a fragment of seven residues,
restrict the selection choosing only these residues. The following
residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN,
SER, THR, TYR and TRP.
res 6p7 If there are six or more polar residues in a fragment of seven residues,
restrict the selection choosing only these residues. The following
residues are treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN,
SER, THR, TYR and TRP.

RESTRICTING SELECTION TO
THE SPECIFIED CHEMICAL ELEMENT
To restrict the selection to certain chemical element, use the keyword ELEMENT (short form: ELE) and the standard chemical symbol. To restrict your selection to iron atoms, for example, you should type the following command:

res ele fe

In addition to real chemical elements, garlic accepts two imaginary elements: "jellium" (J) and "quarkonium" (Q). Jellium is inert and it never binds to neighboring atoms, no matter how close they are. Quarkonium binds to other quarkonium atoms which have adjacent atomic serial numbers. For example, if some quarkonium atom has serial number i, it may form bonds with quarkonium atoms i-1 and i+1. The interatomic distance is not important! Both elements were introduced to enable drawing of special objects. Quarkonium may be used to draw polygonal lines in three dimensions. The original idea was to adapt garlic for visualization of some medical data. For example, quarkonium may be used to represent blood vessels and jellium to represent retraction balls characteristic for broken axons in human brain. By the way, quarkonium is a serious thing in high energy physics, but there it looks quite different. Note that symbols J and Q are not used in the periodic table of elements.

NOTES
(1) The command RESTRICT resets the editing mode to default (no editing).

RELATED COMMANDS
SELECT overwrites the previous selection. ADD expands the previous selection.

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SAV, SAVE

NAME
SAV, SAVE - save atomic data to the specified file.

SYNOPSIS
SAV file_name
SAV file_name SEL
SAVE file_name
SAVE file_name SEL

DESCRIPTION
Save atomic data to the specified file. By default, all atoms are saved. If keyword SEL is used, only selected atoms are saved. No header is written, just ATOM and HETATM records. You may copy and paste the header from the original (input) file. Coordinates will be expressed in the internal coordinate system (the geometric center used as the origin). Don't forget that Unix (Linux) file names are case sensitive. If the specified file exists already, it will be overwritten without warning!

RELATED COMMANDS
LOA (LOAD) loads the specified structure. DIS (DISCARD) discards the specified structure.

garlic-1.6/commands/sca.html0000644000000000000000000002441110376322003016012 0ustar rootroot00000000000000 SCA, SCALE

SCA, SCALE

NAME
SCA, SCALE - select hydrophobicity scale.

SYNOPSIS
SCA keyword
SCALE keyword

DESCRIPTION
The command SCALE selects the specified hydrophobicity scale. Since version 1.4, six scales are available: Eisenberg normalized consensus scale, Kyte-Doolittle hydropathy scale and four experimentally determined scales from the Stephen White laboratory . The scale is assigned to the structure which is currently being handled (the structure which was caught using the command CATCH). It is also used as default hydrophobicity scale for the sequence in the main sequence buffer. The hydrophobicity scale is used to calculate the averaged hydrophobicity and hydrophobic moment. It may be also used to color the protein structure according to hydrophobicity.

Hard-coded program default is Eisenberg scale.

KEYWORDS
KEYWORD
(SHORT) 		KEYWORD
(LONG) 		DESCRIPTION
EIS EISENBERG Default: Eisenberg normalized consensus hydrophobicity
scale (reference 1, see the bottom of this page!).
KD KD Kyte-Doolittle hydropathy scale (reference 2).
INT INTERFACE Interface scale from the Stephen White laboratory (ref. 3).
OCT OCT Octanol scale from the Stephen White laboratory (ref. 4).
The keyword OCT was introduced in version 1.4 of garlic,
to replace the keyword WHI (WHITE).
IN2 IN2 Modified interface scale: HIS, ASP and GLU neutral.
DIF DIFFERENTIAL Differential scale: octanol minus interface.

HYDROPHOBICITY SCALES
The table below contains numeric data for four hydrophobicity scales which are used in garlic. The original scales from the Stephen White laboratory contain the free energy changes for a transfer of whole residues from water to bilayer interface or octanol. In garlic, these free energy changes are multiplied by minus one and used as hydrophobicity values. The experimental values and nice theoretical explanations may be found at:
http://blanco.biomol.uci.edu/hydrophobicity_scales.html
NAME EIS KD INT OCT IN2 DIF
ALA 0.62 1.80 -0.17 -0.50 -0.17 -0.33
ARG -2.53 -4.50 -0.81 -1.81 -0.81 -1.00
ASN -0.78 -3.50 -0.42 -0.85 -0.42 -0.43
ASP -0.90 -3.50 -1.23 -3.64 0.07 -2.41
CYS 0.29 2.50 0.24 0.02 0.24 -0.22
GLN -0.85 -3.50 -0.58 -0.77 -0.58 -0.19
GLU -0.74 -3.50 -2.02 -3.63 0.01 -1.61
GLY 0.48 -0.40 -0.01 -1.15 -0.01 -1.14
HIS -0.40 -3.20 -0.96 -2.33 -0.17 -1.37
ILE 1.38 4.50 0.31 1.12 0.31 0.81
LEU 1.06 3.80 0.56 1.25 0.56 0.69
LYS -1.50 -3.90 -0.99 -2.80 -0.99 -1.81
MET 0.64 1.90 0.23 0.67 0.23 0.44
PHE 1.19 2.80 1.13 1.71 1.13 0.58
PRO 0.12 -1.60 -0.45 -0.14 -0.45 0.31
SER -0.18 -0.80 -0.13 -0.46 -0.13 -0.33
THR -0.05 -0.70 -0.14 -0.25 -0.14 -0.11
TRP 0.81 -0.90 1.85 2.09 1.85 0.24
TYR 0.26 -1.30 0.94 0.71 0.94 -0.23
VAL 1.08 4.20 -0.07 0.46 -0.07 0.53
ASX -0.84 -3.50 -0.83 -2.25 -0.18 -1.38
GLX -0.80 -3.50 -1.30 -2.20 -0.29 -0.90
UNK 0.00 -0.49 -0.14 -0.52 -0.38 -0.29

EXAMPLES
COMMAND DESCRIPTION
sca eis
Use the scale prepared by David Eisenberg.
sca int Use the experimental interface scale from
the Stephen White laboratory.

NOTES
(1) Many hydrophobicity scales may be found in literature. However, most of these scales are mutually highly correlated.

(2) The keyword WHI (WHITE) was replaced by the keyword OCT (OCTANOL) in version 1.4 of garlic!

RELATED COMMANDS
PLOT is used to draw averaged hydrophobicity and other hydrophobicity functions. color HYPHOB is used to color the structure according to hydrophobicity of residues.

REFERENCES
(1) Eisenberg, D., Schwarz, E., Komaromy, M. and Wall, R. (1984). J. Mol. Biol. 179, p. 125.
(2) Kyte, J. and Doolittle, R. F. (1982). J. Mol. Biol. 157, p. 105.
(3) Wimley, W. C. and White, S. H. (1996). Nature Struct. Biol. 3, p. 842.
(4) Wimley, W. C., Creamer, T. P. and White, S. H. (1996). Biochemistry 35, p. 5109.
(5) White, S. H. and Wimley, W. C. (1998). Biochim. Biophys. Acta 1376, p 339.
(6) White, S. H. and Wimley, W. C. (1999). Annu. Rev. Biophys. Biomol. Struc. 28, p. 319.

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FON, FONT

NAME
FON, FONT - change font.

SYNOPSIS
FON font_name
FONT font_name

DESCRIPTION
Change default font. At present, garlic uses only one font for input, output and main window. Try to execute xlsfonts on your system, to obtain a list of fonts. The initial font is set in .garlicrc file. Examples:

fon 10x20
fon olglyph-19

RELATED COMMANDS
FG changes the text color used to draw strings in the main window. TFG changes the text color used to draw strings in input and output window.

garlic-1.6/commands/dis.html0000644000000000000000000000362710345613521016035 0ustar rootroot00000000000000 DIS, DISCARD

DIS, DISCARD

NAME
DIS, DISCARD - discard the specified structure.

SYNOPSIS
DIS identifier
DIS ALL
DIS *
DISCARD identifier
DISCARD ALL
DISCARD *

DESCRIPTION
Discard the specified structure (macromolecular complex). The memory used to store the structure is freed. If keyword ALL is used (or asterisk, *), all structures will be discarded. Examples:

COMMAND DESCRIPTION
dis 1 Discard the structure number 1.
dis 7 Discard the structure number 7.
dis * Discard all. Nothing will be loaded
after this command.

NOTES
(1) Sometimes you will forget the identifiers, especially when working with many structures. Move the mouse pointer over the structure which should be discarded. The identifier will be displayed in the output window (bottom right corner of the garlic window). The number in parentheses is the identifier you need. In the example below, the identifier is equal to one.



(2) If you discard everything, the indexing will be reset too. The first structure you load after discarding everything will be assigned index "1" (one).

(3) The command DISCARD resets the editing mode to default (no editing).

RELATED COMMANDS
LOAD (READ) loads the specified file.

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DIHEDRAL ANGLES

dihedral angles, phi, psi, omega, chi1, chi2, chi3, chi4, chi5, rotamers, dihedral angle, definitions, garlic, Damir Zucic.
MAIN CHAIN DIHEDRAL ANGLES
The main chain dihedral angles are defined as follows:

(1) The phi angle is the angle of right-handed rotation around N-CA bond, the value being zero if CA-C bond is cis to C-N bond. Range: from -180 to 180 degrees.

(2) The psi angle is the angle of right-handed rotation around CA-C bond, the value being zero if C-N bond is cis to N-CA bond. Range: from -180 to 180 degrees.

(3) The omega angle is the angle of right-handed rotation about C-N bond, the value being zero if CA-C bond of the preceding residue is cis to N-CA bond. Most residues in a typical protein are involved in the formation of two peptide bonds. The peptide bond formed by the residues I and I + 1 is assigned to the residue I + 1. The same applies to the omega angle. For that reason no omega angle is assigned to the first residue.

Since version 1.2, garlic uses the following procedure to calculate the main chain dihedral angles:

(1) In the first attempt, the coordinates of the main chain atoms are used to calculate the dihedral angles phi and psi. The phi angle will be missing for the first residue in each chain. The psi angle will be missing for the last residue in each chain.

(2) In the second attempt, the missing phi angles will be calculated using the coordinates of H (hydrogen) atoms, if available. The missing psi angles will be calculated using the coordinates of O (oxygen) atoms.





SIDE CHAIN DIHEDRAL ANGLES
For each side chain dihedral angle, the coordinates of four atoms are required. The table below contains the list of atoms and the range of values, for each side chain angle and for each residue. In garlic, the angle chi1 is not calculated for ALA and GLY. The angle chi2 is not calculated for ALA, CYS, GLY, SER, THR and VAL. The angle chi3 is calculated for ARG, GLN, GLU, LYS and MET, the angle chi4 is calculated for ARG and LYS and the angle CHI5 is calculated only for ARG.

CHI1
SIDE
CHAIN 		AXIS ATOMS USED TO
DEFINE ANGLE 		ZERO VALUE FORMAL RANGE
ARG CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
ASN CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
ASP CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
CYS CA-CB N-CA-CB-SG SG cis to N from -180 to +180 deg
GLN CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
GLU CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
HIS CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
ILE CA-CB N-CA-CB-CG1 CG1 cis to N from -180 to +180 deg
LEU CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
LYS CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
MET CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
PHE CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
PRO CA-CB N-CA-CB-CG CG cis to N CA-CB is part of ring
SER CA-CB N-CA-CB-OG OG cis to N from -180 to +180 deg
THR CA-CB N-CA-CB-OG1 OG1 cis to N from -180 to +180 deg
TRP CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
TYR CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
VAL CA-CB N-CA-CB-CG1 CG1 cis to N from -180 to +180 deg
CHI2
ARG CB-CG CA-CB-CG-CD CD cis to CA from -180 to +180 deg
ASN CB-CG CA-CB-CG-OD1 OD1 cis to CA from -180 to +180 deg
ASP CB-CG CA-CB-CG-OD1 OD1 cis to CA from -180 to +180 deg
GLN CB-CG CA-CB-CG-CD CD cis to CA from -180 to +180 deg
GLU CB-CG CA-CB-CG-CD CD cis to CA from -180 to +180 deg
HIS CB-CG CA-CB-CG-ND1 ND1 cis to CA from -180 to +180 deg
ILE CB-CG1 CA-CB-CG1-CD CD cis to CA from -180 to +180 deg
LEU CB-CG CA-CB-CG-CD1 CD1 cis to CA from -180 to +180 deg
LYS CB-CG CA-CB-CG-CD CD cis to CA from -180 to +180 deg
MET CB-CG CA-CB-CG-SD SD cis to CA from -180 to +180 deg
PHE CB-CG CA-CB-CG-CD1 CD1 cis to CA from -180 to +180 deg
PRO CB-CG CA-CB-CG-CD CD cis to CA CB-CG is part of ring
TRP CB-CG CA-CB-CG-CD1 CD1 cis to CA from -180 to +180 deg
TYR CB-CG CA-CB-CG-CD1 CD1 cis to CA from -180 to +180 deg
CHI3
ARG CG-CD CB-CG-CD-NE NE cis to CB from -180 to +180 deg
GLN CG-CD CB-CG-CD-OE1 OE1 cis to CB from -180 to +180 deg
GLU CG-CD CB-CG-CD-OE1 OE1 cis to CB from -180 to +180 deg
LYS CG-CD CB-CG-CD-CE CE cis to CB from -180 to +180 deg
MET CG-SD CB-CG-SD-CE CE cis to CB from -180 to +180 deg
CHI4
ARG CD-NE CG-CD-NE-CZ CZ cis to CG from -180 to +180 deg
LYS CD-CE CG-CD-CE-NZ NZ cis to CG from -180 to +180 deg
CHI5
ARG NE-CZ CD-NE-CZ-Nh1 Nh1 cis to CD from -180 to +180 deg




garlic-1.6/commands/gro.html0000644000000000000000000001071310404015061016026 0ustar rootroot00000000000000 GRO, GROUP

GRO, GROUP

NAME
GRO, GROUP - group structures: catch more than one structure.

SYNOPSIS
GRO identifier1 identifier2 ... identifierN
GRO ALL
GRO SAV filename
GRO SSC filename
GROUP identifier1 identifier2 ... identifierN
GROUP ALL
GROUP SAVE filename
GROUP SSC filename

DESCRIPTION
The command GROUP may be used to catch more than one structure. It is possible to group only one structure, but this doesn't make much sense. A typical usage will be to unite some inhibitor with a substrate.

The structures which form the group will be rotated about the common rotation axis and translated as a single object, except it the keyword ALL is used. In that case, each structure will retain its own rotation center (the old one).

Slab and color fading will be changed simultaneously for all structures. It is recommended to adjust slab and color fading before forming the group. Use much wider slab than usual!

Many other commands will be applied simultaneously for all structures (color, BACKBONE etc.). The exceptions are SAVE , EDIT and REPLACE , which use only default structure (the one which was caught last or loaded as the last structure).

To break the group of structures, i.e. to cancel the command GROUP, execute the command CATCH with a single identifier as a command parameter, to catch only one structure. The command DISCARD may also be used to break the group of structures. Two other commands which cancel GROUP are CREATE and LOAD .

GROUP ALL
The keyword ALL may be used to group all structures into a single object. Each structure will retain its old rotation center. To break the group, use the command CATCH to catch only one structure.

GROUP SAVE filename
The keyword SAVE may be used to save the entire group as a single file. Each structure will be stored as a separate chain. If any of the structures contained more than one chain, it will be stored as a single chain. The first structure will be stored as the chain A, the second as the chain B etc. If there are more than 26 structures, some chain identifiers may be used more than once. The original chain identifiers will be lost. The original atomic serial numbers and residue serial numbers will be replaced by new serials. These changes will affect only data stored to the output file. After breaking the group, each structure will remain intact. The file name is case sensitive.

GROUP SSC filename
The keyword SSC may be used to save the entire group into a single file. All structures will be stored as a single chain. The original chain identifiers will be lost. The original atomic serial numbers and residue serial numbers will be replaced by new serials. These changes will affect only data stored to the output file. After breaking the group, each structure will remain intact. The file name is case sensitive.

EXAMPLES
COMMAND DESCRIPTION
gro 1 2 4 Group structures 1, 2 and 4. Define a single rotation center
for all structures.
gro all Group all structures. Each structure will retain its old
rotation center.
group 1 3
group save united.pdb 		Group structures 1 and 3 and store as a single structure
consisting of two chains to the output file united.pdb .
gro 2 5
gro ssc xyz.pdb 		Group structures 2 and 5 and store as a single chain
to the output file called xyz.pdb .

RELATED COMMANDS
CATCH is used to catch only one structure. The command CATCH breaks the group formed by the command GROUP.

garlic-1.6/commands/tfg.html0000644000000000000000000000330010345616605016030 0ustar rootroot00000000000000 TFG

TFG

NAME
TFG - change the color used to draw text in input and output window.

SYNOPSIS
TFG color

DESCRIPTION
Change the color used to draw text in input and output window. The color should be specified in one of the formats recognized by your X server. Both color names and numerical specification are accepted.

This command does not affect the output window in the sequence comparison mode. Check the command COMPARE .

EXAMPLES
COMMAND DESCRIPTION
tfg white White
tfg DarkSlateGray Dark dark slate gray
tfg #3000a0007000 Kind of green
tfg rgb:0/0/8 Dark blue
tfg rgbi:0.0/0.0/0.5 The same dark blue as above

Read the file rgb.txt (in /lib/X11/ directory) and the man page with a general description of the X window system (man X), to learn other color specification standards.

RELATED COMMANDS
TBG changes the background color used to draw input and output window.

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FG, FOREG, FOREGROUND

NAME
FG, FOREG, FOREGROUND - change the main window foreground color.

SYNOPSIS
FG color
FOREG color
FOREGROUND color

DESCRIPTION
Change the main window foreground color. The color should be specified in one of the formats recognized by your X server. Both color names and numerical specification are accepted. This color is used to draw labels and titles. Note that this color is not used to draw atoms and bonds.

This command does not affect the main window in the sequence comparison mode. Check the command COMPARE .

EXAMPLES
COMMAND DESCRIPTION
fg white White
fg DarkSlateGray Dark dark slate gray
fg #3000a0007000 Kind of green
fg rgb:0/0/8 Dark blue
fg rgbi:0.0/0.0/0.5 The same dark blue as above

Read the file rgb.txt (in /lib/X11/ directory) and the man page with a general description of the X window system (man X), to learn other color specification standards.

RELATED COMMANDS
BG (BACKG, BACKGROUND) changes the main window background color.

garlic-1.6/commands/rad.html0000644000000000000000000000270610345615713016026 0ustar rootroot00000000000000 RAD, RADIUS

RAD, RADIUS

NAME
RAD, RADIUS - set sphere radius.

SYNOPSIS
RAD value
RADIUS value

DESCRIPTION
Set the sphere radius for selection. The value should be given in angstroms. The command SELECT SPHERE may be used to select only the atoms which fit into the sphere of a given radius around the current geometric center.

EXAMPLES
COMMAND DESCRIPTION
rad 4.5 Set radius value to 4.5 angstroms.
sel 210-212
cen
rad 10
sel sphere
sel com
hide 		Select residues from 210 to 212,
redefine the geometric center,
set sphere radius to 10 angstroms
and select atoms in a given sphere.
Select all atoms outside the given
sphere and hide them.

RELATED COMMANDS
SELECT SPHERE is used to select atoms in a sphere around the current geometric center. center is used to redefine the position of the geometric center.

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Kkɭ[1>sҺ(L[Rަqve^e ;Muv -GQ@A<ޢ.mFrM>ko}.:|Kpv/#Ǩ^mykER@[I wzKjҳI9I*rƸړ11$ƨ Ӓjr b랕sM0y/+@ǷRDƘO=jCHX~x/w| Er3Ҳ䑥rrOOʺy#95՜&ש)IQEd`QEQEQEQEQEQEQEQEQEQEQEQEQEQEQEQEQEQEQEi>\*9ANmZZ-AHA}Ir"x0#s犏ºvS̮@ikcSX#vA*B U4krY3 CWou2e\Cf`;/BĊe`4qRܒy WHE, WHEEL

WHE, WHEEL

NAME
WHE, WHEEL - draw helical wheel plot.

SYNOPSIS
SHORT FORM LONG FORM
WHE
WHE CLO
WHE start_index end_index
WHE start_index end_index CLO
WHE OFF 		WHEEL
WHEEL CLOCKWISE
WHEEL start_index end_index
WHEEL start_index end_index CLOCKWISE
WHEEL OFF

DESCRIPTION
Draw helical wheel plot for the given sequence or sequence fragment. Helical wheel may be used to recognize the amphiphilic character of the specified sequence fragment. The sequence from the main sequence buffer (or part of it) is used as input. Additional input: the rotation angle between adjacent residues and hydrophobicity values. The angle should correspond to certain structural motif. Default (hard-coded) angle is 100 degrees, which corresponds to alpha helix, but this may be changed to some arbitrary value, using the command ANGLE. The value of 160 degrees is suitable for beta strand and 115 or 125 is suitable for 3-10 helix.

While helical wheel may be drawn for any sequence length, it makes sense only for short sequence fragments (up to about twenty residues). Hydrophobic residues will be colored in shades of red, while hydrophilic residues will be colored blue. Color intensity depends on the hydrophobicity: very hydrophobic residues will be intensely red and weakly hydrophobic residues will be almost white. Very hydrophilic residues will be intensely blue and weakly hydrophilic residues will be almost white. The command SCALE may be used to select the hydrophobicity scale.

The command WHEEL is usually used in combination with some other commands. See the examples below.



KEYWORDS AND PARAMETERS
The command WHEEL may be used alone, combined with one of two keywords (OFF and CLOCKWISE) or with two residue numbers. Note that from version 1.4, residue array indices are used instead of serial indices! There was some mess with the structures which consist of multiple chains, so the actual residue numbers (related to array indices) proved to be more reliable than the serial numbers. If you specify the residue range from 1 to 10, the residues having the array indices between 0 and 9 will be used. This is because the lowest array index in the C programming language is zero, not one.

If used alone, the helical wheel will be drawn for the entire sequence stored in the main sequence buffer. If this sequence is large the plot will be useless. Two residue numbers may be used to specify the residue range.

By default, residues are drawn counterclockwise. This arrangement of residues gives the top view of a helix. The keyword CLO (long form: CLOCKWISE) may be used to force clockwise arrangement of residues (the bottom view of a helix).

The keyword OFF is used to return to the main drawing mode (the structure drawing mode).

EXAMPLES
COMMAND DESCRIPTION
seq = asp ile met ala glu ile
scale eis
angle 100
wheel 		Initialize the sequence fragment,
select Eisenberg hydrophobicity scale,
set angle to 100 degrees and draw
helical wheel. It is assumed that
that the specified sequence fragment
belongs to alpha helix.
load 2por.pdb
seq from 1
scale eis
angle 160
wheel 2-10 		Load porin coordinates, copy the sequence
of this protein to the main sequence
buffer, select Eisenberg hydrophobicity
scale, set angle to 160 degrees and draw
helical wheel for residues from 2 to 10.
It is assumed that the specified sequence
fragment belongs to beta strand.
whe clo Draw residues clockwise. This
gives the bottom view of a helix,
which is more common in books.
whe off Return to default drawing mode.
Instead using this command,
you can hit the ESCAPE key.

NOTES
(1) Instead using the command WHEEL OFF, the ESCAPE key may be pressed to return to the main drawing mode.

(2) Don't forget that WHEEL uses only the sequence stored to the main sequence buffer. Read description of the command SEQ (SEQUENCE) to learn how to initialize this buffer.

RELATED COMMANDS
SEQUENCE is used to copy, define or load the sequence. ANGLE defines the rotation angle between adjacent residues. SCALE is used to specify the hydrophobicity scale.

garlic-1.6/commands/pat.html0000644000000000000000000000672110345615470016045 0ustar rootroot00000000000000 PAT, PATTERN

PAT, PATTERN

NAME
PAT, PATTERN - define sequence pattern.

SYNOPSIS
PAT = name_11 name_12 ... name_1m / ... / name_k1 name_k2 ... name_kn
PAT TOL number_of_allowed_errors
PATTERN = name_11 name_12 ... name_1m / ... / name_k1 name_k2 ... name_kn
PATTERN TOLERANCE number_of_allowed_errors

DESCRIPTION
The command PATTERN (garlic version 1.4 or later) may be used to define a sequence pattern. It is more general than the command SEQUENCE. Each pattern is a set of name lists, separated by slashes (/). In the following example, a simple pattern of three residues is defined:

PAT = ASP ASN / PHE TYR TRP / ARG LYS

The first residue may be matched by either ASP or ASN, the second residue may be matched by PHE, TYR or TRP, while the third residue may be matched by ARG or LYS.

The macromolecular structure may be searched for the given pattern, using the command SELECT PATTERN (short form: SEL PAT). The commands RESTRICT and ADD may be also used to search for the fiven pattern. For the pattern defined above, the following fragments will be selected:

ASP PHE ARG
ASP PHE LYS
ASP TYR ARG
ASP TYR LYS
ASP TRP ARG
ASP TRP LYS
ASN PHE ARG
ASN PHE LYS
ASN TYR ARG
ASN TYR LYS
ASN TRP ARG
ASN TRP LYS

WILDCARDS
The command PATTERN may be combined with wildcards. The character * (asterisk) may be placed at any position in the pattern string, though it does not make much sense at the first and at the last position. Example:

PAT = ARG LYS HIS / * / ARG LYS HIS / * / ARG LYS HIS

PATTERN TOLERANCE
TOLERANCE (short form: TOL) is the only keyword which may be combined with the command PATTERN. It may be used to define the pattern tolerance, i.e. the maximal number of allowed errors which may be tolerated while searching for the specified pattern.

DELETIONS AND INSERTIONS
It is not possible to handle deletions and insertions directly. However, a number of different patterns may be incorporated into a simple script, which may be used to handle deletions and insertions. The example below is a screen shot of one such script (loaded into vi editor). The script contains three patterns of different length. Each pattern was written as a single line but it was wrapped by the editor because of length. Note that many consecutive wildcards are used in this example.



NOTES
(1) The maximal number of residue names in each list is 30 (more than enough for 20 standard residue names). The maximal number of lists in a pattern is 100. If this is not enough, change MAX_PATT_LENGTH in defines.h file.

RELATED COMMANDS
The command SEQUENCE, combined with the keyword = (equality sign), may be used to define a fixed sequence pattern. Of course, only one residue at each position may be specified with the command SEQUENCE. The commands SELECT, ADD and RESTRICT may be used to search the macromolecular structure for the specified pattern.

garlic-1.6/commands/pau.html0000644000000000000000000000142710345615524016044 0ustar rootroot00000000000000 PAU, PAUSE

PAU, PAUSE

NAME
PAU, PAUSE - pause script execution.

SYNOPSIS
PAU
PAUSE

DESCRIPTION
Pause script execution. This may be useful if using garlic for lectures and conference presentations. The script execution will be paused until the return key is pressed.

RELATED COMMANDS
Use EXE (EXECUTE) to load and execute garlic script. Use LOG to log your garlic session. The log file may be modified into the script file later (or even left unchanged).

garlic-1.6/commands/pos.html0000644000000000000000000000176110345615646016066 0ustar rootroot00000000000000 POS, POSITION

POS, POSITION

NAME
POS, POSITION - move the origin of the internal coordinate system to the specified position.

SYNOPSIS
POS x y z
POSITION x y z

DESCRIPTION
An internal coordinate system is assigned to each structure. The command POS (POSITION) sets the position of this origin. Three coordinates (x, y and z) should be specified.

Initially, the position of geometric center is used as the internal system origin for each structure. When loaded, this origin is set into the point (0, 0, 0).

RELATED COMMANDS
CEN (center) redefines the internal system origin. MOV (MOVE) chooses the object which should be moved (structure, plane, membrane or all).

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Garlic Commands

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
The image in the main window is controled by CONTROLS and by COMMANDS. This page contains the list of garlic commands.

Garlic commands are strings, consisting of one or more words. A command is executed when you press the RETURN key (this key is labeled ENTER on some keyboards). Note that ENTER key on the numeric keypad (the one in the bottom right corner of your keyboard) is NOT the right key! Commands will be displayed in the area called the input window.

The input window is placed at the bottom of the main garlic window, left justified. You don't have to the click into this area to enter the command string - just type it. The input window is capable to display a single error message (top) and a single command (bottom).

You can access previously executed commands by using arrow keys on your keyboard (the UP arrow scans the history buffer backwards and DOWN arrow in the opposite direction).

This page contains the alphabetic list of garlic commands with a short description and with link to detailed description.

Commands are generally case insensitive, but file names are case sensitive because unix (linux) is case sensitive.

SHORT
FORM 		LONG FORM SHORT DESCRIPTION
ADD ADD Expand current selection.
ANG ANGLE Define angle.
ATO ATOMS Change atom drawing style.
BAC BACKBONE Draw backbone.
BACKG BACKGROUND The same as BG.
BAL BALLS Set the ball radius.
BG BACKGROUND Change main window background color.
BLU BLUR Blur (soften) the image in the main window.
BON BONDS Change bond drawing style or refresh bonds.
CAT CATCH Catch the specified structure.
CEN CENTER Change the internal coordinate system origin.
COL COLOR Set color.
COM COMPARE Compare two sequences.
CRE CREATE Create structure.
DIS DISCARD Discard structure.
DOC DOCK Prepare two structures for docking.
DUM DUMP Dump some numeric data to console or to file.
EDI EDIT Edit structure.
EXE EXECUTE Execute garlic script.
EXI EXIT Quit garlic session.
EXP EXPAND The same as ADD.
FAD FADING Change color fading style or parameter(s).
FG FOREGROUND Change main window foreground color.
FON FONT Change font.
FOREG FOREGROUND The same as FG.
GRO GROUP Group (catch simultaneously) the specified structures.
HID HIDE Hide selected atoms.
HYB HYBONDS Generate hydrogen bonds.
IGN IGNORE Ignore (this command does nothing).
LAB LABELS Show labels.
LOA LOAD Load the specified file.
LOG LOG Write commands to log file.
MEM MEMBRANE Membrane manipulation.
MON MONO Switch to mono mode.
MOV MOVE Define which object should be moved.
NEI NEIGHBORHOOD Show or hide the sequence neighborhood.
PAT PATTERN Define sequence pattern.
PAU PAUSE Pause execution (useful in scripts).
PLA PLANE Plane manipulation.
PLO PLOT Plot averaged hydrophob. and/or hydrophobic moment.
POS POSITION Move structure to specified position.
PRO PROBE Set the bond probe radius (used to draw nice bonds).
QUI QUIT The same as exit.
RAD RADIUS Define sphere radius (used for selection).
RAM RAMACHANDRAN Draw Ramachandran plot.
REA READ The same as LOAD.
REF REFRESH Switch graphics refreshing on or off.
REG REGISTER Register garlic.
REP REPLACE Replace selected residues.
RES RESTRICT Restrict current selection.
ROT ROTATE Rotate structure.
SAV SAVE Save atomic data to file.
SCA SCALE Select hydrophobicity scale.
SEL SELECT Select atoms.
SEQ SEQUENCE Sequence buffer manipulation.
SET SET Set the specified dihedral angle.
SHO SHOW Show selected atoms.
SLA SLAB Change slab style or parameter(s).
SSB SSB Change drawing style for disulfide bonds.
STE STEREO Switch to stereo mode.
STI STICKS Set the stick radius.
STR STRUCTURE Secondary structure manipulation.
TAG TAG Assign tag (short text) to structure.
TAK TAKE The same as CATCH.
TBG TEXT_BACKGROUND Change text background color.
TFG TEXT_FOREGROUND Check text foreground color.
TIT TITLE Add title to the main window.
TRA TRANSLATE Translate structure.
VEN VENN Draw Venn diagram.
WHE WHEEL Draw helical wheel.
WIN WINDOW Set sliding window width.
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MON, MONO

NAME
MON, MONO - switch to mono mode.

SYNOPSIS
MON
MONO

DESCRIPTION
Switch to mono mode, i.e. switch stereo off.

RELATED COMMANDS
Use STEREO to switch to stereo mode. STEREO OFF does the same job as MONO.

garlic-1.6/commands/col.html0000644000000000000000000001701310361462547016035 0ustar rootroot00000000000000 COL, color

COL, color

NAME
COL, color - change the color of selected atoms and their corresponding bonds.

SYNOPSIS
COL color_scheme_name
COL left_1 middle_1 right_1 ... ... ... left_N, middle_N, right_N

DESCRIPTION
Change the color used to draw selected atoms and their corresponding bonds. Half of each bond belongs to one atom, while half of the same bond belongs to another atom. The easy way to specify color is to use the predefined color scheme. The powerfull (but more complicated) way to specify color is to issue detailed color specification. From version 1.5, default color scheme is COLD.

color USAGE
In garlic, colors are used to create 3D illusions. In most color schemes, the atoms close to the observer have bright colors, while distant atoms have dark colors. Atoms and bonds look like three-dimensional objects because one side is brighter than the other. Here are some technical details about color usage:

At least one and at most eight surfaces are assigned to each structure. These surfaces are equidistant planes, spheres or cylinders. The surface which is nearest to the observer is called "front surface", while the most distant surface is called "back surface". To each surface, three colors are assigned: left, middle and right color. In most color schemes, left color is bright and right color is dark. Atoms may be divided in three groups:

(1) Atoms which are in front of the front surface;
(2) Atoms which are behind the back surface;
(3) All other atoms, positioned in the sandwich between two surfaces.

All atoms which are in front of the front surface are drawn using the same set of three colors which assigned to front surface. Atoms behind the back surface are colored using three colors assigned to back surface. Colors for atoms laying between two surfaces are prepared by linear interpolation of colors assigned to these two surfaces. This is what I call color fading (this term was not the best choice I could make, sorry).

In a special case, when only one surface is used, color does not depend on distance.

Almost all predefined color schemes typically define two surfaces, i.e. a total of six colors. There are some exceptions: color schemes HOT and COLD use three surfaces, while MONOCHROME uses only one.

Planes, spheres and cylinders
For most proteins and other molecules, planar fading is the best choice. In this case, a set of planes, perpendicular to z axis is used. Concentric spheres may be used when working with large globular proteins, while cylinders may be used for beta-barrel proteins, like porins. The axis of concentric cylinders is parallel to y.

USING PREDEFINED color SCHEMES
Twenty predefined color schemes are available:

SCHEME NAME DESCRIPTION
RED Red color scheme; distant atoms are dark
GREEN Green, distant atoms are dark
BLUE BLUE (deep sea), distant atoms are dark
YELLOW Yellow, distant atoms are dark
CYAN Cyan (cloudless sky), distant atoms are dark
MAGENTA Magenta, distant atoms are dark
WHITE Shades of gray, distant atoms almost black
YELLOW-GREEN Somewhere between yellow and green,
distant atoms dark
CYAN-GREEN Somewhere between green and blue-green,
distant atoms dark
CYAN-BLUE Somewhere between blue and blue-green,
distant atoms dark
MAGENTA-BLUE Somewhere between blue and magenta,
distant atoms are dark
MAGENTA-RED Somewhere between red and magenta,
distant atoms are dark
ORANGE Orange, distant atoms are dark
HOT The nearest atoms are yellow, atoms in the middle are orange
and distant atoms are dark red
COLD Default color scheme: the nearest atoms are cyan, atoms in
the middle are cyan-blue and distant atoms are dark blue
MODEL Use different colors for different NMR models
MONOCHROME Edge black, central region white, distance independent
CPK Modified Corey-Pauling-Kultun color scheme,
distant atoms are dark
size Residues are colored according to the side chain size.
ZEbrA Residues with even serial number are red, odd residues
cyan-blue, distant atoms are dark
WEIGHTED Residues are colored according to the absolute value
of weighted hydrophobicity. For more details, read
the source file color_weighted.c !
CHAIN Use color to distinguish chains;
distant atoms are should be dark
HYPHOB Assign color according to hydrophobicity;
distant atoms are dark

Do not abbreviate the color scheme name! Case is not important. Some selected schemes are shown below.



DETAILED color SPECIFICATION
Most users should be satisfied with predefined color schemes. Anyway, it is fairly easy to use colors which are not available through predefined schemes. To define N color planes (up to eight), you have to define 3 * N colors. The keyword OLD may be used to leave the previous value unchanged. Here are some examples:

col yellow orange red red DarkRed black Define two color surfaces
with six colors.
col rgb:ffff/ffff/4444 rgb:ffff/dddd/0000 DarkRed One color surface,
three colors.
col old old old black black black Leave the front colors unchanged,
set all back colors to black.

Be careful with the keyword OLD - it may be used only if the currently used color scheme has at least as many colors as a new one.

RELATED COMMANDS
FADING may be used to change the position of outer color surfaces and to switch color fading on and off.

garlic-1.6/commands/hid.html0000644000000000000000000000102410345614140016005 0ustar rootroot00000000000000 HID, HIDE

HID, HIDE

NAME
HID, HIDE - hide selected atoms.

SYNOPSIS
HID
HIDE

DESCRIPTION
Hide selected atoms and associated bonds.

RELATED COMMANDS
SHOW shows selected atoms and associated bonds.

garlic-1.6/commands/com.html0000644000000000000000000001452710345613436016042 0ustar rootroot00000000000000 COM, COMPARE

COM, COMPARE

NAME
COM, COMPARE - compare two sequences.

SYNOPSIS
COM
COM minimal_score segment_width
COM OFF
COM COR serial1 serial2
COM ZOO zoom_factor
COMPARE
COMPARE minimal_score segment_width
COMPARE OFF
COMPARE CORNER serial1 serial2
COMPARE ZOOM zoom_factor

DESCRIPTION
Compare two sequences. Garlic mantains two sequence buffers: the main sequence buffer and the reference sequence buffer. After initializing both buffers, the command COMPARE may be used to prepare the plot with comparison of these two sequences. Matching residues will be marked by dots or squares, depending on the zoom factor. Dots or squares which represent residue pairs which match exactly will be colored yellow, while residues which are different but have similar properties will be colored red. The reference sequence will be assigned to the horizontal (x) axis, while another (investigated) sequence will be assigned to the vertical (y) axis.

The plot will contain only residues which belong to the segments for which the score of matching residues is equal to or larger than minimal score. The minimal score (the number of matching pairs) and the width of the segment used for comparison may be specified by the user. Hard-coded defaults are SEGMENT_WIDTH and MINIMAL_SCORE, defined in defines.h file. The values used in the original garlic package: SEGMENT_width=5, MINIMAL_SCORE=5.

SCORING
Two sequences are compared using fixed width segments. The matrix shown below is used to identify matching residues. It was inspired by Dayhoff PAM250 matrix. However, while PAM250 matrix contains a range of values, both positive and negative, the only values used in the substitution matrix below are zero and one. One is used to identify matching residue pairs and zero for pairs which do not match.



The scoring scheme used in garlic is much simpler than the elaborate schemes used in advanced programs for sequence alignments. However, this scheme is still quite useful and I believe that many users will like to play with the various segment widths and scores.

KEYWORDS AND PARAMETERS
All keywords and associated parameters are explained in the table below. Note that the minimal score may not exceed the segment width.

KEYWORD AND/OR
PARAMETERS 		DESCRIPTION
None Draw sequence comparison, using default segment
width and default minimal score.
OFF Return to the main drawing mode. The same may
be achieved by hiting the ESCAPE key.
minimal_score segment_width Draw sequence comparison, using the specified
segment width and the specified minimal score.
Both parameters should be positive.
CORNER ref_offset main_offset Draw sequence comparison, but skip some leading
residues. Skip (ref_offset - 1) residues of
the reference sequence and (main_offset - 1)
residues of the main sequence.

MOUSE USAGE
The pointing device (mouse) may be used to find the residue serial numbers and names for matching pairs and residues which follow after them. After a chosen pair is reached with the pointer, the information about this pair and residues which follow them will be available in the output window (the bottom right corner). Color codes: yellow is used for residues which are equal, magenta for acceptable substitutions and red for mismatching residues.



EXAMPLES
COMMAND DESCRIPTION
load 9PAP.pdb
sel het
sel com
seq from 1
seq copy
load 1HUC.pdb
sel a,b/*/*/*
seq from 2
compare 8 10 		Load the structure of papain, select all hetero atoms and
then select the complement of this selection. The purpose
of this trick is to exclude all hetero atoms from selection.
Extract the sequence and copy it to the reference buffer.

After that, load the structure of human cathepsin B, select
chains A and B (one molecules consists of two chains), extract
the sequence and compare it with the content of the reference
buffer. The minimal score is 8 and the segment width is 10.
load 9PAP.pdb
sel het
sel com
seq from 1
seq copy
seq load sample.fasta
compare 6 7 		Load the structure of papain and copy the sequence to the
reference buffer using the same method as in the previous
example. Read the second sequence from the specified FASTA
file (one letter codes). Compare two sequences, using the
specified minimal score and segment width (5/7).
This is the typical usage of sequence comparison: compare
a fresh sequence with the sequence of a solved structure.
com zoom 4 Change zoom factor to 4.
com cor 100 100 Skip the first hundred residues of both sequences.

NOTES
(1) You don't need protein 3D structures to compare two sequences. The minimal information required for protein comparison is the primary structure, i.e. the protein sequence.

RELATED COMMANDS
The command SEQ (SEQUENCE) is used to manipulate the content of the main sequence buffer and of the reference sequence buffer. LOAD is used to load the PDB file. SELECT, ADD and RESTRICT are used for selection.

garlic-1.6/commands/ven.html0000644000000000000000000000560710345616726016060 0ustar rootroot00000000000000 VEN, VENN

VEN, VENN

NAME
VEN, VENN - draw Venn diagram.

SYNOPSIS
VEN
VEN OFF
VEN start_index end_index
VENN
VENN OFF
VENN start_index end_index

DESCRIPTION
Draw Venn diagram for the given protein sequence or sequence fragment. Venn diagram gives the quick statistical overview of the protein sequence: count of residues and residue types. It is primarily intended for students. Experts will not find this routine very interesting.



KEYWORDS AND PARAMETERS
The command VENN may be used alone, combined with the keyword OFF or with two residue numbers. Note that from version 1.4, residue array indices are used instead of serial indices! There was some mess with the structures which consist of multiple chains, so the actual residue numbers (related to array indices) proved to be more reliable than the serial numbers. If you specify the residue range from 1 to 100, the residues having the array indices between 0 and 99 will be used. This is because the lowest array index in the C programming language is zero, not one.

If used alone, the Venn diagram will be drawn for the entire sequence stored in the main sequence buffer. Two residue array indices (shifted for one) may be used to specify the residue range. The keyword OFF is used to return to the main drawing mode (structure drawing mode).

EXAMPLES
COMMAND DESCRIPTION
load 2por.pdb
seq from 1
ven 		Load the specified structure (porin),
copy the sequence from this structure
to the main sequence buffer and draw
Venn diagram.
ven 1-100 Prepare Venn diagram with counts, but
only for the first hundred residues,
having the array indices from 0 to 99.
ven off Return to default drawing mode.
Instead using this command,
you can hit the ESCAPE key.

NOTES
(1) Instead using the command VENN OFF, the ESCAPE key may be pressed to return to the main drawing mode.

(2) Ven diagram is a term from the set theory, which is part of mathematics. Different sorts of Venn diagrams may be found in different branches of science.

RELATED COMMANDS
SEQUENCE is used to copy, define or load the sequence.

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RAM, RAMACHANDRAN

NAME
RAM, RAMACHANDRAN - draw Ramachandran plot.

SYNOPSIS
RAM
RAM SEL
RAM OFF
RAMACHANDRAN
RAMACHANDRAN SEL
RAMACHANDRAN OFF

DESCRIPTION
Draw Ramachandran plot (only for proteins). The main chain torsion angles, phi and psi, are used to prepare two-dimensional scatter plot. Residues for which both phi and psi angle may be calculated will be shown as small circles. The horizontal axis (abscisa) is used for phi values, while the vertical axis (ordinate) is used for psi values. Blue color is used for trans residues, magenta for cis residues and red for bad residues. Trans residues are drawn first, followed by cis residues. Bad residues are drawn last. A residue is treated as bad if peptide unit associated with this residue is not planar. Peptide unit is considered as non-planar if it is twisted for more than 20 degrees. Terminal residues will be missing, because at least one of dihedral angles is not defined for such residues.

DIHEDRAL ANGLES
Click here for definitions of dihedral angles.

KEYWORDS
If used without any keyword, the command RAM will prepare the Ramachandran plot for protein structure(s) which are currently being handled ("caught"). Keyword OFF is used to switch off the Ramachandran plot, i.e. to return to the main drawing mode (atomic structure display). If keyword SEL (SELECTED) is used, only the residues which are currently selected will be visible in the Ramachandran plot. A residue is treated as selected if the first atom of this residue is selected. For proteins, this is usually N (nitrogen) atom. Here is the overview:

KEYWORD DESCRIPTION
ram sel Draw Ramachandran plot for selected residues.
ram off Return to default drawing mode (atomic structure).
Instead using this command, you can hit the ESCAPE key.

MOUSE USAGE
Pointing device (mouse) may be used to identify individual residues in Ramachandran plot. Just place the mouse pointer above the selected residue and the most important data for this residue will be shown in the output window. The output window will look like this:



EXAMPLE OF RAMACHANDRAN PLOT
The example below show the Ramachandran plot for photosynthetic reaction center from Rhodopseudomonas viridis.



EXAMPLES
COMMAND DESCRIPTION
ram Draw Ramachandran plot for all residues.
ram off Return to default drawing mode (atomic structure).
ram sel Draw Ramachandran plot for selected residues.
sel pro
ram sel 		Select all prolines and draw Ramachandran
plot for prolines.
sel cis
ram sel 		Select all residues in cis conformation and
draw Ramachandran plot for them.
sel bad
ram sel 		Select bad residues (peptide unit not planar)
and draw Ramachandran plot.
sel tra
ram sel 		Select all residues in trans conformation and
draw Ramachandran plot.

NOTES
(1) Instead using the command RAMA OFF, the ESCAPE key may be pressed to return to the main drawing mode.

(2) G. N. Ramachandran devised in the late 1960's the steric constraints for amino acid residues in proteins. As the number of high resolution structures is increasing, it appears evident that these old constrains are becoming obsolete. If you are interested in this problem, read this article:

http://xray.bmc.uu.se/~gerard/rama/ramarev.html

RELATED COMMANDS
SEL may be used to select a portion of protein structure, to reduce the amount of data in Ramachandran plot.

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SLA, SLAB

NAME
SLA, SLAB - change slab.

SYNOPSIS
SLA keyword
SLA FRONT shift
SLA BACK shift
SLAB keyword
SLAB FRONT shift
SLAB BACK shift

DESCRIPTION
Change the slab. Slab is used to cut the slice out from the structure and to hide the rest. Two slab surfaces are used: the front slab surface, which is the one closer to the observer and the back slab surface. There are three versions of this command:

(1) SLAB FRONT shift ----> move the front slab surface;
(2) SLAB BACK shift ----> move the back slab surface;
(3) SLAB keyword ----> switch slab off or change the type of the surfaces.

SLAB FRONT shift
This command moves the front slab surface. It is recommended to use this command in scripts - in interactive mode, use controls (keys DEL and ENTER on numeric keypad). The shift value should be given in angstroms. Positive shift moves the front slab surface away from the observer. FRONT may be abbreviated to FRO.

SLAB BACK shift
This command moves the back slab surface. It is recommended to use this command in scripts - in interactive mode, use controls (keys 1 and 3 on the numeric keypad). The shift value should be given in angstroms. Positive shift moves the back slab surface away from the observer. BACK may be abbreviated to BAC.

SLAB keyword
Some keywords may be used to change the type of slab surfaces and to switch slab off. Here is the list of keywords:

SHORT FORM LONG FORM DESCRIPTION
OFF OFF Switch slab off: all parts
of the structure should be visible.
PLA PLANE Use planes as slab surfaces
SPH SPHERE Use spheres as slab surfaces
CYL CYLINDER Use cylinders as slab surfaces
HALF-SPH HALF-SPHERE Use spheres as slab surfaces, but
hide the back half of the structure.
HALF-CYL HALF-CYLINDER Use cylinders as slab surfaces, but
hide the back half of the structure.

For most structures, the planar slab is the best choice. Spherical and semi-spherical slab may be useful when working with large globular proteins, while cylindrical and semi-cylindrical slab is useful when working with beta-barrel proteins (like porins). The cylinder axis is parallel to y axis (vertical from user's standpoint).

EXAMPLES
COMMAND DESCRIPTION
slab off Switch slab off
slab front 4.5 Move the front slab surface 4.5 angstroms
away from the observer
slab back -2.8 Move the back slab surface 2.8 angstroms
closer to the observer
slab half-sph Change slab to semi-spherical
garlic-1.6/commands/cat.html0000644000000000000000000000431410345613313016016 0ustar rootroot00000000000000 CAT, CATCH

CAT, CATCH

NAME
CAT, CATCH - catch the specified macromolecular complex.

SYNOPSIS
CAT identifier
CATCH identifier

DESCRIPTION
Catch the specified structure (macromolecular complex). The structure is a set of atoms read from a single file. Thus, every file is treated as a separate structure. The structure identifier is positive integer. The value zero is not used; structures are numbered 1, 2, 3, etc. When you catch a single structure, all transformations (rotations, translations etc.) are applied to this structure, leaving other structures intact. Selection (commands SELECT, ADD, RESTRICT) are also applied only to this structure. The command CATCH is used when working with more than one structure - for example, when docking an inhibitor to a substrate. When only one structure (file) is loaded, this command has no purpose. Examples:

COMMAND DESCRIPTION
cat 1 Catch the structure number 1.
cat 7 Catch the structure number 7.

NOTES
(1) Sometimes you will forget the identifiers, especially when working with many structures. Move the mouse pointer over the structure you want to catch. The identifier will be displayed in the output window (bottom right corner of the garlic window). The number in parentheses is the identifier you need. In the example below, the identifier is equal to one.


(2) The command CATCH resets the editing mode to default (no editing).

RELATED COMMANDS
TAK (TAKE) does exactly the same job as CATCH. DIS (DISCARD) is used to discard the macromolecular complex (structure). GRO (GROUP) is used to catch more than one structure simultaneously.

garlic-1.6/commands/nei.html0000644000000000000000000001013210345615437016026 0ustar rootroot00000000000000 NEI, NEIGHBORHOOD

NEI, NEIGHBORHOOD

NAME
NEI, NEIGHBORHOOD - hide or show the sequence neighborhood.

SYNOPSIS
NEI
NEI VER
NEI OFF
NEIGHBORHOOD
NEIGHBORHOOD VERBOSE
NEIGHBORHOOD OFF

DESCRIPTION
Hide or show the sequence neighborhood of the residue covered by the pointer. When you cross an atom or bond with the mouse pointer, the output window will contain some useful information about this atom. In addition to this, the top portion of the main window will contain some data about the residues before and after the residue to which this atom belongs. The central residue will be enclosed in a small rectangle. The entire sequence neighborhood will be enclosed in a wide rectangle.

Just below the central residue there will be a small black rectangle with a blue arrow. This arrow shows the approximate direction of the main chain.



If you are not interested in the sequence neighborhood, execute the command:

nei off

If you want to remove the sequence neighborhood permanently, find this section in the configuration file .garlicrc and use the keyword "no" instead of the previus keyword ("verbose" or "yes"):

# Sequence neighborhood of the residue under the pointer may be hidden,
# visible and short or visible and verbose (no/yes/verbose):

show sequence neighborhood: verbose

By default, the sequence neighborhood will be visible and verbose.

KEYWORDS
If used without any keyword, the command NEI will make the sequence neighborhood visible and short. The string at the top of the main window will contain only residue names, without serial numbers and chain identifiers. The keyword VER (long form: VERBOSE) may be used to force writing of residue serial numbers and chain identifiers in addition to residue names. The keyword OFF is used to hide the sequence neighborhood.

The keyword VER (VERBOSE) was introduced in version 1.4 of the program. The verbose output was set as default in the configuration file, .garlicrc.

EXAMPLES
COMMAND DESCRIPTION
nei off Hide the sequence neighborhood.
nei Show short sequence neighborhood (residue names, without serial numbers and chain identifiers).
nei ver Show verbose sequence neighborhood (residue names, serial numbers and chain identifiers).

NOTES
(1) Residues in the sequence neighborhood are listed in direction from amino- to carboxyl-terminal residue.

(2) If the current residue is close to the polypeptide chain end, it will be displaced from the central position.

(3) The half-width of the sequence neighborhood is defined as NEIGH_HALF_WIDTH in defines.h; the total number of residues in the sequence neighborhood is:

2 * NEIGH_HALF_WIDTH + 1.

Default NEIGH_HALF_WIDTH value is 11 which gives 23 residues in the sequence neighborhood. The actual number of visible residues depends on the size of the main window and on the font size. Default font size is 10x20. If this is too large, use 9x15 or 7x14 - these fonts are still readable, but on small displays more suitable if you want the entire sequence neighborhood to be visible.

RELATED COMMANDS
FONT is used to change the font. For example:

fon 7x14

may be used to choose reasonably small (but readable) font.

garlic-1.6/commands/blu.html0000644000000000000000000000546410345613211016035 0ustar rootroot00000000000000 BLU, BLUR

BLU, BLUR

NAME
BLU, BLUR - blur (soften) the image in the main window.

SYNOPSIS
BLU width height
BLU OFF
BLUR width height
BLUR OFF

DESCRIPTION
The command BLUR (short form: BLU) will blur (soften) the image in the main window. The color of each pixel in the main window will be replaced with the averaged color of

width x height

pixels surrounding this pixel. The original color of this pixel will be used too, weighted equally as all other pixels. The contrast will be reduced. Larger blur rectangle will result in softer image. The textual content of the main window (titles, labels) will remain unchanged. Default blur rectangle width and height: 3x3 pixels (see the configuration file, .garlicrc ).

Use the command BLUR OFF (short form: BLU OFF) to switch blur off.

EXAMPLES
COMMAND DESCRIPTION
blur Soften the image in the main window,
using default blur rectangle.
blur 4 4 Soften the image in the main window,
using 16 pixels to calculate color
of the central pixel.
blur off Switch blur off.

The following eight images show the water molecule on two different backgrounds, white and black. No blur was applied on two images in the leftmost column.
blur off
bg black 		blur 3 3
bg black 		blur 6 6
bg black 		blur 12 12
bg black
blur off
bg white 		blur 3 3
bg white 		blur 6 6
bg white 		blur 12 12
bg white

RELATED COMMANDS
BG changes the background color.

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ADD, EXP, EXPAND

NAME
ADD, EXP, EXPAND - add specified atoms to current selection.

SYNOPSIS
ADD chain_identifiers/residue_serials/residue_names/atom_names
ADD residue_ranges
ADD residue_names
ADD ATO atomic_ranges
ADD ATOMS atomic_ranges
ADD keyword
ADD ELE chemical_symbol
ADD ELEMENT chemical_symbol

DESCRIPTION
Add specified atoms to current selection. Atoms are added according to the specified cryteria. The command EXPAND does exactly the same job as ADD. The essential difference between ADD and SELECT is that ADD does not overwrite the previous selection. Four types of selection are available:

(1) detailed selection;
(2) selection by residue serial numbers;
(3) selection by residue names;
(4) special selection (by keyword);
(5) selection by chemical symbol;
(6) selection by atom serial number.

DETAILED SELECTION
In this case four data types are specified simultaneously: chain identifiers, residue serial numbers, residue names and atom names. It is not possible to specify atomic serial numbers. The selection string should contain exactly three slashes, separating different data types:

chain_identifiers/residue_serials/residue_names/atom_names.

Both uppercase and lowercase characters are accepted. Space ( ), comma (,) and semicolon (;) may be used as separators.

Chain identifiers are single alphabetic characters. Asterisk (*) may be used to select all chains. The keyword EXC (EXCEPT) may be used to exclude one or more chains from selection.

Residue serial numbers consist of digits. Minus may be used to specify a range of residue serial numbers. For example, 1-100 specifyes residues from 1 to 100, including these two. Asterisk (*) may be used to specify all residue serials. The keyword EXC (EXCEPT) may be used to exclude serial numbers or ranges from selection.

Residue names are expected in three letters code. Asterisk (*) may be used to specify all residue names. The keyword EXC (EXCEPT) may be used to exclude one or more names from selection. Non-standard names are accepted.

The names of atoms are expected as used in the input file; do not replace them with pure chemical symbols. C alpha, for example, should be specified as CA or ca (case is not important), if coordinates are read from PDB file. Asterisk (*) may be used to select all atoms, while EXC may be used to exclude some atoms from selection. Examples:

add a/*/*/* Add all atoms from chain A to current selection.
add * exc m/*/*/ca Add CA atoms from all chains except chain M.
add */*/*/* exc ca,c,n,o Add all atoms except CA, C, N and O.
add a/* exc 72-112/*/ca Add CA atoms from chain A, but exclude residues from 72 to 112.

SELECTION BY RESIDUE SERIAL NUMBERS
To select all atoms in a single residue, a residue range or in a number of residues and residue ranges, a simple syntax may be used. The selection string should contain no slashes. Keyword EXC (EXCEPT) is accepted, but asterisk (*) will be missintepreted. Minus may be used to specify residue ranges. Comma (,), semicolon (;) and space ( ) may be used as separators. Examples:

add 1-100 Add residues from 1 to 100 to current selection.
add 1-100 exc 20-40 Add residues 1-100 but exclude 20-40.
add 1, 4, 8, 11-48 exc 20-32 Add residues 1, 4, 8 and 11-48 but exclude 20-32.

SELECTION BY ATOMIC SERIAL NUMBERS
To add a single atom by the atomic serial number, combine the command ADD and the keyword ATO (ATOMS). For example, to add the atom number 102 to the current selection type:

add ato 102

The same keyword may be used to add a range of atoms or to add two or more ranges. Examples:

add ato 1-100 Add atoms which have serial numbers in the range between 1 and 100.
add 1-20 40-50 Add atoms which have serial numbers between 1 and 20 and between 40 and 50.

Do not combine the keywords EXC (EXCLUDE) and ATO (ATOMS).

SELECTION BY RESIDUE NAMES
Three letters code should be used. Asterisk (*) and keyword EXC (EXCEPT) are not accepted. Example:

add phe,tyr,trp Add PHE, TYR and TRP to current selection.

SPECIAL SELECTION KEYWORDS
Some special keywords may be combined with ADD to select residues or atoms according to some properties. It is also possible to select the complement, i.e. all atoms which were not selected previously. A single keyword should be used; asterisk (*) and keyword EXC (EXCEPT) are not accepted.

add *
add all 		Add all atoms to current selection, i.e. select all.
add abo
add above 		Add atoms above the plane.
add aci
add acidic 		Add acidic amino acids (GLU and ASP).
add ali
add aliphatic 		Add aliphatic amino acids (ILE, LEU and VAL).
add alt Add atoms at alternate positions.
add bad Add bad residues. A residue is treated as bad if the
peptide bond assigned to this residue is non-planar.
The peptide bond is non-planar if the omega angle is
different for 20 or more degrees from 0 or 180 degrees.
add bas
add basic 		Add basic amino acids (ARG, LYS and HIS).
add bel
add below 		Add atoms below the plane.
add cha
add charged 		Add charged amino acids (ARG, LYS, HIS, GLU and ASP).
add cis Add cis residues.
add com
add complement 		Add atoms which were not select previously.
add het
add hetero 		Add hetero atoms (heme groups, water etc.).
add pho
add hydrophobic 		Add hydrophobic amino acids
(ALA, ILE, LEU, MET, PHE, TRP, VAL, TYR, CYS, GLY and HIS).
add mai
add main_chain 		Add main chain atoms (CA, C, N and O).
add mod serial_number
add model serial_number 		Add model specified by serial_number.
NMR structure is a set of models. Example: add mod 1
add neg
add negative 		Add negatively charged amino acids (GLU and ASP).
add pat
add pattern 		Add the sequence pattern. The command
PAT (PATTERN) is used to define the sequence pattern.
add pol
add polar 		Add polar amino acids
(ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TRP and TYR).
add pos
add positive 		Add positively charged amino acids (ARG, LYS and HIS).
add seq
add sequence 		Add sequence fragments which match the sequence stored
to the sequence buffer. The sequence buffer should be
initialized before executing this command.
add sid
add side_chains 		Add atoms which belong to side chains (all except CA, C, N and O).
add sma
add small 		Add small amino acids
(GLY, ALA, SER, THR, CYS, VAL, PRO, ASP and ASN).
add sph
add sphere 		Add atoms inside the sphere. Use the command
RAD (RADIUS) to set the sphere radius.
add tin
add tiny 		Add tiny amino acids (GLY,ALA and SER).
add tm Add the transmembrane part
(useful for membrane proteins).
add tra
add trans 		Add trans residues.
add tri
add triplet 		If there are three (or more) positively charged residues in a fragment
of up to five protein residues, add these residues to the current set
of selected atoms. Detailed explanation may found in the article:
D. Juretic, L. Zoranic and D. Zucic,
Basic charge clusters and predictions of membrane protein topology,
Journal of Chemical Information and Computer Sciences 42, No. 3,
620-632 (2002).
add 2c3 If there are two (or more) charged residues in a fragment of
three residues, add these residues to the current selection.
add 2cz3 If there are two (or more) charged or zwitterionic residues in
a fragment of three residues, add these residues to the current
selection.
add 2nz3
add 3c4
add 3cz4
add 3nz4
add 3c5
add 3cz5
add 3nz5
add 3p5
add 4c5
add 4cz5
add 4nz5
add 3c6
add 3cz6
add 3nz6
add 4c6
add 4cz6
add 4nz6
add 5c6
add 5cz6
add 5nz6
add 4c7
add 4cz7
add 4nz7
add 5c7
add 5cz7
add 5nz7
add 5p7
add 6p7
add 4c9
add 4cz9
add 4nz9
add 5c9
add 5cz9
add 5nz9 		Analogous to add 2c3 and add 2cz3, where c stands for charged ,
cz for charged or zwitterionic , nz for negative or zwitterionic
and p for polar . The same selection criteria may be defined
using patterns, but these short keywords are more practical.
add 3p5 If there are three or more polar residues in a fragment of five residues,
add these residues. The following residues are treated as polar:
ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP.
add 5p7 If there are five or more polar residues in a fragment of five residues,
add these residues to the current selection. The following residues are
treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR,
TYR and TRP.
add 6p7 If there are six or more polar residues in a fragment of five residues,
add these residues to the current selection. The following residues are
treated as polar: ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR,
TYR and TRP.

EXPANDING SELECTION WITH
THE SPECIFIED CHEMICAL ELEMENT
To add certain chemical element to the selection, use the keyword ELEMENT (short form: ELE) and the standard chemical symbol. To expand your selection with iron atoms, for example, you should type the following command:

add ele fe

In addition to real chemical elements, garlic accepts two imaginary elements: "jellium" (J) and "quarkonium" (Q). Jellium is inert and it never binds to neighboring atoms, no matter how close they are. Quarkonium binds to other quarkonium atoms which have adjacent atomic serial numbers. For example, if some quarkonium atom has serial number i, it may form bonds with quarkonium atoms i-1 and i+1. The interatomic distance is not important! Both elements were introduced to enable drawing of special objects. Quarkonium may be used to draw polygonal lines in three dimensions. The original idea was to adapt garlic for visualization of some medical data. For example, quarkonium may be used to represent blood vessels and jellium to represent retraction balls characteristic for broken axons in human brain. By the way, quarkonium is a serious thing in high energy physics, but there it looks quite different. Note that symbols J and Q are not used in the periodic table of elements.

NOTES
(1) The command ADD resets the editing mode to default (no editing).

RELATED COMMANDS
EXPAND does exactly the same job as ADD. SELECT overwrites the previous selection. RESTRICT restrics the previous selection.

garlic-1.6/commands/mov.html0000644000000000000000000000637310345615413016062 0ustar rootroot00000000000000 MOV, MOVE

MOV, MOVE

NAME
MOV, MOVE - define which object should be moved.

SYNOPSIS
MOV STR
MOV MEM
MOV PLA
MOV ALL
MOVE STRUCTURE
MOVE MEMBRANE
MOVE PLANE
MOVE ALL

DESCRIPTION
This command defines which object should be moved when rotation and translation controls or commands are used. When a PDB file is read, a new structure is stored into program memory. A single plane (initially invisible) is associated with each structure. On request (after the first execution of the command MEMBRANE), a single membrane may also be added to the structure. By default, the movement controls are affecting both the atomic structure and the associated objects (the plane and the membrane, if initialized). The command MOV (MOVE) may be used to change the action of the movement controls, to move only the choosen object.

The command MOVE affects only the molecule which is currently being handled (the structure which is "caught").

KEYWORDS
KEYWORD
(SHORT) 		KEYWORD
(LONG) 		DESCRIPTION
STR STRUCTURE Move only the structure (atoms), leaving the
plane and the membrane at the current position.
MEM MEMBRANE Move only the membrane, leaving the structure
(atoms) and the plane at the current position.
PLA PLANE Move only the plane, leaving the structure
(atoms) and the membrane at the current position.
ALL ALL Move all (atoms + plane + membrane).

EXAMPLES
COMMAND DESCRIPTION
mov pla
Move the plane leaving the structure
and the membrane at the current position.
mov all Move structure, plane and membrane.
This is default action.

NOTES
(1) The plane and the membrane are affected by rotation and translation controls and commands. Slab and color fading do not affect these objects.

(2) Never use two keywords with the command MOVE! If you want to move the plane and the membrane, for example, you should move it one by one!

RELATED COMMANDS
PLA (PLANE) is used to manipulate the plane associated with the molecular structure. MEM (MEMBRANE) is used to generate and manipulate the membrane. CATCH is used to catch the specified structure.

garlic-1.6/commands/residues.html0000644000000000000000000006677010361661754017122 0ustar rootroot00000000000000 Garlic Template File

Garlic Template File

residues.pdb

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This page contains the template file for garlic. This file contains the template residues, which are used as basic building blocks required to create a new polypeptide. If you don't have the template file, save this html file as text and remove all lines which do not contain the string ATOM at the beginning. Don't forget to check the bottom lines.

Recommended locations (listed in search order):

Special template file residues.pdb in the current working directory
User's private template file $HOME/garlic/residues.pdb
User's private template file (alternative location) $HOME/garlic/residues.pdb
System-wide file (linux) /usr/share/garlic/residues.pdb
Alternative system-wide file (some systems) /usr/local/lib/garlic/residues.pdb

Garlic uses only one template file. The program first looks in the current working directory, then in $HOME directory etc. until the template file is found. If template file is not available at all, some commands (like CREATE and REPLACE) will fail to work, but the program will not crash. 
ATOM      1  N   ALA     1     -20.307  17.277  25.298  1.00  0.18              
ATOM      2  CA  ALA     1     -20.293  16.365  24.112  1.00  0.19              
ATOM      3  C   ALA     1     -18.873  16.278  23.541  1.00  0.20              
ATOM      4  O   ALA     1     -18.190  17.275  23.428  1.00  0.25              
ATOM      5  CB  ALA     1     -21.238  16.916  23.045  1.00  0.24              
ATOM      6  H   ALA     1     -19.804  18.120  25.278  1.00  0.19              
ATOM      7  HA  ALA     1     -20.622  15.383  24.409  1.00  0.18              
ATOM      8  HB  ALA     1     -21.767  17.771  23.437  1.00  1.03              
ATOM      9  HB  ALA     1     -20.670  17.215  22.176  1.00  1.00              
ATOM     10  HB  ALA     1     -21.949  16.156  22.760  1.00  1.09              
ATOM     11  N   ARG     2     -18.461  15.068  23.192  1.00  0.36              
ATOM     12  CA  ARG     2     -17.108  14.831  22.625  1.00  0.36              
ATOM     13  C   ARG     2     -17.200  13.824  21.484  1.00  0.30              
ATOM     14  O   ARG     2     -17.868  12.814  21.598  1.00  0.30              
ATOM     15  CB  ARG     2     -16.196  14.274  23.713  1.00  0.44              
ATOM     16  CG  ARG     2     -15.991  15.334  24.791  1.00  0.76              
ATOM     17  CD  ARG     2     -15.008  14.797  25.834  1.00  1.23              
ATOM     18  NE  ARG     2     -15.444  15.244  27.185  1.00  1.90              
ATOM     19  CZ  ARG     2     -14.847  14.759  28.240  1.00  2.72              
ATOM     20  Nh1 ARG     2     -13.673  14.207  28.102  1.00  3.38              
ATOM     21  Nh2 ARG     2     -15.449  14.840  29.395  1.00  3.41              
ATOM     22  H   ARG     2     -19.080  14.321  23.320  1.00  0.39              
ATOM     23  HA  ARG     2     -16.702  15.755  22.254  1.00  0.40              
ATOM     24  HB  ARG     2     -16.648  13.394  24.149  1.00  0.54              
ATOM     25  HB  ARG     2     -15.243  14.004  23.284  1.00  0.52              
ATOM     26  HG  ARG     2     -15.593  16.232  24.346  1.00  1.17              
ATOM     27  HG  ARG     2     -16.935  15.559  25.265  1.00  1.11              
ATOM     28  HD  ARG     2     -14.990  13.717  25.799  1.00  1.78              
ATOM     29  HD  ARG     2     -14.018  15.178  25.632  1.00  1.69              
ATOM     30  HE  ARG     2     -16.171  15.891  27.280  1.00  2.34              
ATOM     31  Hh1 ARG     2     -13.244  14.162  27.199  1.00  3.40              
ATOM     32  Hh1 ARG     2     -13.202  13.832  28.898  1.00  4.14              
ATOM     33  Hh2 ARG     2     -16.349  15.268  29.460  1.00  3.47              
ATOM     34  Hh2 ARG     2     -15.007  14.474  30.213  1.00  4.18              
ATOM     35  N   ASN     3     -16.516  14.122  20.389  1.00  0.23              
ATOM     36  CA  ASN     3     -16.511  13.242  19.206  1.00  0.22              
ATOM     37  C   ASN     3     -15.108  13.209  18.611  1.00  0.21              
ATOM     38  O   ASN     3     -14.478  14.235  18.461  1.00  0.29              
ATOM     39  CB  ASN     3     -17.499  13.783  18.172  1.00  0.25              
ATOM     40  CG  ASN     3     -18.879  13.944  18.814  1.00  0.28              
ATOM     41  OD1 ASN     3     -19.878  13.516  18.270  1.00  1.09              
ATOM     42  ND2 ASN     3     -18.984  14.560  19.961  1.00  1.16              
ATOM     43  H   ASN     3     -16.007  14.953  20.385  1.00  0.26              
ATOM     44  HA  ASN     3     -16.802  12.256  19.501  1.00  0.22              
ATOM     45  HB  ASN     3     -17.163  14.742  17.812  1.00  0.27              
ATOM     46  HB  ASN     3     -17.571  13.097  17.340  1.00  0.29              
ATOM     47  HD2 ASN     3     -19.865  14.666  20.382  1.00  1.18              
ATOM     48  HD2 ASN     3     -18.188  14.915  20.404  1.00  1.98              
ATOM     49  N   ASP     4     -14.646  12.011  18.281  1.00  0.22              
ATOM     50  CA  ASP     4     -13.290  11.823  17.688  1.00  0.23              
ATOM     51  C   ASP     4     -13.353  10.783  16.560  1.00  0.26              
ATOM     52  O   ASP     4     -13.923   9.723  16.723  1.00  0.37              
ATOM     53  CB  ASP     4     -12.317  11.360  18.770  1.00  0.24              
ATOM     54  CG  ASP     4     -12.487   9.860  19.000  1.00  0.34              
ATOM     55  OD1 ASP     4     -13.592   9.399  18.774  1.00  0.30              
ATOM     56  OD2 ASP     4     -11.499   9.262  19.390  1.00  0.57              
ATOM     57  H   ASP     4     -15.232  11.245  18.441  1.00  0.25              
ATOM     58  HA  ASP     4     -12.947  12.761  17.282  1.00  0.25              
ATOM     59  HB  ASP     4     -11.302  11.560  18.460  1.00  0.28              
ATOM     60  HB  ASP     4     -12.519  11.886  19.691  1.00  0.29              
ATOM     61  N   CYS     5     -12.755  11.118  15.426  1.00  0.19              
ATOM     62  CA  CYS     5     -12.735  10.212  14.247  1.00  0.18              
ATOM     63  C   CYS     5     -11.387  10.282  13.528  1.00  0.17              
ATOM     64  O   CYS     5     -10.854  11.350  13.300  1.00  0.22              
ATOM     65  CB  CYS     5     -13.830  10.645  13.279  1.00  0.21              
ATOM     66  SG  CYS     5     -13.702  12.314  12.591  1.00  0.48              
ATOM     67  H   CYS     5     -12.320  11.996  15.387  1.00  0.23              
ATOM     68  HA  CYS     5     -12.923   9.205  14.564  1.00  0.20              
ATOM     69  HB  CYS     5     -13.843   9.950  12.454  1.00  0.29              
ATOM     70  HB  CYS     5     -14.779  10.571  13.783  1.00  0.36              
ATOM     71  HG  CYS     5     -14.465  12.816  12.884  1.00  1.05              
ATOM     72  N   GLN     6     -10.853   9.121  13.180  1.00  0.36              
ATOM     73  CA  GLN     6      -9.537   9.034  12.469  1.00  0.44              
ATOM     74  C   GLN     6      -9.597   7.976  11.351  1.00  0.45              
ATOM     75  O   GLN     6     -10.108   6.893  11.547  1.00  0.58              
ATOM     76  CB  GLN     6      -8.455   8.664  13.479  1.00  0.54              
ATOM     77  CG  GLN     6      -7.073   8.995  12.898  1.00  0.74              
ATOM     78  CD  GLN     6      -6.557  10.290  13.531  1.00  1.23              
ATOM     79  OE1 GLN     6      -6.781  11.372  13.028  1.00  1.93              
ATOM     80  NE2 GLN     6      -5.860  10.221  14.633  1.00  1.76              
ATOM     81  H   GLN     6     -11.351   8.307  13.403  1.00  0.44              
ATOM     82  HA  GLN     6      -9.303   9.992  12.038  1.00  0.52              
ATOM     83  HB  GLN     6      -8.606   9.223  14.392  1.00  0.62              
ATOM     84  HB  GLN     6      -8.513   7.615  13.699  1.00  0.53              
ATOM     85  HG  GLN     6      -6.384   8.193  13.114  1.00  1.07              
ATOM     86  HG  GLN     6      -7.145   9.127  11.830  1.00  0.95              
ATOM     87  HE2 GLN     6      -5.521  11.040  15.049  1.00  2.25              
ATOM     88  HE2 GLN     6      -5.674   9.349  15.042  1.00  2.11              
ATOM     89  N   GLU     7      -9.064   8.328  10.190  1.00  0.29              
ATOM     90  CA  GLU     7      -9.049   7.403   9.010  1.00  0.28              
ATOM     91  C   GLU     7      -7.686   7.419   8.299  1.00  0.26              
ATOM     92  O   GLU     7      -7.148   8.467   8.000  1.00  0.35              
ATOM     93  CB  GLU     7     -10.129   7.836   8.034  1.00  0.35              
ATOM     94  CG  GLU     7     -11.459   7.206   8.446  1.00  0.41              
ATOM     95  CD  GLU     7     -12.574   7.746   7.549  1.00  0.87              
ATOM     96  OE1 GLU     7     -12.323   8.763   6.924  1.00  1.57              
ATOM     97  OE2 GLU     7     -13.617   7.109   7.538  1.00  1.56              
ATOM     98  H   GLU     7      -8.674   9.224  10.127  1.00  0.32              
ATOM     99  HA  GLU     7      -9.262   6.412   9.338  1.00  0.30              
ATOM    100  HB  GLU     7     -10.214   8.903   8.055  1.00  0.38              
ATOM    101  HB  GLU     7      -9.865   7.519   7.035  1.00  0.38              
ATOM    102  HG  GLU     7     -11.405   6.132   8.340  1.00  0.61              
ATOM    103  HG  GLU     7     -11.679   7.452   9.475  1.00  0.66              
ATOM    104  N   GLY     8      -7.151   6.234   8.041  1.00  0.56              
ATOM    105  CA  GLY     8      -5.835   6.094   7.357  1.00  0.58              
ATOM    106  C   GLY     8      -5.892   4.945   6.343  1.00  0.54              
ATOM    107  O   GLY     8      -6.415   3.885   6.628  1.00  0.51              
ATOM    108  H   GLY     8      -7.651   5.435   8.316  1.00  0.81              
ATOM    109  HA  GLY     8      -5.598   7.013   6.848  1.00  0.65              
ATOM    110  HA  GLY     8      -5.077   5.885   8.095  1.00  0.56              
ATOM    111  N   HIS     9      -5.343   5.186   5.162  1.00  0.28              
ATOM    112  CA  HIS     9      -5.323   4.163   4.075  1.00  0.29              
ATOM    113  C   HIS     9      -3.961   4.180   3.378  1.00  0.30              
ATOM    114  O   HIS     9      -3.437   5.233   3.066  1.00  0.50              
ATOM    115  CB  HIS     9      -6.415   4.486   3.051  1.00  0.34              
ATOM    116  CG  HIS     9      -7.790   4.408   3.717  1.00  0.36              
ATOM    117  ND1 HIS     9      -8.354   5.354   4.314  1.00  0.43              
ATOM    118  CD2 HIS     9      -8.677   3.349   3.788  1.00  0.46              
ATOM    119  CE1 HIS     9      -9.496   5.008   4.752  1.00  0.50              
ATOM    120  NE2 HIS     9      -9.788   3.742   4.463  1.00  0.50              
ATOM    121  H   HIS     9      -4.942   6.069   5.014  1.00  0.33              
ATOM    122  HA  HIS     9      -5.501   3.186   4.494  1.00  0.30              
ATOM    123  HB  HIS     9      -6.264   5.483   2.663  1.00  0.36              
ATOM    124  HB  HIS     9      -6.371   3.778   2.237  1.00  0.41              
ATOM    125  HD1 HIS     9      -7.966   6.246   4.430  1.00  0.51              
ATOM    126  HD2 HIS     9      -8.513   2.366   3.373  1.00  0.57              
ATOM    127  HE1 HIS     9     -10.157   5.667   5.297  1.00  0.62              
ATOM    128  N   ILE    10      -3.412   2.996   3.147  1.00  0.20              
ATOM    129  CA  ILE    10      -2.084   2.856   2.475  1.00  0.22              
ATOM    130  C   ILE    10      -2.133   1.649   1.498  1.00  0.19              
ATOM    131  O   ILE    10      -2.638   0.603   1.845  1.00  0.19              
ATOM    132  CB  ILE    10      -1.018   2.598   3.544  1.00  0.28              
ATOM    133  CG1 ILE    10      -0.940   3.822   4.469  1.00  0.30              
ATOM    134  CG2 ILE    10       0.340   2.380   2.864  1.00  0.36              
ATOM    135  CD1 ILE    10       0.029   3.539   5.629  1.00  1.04              
ATOM    136  H   ILE    10      -3.906   2.196   3.434  1.00  0.26              
ATOM    137  HA  ILE    10      -1.841   3.758   1.955  1.00  0.22              
ATOM    138  HB  ILE    10      -1.282   1.724   4.112  1.00  0.32              
ATOM    139  HG1 ILE    10      -0.589   4.677   3.909  1.00  0.80              
ATOM    140  HG1 ILE    10      -1.920   4.039   4.864  1.00  0.74              
ATOM    141  HG2 ILE    10       0.263   2.610   1.812  1.00  0.89              
ATOM    142  HG2 ILE    10       1.082   3.022   3.313  1.00  0.97              
ATOM    143  HG2 ILE    10       0.644   1.352   2.980  1.00  1.01              
ATOM    144  HD1 ILE    10       0.183   2.476   5.731  1.00  1.68              
ATOM    145  HD1 ILE    10       0.977   4.018   5.436  1.00  1.64              
ATOM    146  HD1 ILE    10      -0.382   3.927   6.549  1.00  1.58              
ATOM    147  N   LEU    11      -1.600   1.848   0.301  1.00  0.27              
ATOM    148  CA  LEU    11      -1.575   0.787  -0.735  1.00  0.30              
ATOM    149  C   LEU    11      -0.233   0.783  -1.459  1.00  0.24              
ATOM    150  O   LEU    11       0.238   1.809  -1.905  1.00  0.24              
ATOM    151  CB  LEU    11      -2.698   1.086  -1.726  1.00  0.39              
ATOM    152  CG  LEU    11      -3.390  -0.197  -2.223  1.00  0.46              
ATOM    153  CD1 LEU    11      -4.099  -0.917  -1.040  1.00  1.23              
ATOM    154  CD2 LEU    11      -4.415   0.243  -3.301  1.00  1.19              
ATOM    155  H   LEU    11      -1.216   2.733   0.120  1.00  0.31              
ATOM    156  HA  LEU    11      -1.737  -0.165  -0.277  1.00  0.33              
ATOM    157  HB  LEU    11      -3.430   1.722  -1.245  1.00  0.53              
ATOM    158  HB  LEU    11      -2.289   1.611  -2.571  1.00  0.41              
ATOM    159  HG  LEU    11      -2.660  -0.865  -2.671  1.00  0.73              
ATOM    160  HD1 LEU    11      -4.377  -0.194  -0.287  1.00  1.69              
ATOM    161  HD1 LEU    11      -4.981  -1.432  -1.378  1.00  1.82              
ATOM    162  HD1 LEU    11      -3.429  -1.642  -0.603  1.00  1.73              
ATOM    163  HD2 LEU    11      -4.595   1.304  -3.213  1.00  1.64              
ATOM    164  HD2 LEU    11      -4.012   0.040  -4.277  1.00  1.87              
ATOM    165  HD2 LEU    11      -5.348  -0.275  -3.188  1.00  1.68              
ATOM    166  N   LYS    12       0.367  -0.394  -1.564  1.00  0.32              
ATOM    167  CA  LYS    12       1.689  -0.552  -2.249  1.00  0.29              
ATOM    168  C   LYS    12       1.677  -1.816  -3.107  1.00  0.25              
ATOM    169  O   LYS    12       1.277  -2.870  -2.658  1.00  0.31              
ATOM    170  CB  LYS    12       2.797  -0.640  -1.216  1.00  0.30              
ATOM    171  CG  LYS    12       2.708   0.582  -0.296  1.00  0.47              
ATOM    172  CD  LYS    12       3.897   0.594   0.672  1.00  0.53              
ATOM    173  CE  LYS    12       3.927  -0.710   1.470  1.00  0.73              
ATOM    174  NZ  LYS    12       4.644  -0.514   2.761  1.00  1.37              
ATOM    175  H   LYS    12      -0.089  -1.166  -1.174  1.00  0.48              
ATOM    176  HA  LYS    12       1.862   0.302  -2.883  1.00  0.31              
ATOM    177  HB  LYS    12       2.681  -1.544  -0.648  1.00  0.37              
ATOM    178  HB  LYS    12       3.755  -0.654  -1.711  1.00  0.35              
ATOM    179  HG  LYS    12       2.722   1.481  -0.893  1.00  0.73              
ATOM    180  HG  LYS    12       1.789   0.548   0.259  1.00  0.64              
ATOM    181  HD  LYS    12       4.815   0.701   0.117  1.00  1.09              
ATOM    182  HD  LYS    12       3.798   1.427   1.352  1.00  1.00              
ATOM    183  HE  LYS    12       2.918  -1.036   1.670  1.00  1.30              
ATOM    184  HE  LYS    12       4.437  -1.473   0.898  1.00  1.42              
ATOM    185  HZ  LYS    12       4.882   0.493   2.876  1.00  1.79              
ATOM    186  HZ  LYS    12       4.031  -0.815   3.547  1.00  1.83              
ATOM    187  HZ  LYS    12       5.514  -1.079   2.765  1.00  2.00              
ATOM    188  N   MET    13       2.125  -1.681  -4.347  1.00  0.26              
ATOM    189  CA  MET    13       2.172  -2.830  -5.301  1.00  0.28              
ATOM    190  C   MET    13       3.485  -2.804  -6.097  1.00  0.30              
ATOM    191  O   MET    13       3.901  -1.774  -6.591  1.00  0.37              
ATOM    192  CB  MET    13       0.978  -2.757  -6.255  1.00  0.35              
ATOM    193  CG  MET    13       0.987  -1.419  -6.993  1.00  1.15              
ATOM    194  SD  MET    13       1.240  -1.464  -8.785  1.00  2.09              
ATOM    195  CE  MET    13       0.185  -0.054  -9.200  1.00  2.25              
ATOM    196  H   MET    13       2.429  -0.788  -4.624  1.00  0.28              
ATOM    197  HA  MET    13       2.121  -3.749  -4.747  1.00  0.28              
ATOM    198  HB  MET    13       1.038  -3.564  -6.970  1.00  0.94              
ATOM    199  HB  MET    13       0.061  -2.853  -5.692  1.00  0.92              
ATOM    200  HG  MET    13       0.043  -0.929  -6.809  1.00  1.89              
ATOM    201  HG  MET    13       1.765  -0.802  -6.569  1.00  1.80              
ATOM    202  HE  MET    13       1.045   0.456  -8.787  1.00  2.50              
ATOM    203  HE  MET    13       0.330   0.718  -9.941  1.00  2.60              
ATOM    204  HE  MET    13       0.101  -0.633 -10.106  1.00  2.53              
ATOM    205  N   PHE    14       4.121  -3.961  -6.207  1.00  0.19              
ATOM    206  CA  PHE    14       5.407  -4.089  -6.950  1.00  0.20              
ATOM    207  C   PHE    14       5.422  -5.373  -7.776  1.00  0.21              
ATOM    208  O   PHE    14       4.987  -6.413  -7.322  1.00  0.35              
ATOM    209  CB  PHE    14       6.569  -4.128  -5.957  1.00  0.22              
ATOM    210  CG  PHE    14       6.335  -3.110  -4.845  1.00  0.20              
ATOM    211  CD1 PHE    14       5.580  -3.441  -3.732  1.00  0.18              
ATOM    212  CD2 PHE    14       6.878  -1.848  -4.937  1.00  0.23              
ATOM    213  CE1 PHE    14       5.371  -2.516  -2.732  1.00  0.17              
ATOM    214  CE2 PHE    14       6.668  -0.922  -3.937  1.00  0.22              
ATOM    215  CZ  PHE    14       5.916  -1.255  -2.835  1.00  0.18              
ATOM    216  H   PHE    14       3.718  -4.745  -5.779  1.00  0.25              
ATOM    217  HA  PHE    14       5.527  -3.242  -7.606  1.00  0.21              
ATOM    218  HB  PHE    14       6.646  -5.107  -5.524  1.00  0.24              
ATOM    219  HB  PHE    14       7.493  -3.890  -6.465  1.00  0.26              
ATOM    220  HD1 PHE    14       5.159  -4.431  -3.641  1.00  0.19              
ATOM    221  HD2 PHE    14       7.479  -1.590  -5.792  1.00  0.27              
ATOM    222  HE1 PHE    14       4.783  -2.782  -1.868  1.00  0.18              
ATOM    223  HE2 PHE    14       7.096   0.067  -4.018  1.00  0.26              
ATOM    224  HZ  PHE    14       5.753  -0.532  -2.052  1.00  0.19              
ATOM    225  N   PRO    15       5.933  -5.274  -8.995  1.00  1.08              
ATOM    226  CA  PRO    15       6.013  -6.426  -9.902  1.00  1.04              
ATOM    227  C   PRO    15       7.369  -6.432 -10.606  1.00  0.87              
ATOM    228  O   PRO    15       7.811  -5.433 -11.141  1.00  1.05              
ATOM    229  CB  PRO    15       4.874  -6.214 -10.911  1.00  1.27              
ATOM    230  CG  PRO    15       4.304  -4.781 -10.660  1.00  1.32              
ATOM    231  CD  PRO    15       5.070  -4.187  -9.461  1.00  1.26              
ATOM    232  HA  PRO    15       5.866  -7.336  -9.362  1.00  1.16              
ATOM    233  HB  PRO    15       5.246  -6.289 -11.920  1.00  1.35              
ATOM    234  HB  PRO    15       4.101  -6.951 -10.754  1.00  1.44              
ATOM    235  HG  PRO    15       4.452  -4.166 -11.535  1.00  1.40              
ATOM    236  HG  PRO    15       3.251  -4.839 -10.433  1.00  1.46              
ATOM    237  HD  PRO    15       5.672  -3.346  -9.780  1.00  1.32              
ATOM    238  HD  PRO    15       4.391  -3.889  -8.685  1.00  1.45              
ATOM    239  N   SER    16       8.025  -7.583 -10.595  1.00  0.29              
ATOM    240  CA  SER    16       9.351  -7.738 -11.238  1.00  0.25              
ATOM    241  C   SER    16       9.398  -9.094 -11.925  1.00  0.26              
ATOM    242  O   SER    16       8.952 -10.084 -11.375  1.00  0.35              
ATOM    243  CB  SER    16      10.444  -7.648 -10.188  1.00  0.27              
ATOM    244  OG  SER    16       9.952  -6.700  -9.252  1.00  0.40              
ATOM    245  H   SER    16       7.599  -8.341 -10.141  1.00  0.33              
ATOM    246  HA  SER    16       9.488  -6.965 -11.965  1.00  0.24              
ATOM    247  HB  SER    16      10.589  -8.595  -9.717  1.00  0.39              
ATOM    248  HB  SER    16      11.367  -7.297 -10.625  1.00  0.35              
ATOM    249  HG  SER    16       9.508  -6.002  -9.741  1.00  0.91              
ATOM    250  N   THR    17       9.946  -9.116 -13.132  1.00  0.19              
ATOM    251  CA  THR    17      10.061 -10.373 -13.925  1.00  0.18              
ATOM    252  C   THR    17      11.385 -10.357 -14.678  1.00  0.17              
ATOM    253  O   THR    17      11.715  -9.370 -15.313  1.00  0.29              
ATOM    254  CB  THR    17       8.903 -10.454 -14.925  1.00  0.20              
ATOM    255  OG1 THR    17       8.956  -9.225 -15.643  1.00  0.28              
ATOM    256  CG2 THR    17       7.548 -10.450 -14.220  1.00  0.31              
ATOM    257  H   THR    17      10.280  -8.267 -13.498  1.00  0.23              
ATOM    258  HA  THR    17      10.030 -11.227 -13.265  1.00  0.19              
ATOM    259  HB  THR    17       8.997 -11.297 -15.585  1.00  0.28              
ATOM    260  HG1 THR    17       8.383  -8.597 -15.200  1.00  0.90              
ATOM    261  HG2 THR    17       7.694 -10.468 -13.151  1.00  1.06              
ATOM    262  HG2 THR    17       7.002  -9.558 -14.491  1.00  1.00              
ATOM    263  HG2 THR    17       6.981 -11.319 -14.517  1.00  1.09              
ATOM    264  N   TRP    18      12.117 -11.458 -14.590  1.00  0.22              
ATOM    265  CA  TRP    18      13.442 -11.587 -15.278  1.00  0.20              
ATOM    266  C   TRP    18      13.562 -12.996 -15.852  1.00  0.19              
ATOM    267  O   TRP    18      13.196 -13.958 -15.204  1.00  0.22              
ATOM    268  CB  TRP    18      14.571 -11.352 -14.277  1.00  0.19              
ATOM    269  CG  TRP    18      14.582  -9.877 -13.861  1.00  0.23              
ATOM    270  CD1 TRP    18      13.809  -9.376 -12.906  1.00  0.27              
ATOM    271  CD2 TRP    18      15.346  -8.932 -14.394  1.00  0.25              
ATOM    272  NE1 TRP    18      14.132  -8.075 -12.880  1.00  0.30              
ATOM    273  CE2 TRP    18      15.096  -7.710 -13.787  1.00  0.29              
ATOM    274  CE3 TRP    18      16.298  -9.007 -15.404  1.00  0.27              
ATOM    275  CZ2 TRP    18      15.785  -6.583 -14.183  1.00  0.33              
ATOM    276  CZ3 TRP    18      16.983  -7.874 -15.795  1.00  0.32              
ATOM    277  Ch2 TRP    18      16.726  -6.665 -15.186  1.00  0.35              
ATOM    278  H   TRP    18      11.763 -12.202 -14.052  1.00  0.23              
ATOM    279  HA  TRP    18      13.512 -10.868 -16.075  1.00  0.21              
ATOM    280  HB  TRP    18      14.418 -11.963 -13.407  1.00  0.20              
ATOM    281  HB  TRP    18      15.515 -11.613 -14.724  1.00  0.18              
ATOM    282  HD1 TRP    18      13.087  -9.894 -12.294  1.00  0.29              
ATOM    283  HE1 TRP    18      13.720  -7.439 -12.260  1.00  0.33              
ATOM    284  HE3 TRP    18      16.506  -9.945 -15.887  1.00  0.25              
ATOM    285  HZ2 TRP    18      15.584  -5.634 -13.708  1.00  0.36              
ATOM    286  HZ3 TRP    18      17.723  -7.937 -16.576  1.00  0.35              
ATOM    287  Hh2 TRP    18      17.264  -5.781 -15.494  1.00  0.39              
ATOM    288  N   TYR    19      14.078 -13.086 -17.069  1.00  0.41              
ATOM    289  CA  TYR    19      14.257 -14.399 -17.759  1.00  0.33              
ATOM    290  C   TYR    19      15.607 -14.436 -18.483  1.00  0.30              
ATOM    291  O   TYR    19      15.983 -13.486 -19.139  1.00  0.32              
ATOM    292  CB  TYR    19      13.133 -14.581 -18.781  1.00  0.36              
ATOM    293  CG  TYR    19      11.787 -14.282 -18.118  1.00  0.38              
ATOM    294  CD1 TYR    19      11.205 -15.200 -17.268  1.00  0.34              
ATOM    295  CD2 TYR    19      11.135 -13.089 -18.359  1.00  0.47              
ATOM    296  CE1 TYR    19       9.991 -14.931 -16.671  1.00  0.39              
ATOM    297  CE2 TYR    19       9.922 -12.821 -17.761  1.00  0.51              
ATOM    298  CZ  TYR    19       9.340 -13.739 -16.912  1.00  0.46              
ATOM    299  OH  TYR    19       8.125 -13.470 -16.313  1.00  0.53              
ATOM    300  H   TYR    19      14.344 -12.258 -17.512  1.00  0.45              
ATOM    301  HA  TYR    19      14.215 -15.196 -17.040  1.00  0.33              
ATOM    302  HB  TYR    19      13.280 -13.902 -19.610  1.00  0.43              
ATOM    303  HB  TYR    19      13.133 -15.597 -19.148  1.00  0.36              
ATOM    304  HD1 TYR    19      11.704 -16.139 -17.071  1.00  0.32              
ATOM    305  HD2 TYR    19      11.580 -12.360 -19.021  1.00  0.54              
ATOM    306  HE1 TYR    19       9.547 -15.660 -16.009  1.00  0.40              
ATOM    307  HE2 TYR    19       9.423 -11.882 -17.958  1.00  0.60              
ATOM    308  HH  TYR    19       7.495 -14.131 -16.609  1.00  1.09              
ATOM    309  N   VAL    20      16.310 -15.550 -18.343  1.00  0.68              
ATOM    310  CA  VAL    20      17.638 -15.729 -18.987  1.00  0.51              
ATOM    311  C   VAL    20      17.763 -17.141 -19.547  1.00  0.46              
ATOM    312  O   VAL    20      17.421 -18.106 -18.892  1.00  0.60              
ATOM    313  CB  VAL    20      18.726 -15.508 -17.933  1.00  0.46              
ATOM    314  CG1 VAL    20      19.513 -14.248 -18.276  1.00  1.11              
ATOM    315  CG2 VAL    20      18.076 -15.336 -16.557  1.00  1.12              
ATOM    316  H   VAL    20      15.933 -16.265 -17.799  1.00  0.81              
ATOM    317  HA  VAL    20      17.760 -15.015 -19.781  1.00  0.57              
ATOM    318  HB  VAL    20      19.388 -16.354 -17.912  1.00  0.67              
ATOM    319  HG1 VAL    20      19.937 -14.338 -19.265  1.00  1.78              
ATOM    320  HG1 VAL    20      18.857 -13.392 -18.246  1.00  1.49              
ATOM    321  HG1 VAL    20      20.309 -14.115 -17.559  1.00  1.64              
ATOM    322  HG2 VAL    20      17.459 -16.195 -16.333  1.00  1.59              
ATOM    323  HG2 VAL    20      18.844 -15.246 -15.801  1.00  1.61              
ATOM    324  HG2 VAL    20      17.465 -14.446 -16.548  1.00  1.71
garlic-1.6/commands/ssb.html0000644000000000000000000000727610357045441016054 0ustar rootroot00000000000000 SSB

SSB

NAME
SSB - change drawing style for disulfide bonds.

SYNOPSIS
SSB style

DESCRIPTION
Change drawing style for disulfide bonds. Disulfide bond style is defined separately from atom style. This command does not affect the ordinary covalent bonds: the command BONDS should be used for that purpose. Note that there is no separate keyword for curved bonds and sticks (nice style): the bond curvature is defined by the command PROBE .

STYLE THICKNESS TYPE
0 Invisible bonds. Fixed width.
1 A single line. Fixed width.
2 Three lines. Fixed width.
3 Five lines. Fixed width.
4 Seven lines. Fixed width.
5 Nine lines. Fixed width.
nic
nice 		Curved bonds, conical sticks or cylindrical sticks,
depending both on the bond probe radius and the atomic
radii. This bond style is available for the following
atomic styles: SMALL, SM2, COVALENT, CO2,
SPACEFILL, SP2, BIG and BI2. Do not combine
the nice bond style with atomic styles 0, 1, 2, 3,
4, 5, 6, 7, BALL and BA2. 		Proportional.
sti
sticks 		Cylindrical sticks. The command BONDS STICKS
(short form: BON STI) is the most convenient
way to draw bonds as sticks. Default stick
radius may be changed by using the command
STICKS (short form: STI). 		Proportional.

NICE BONDS
Nice bonds may be curved or straight, cylindrical or conical, depending on bond probe radius. If this radius is small (like 0.8 angstroms), the bonds will be curved. Probe radius of 10 angstroms will give the straight bonds. If you want to draw the chemical bonds as cylindrical sticks, it is more convenient to use the command BONDS STICKS. If your atoms are drawn using different radii, the bonds will appear conical. For more details, read also the text about the command BONDS .

NOTES
(1) Invisible disulfide bonds (style 0) are not treated as hidden - they are just invisible.

(2) The nice bond style is allowed for ordinary covalent bonds and for disulfide bonds, but not for hydrogen bonds.

(4) Remember that the nice disulfide bond style works only for the following atomic styles: SMALL, SM2, COVALENT, CO2, SPACEFILL, SP2, BIG and BI2.

RELATED COMMANDS
PRO (PROBE) is used to set the probe radius. ATO (ATOMS) is used to change the drawing style for atoms. SSB is used to change the bond drawing style for disulfide bonds. STI (STICKS) is used to change the stick radius. BALLS is used to set the ball radius.

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TAG

NAME
TAG - assign tag (short text) to a structure.

SYNOPSIS
TAG "tag"
TAG OFF

DESCRIPTION
If used without keyword OFF, this command assigns the specified tag to the structure which is currently handled. If used with keyword OFF, this command hides tag. Tag may contain up to 128 characters.

EXAMPLES
COMMAND DESCRIPTION
tag "PORIN" Add the tag "PORIN" to a structure
which is currently handled (caught)
tag off Hide tag

RELATED COMMANDS
The command LABELS assigns labels to selected atoms. TITLE adds the title to the main window. Both labels and tag move along with the structure. Note that tag is assigned to the structure, labels to atoms and title is assigned to the main window.

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ROT, ROTATE

NAME
ROT, ROTATE - rotate the structure for the given angle around the given axis.

SYNOPSIS
ROT axis angle

DESCRIPTION
Rotate the structure. The axis should be specified with one letter (x, y or z) and the angle should be given in degrees.

EXAMPLES
COMMAND DESCRIPTION
rot z 90 Rotate around z for 90 degrees (counterclockwise).
rot x -0.5 Rotate around x for -0.5 degrees (clockwise).

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WIN, WINDOW

NAME
WIN, WINDOW - set the sliding window width.

SYNOPSIS
WIN value
WINDOW value

DESCRIPTION
Set the sliding window width. The value is stored as an internal variable and used to calculate and draw average hydrophobicity and hydrophobic moment. The hard-coded default value is 11 residues. The minimal value is 1. The command PLOT may be used to plot the averaged hydrophobicity and/or hydrophobic moment.

EXAMPLES
COMMAND DESCRIPTION
win 20 Set the sliding window width to 20.
win 8
plot mom 		Set the sliding window width to 8
and draw hydrophobic moment.

RELATED COMMANDS
PLOT is used to draw averaged hydrophobicity and/or the hydrophobic moment. ANGLE is used to set the rotation angle between adjacent residues (important for hydrophobic moment, not for averaged hydrophobicity). DUMP is used to dump hydrophobicity functions to the console or to the specified file.

garlic-1.6/commands/sel.html0000644000000000000000000003411210417442657016044 0ustar rootroot00000000000000 SEL, SELECT

SEL, SELECT

NAME
SEL, SELECT - select specified atoms. Overwrite the previous selection.

SYNOPSIS
SEL chain_identifiers/residue_serials/residue_names/atom_names
SEL residue_ranges
SEL residue_names
SEL ATO atomic_ranges
SEL keyword
SEL ELE chemical_symbol
SELECT chain_identifiers/residue_serials/residue_names/atom_names
SELECT residue_ranges
SELECT residue_names
SELECT ATOMS atomic_ranges
SELECT keyword
SELECT ELEMENT chemical_symbol

DESCRIPTION
Select specified atoms. Atoms are selected according to the specified cryteria. Six types of selection are available:

(1) detailed selection;
(2) selection by residue serial numbers;
(3) selection by residue names;
(4) special selection (by keyword);
(5) selection by chemical symbol;
(6) selection by atom serial number.

DETAILED SELECTION
In this case four data types are specified simultaneously: chain identifiers, residue serial numbers, residue names and atom names. It is not possible to specify atomic serial numbers. The selection string should contain exactly three slashes, separating different data types:

chain_identifiers/residue_serials/residue_names/atom_names.

Both uppercase and lowercase characters are accepted. Space ( ), comma (,) and semicolon (;) may be used as separators.

Chain identifiers are single alphabetic characters. Asterisk (*) may be used to select all chains. The keyword EXC (EXCEPT) may be used to exclude one or more chains from selection.

Residue serial numbers consist of digits. Minus may be used to specify a range of residue serial numbers. For example, 1-100 specifyes residues from 1 to 100, including these two. Asterisk (*) may be used to specify all residue serials. The keyword EXC (EXCEPT) may be used to exclude serial numbers or ranges from selection.

Residue names are expected in three letters code. Asterisk (*) may be used to specify all residue names. The keyword EXC (EXCEPT) may be used to exclude one or more names from selection. Non-standard names are accepted.

The names of atoms are expected as used in the input file; do not replace them with pure chemical symbols. C alpha, for example, should be specified as CA or ca (case is not important), if coordinates are read from PDB file. Asterisk (*) may be used to select all atoms, while EXC may be used to exclude some atoms from selection. Examples:

sel a/*/*/* Select all atoms from chain A.
sel * exc m/*/*/ca Select CA atoms from all chains except chain M.
sel */*/*/* exc ca,c,n,o Select all atoms except CA, C, N and O.
sel a/* exc 72-112/*/ca Select CA atoms from chain A, but exclude residues from 72 to 112.

SELECTION BY RESIDUE SERIAL NUMBERS
To select all atoms in a single residue, a residue range or in a number of residues and residue ranges, a simple syntax may be used. The selection string should contain no slashes. Keyword EXC (EXCEPT) is accepted, but asterisk (*) will be missintepreted. Minus may be used to specify residue ranges. Comma (,), semicolon (;) and space ( ) may be used as separators. Examples:

sel 1-100 Select residues from 1 to 100.
sel 1-100 exc 20-40 Select residues 1-100 but exclude 20-40.
sel 1, 4, 8, 11-48 exc 20-32 Select residues 1, 4, 8 and 11-48 but exclude 20-32.

SELECTION BY ATOMIC SERIAL NUMBERS
To select a single atom by the atomic serial number, combine the command SEL (SELECT) and the keyword ATO (ATOMS). For example, to select the atom number 102 type:

sel ato 102

The same keyword may be used to select a range of atoms or two or more ranges. Examples:

sel ato 1-100 Select atoms which have serial numbers in the range between 1 and 100.
sel 1-20 40-50 Select atoms which have serial numbers between 1 and 20 and between 40 and 50.

Do not combine the keywords EXC (EXCLUDE) and ATO (ATOMS).

SELECTION BY RESIDUE NAMES
Three letters code should be used. Asterisk (*) and keyword EXC (EXCEPT) are not accepted. Example:

sel phe,tyr,trp Select PHE, TYR and TRP.

SPECIAL SELECTION KEYWORDS
Some special keywords may be combined with SEL (SELECT) to select residues or atoms according to some properties. It is also possible to select the complement, i.e. all atoms which were not selected previously. A single keyword should be used; asterisk (*) and keyword EXC (EXCEPT) are not accepted.

sel *
sel all 		Select all atoms (select all).
sel abo
sel above 		Select atoms above the plane.
sel aci
sel acidic 		Select acidic amino acids (GLU and ASP).
sel ali
sel aliphatic 		Select aliphatic amino acids (ILE, LEU and VAL).
sel alt Select atoms at alternate positions.
sel bad Select bad residues. A residue is treated as bad if the
peptide bond assigned to this residue is non-planar.
The peptide bond is non-planar if the omega angle is
different for 20 or more degrees from 0 or 180 degrees.
sel bas
sel basic 		Select basic amino acids (ARG, LYS and HIS).
sel bel
sel below 		Select atoms below the plane.
sel cha
sel charged 		Select charged amino acids (ARG, LYS, HIS, GLU and ASP).
sel cis Select cis residues.
sel com
sel complement 		Select atoms which were not selected previously.
sel het
sel hetero 		Select hetero atoms (heme groups, water etc.).
sel pho
sel hydrophobic 		Select hydrophobic amino acids
(ALA, ILE, LEU, MET, PHE, TRP, VAL, TYR, CYS, GLY and HIS).
sel mai
sel main_chain 		Select main chain atoms (CA, C, N and O).
sel mod serial_number
sel model serial_number 		Select model specified by serial_number.
NMR structure is a set of models. Example: sel mod 1
sel neg
sel negative 		Select negatively charged amino acids (GLU and ASP).
sel pat
sel pattern 		Select the sequence pattern. The command
PAT (PATTERN) is used to define the sequence pattern.
sel pol
sel polar 		Select polar amino acids
(ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TRP and TYR).
sel pos
sel positive 		Select positively charged amino acids (ARG, LYS and HIS).
sel seq
sel sequence 		Select sequence fragments which match the sequence stored
to the sequence buffer. The sequence buffer should be
initialized before executing this command.
sel sid
sel side_chains 		Select atoms which belong to side chains (all except CA, C, N and O).
sel sma
sel small 		Select small amino acids
(GLY, ALA, SER, THR, CYS, VAL, PRO, ASP and ASN).
sel sph
sel sphere 		Select atoms inside the sphere. Use the command
RAD (RADIUS) to set the sphere radius.
sel tm Select the transmembrane part
(useful for membrane proteins).
sel tra
sel trans 		Select trans residues.
sel tri
sel triplet 		If there are three (or more) positively charged residues in a fragment
of up to five protein residues, select these residues. Detailed
explanation may be found in the article:
D. Juretic, L. Zoranic and D. Zucic,
Basic charge clusters and predictions of membrane protein topology,
Journal of Chemical Information and Computer Sciences 42, No. 3,
620-632 (2002).
sel 2c3 If there are two (or more) charged residues in a fragment of three
residues, select these residues.
sel 2cz3 If there are two (or more) charged or zwitterionic residues in a
fragment of three residues, select these residues.
sel 2nz3
sel 3c4
sel 3cz4
sel 3nz4
sel 3c5
sel 3cz5
sel 3nz5
sel 3p5
sel 4c5
sel 4cz5
sel 4nz5
sel 3c6
sel 3cz6
sel 3nz6
sel 4c6
sel 4cz6
sel 4nz6
sel 5c6
sel 5cz6
sel 5nz6
sel 4c7
sel 4cz7
sel 4nz7
sel 5c7
sel 5cz7
sel 5nz7
sel 5p7
sel 6p7
sel 4c9
sel 4cz9
sel 4nz9
sel 5c9
sel 5cz9
sel 5nz9 		Analogous to sel 2c3 and sel 2cz3, where c stands for charged ,
cz for charged or zwitterionic , nz for negative or zwitterionic
and p for polar . The same selection criteria may be defined
using patterns, but these short keywords are more practical.
sel 3p5 If there are three or more polar residues in a fragment of five residues,
select these residues. The following residues are treated as polar:
ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP.
sel 5p7 If there are five or more polar residues in a fragment of seven residues,
select these residues. The following residues are treated as polar:
ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP.
sel 6p7 If there are six or more polar residues in a fragment of seven residues,
select these residues. The following residues are treated as polar:
ARG, LYS, HIS, ASP, GLU, ASN, GLN, SER, THR, TYR and TRP.

SELECTING CHEMICAL ELEMENTS
To select certain chemical element, use the keyword ELEMENT (short form: ELE) and the standard chemical symbol. To select iron, for example, you should type the following command:

sel ele fe

In addition to real chemical elements, garlic accepts two imaginary elements: "jellium" (J) and "quarkonium" (Q). Jellium is inert and it never binds to neighboring atoms, no matter how close they are. Quarkonium binds to other quarkonium atoms which have adjacent atomic serial numbers. For example, if some quarkonium atom has serial number i, it may form bonds with quarkonium atoms i-1 and i+1. The interatomic distance is not important! Both elements were introduced to enable drawing of special objects. Quarkonium may be used to draw polygonal lines in three dimensions. The original idea was to adapt garlic for visualization of some medical data. For example, quarkonium may be used to represent blood vessels and jellium to represent retraction balls characteristic for broken axons in human brain. By the way, quarkonium is a serious thing in high energy physics, but there it looks quite different. Note that symbols J and Q are not used in the periodic table of elements.

NOTES
(1) The command SELECT resets the editing mode to default (no editing).

(2) The keyword TM may be used to select the transmembrane part of the protein. In addition to the atoms which lay between two planes which define the membrane, some outside atoms will be taken into account, if they don't lay more than two anstroms from the nearest plane. This should ensure that some hydrophobic residues close to the edge will not be excluded from the selection.

RELATED COMMANDS
ADD expands the previous selection. RESTRICT restrics the previous selection.

garlic-1.6/commands/lab.html0000644000000000000000000000176310345614335016017 0ustar rootroot00000000000000 LAB, LABELS

LAB, LABELS

NAME
LAB, LABELS - show or hide labels.

SYNOPSIS
LAB
LABELS
LAB OFF
LABELS OFF

DESCRIPTION
If used without keyword OFF, this command shows labels for selected atoms. If used with keyword OFF, this command hides labels. Each label contains:
(1) residue name;
(2) residue sequence number;
(3) chain identifier;
(4) atom name;
(5) alternate location indicator.

RELATED COMMANDS
TITLE adds the title to the main window. TAG assigns the specified tag to a structure. Both labels and tag move along with the structure. Note that tag is assigned to the structure, labels to atoms and title is assigned to the main window.

garlic-1.6/commands/dummy_atoms.html0000644000000000000000000000353010364510242017602 0ustar rootroot00000000000000 Jellium (J) and Quarkonium (Q)

Jellium (J) and Quarkonium (Q)

In addition to real chemical elements, garlic accepts two imaginary elements: "jellium" (J) and "quarkonium" (Q). Jellium is inert and it never binds to neighboring atoms, no matter how close they are. Quarkonium binds to other quarkonium atoms which have adjacent atomic serial numbers. For example, if some quarkonium atom has serial number i, it may form bonds with quarkonium atoms i-1 and i+1. The interatomic distance is not important! Quarkonium is capable to form at most two bonds. To break the polygonal line, skip one serial index. For example, if three consecutive Q atoms in PDB file have serial numbers i-1, i and i+2, the atoms i-1 and i will be bound, but there will be no bond between atoms i and i+2. The same trick may be used to force Q atom to form no bonds: use indices i-2, i and i+2.

Both elements were introduced to enable drawing of special objects. Quarkonium may be used to draw polygonal lines in three dimensions. The original idea was to adapt garlic for visualization of some medical data. For example, quarkonium may be used to represent blood vessels and jellium to represent retraction balls characteristic for broken axons in human brain.

By the way, quarkonium is a serious thing in high energy physics, but there it looks quite different. The term jellium is used is solid state physics (jellium model for electrons in solid). Note that symbols J and Q are not used in the periodic table of elements. For that reason these two terms were abused in garlic. If I should be thrown through the window at the next meeting of Croatian Physical Society, please note that my colleague Dario Faj deserves the same treatment, he was also involved in this dirty job.

garlic-1.6/commands/loa.html0000644000000000000000000000337310345614572016036 0ustar rootroot00000000000000 LOA, LOAD, REA, READ

LOA, LOAD, REA, READ

NAME
LOA, LOAD, REA, READ - load the specified file.

SYNOPSIS
LOA file_name
LOAD file_name
REA file_name
READ file_name

DESCRIPTION
Load and display the specified file. The file content will be treated as a separate structure. The unique structure identifier (positive integer) will be assigned to this structure. The structure will be placed in the middle of the screen.

You can load any file more than once. A total number of structures which may be simultaneously loaded depends on the available memory. The hard-coded maximum is 1000, which should be more than enough.

The command LOAD may be written in uppercase, lowercase or mixed case, but the file name should be specified in correct case - unix file names are case sensitive.

SEARCH PATH
One or more directories will be searched to find the specified file, in the following order:

(1) the current working directory;
(2) directory specified in the environment variable MOL_DIR;
(3) all directories specified in the environment variable MOL_PATH.

The recommended environment variable is MOL_PATH.

NOTES
(1) The command LOAD resets the editing mode to default (no editing).

RELATED COMMANDS
DIS (DISCARD) discards the specified structure. SAV (SAVE) saves the atomic data to a file.

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BAC, BACKBONE

NAME
BAC, BACKBONE - draw backbone.

SYNOPSIS
BAC
BAC OFF
BAC bond_style

DESCRIPTION
Draw polypeptide (protein) backbone, by connecting neighbouring CA (C alpha) atoms. All other atoms in the selected portion of the structure will be hidden. At present, five bond styles are available, all of them fixed in size.

If this command is specified without any arguments, default bond style (5) will be used.

The command BAC OFF hides the backbone and shows atoms and bonds which were visible before.

STYLE THICKNESS TYPE
0 Invisible bonds Fixed width.
1 single, thin line Fixed width.
2 Three lines Fixed width.
3 Five lines Fixed width.
4 Seven lines Fixed width.
5 Nine lines Fixed width.

NOTES
(1) Invisible bonds (style 0) are not treated as hidden - they are just invisible.

RELATED COMMANDS
BON (BONDS) changes drawing style for bonds, but does not affect the backbone. ATO (ATOMS) command may be used to add atoms to the backbone. It is recommended to show only CA atoms, using BALL or SPACEFILL style.

garlic-1.6/commands/seq.html0000644000000000000000000001576710345616254016064 0ustar rootroot00000000000000 SEQ, SEQUENCE

SEQ, SEQUENCE

NAME
SEQ, SEQUENCE - manipulate the content of the sequence buffer.

SYNOPSIS
SEQ = three_letters_code
SEQ LOAD filename
SEQ READ filename
SEQ FROM structure_identifier
SEQ COPY
SEQ SAVE filename
SEQ SWN filename
SEQ RESET

DESCRIPTION
The command SEQ (long form: SEQUENCE) manipulates the content of the main sequence buffer. Garlic mantains two sequence buffers: the main buffer and the reference buffer. The main sequence buffer is used to prepare the average hydrophobicity plot, the hydrophobic moment plot, helical wheel plot and for some other operations which require the sequence information. The reference sequence buffer is used for sequence comparison and other operations which require two sequences.

Both buffers store the following sequence information:
(1) The number of residues.
(2) The sequence in the form of three letters code. Uppercase letters are used.
(3) Disulfide bond flag, if information about disulfide bonds is available.
(4) Residue serial numbers.
(5) Raw hydrophobicity values (replaced by average value for exotic residues).

In addition, the main sequence buffer contains the following information:
(6) The average hydrophobicity. width.
(7) The hydrophobic moment.

As sequence information may be given independently from any structure, atomic coordinates are not required for most sequence manipulation routines. Thus, garlic may be used as the sequence analysing tool.

All version of the command SEQ, except one, are used to manipulate the content of the main sequence buffer. The only exception is SEQ COPY, which copies the content of the main sequence buffer to the reference buffer. This is the only way to store information to the reference buffer.

SEQ = three_letters_code
The command SEQ may be used with the keyword = (equal sign) to define sequence at garlic command prompt. This may be practical to define a short sequence fragment. This fragment may be used for helical wheel plot, or to locate the given sequence fragment in a structure which is being investigated. The syntax:

SEQ = three_letters_code

Example:

seq = ala phe tyr trp asn

The sequence fragment will be converted to uppercase. The sequence is not checked for exotic residues so you can use the non-standard codes. However, the routine which assigns the hydrophobicity values will fail to recognize them. The average hydrophobicity value (calculated for the current scale) will be assigned to these residues. At present, 23 codes are recognized:


SEQ LOAD filename
The keyword LOAD (or READ, short forms LOA and REA) may be used to read the sequence from the specified file. Garlic is capable to recognize two types of input file formats: FASTA files (one letter code) and files which contain three letters code in a free format.

If input file contains the symbol > (greater than) in the first column of the first useful line, the file is treated as one letter protein code in FASTA format. Empty lines are ignored. The lines beginning with the symbol # (numbersign) in the first column are treated as comments (ignored too). Thus, the lines which are not empty and do not contain the symbol # in the first column are treated as useful.

If input file is not recognized as FASTA file, it is expected to contain the three letters code in a free format. Empty lines and all lines which contain # in the first column are ignored. All other lines are treated as useful. Digits (serial numbers, for example) are ignored. The following characters are threated as separators:
(1) space
(2) tab
(3) comma (,)
(4) semicolon (;)
(5) newline (line feed)

If input file contains at least one bad code (a residue name which consists of four letters, for example) the reading will fail. The hard-coded maximal number of residues is 20000, but it may be easily changed (see MAXRESIDUES in the header file defines.h).

Example:
load sample.fasta

SEQ FROM structure_identifier
The keyword FROM (short form: FRO) may be used to copy the sequence from the specified structure to the main sequence buffer. Only selected residues are copied. Residue is treated as selected if the first atom is selected. For proteins, this is typically N (nitrogen). Residue insertion codes are ignored! Thus, the same residue serial index (number) may appear more than once in the array of residue serial numbers.

Example:
seq from 1

SEQ COPY
The command SEQ COPY (short form: SEQ COP) copies the sequence from the main sequence buffer to the reference buffer. This is the only way to initialize the reference buffer. This command must be executed (i.e., the keyword COPY must be used) before executing commands which require two sequences for proper operation. The main sequence buffer may be initialized prior to SEQ COPY by using one of the keywords described above (=, LOAD or FROM).

Example:
seq copy

SEQ SAVE filename
The command SEQ SAVE (short form: SEQ SAV) saves the sequence to the specified file. Ten codes (each consisting of up to three letters) are written per line, separated by space. Serial numbers are not included (but see the keyword SWN).

Example:
seq save 9pap.seq

SEQ SWN filename
The command SEQ SWN saves the sequence to the specified file. Both residue names and serial numbers are written to the output file. Insertion codes will be missing! Five serial numbers and residue names are written per line, separated by space.

Example:
seq swn 9pap.seq

SEQ RESET
Reset (clear) the main sequence buffer. The command SEQ RESET (short form: SEQ RES) sets the number of residues in the main sequence buffer to zero. The storage is not freed, so the buffer may be used again later.

Example:
seq reset

RELATED COMMANDS
PLOT prepares the average hydrophobicity and/or hydrophobic moment plot. COMPARE compares two sequences. VENN draws Venn diagram. WHEEL draws helical wheel plot. SEL SEQ selects portions of the structure which contain the sequence stored to the main sequence buffer. To use any of these commands, the main sequence buffer (to use COMPARE both buffers) must be initialized by using the command SEQ. STR defines the secondary structure and CREATE may be used to create a new peptide.

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PLA, PLANE

NAME
PLA, PLANE - manipulate the plane associated with the structure.

SYNOPSIS
PLA
PLA RAD value
PLA TRA value
PLA OFF
PLANE
PLANE RADIUS value
PLANE TRANSPARENCY value
PLANE OFF

DESCRIPTION
When a PDB file is read, a new structure is stored into program memory. A single plane is associated with this structure. By default, the plane is invisible and movement controls are affecting both the structure and the associated plane. The command PLANE may be used to make the plane visible, to set the plane transparency or radius, or to hide the plane.

Plane is represented by an ellipse. One side of this ellipse will be colored blue and other side will be colored orange-red. Blue side is treated as top (upper) side, while orange-red side is treated as bottom side. Far side of the plane is dark.

The transparency value should be between 0 and 1. If the transparency is equal to zero the plane is opaque. Default plane transparency is 0.4 (hard-coded). The initial (default) plane radius is based on the spacial extent of the structure. The image below shows two semi-transparent planes: the left plane is seen from above, while the right plane is seen from below. The transparency is equal to 0.3 for both planes.



Plane may be used for different purposes:
(1) To distinguish protein domains. Many soluble proteins fold into two domains. Plane may be used to outline the border between these domains.
(2) Atoms may be selected according to their position with respect to plane. The command SEL ABO (SELECT ABOVE) selects atoms which are above the plane. The command SEL BEL (SELECT BELOW) selects atoms which are below the plane. The image below shows what may be achieved when applying different drawing styles to atoms on different sides of the plane.
(3) To represent the cellular membrane. Since version 1.2, garlic is capable to represent the membrane directly, so this usage of planes is obsolete.



KEYWORDS
KEYWORD
(SHORT) 		KEYWORD
(LONG) 		DESCRIPTION
OFF OFF Hide plane.
RAD RADIUS Set plane radius (value should be given in angstroms).
TRA TRANSPARENCY Set plane transparency (between 0 and 1).

EXAMPLES
COMMAND DESCRIPTION
plane Make the plane visible.
pla rad 20 Change plane radius to 20 angstroms.
pla tra 0.3 Change plane transparency (new value: 0.3).
plane off Hide plane.

NOTES
(1) By default, the plane moves with the structure. If movement controls affect only the plane, be sure to make it visible. Otherwise, you may push the plane far away from the object to which this plane belongs.

(2) In garlic source code, each plane is defined by the plane center (three coordinates) and by the normal vector (three-component vector).

(3) At present, garlic associates only one plane with each structure. If for some reason you need two planes (for example, to simulate the cellular membrane), use the following trick:
(3.1) Prepare the structure and its associated plane (the first plane).
(3.2) Load another structure (something small, like a single residue) and hide it.
(3.3) Make the plane (which is associated with this small structure) visible.
(3.4) Change radius and transparency for the second plane.
(3.5) Set the position and orientation of this plane.
If you learn this trick, you will be able to prepare images like this one:



RELATED COMMANDS
LOAD is used to load the structure (PDB file). MOVE is used to define which object should be moved. POSITION is used to place the chosen object (structure, plane, membrane or all) to arbitrary position. SELECT ABOVE selects atoms above the plane, while SELECT BELOW selects atoms below the plane.

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STE, STEREO

NAME
STE, STEREO - switch to stereo mode.

SYNOPSIS
STE
STEREO
STE OFF
STEREO OFF

DESCRIPTION
Switch to stereo mode. If keyword OFF is added, switch stereo off, i.e. switch to mono mode.

RELATED COMMANDS
Use MONO to switch to mono mode. It does exactly the same job as STEREO OFF.

garlic-1.6/commands/tbg.html0000644000000000000000000000331110345616567016035 0ustar rootroot00000000000000 TBG

TBG

NAME
TBG - change the background color used to draw input and output window.

SYNOPSIS
TBG color

DESCRIPTION
Change the background color used to draw input and output window. The color should be specified in one of the formats recognized by your X server. Both color names and numerical specification are accepted.

This command does not affect the output window in the sequence comparison mode. Check the command COMPARE .

EXAMPLES
COMMAND DESCRIPTION
tbg white White
tbg DarkSlateGray Dark dark slate gray
tbg #3000a0007000 Kind of green
tbg rgb:0/0/8 Dark blue
tbg rgbi:0.0/0.0/0.5 The same dark blue as above

Read the file rgb.txt (in /lib/X11/ directory) and the man page with a general description of the X window system (man X), to learn other color specification standards.

RELATED COMMANDS
TFG changes the foreground (text) color used in input and output window.

garlic-1.6/commands/log.html0000644000000000000000000000257010345614626016042 0ustar rootroot00000000000000 LOG

LOG

NAME
LOG - write interactive commands into the log file.

SYNOPSIS
LOG file_name
LOG OFF

DESCRIPTION
Use this command to log your garlic session into the specified file. The log file may be modified later and used as garlic script. LOG OFF closes the log file and stops logging.

NOTES
(1) If you logged the entire garlic session and want to use your log file as script, do not forget to remove the keyword QUIT (EXIT) which was used to end the garlic session!

(2) Lines which have # in the first column are treated as comments. Empty lines are ignored.

(3) Use PAUSE to pause the program execution. This is useful if preparing lecture or presentation, otherwise the script will run till the end without stopping.

(4) You can start and stop logging at any moment during your garlic session. Do not use the same log file name twice if you want to keep the old file - it will be overwritten.

RELATED COMMANDS
Exe executes the garlic script. PAUSE pauses the script execution.

garlic-1.6/commands/set.html0000644000000000000000000000223410345616305016045 0ustar rootroot00000000000000 SET

SET

NAME
SET - set dihedral angle

SYNOPSIS
SET PHI value
SET PSI value
SET OME value
SET OMEGA value
SET CHI1 value
SET CHI2 value
SET CHI3 value
SET CHI4 value
SET CHI5 value

DESCRIPTION
The command SET may be used to set the chosen dihedral angle. The value of the angle should always be given in degrees. The keyword OMEGA may be abbreviated to OME. Do not abbreviate the keywords CHI1, CHI2, CHI3, CHI4 and CHI5.

DIHEDRAL ANGLES
Click here for definitions of dihedral angles.

EXAMPLES
set phi -179.0
set ome 0
set chi1 62
set chi2 178.50

RELATED COMMANDS
The command EDIT may be used to change dihedral angles by using rotational controls.

garlic-1.6/commands/hyb.html0000644000000000000000000000267110345614162016040 0ustar rootroot00000000000000 HYB, HYBONDS

HYB, HYBONDS

NAME
HYB, HYBONDS - generate hydrogen bonds.

SYNOPSIS
HYB
HYB style
HYB OFF
HYBONDS
HYBONDS style
HYBONDS OFF

DESCRIPTION
Generate hydrogen bonds for the entire structure. Show hydrogen bonds for visible atoms. At present, some very simple geometric restrains are used to generate hydrogen bonds. Check the configuration file (.garlicrc) and the source file gen_hybonds.c to learn more about these restrains.

Keyword OFF may be used to hide hydrogen bonds.

For hydrogen bonds, there is no proportional ("nice") style. The only available styles are 0, 1, 2, 3, 4 and 5.

Default style used to draw hydrogen bonds is 1 (a single line of fixed width). You can change it by specifying the style. Examples:

hyb Generate hydrogen bonds and
show them using default style (1).
hyb 4 Generate hydrogen bonds and
show them using style 4 (four lines).
hyb off Hide hydrogen bonds
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BG, BACKG, BACKGROUND

NAME
BG, BACKG, BACKGROUND - change the main window background color.

SYNOPSIS
BG color
BACKG color
BACKGROUND color

DESCRIPTION
Change the main window background color. The color should be specified in one of the formats recognized by your X server. Both color names and numerical specification are accepted.

This command does not affect the main window in the sequence comparison mode. Check the command COMPARE .

EXAMPLES
COMMAND DESCRIPTION
bg white White
bg DarkSlateGray Dark dark slate gray
bg #3000a0007000 Kind of green
bg rgb:0/0/8 Dark blue
bg rgbi:0.0/0.0/0.5 The same dark blue as above

Read the file rgb.txt (in /lib/X11/ directory) and the man page with a general description of the X window system (man X), to learn other color specification standards.

RELATED COMMANDS
FG (FOREG, FOREGROUND) changes the main window foreground (text) color.

garlic-1.6/commands/pro.html0000644000000000000000000000545310345615665016070 0ustar rootroot00000000000000 PRO, PROBE

PRO, PROBE

NAME
PRO, PROBE - set the bond probe radius.

SYNOPSIS
PRO value
PROBE value

DESCRIPTION
Set the bond probe radius. The bond probe is used to draw nice bonds (cones and sticks, curved or straight). Small probe (about 0.8 angstroms) is used to obtain curved bond shapes, while large probe (about 10 angstroms) may be used to draw cones or sticks. Be sure to read the text about the command BONDS to learn how to create nice images, playing with commands PROBE, ATOMS and BONDS. Default probe radius is 0.8 angstroms, but this may be changed in the configuration file .garlicrc .

One and only one bond probe radius is assigned to each loaded structure. The bond probe radius may be changed separately for each structure. The command PROBE affects only the structure which is currently "caught" (see the command CATCH ) .

EXAMPLES
The images below show the same structure (adrenalin) drawn using two different probes: 0.8 angstroms (curved bonds, the left image) and 10 angstroms (conical sticks, the right image). In both cases all atoms were drawn using the small atomic style with enhanced contrast (ATOMS SM2). Bonds were drawn using the nice bond style (BONDS NICE).

probe 0.8 probe 10

NOTES
(1) Do not confuse the bond probe with the surface probe. The bond probe is used to draw bonds, while the surface probe is used to generate surface points. Read the text about the command SURFACE to learn more about the surface probe.

(2) To draw sticks, it is more convenient to use the commands BONDS STICKS and STICKS. The keyword STICKS (short form STI) of the command BONDS is used to draw bonds as sticks, while the separate command STICKS is used to define the stick radius. (3) To draw balls and sticks, it is convenient to use commands BALLS, STICKS, BONDS STICKS and ATOMS BALLS.

RELATED COMMANDS
BONDS is used to define drawing style for bonds. SSB is used to define drawing style for disulfide bonds. ATOMS is used to define drawing style for atoms. STICKS is used to define the radius of sticks. BALLS is used to define the radius of balls.

garlic-1.6/commands/sti.html0000644000000000000000000000322010345616434016050 0ustar rootroot00000000000000 STI, STICKS

STI, STICKS

NAME
STI, STICKS - set the radius of sticks.

SYNOPSIS
STI value
STICKS value

DESCRIPTION
Set the stick radius. The stick radius is used to draw selected bonds as sticks. To draw bonds as sticks, execute the command BONDS STICKS (short form: BON STI). Default radius is 0.15 angstroms, but this may be changed in the configuration file .garlicrc .

One and only one stick radius is assigned to each loaded structure. Thus, after the command BONDS STICKS, all selected bonds will be drawn as sticks of the same radius. The stick radius may be changed separately for each structure. The command STICKS affects only the structure which is currently "caught" (see the command CATCH ) .

EXAMPLES
The image below shows the adrenalin molecule drawn using default stick radius and default ball radius. Bonds were drawn as sticks (BON STI) while atoms were drawn as specular balls (ATO BA2).



RELATED COMMANDS
BONDS is used to define drawing style for bonds. SSB is used to define drawing style for disulfide bonds. ATOMS is used to define drawing style for atoms. PROBE is used to define the bond probe radius (the alternative way to draw bonds as sticks).

garlic-1.6/commands/cre.html0000644000000000000000000000674210364510160016024 0ustar rootroot00000000000000 CRE, CREATE

CRE, CREATE

NAME
CRE, CREATE - create structure

SYNOPSIS
CRE
CREATE

DESCRIPTION
Create structure, using the sequence from the main sequence buffer and the secondary structure from the main secondary structure buffer. At present (version 1.6), garlic is capable to create polypeptides only. Do not use this command to create DNA or RNA structure.

Both buffers have to be initialized before issuing the command CREATE. A typical use will be to create a short peptide, which will be tryed as an inhibitor for a larger, experimentally determined structure.

The present version (garlic 2.1) will correctly interpret the secondary structure codes for alpha helix (H), 3-10 helix (G) and beta strand (E), while coil (C) and turn (T) will be treated the same way as beta strand.

TEMPLATE RESIDUES
The new structure will be created using the residues from the template file. The template file contains 20 standard residues. This file should be named residues.pdb and stored to at least one of the following directories (listed in the search order):
(1) The current working directory.
(2) $HOME (user's home directory).
(3) $HOME/garlic (garlic subdirectory of the user's home directory).
(4) /usr/share/garlic (location for the system-wide file).
(5) /usr/local/lib/garlic (alternative location for the system-wide file).
(6) /usr/lib/garlic (another alternative location for the system-wide file).

If you want to add some extra residues (like modified amino-acids) to the template file, make your own copy of the file residues.pdb and keep it either in $HOME/garlic subdirectory or in your favorite working directory. It is very easy to add residues to the template file: just copy and paste the chosen exotic residue from the PDB file where you have it to the end of garlic template file. Be sure to include hydrogen atoms! There is one more thing: be sure that your residue does not have the same residue serial number as the preceding residue. You don't have to worry about the position and the orientation of your residue.

If you don't have the file residues.pdb, click here for html version. It is very easy to convert this version to the plain PDB, just save it as the plain text.

EXAMPLE
seq = asp ala phe tyr trp asn
str = eeeeee
cre 		Define a short sequence (six residues),
use extended structure for all residues
and create the short peptide.

NOTES
(1) The command CREATE resets the editing mode to default (no editing).

RELATED COMMANDS
Use SEQUENCE to prepare the protein sequence and STRUCTURE to prepare the secondary structure. The secondary structure buffer is initially filled with MAXRESIDUES codes for extended structure (EEEEEEEE...). MAXRESIDUES is defined in the source file defines.h . BONDS REFRESH may be used to fix bad bonds, which may sometimes be generated after executing the command CREATE.

garlic-1.6/commands/bal.html0000644000000000000000000000260610345613161016010 0ustar rootroot00000000000000 BAL, BALLS

BAL, BALLS

NAME
BAL, BALLS - set the ball radius.

SYNOPSIS
BAL value
BALLS value

DESCRIPTION
Set the ball radius (in angstroms). The ball radius is used to draw the selected atoms as balls. To draw atom as balls, execute the command ATOMS BA2 (specular balls) or ATOMS BALLS (balls with lower contrast). Short forms: ATO BA2, ATO BAL. Default ball radius is 0.40 angstroms, but this may be changed in the configuration file .garlicrc .

The ball radius may be set individually for each atom. Just select a single atom or more atoms and execute the command BAL with a single parameter (a new ball radius). The command BALLS affects the selected atom of the structure which is currently "caught" (see the command CATCH ) .

RELATED COMMANDS
BONDS is used to define drawing style for bonds. SSB is used to define drawing style for disulfide bonds. ATOMS is used to define drawing style for atoms. STICKS is used to define the sticks radius (many people like to draw structures as balls and sticks).

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EXE, EXECUTE

NAME
EXE, EXECUTE - load and execute garlic script.

SYNOPSIS
EXE file_name
EXECUTE file_name

DESCRIPTION
Load and execute the specified garlic script. The garlic script file should contain garlic commands. There is only one command which is not executed if added into garlic script: the EXE command. This is done to avoid endless loops; the script which executes itself will generate an endless loop. If you don't like it, change to source file execute_command1.c (use the source, Luke!). Examples:

COMMAND DESCRIPTION
exe dance.script Execute the script which loads trp.pdb
and forces this molecule to play something
similar to Argentinian tango.

RELATED COMMANDS
LOG may be used to store commands used during a garlic session. The log file may be used later as a script.

garlic-1.6/commands/bon.html0000644000000000000000000001512410361657455016043 0ustar rootroot00000000000000 BON, BONDS

BON, BONDS

NAME
BON, BONDS - change drawing style for bonds or refresh (reset) bonds.

SYNOPSIS
BON style
BON REF
BONDS style
BONDS REFRESH

DESCRIPTION
Change drawing style for bonds or refresh (reset) bonds. Bond style is defined separately from atom style. If used to set the bond style, this command does not affect disulfide bonds: the command SSB should be used for that purpose. Note that there is no separate keyword for curved bonds and sticks (nice style): the bond curvature is defined by the command PROBE .

REFRESHING (RESETING) BONDS
The commands CREATE, REPLACE and EDIT may sometimes generate bad bonds. The same may happen if you load the structure which contains some bad coordinates (side chains are too close, for example). If you have spotted bad bonds in your structure, do the following:

(1) Use the command EDIT (EDIT CLICK works fine) to move side chains, individual atoms or groups of atoms away from bad position.

(2) Execute the command BONDS REFRESH. The keyword REFRESH was introduced in version 1.5; it is not available in the earlier versions of this program!

(3) Check are there any bad bonds left. If you can see them, repeat the procedure. Please note that after replacing deeply buried small side chain with a large one you may be missing space - neighbors might be too close!

Refreshing of bonds affects ordinary bonds, as well as disulfide and pseudo-bonds. Pseudo-bonds are bonds connecting pseudo-atoms (quarkonium and jellium). Backbone data and dihedral angles will be updated too.

STYLE THICKNESS TYPE
0 Invisible bonds. Fixed width.
1 A single line. Fixed width.
2 Three lines. Fixed width.
3 Five lines. Fixed width.
4 Seven lines. Fixed width.
5 Nine lines. Fixed width.
nic
nice 		Curved bonds, conical sticks or cylindrical sticks,
depending both on the bond probe radius and the atomic
radii. This bond style is available for the following
atomic styles: SMALL, SM2, COVALENT, CO2,
SPACEFILL, SP2, BIG and BI2. Do not combine
the nice bond style with atomic styles 0, 1, 2, 3,
4, 5, 6, 7, BALL and BA2. 		Proportional.
sti
sticks 		Cylindrical sticks. The command BONDS STICKS
(short form: BON STI) is the most convenient
way to draw bonds as sticks. Default stick
radius may be changed by using the command
STICKS (short form: STI). 		Proportional.

The image below shows all drawing styles for bonds. To reproduce this image, execute the script bonds.script; the file trp.pdb (tryptophan) is required as input.



NICE BONDS
Nice bonds may be curved or straight, cylindrical or conical, depending on the bond probe radius. If this radius is small (like 0.8 angstroms), the bonds will be curved. Probe radius of 10 angstroms will give the straight bonds. If you want to draw the chemical bonds as cylindrical sticks, use the same atomic radius for all atoms and a relatively large probe. It is, however, more convenient to use the command BONDS STICKS (short form: BON STI) to draw cylindrical sticks. The command BONDS STICKS may be combined with the command STICKS, which is used to adjust the stick radius. If your atoms are drawn using different radii (and this is true for most atomic styles), the bonds will appear conical. This is one of the things which make garlic different from most other programs: in garlic, conical sticks are just the special case of nice bonds. Most other programs are capable to draw just simple cylindrical sticks.

The images below shows the same structure (adrenalin) drawn using two different bond probes: 0.8 angstroms (curved bonds, the left image) and 10 angstroms (conical sticks, the right image). In both cases all atoms were drawn using the small atomic style with enhanced contrast (ATOMS SM2).

probe 0.8 probe 10

EXAMPLES
In this example, four drawing styles for atoms were combined with nice bonds, drawn with four different probe radii. The following drawing styles were used (vertical, from top to bottom): sm2, co2, sp2 and bi2. Probe radii (angstroms, from left to right): 0.25, 0.50, 1.00 and 2.00. A single benzene molecule was used to prepare this image.



NOTES
(1) Invisible bonds (style 0) are not treated as hidden - they are just invisible.

(2) A good performance and fairly good contrast may be achieved choosing atom drawing style 0 (no pixels) and bond drawing style 2 (line width of three pixels).

(3) The nice bond style is allowed for ordinary covalent bonds and for disulfide bonds, but not for hydrogen bonds.

(4) Remember that the nice bond style works only for the following atomic styles: SMALL, SM2, COVALENT, CO2, SPACEFILL, SP2, BIG and BI2.

(5) The keyword REFRESH is available since version 1.5!

RELATED COMMANDS
PRO (PROBE) is used to set the probe radius. ATO (ATOMS) is used to change the drawing style for atoms. SSB is used to change the bond drawing style for disulfide bonds. STI (STICKS) is used to change the stick radius. BALLS is used to set the ball radius.

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_\!& j+7kC%&D%WYG $ay czF# I W"Y;hgWXd#x{٢<\L%}ɑuJǼZ&Jy~o}ks;6k#BB}zQ$H%f4Lj #J|[-ް&.,w"s1YLfϚdn#ρ>m"SQ5Sq>A7Mv*U/UU+84g~-Q[.eW5UݒoPw辧jNܡ·ixb =^m|ȒJ漕qe ǃYT:g=1.ٮ쬍'pljmpTd {ٖP{s0݌ m f =FhAP2b{ {aa'cZ~@1kDt<(0uZr'0Ǜ"0D4e:a#70t`A*9KtR&2,c(b,gaH IGN, IGNORE

IGN, IGNORE

NAME
IGN, IGNORE - do nothing.

SYNOPSIS
IGN
IGNORE

DESCRIPTION
This command does nothing. It is absolutely useless. Do not use it to pause the program execution - PAUSE should be used for this purpose.

garlic-1.6/commands/plo.html0000644000000000000000000002055210445774062016055 0ustar rootroot00000000000000 PLO, PLOT

PLO, PLOT

NAME
PLO, PLOT - draw hydrophobicity function(s).

SYNOPSIS
PLO HYD
PLO HYD start_index end_index
PLO WEI
PLO WEI start_index end_index
PLO MOM
PLO MOM start_index end_index
PLO SID
PLO SID start_index end_index
PLO F1
PLO F2
PLO F3
PLO F4
PLO F5
PLO F6
PLO F7
PLO OFF
PLOT HYDROPHOBICITY
PLOT HYDROPHOBICITY start_index end_index
PLOT WEIGHTED
PLOT WEIGHTED start_index end_index
PLOT MOMENT
PLOT MOMENT start_index end_index
PLO SIDED
PLO SIDED start_index end_index
PLOT F1
PLOT F2
PLOT F3
PLOT F4
PLOT F5
PLOT F6
PLOT F7
PLOT OFF

DESCRIPTION
Draw averaged hydrophobicity, weighted hydrophobicity, hydrophobic moment, sided hydrophobicity or some other hydrophobicity function. Two or more keywords may be combined in the same line. All hydrophobicity functions will be calculated using the sequence from the main sequence buffer, the current sliding window width (if required) and the current hydrophobicity scale. To calculate the hydrophobic moment one more parameter is required: the rotation angle between adjacent residues.

Seven additional hydrophobicity functions may be found in these source files:
F1: hyphob_function1.c
F2: hyphob_function2.c
F3: hyphob_function3.c
F4: hyphob_function4.c
F5: hyphob_function5.c
F6: hyphob_function6.c
F7: hyphob_function7.c

The averaged hydrophobicity will be shown as red line and the hydrophobic moment will be shown as blue line. The sided hydrophobicity (on one side and on another side) will be represented by two lines (magenta and violet). Weighted hydrophobicity will be colored violet too. The information about the residue covered by the pointer (mouse) will be visible in the output window (bottom right corner of the main window), while the sequence neighborhood of the current residue will be visible above the plot (top of the main window).

If the entire sequence is used for calculation, there is a chance that plot will contain the straight line at the end. This portion of the plot refers to solvent molecules, which are typically stored to the end of PDB file. This trailing line may be easily removed by adjusting the range of residue numbers. Here are two examples:

The first image was prepared using all residues from 200 to the last one, including solvent molecules.



The second image was prepared using residues from 200 to 280, omitting the solvent molecules.



KEYWORDS
KEYWORD
(SHORT) 		KEYWORD
(LONG) 		DESCRIPTION
OFF OFF Return to the main drawing mode (draw atomic coordinates).
Instead using this command, you can hit the ESCAPE key.
HYD HYDROPHOBICITY Draw averaged hydrophobicity.
WEI WEIGHTED Draw weighted hydrophobicity.
MOM MOMENT Draw hydrophobic moment.
SID SIDED Draw sided hydrophobicity for both sides (two lines).
F1 F1 Draw hydrophobicity function F1 (hyphob_function1.c).
F2 F2 Draw hydrophobicity function F2 (hyphob_function2.c).
F3 F3 Draw hydrophobicity function F3 (hyphob_function3.c).
F4 F4 Draw hydrophobicity function F4 (hyphob_function4.c).
F5 F5 Draw hydrophobicity function F5 (hyphob_function5.c).
F6 F6 Draw hydrophobicity function F6 (hyphob_function6.c).
F7 F7 Draw hydrophobicity function F7 (hyphob_function7.c).

PARAMETERS
PARAMETER
(SHORT) 		DESCRIPTION
start_index The actual number of the first residue.
Note that serial numbers are not used!
end_index The actual number of the last residue.

MOUSE USAGE
Mouse may be used to retrieve the information about averaged hydrophobicity and hydrophobic moment for a given residue. This residue is treated as the central residue of the current sliding window. The numerical data, along with residue name and serial number will be visible in the output window (bottom right corner). The sequence neighborhood of this residue will be visible above the plot. The information will be associated with the residue which has the same horizontal position (x coordinate) as the mouse pointer.



EXAMPLES
COMMAND DESCRIPTION
load 2por.pdb
seq from 1
scale eis
win 7
angle 180
plot hyd mom 1-300 		Load porin coordinates, copy sequence to
the main sequence buffer, select Eisenberg
hydrophobicity scale, set window width to 7
and set angle to 180 degrees. Draw averaged
hydrophobicity and hydrophobic moment for
residues from 1 to 300.
seq load sample.fasta
scale eis
angle 100
plot mom 		Read the file sample.fasta, which contains
the protein sequence in FASTA format (one
letter code), select Eisenberg scale, set
angle to 100 and draw hydrophobic moment.
plot off Return to default drawing mode.
Instead using this command, you can hit the ESCAPE key.

MATHEMATICAL BACKGROUND
Both the averaged hydrophobicity and the hydrophobic moment are calculated using a rectangular sliding window. If there are N residues in the sliding window, the averaged hydrophobicity is equal to:

Hydrophobic moment is equal to:

If you are searching for amphipatic alpha helices, set alpha to 100 degrees. To identify amphipatic beta strands, use 180 degrees. You can change alpha by using the command ANGLE.

NOTES
(1) Instead using the command PLOT OFF, the ESCAPE key may be pressed to return to the main drawing mode.

(2) PLOT uses only the sequence stored to the main sequence buffer. Read description of the command SEQ (SEQUENCE) to learn how to initialize this buffer.

(3) If you plot both the averaged hydrophobicity and the hydrophobic moment, the output window (bottom right corner) will contain the hydrophobic moment of the central residue.

(3) Every time you change hydrophobicity scale, don't forget to refresh the plot (i.e., execute the command PLOT once more).

RELATED COMMANDS
SEQUENCE is used to copy, define or load the sequence. ANGLE defines the rotation angle between adjacent residues. SCALE is used to specify the hydrophobicity scale. WINDOW is used to set the sliding window width.

garlic-1.6/commands/str.html0000644000000000000000000001247410346116674016076 0ustar rootroot00000000000000 STR, STRUCTURE

STR, STRUCTURE

NAME
STR, STRUCTURE - manipulate the content of the secondary structure buffer.

SYNOPSIS
STR = one_letter_code
STR LOAD filename
STR READ filename
STR FROM structure_identifier
STR COPY
STR SAVE filename
STR RESET

DESCRIPTION
The command STR (long form: STRUCTURE) manipulates the content of the main secondary structure buffer. Garlic mantains two secondary structure buffers: the main buffer and the reference buffer. The main secondary structure buffer is used to create a new structure and to replace a portion of an existing structure.

By default, the entire main secondary structure buffer is initially filled with codes for extended structure (i.e. filled with EEEEEEEE...). The number of codes is set to MAXRESIDUES (defined in defines.h). This is done once, when the program starts. When you change the content of this buffer, the leading portion of the buffer will be filled with the last secondary structure and the remainder will be filled with old codes. Use the command STR RESET to reinitialize the buffer before using the command CREATE.

Both buffers store the following secondary structure information:
(1) The length of the secondary structure.
(2) The secondary structure (one letter codes). The codes are:

C = coil,
E = strand,
G = 3-10 helix,
H = alpha helix,
T = turn.

As the secondary structure information may be defined independently from any structure, atomic coordinates are not required for most secondary structure manipulation routines.

All versions of the command STR, except one, are used to manipulate the content of the main secondary structure buffer. The only exception is STR COPY, which copies the content of the main secondary structure buffer to the reference buffer. This is the only way to initialize the reference buffer.

STR = one_letter_code
The command STR may be used with the keyword = (equal sign) to define the secondary structure at garlic command prompt. This may be practical to define the secondary structure of a short peptide or a small protein. The syntax:

STR = one_letter_code

Example:

str = ccccccchhhhhhhcttteeeeecccccccccccccc

The secondary structure will be converted to uppercase. If at least one bad code is found, the command will fail and the main secondary structure buffer will be left empty. Space, comma and tab may be used as separators.

STR LOAD filename
The keyword LOAD (or READ, short forms LOA and REA) may be used to read the secondary structure from the specified file. The input file should be written in a format similar to FASTA. Empty lines and lines beginning with # will be ignored. The number of codes per line is arbitrary. Example:



The following characters are threated as separators:
(1) space
(2) tab
(3) comma (,)

If input file contains at least one bad code (a residue name which consists of four letters, for example) the reading will fail. The hard-coded maximal number of residues is 20000, but it may be easily changed (see MAXRESIDUES in the header file defines.h).

Example:
load secstr.fasta

STR FROM structure_identifier
The keyword FROM (short form: FRO) may be used to copy the secondary structure from the specified atomic structure to the main secondary structure buffer. Only the structure of selected residues is copied. Residue is treated as selected if the first atom is selected. For proteins, this is typically N (nitrogen).

Example:
str from 1

STR COPY
The command STR COPY (short form: STR COP) copies the secondary structure from the main secondary structure buffer to the reference buffer. This is the only way to initialize the reference buffer. This command must be executed (i.e., the keyword COPY must be used) before executing commands which require two secondary structures for proper operation. The main secondary structure buffer may be initialized prior to STR COPY by using one of the keywords described above (=, LOAD or FROM).

Example:
str copy

STR SAVE filename
The command STR SAVE (short form: STR SAV) saves the secondary structure to the specified file. The output file will be written in FASTA format.

Example:
str save 9pap.secstr

STR RESET
Reset (initialize) the main secondary structure buffer. The short form is STR RES. The command STR RESET sets the number of codes in the main secondary structure buffer to MAXRESIDUES (defined in defines.h) and fills the entire buffer with codes for extended structure (EEEEEEEE...).

Example:
str reset

RELATED COMMANDS
SEQ may be used to define the sequence. CREATE may be used to create a new peptide.

garlic-1.6/commands/exi.html0000644000000000000000000000122510345613763016043 0ustar rootroot00000000000000 EXI, EXIT, QUI, QUIT

EXI, EXIT, QUI, QUIT

NAME
EXI, EXIT, QUI, QUIT - quit garlic session (exit from garlic).

SYNOPSIS
EXI
EXIT
QUI
QUIT

DESCRIPTION
Quit garlic session, i.e. exit from garlic. The main garlic window will be closed, memory freed etc. At present, garlic is not capable to save any data (this will be changed, of course), so there are no warning messages.

garlic-1.6/commands/doc.html0000644000000000000000000001563110357045361016025 0ustar rootroot00000000000000 DOC, DOCK

DOC, DOCK

NAME
DOC, DOCK - prepare two structures for docking.

SYNOPSIS
DOC identifier_1 identifier_2
DOC OFF
DOCK identifier_1 identifier_2
DOCK OFF

DESCRIPTION
The command DOCK prepares two structures for docking. Before executing this command, two molecules (structures) have to be loaded. For each structure a region on the surface should be selected as a candidate region for interaction with another molecule. For example, if the first molecule is the substrate, the active site has to be identified as the region where the inhibitor should be placed. Assuming that another molecule is the inhibitor, the side which is expected to interact with the substrate should be identified.

When both molecules are ready for docking, the command DOCK should be executed. The identifiers of both molecules have to be issued as arguments. Both molecules will be translated and rotated to position and orientation suitable for docking. The first molecule will be moved to the bottom of the main window, with the selected region visible on the upper side. The second molecule will be placed atop the first molecule, with the selected region facing the first molecule.

Further, a special docking window will be opened, showing the orthogonal projections of polar side chains as symbols. The polar side chains of both molecules are projected to the plane associated with the first molecule. Cyan symbols belong to the bottom molecule (the first one) and red symbols belong to the top molecule. Hydrogen bond donors are shown as crosses, acceptors as circles, and side chains which are both hydrogen bond donors and acceptors are shown as crosses in circles.

The user might be able to combine two structures, using the information visible in both the main garlic window and in docking window. However, this routine is still quite naive, so don't expect too much. Docking is not an easy game. I hope that this command will be useful at least for educational purpose.

KEYWORDS
The keyword OFF is the only keyword which may be used with the command DOCK. DOCK OFF is used to hide docking window.

KEYWORD DESCRIPTION
OFF Hide docking window.

PARAMETERS
Except when used in combination with the keyword OFF, the command DOCK should be followed by two structure identifiers. If you have forgotten these numbers, just move the mouse pointer over the structure(s) and find the identifier(s) in the output window (the bottom right corner). The order is important: the first molecule will be placed to the bottom of the main window, while the second will be placed atop the first one.

PARAMETER DESCRIPTION
identifier_1 Identifier of the first molecule.
(substrate, for example).
identifier_2 Identifier of the second molecule.
(inhibitor, for example).

EXAMPLE
The example below shows how to prepare two structures for docking. In this example, the first structure is papain (reference 1) and the second structure is stefin (reference 2). The structure of the complex is known ( PDB code 1STF).

STEP1:
Load the first structure:
load file1.pdb
Change the color. Cyan-blue might be
a good choice:
color cyan-blue 		STEP 2:
Make the plane visible:
plane
Prepare to move the plane:
move plane
Use plane to divide structure in two parts.
The active site should be above the plane.
Change drawing style for atoms or bonds.
Here the spacefill style is used. This is
bad idea if using slow machine.
sel above
atom sp2
Reset movement controls:
move all
STEP 3:
Push the first structure to the corner.
Load the second structure:
load file2.pdb
Change color. Red is recommended here:
color red 		STEP 4:
Make the plane visible and divide the
second structure in two parts. Change
drawing style for atoms or bonds.
plane
move plane
(... now rotate and translate the plane)
sel above
atom sp2
Reset movement controls:
move all
STEP 5:
Execute DOCK command:
dock 1 2 		Rotate the second (top) structure. Check
the relative arrangement of hydrogen bond
donors and acceptors. The projections of
these side chains are given in docking
window.

NOTES
(1) If two structures are close, some important atoms might be invisible (hidden by some closer atoms). Use slab to cut slices through structure(s).

(2) Don't forget to catch the right structure before applying some transformation. By default, after the command DOCK is executed, the movement controls are attached to the second (top) structure.

RELATED COMMANDS
LOAD is used to load the specified file (structure, molecule). MOVE is used to define which object should be moved (structure, plane or both). PLANE is used to manipulate the plane associated with the structure. CATCH is used to attach the movement controls to a chosen structure.

REFERENCES
(1) Kamphuis, I. G., Kalk, K. H., Swarte, M. B. A. and Drenth, J. (1984). J. Mol. Biol. 179, p. 233.

(2) Stubbs, M. T., Laber, B., Bode, W., Huber, R., Jerala, R., Lenarcic, B. and Turk, V. (1990). EMBO J. 9, p. 1939.

garlic-1.6/commands/tit.html0000644000000000000000000000356210345616674016070 0ustar rootroot00000000000000 TIT, TITLE

TIT, TITLE

NAME
TIT, TITLE - add, move or remove the specified title.

SYNOPSIS
TIT identifier OFF
TIT identifier screen_x screen_y
TIT identifier screen_x screen_y "title_string"
TITLE identifier OFF
TITLE identifier screen_x screen_y
TITLE identifier screen_x screen_y "title_string"

DESCRIPTION
The keyword TITLE may be used to add, move or remove the title to or from the main window. Up to 100 titles may be added to the main window, to explain the content. The title position may be specified through screen_x and screen_y. Each title has the unique identifier. The identifier is a number between 0 and 99 (these two values are allowed too). The title string should be included into quotes.

EXAMPLES
COMMAND DESCRIPTION
tit 8 50 50 "This is porin" Add the title number 8 to the main window,
close to the top left corner
tit 8 100 400 Move the title number 8 to a new position
tit 8 off Remove (hide) the title number 8

RELATED COMMANDS
The command LABELS assigns labels to selected atoms. TAG assigns the specified tag to a structure. Both labels and tag move along with the structure. Note that tag is assigned to the structure, labels to atoms and title is assigned to the main window.

garlic-1.6/commands/dum.html0000644000000000000000000001252710445773631016054 0ustar rootroot00000000000000 DUM, DUMP

DUM, DUMP

NAME
DUM, DUMP - dump selected numeric data to the console (standard output) or the the specified file.

SYNOPSIS
SHORT FORM LONG FORM
DUM HYD
DUM HYD filename
DUM AVE
DUM AVE filename
DUM WEI
DUM WEI filename
DUM F1
DUM F1 filename
DUM F2
DUM F2 filename
DUM F3
DUM F3 filename
DUM F4
DUM F4 filename
DUM F5
DUM F5 filename
DUM F6
DUM F6 filename
DUM F7
DUM F7 filename 		DUMP HYDROPHOBICITY
DUMP HYDROPHOBICITY filename
DUMP AVERAGE
DUMP AVERAGE filename
DUMP WEIGHTED
DUMP WEIGHTED filename
DUMP F1
DUMP F1 filename
DUMP F2
DUMP F2 filename
DUMP F3
DUMP F3 filename
DUMP F4
DUMP F4 filename
DUMP F5
DUMP F5 filename
DUMP F6
DUMP F6 filename
DUMP F7
DUMP F7 filename

DESCRIPTION
The command DUM (DUMP) may be used to dump selected numeric data to the console (standard output) or to the specified file. At present (version 1.6), the command DUMP may be used to dump hydrophobicity functions. Note that the selected hydrophobicity function should be calculated first, which is forced by executing the command PLOT (for example, PLOT AVERAGE will force the calculation of the average hydrophobicity). The output consists of two columns: The first column contains the residue serial number (integer) and the second column contains the requested value (floating point value). Sample output: 
# Raw hydrophobicity
       0    -3.63
       1     0.46
       2    -2.80
       3     1.25
       4    -0.46
       5    -1.15
       6    -3.64
       7    -0.50
       8    -1.81
       9     0.67
      10    -1.15
The first line is just a comment.

The simplest hydrophobicity function are the raw hydrophobicity and the average hydrophobicity. The weighted hydrophobicity was introduced in version 1.6. The hydrophobicity functions F1, F2, F3, F4 and F5 were introduced in version 1.4, and functions F6 F7 were introduced in version 1.6. These hydrophobicity functions are described in the following source files:
F1: hyphob_function1.c
F2: hyphob_function2.c
F3: hyphob_function3.c
F4: hyphob_function4.c
F5: hyphob_function5.c
F6: hyphob_function6.c
F7: hyphob_function7.c

KEYWORDS
KEYWORD
(SHORT) 		KEYWORD
(LONG) 		DESCRIPTION
HYD HYDROPHOBICITY Dump raw hydrophobicity values.
AVE AVERAGE Dump average hydrophobicity, using
the current sliding window width.
WEI WEIGHTED Dump weighted hydrophobicity, defined in
the source file weighted_hydrophobicity.c .
F1 F1 Dump hydrophobicity function F1.
F2 F2 Dump hydrophobicity function F2.
F3 F3 Dump hydrophobicity function F3.
F4 F4 Dump hydrophobicity function F4.
F5 F5 Dump hydrophobicity function F5.
F6 F6 Dump hydrophobicity function F6.
F7 F7 Dump hydrophobicity function F7.

EXAMPLES
COMMAND DESCRIPTION
dump ave Dump average hydrophobicity to the console.
dump hyd raw.data Dump raw hydrophobicity values to the file
called raw.data (file names are case sensitive).

NOTES
(1) A very simple output format was choosen to make it compatible with popular drawing programs.

RELATED COMMANDS
PLOT is used to draw the specified hydrophobicity function. It should be used before the command dump, to force the calculation of the specified hydrophobicity function. The only exception is raw hydrophobicity (keyword HYD) - it is assigned automatically.
WINDOW is used to define the sliding window width, which affects the average hydrophobicity function.

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( #8J׍r")X!"r3)b] h]c\ִ4[=oT ,WsUNR P@@@؃+%!0$-#%p. [Qڊ`ǘ,1=Ihhf^ B܅]ZI [oK= OPe|8>?PU!(Y X3L{hÉp鲮hi셫]M^E֐[oȆmP:UP$>1pN7x4]=˽=* )],`^Xhp ǑPځjՀikՅ̍TjXՆo_$T_]*B ]C`@ bq˚}Qz" &% ƗHƽ`PB( ,Ǘ ;:jiE̅8[>]݆p^@ նMWR|8CLJUك$@%X7,؂/+bPފ\ ,WU-c3Fjh5F؃hYmcԥocVc, E1D΄x @&p'9.L>HhHG5Wz a[W8>cM[c8>Ou-1@B"d6[GƬSzhV+`0 zT՝2litVt^yp`sqNʼn#k/IP4>iŬRdNejk`k@jLp://Ȇx& mh;cqް_ZRPC8*ik*8) nml^^mmۮo`l:` I>l֜]&LxLN(֝ll>ֆA7Pq->0GTLnrN(hh"FloopmQ<`G81(dDf(*(7o(QM1 5n?PpUlEg,P/mWqܮ1ACzDqrAq!O;n(*8η(4 mr凓(b5sr>pŎs9sD=WtAqvrp88'pCo(EtPvG'rI&)(NwuPu&u*uWu(Pmf;D^7vuG>fhĖj#wjUhvjnLlv.vo'tmYmrgwtdž؆DPoznl]D+nV4q]Wq'7y;garlic-1.6/commands/ref.html0000644000000000000000000000306510364510405016024 0ustar rootroot00000000000000 REF, REFRESH

REF, REFRESH

NAME
REF, REFRESH - switch refreshing on or off.

SYNOPSIS
REF
REFRESH
REF OFF
REFRESH OFF

DESCRIPTION
Most of garlic commands require redrawing of the main window. This may slow down the execution of the program. To save some time, the refreshing may be switched off. Just execute the command:

ref off

(the long form is REFRESH OFF). After that, a number of time-consuming commands may be executed, and refreshing may be turned on again. To switch on refreshing, execute the command REF without the keyword OFF:

ref

This trick is very useful with scripts. Put the command REF OFF close to the top of the script and do not forget to put the command REF (without the keyword OFF!) to the bottom of the script. Try the sample scripts atoms.script , bonds.script and colors.script . The refreshing trick is used in these scripts.

If refreshing is switched off, you will see the message in the middle of the main garlic window (yellow text "Refreshing off" on red background).



garlic-1.6/commands/mem.html0000644000000000000000000001246310345615214016033 0ustar rootroot00000000000000 MEM, MEMBRANE

MEM, MEMBRANE

NAME
MEM, MEMBRANE - generate and manipulate the membrane associated with the structure.

SYNOPSIS
SHORT FORM LONG FORM
MEM
MEM BET
MEM RAD value
MEM THI value
MEM TRA value
MEM OFF 		MEMBRANE
MEMBRANE BETA
MEMBRANE RADIUS value
MEMBRANE THICKNESS value
MEMBRANE TRANSPARENCY value
MEMBRANE OFF

DESCRIPTION
The command MEM (MEMBRANE) may be used to associate the membrane with a protein structure. By default, no membrane is associated with the structure when it is loaded into memory. The membrane is initialized after the first execution of the command membrane. The membrane is useful when analysing some membrane protein, but it does not make much sense when working with a soluble protein.

The experimental determination of the structure of fluid lipid bilayers in The Stephen White Laboratory at UC Irvine has revealed a significant thermal motion of lipid molecules. This means that there is no clear edge of the biological membrane. However, the model used in garlic is just the opposite: the membrane is represented by two parralel planes, with clear external edges. The membrane thickness is also precisely defined. The idea was to give at least a bad model of the membrane, to allow selection of the transmembrane region. Please be sure to read those beatifull pages from Stephen White Laboratory!

The planes used to simulate the membrane are represented as elliptical surfaces. The inner sides are colored orange-red, while the outer sides of the membrane are colored blue. The transparency of these planes may be adjusted, but not individually. The allowed range of transparency from 0 to 1. If the transparency is equal to zero both planes will be opaque. Default transparency is 0.4 (hard-coded).

In addition to the transparency, the membrane thickness and the radius of both planes may be adjusted (keywords THICKNESS and RADIUS, short forms THI and RAD). Default radius will be 50% larger than the membrane thickness. Default membrane thickness is 30 angstroms. It is not possible to change default membrane thickness through .garlicrc file. If you want to change it, modify the hard-coded value in the source file defines.h and recompile the program.

If working with beta barrel protein (porin-like membrane proteins), the keyword BETA may be used to improve membrane placement.

KEYWORDS
KEYWORD
(SHORT) 		KEYWORD
(LONG) 		DESCRIPTION
OFF OFF Hide membrane.
BET BETA Attach membrane to beta barrel protein (porin).
THI THICKNESS Set the membrane thickness (in angstroms).
RAD RADIUS Set the radius of both planes (use angstroms).
THI THICKNESS Set the membrane thickness (in angstroms).
TRA TRANSPARENCY Set the transparency of both planes
(between 0 and 1).

EXAMPLES
COMMAND DESCRIPTION
mem Initialize the membrane and make it visible.
mem rad 20 Change the radius of both planes to 20 angstroms.
mem tra 0.3 Change the transparency of both planes (new value: 0.3).
mem thi 20
mem beta 		Change membrane thickness and attach membrane to beta
barrel protein.
mem off Hide membrane.

NOTES
(1) By default, the membrane moves with the structure. If movement controls affect only the membrane, be sure to make it visible. Otherwise, you may push the membrane far away from the object to which this membrane belongs.

RELATED COMMANDS
LOAD is used to load the structure (PDB file). MOVE is used to define which object should be moved. POSITION is used to place the chosen object (structure, plane, membrane or all) to arbitrary position.

garlic-1.6/commands/reg.html0000644000000000000000000000217110345615777016043 0ustar rootroot00000000000000 REG, REGISTER

REG, REGISTER

NAME
REG, REGISTER

SYNOPSIS
REG
REGISTER

DESCRIPTION
Register garlic: send a short e-mail to the author. This command will fail if your machine is not connected to the Internet. The only content of the message will be the word 'Hi!'. Your registration will not be abused, i.e. your e-mail address will not be given to spammers or anyone else. The registration will be used just to count garlic users.

If your machine is not connected to the Internet, send an e-mail from some other machine. Questions, comments and suggestions are welcome.

The author may be reached at:
zucic@garlic.mefos.hr
zucic@mia.os.carnet.hr

Author's home page:
http://garlic.mefos.hr/zucic

REGISTER GARLIC - by registering, you are supporting further development of this program!
garlic-1.6/commands/prepro_hint.gif0000644000000000000000000000305307501343240017377 0ustar rootroot00000000000000GIF89aطZ"!Created with The GIMP,0I8`(dih¾p,4xpH,Ȥrl:R=k'JX0,&_);garlic-1.6/commands/tra.html0000644000000000000000000000167710345616712016054 0ustar rootroot00000000000000 TRA, TRANSLATE

TRA, TRANSLATE

NAME
TRA, TRANSLATE - translate the structure for the given shift in the given direction.

SYNOPSIS
TRA axis shift

DESCRIPTION
Translate the structure. The axis should be specified with one letter (x, y or z) and the shift should be given in angstroms.

EXAMPLES
COMMAND DESCRIPTION
tra x 40 Move to the right, 40 angstroms.
tra y -0.5 Move up, 0.5 angstroms (y points down).

garlic-1.6/commands/edi.html0000644000000000000000000002577310364510355016027 0ustar rootroot00000000000000 EDI, EDIT

EDI, EDIT

NAME
EDI, EDIT - edit structure

SYNOPSIS
SHORT FORM LONG FORM
EDI OFF
EDI ATO
EDI BON atom1 atom2
EDI CLI
EDI DIM
EDI MAI
EDI OME
EDI PHI
EDI PSI
EDI SID
EDIT OFF
EDIT ATOMS
EDIT BOND atom1 atom2
EDIT CLICK
EDIT DIMENSIONS
EDIT MAIN
EDIT OMEGA
EDIT PHI
EDIT PSI
EDIT SIDE

DESCRIPTION
The command EDI (EDIT), combined with one of associated keywords (except OFF), switches the program to editing mode. This will work for garlic version 1.2 or later. The keyword OFF may be used to switch the program to default mode (no editing). The command EDIT should always be combined with one of the keywords. The most comfortable keyword is CLI (CLICK): after executing the command EDI CLI (long form: EDIT CLICK), use the pointer (mouse) to pick one bond (torsion angle) for editing. Click the left mouse button.

The keywords ATO (ATOMS) and DIM (DIMENSIONS) are reserved for special purposes and should not be used to edit real molecular structures, unless you want to introduce (or to fix) some distortion. These keywords may be used to prepare some artificial structures, made from quarkonium and jellium atoms.

To avoid the accidental modification of the structure, a little sea creature will be visible at the position of the chosen bond or atom. If editing (moving) more than one bond (atom), the creature will be drawn at the position of the first bond (atom). If editing bonds (torsion angles), you will see a little seahorse. If editing atoms (keyword ATOMS) or dimensions (keyword DIMENSIONS) you will see a little squid. Why I have chosen these animals? Seahorse is a poor swimmer but has excellent maneuverability. Squid known hot to use jet propulsion for fast translation. These little creatures will warn you that you are working in editing mode. They will disappear after executing the command EDIT OFF.

The squid will be visible if using
keywords DIMENSIONS or ATOMS
and the seahorse will be visible if using
keywords BOND, BOND, CLICK,
MAIN, OMEGA, PHI, PSI or SIDE.

EDIT OFF
The keyword OFF may be used to switch the program to default mode (no editing, just viewing). The editing symbol (seahorse - if editing bonds or squid - if editing atoms) will disappear from the screen.

EDIT ATOMS
The command EDIT ATOMS (short form: EDI ATO) may be used to translate selected atoms. Normally, you will not use the keyword ATOMS if working with a real molecular structure. This keyword is intended for usage with artificial structures, consisting of polygonal lines. In rare cases, you may use this command to distort the molecular structure, for example to test your own molecular dynamics program. Do not use this keyword unless you really know what you are doing!

The translation of atoms is done by using the keys /, *, +, -, 5 and 0 on numeric keypad.

EDIT BOND atom1 atom2
The command EDIT BOND (short form: EDI BON) should be followed by serial numbers of two atoms which form the bond. The keyword BOND may be used in scripts, to specify a single bond angle for editing. In interactive mode, the keyword CLICK is much more comfortable. Garlic will not allow the editing of the specified bond angle in two cases:
(1) If the specified two atoms do not form an ordinary covalent bond. Disulfide bonds are not counted as such.
(2) If these atoms form a covalent bond, but this bond in part of a closed structure (a ring).

The bond rotation may be done by using the keys 7 and 9 on numeric keypad. Garlic is capable to recognize the bond angle. For dihedral angles phi and psi, an auxiliary plot will be drawn to the bottom right corner of the main window. For dihedral angle omega, the auxiliary plot will be drawn to the bottom of the main window.

EDIT CLICK
The command EDIT CLICK (short form: EDI CLI) is the most comfortable way to chose a single bond angle for editing. Just execute this command and click a single bond. If this bond is as an ordinary covalent bond and if it is not part of some closed structure (a ring), the bond angle editing will be allowed. The seahorse will appear close to the place where the click occurred. Use the keys 7 and 9 on the numeric keypad to change the bond angle.

The keyword CLICK may be used to pick both the main chain bonds as well as side chain bonds. It may not replace the commands MAIN and SIDE, because these two keyword activate the simultaneous editing of two dihedral angles.

Be sure to select all atoms (residues) before using the command EDIT CLICK!

In some cases, a small auxiliary plot will appear in the main window. This means that you have chosen one of the main chain dihedral angles for editing. More details about these auxiliary plots may be found below (see EDIT MAIN).

EDIT DIMENSIONS
The command EDIT DIMENSIONS (short form: EDI DIM) may be used to resize the selected portion of the structure. Normally, you will not use the keyword DIMENSIONS if you are working with a real molecular structure. The translational controls should be used to change each of three dimensions independently: 0 and 5 may be used to change the depth of the structure, / and * to change the width and + and - to change the height of the structure. To resize the structure proportionally change all three dimensions consecutively. Be careful with the command EDIT DIMENSIONS!

EDIT MAIN
Change the main chain dihedral angles phi and psi, for all selected residues. A residue is treated as selected if the first atom of this residue is selected. Click here for detailed definitions of dihedral angles.

The current pair of values and the allowed regions for phi and psi will be visible in the auxiliary Ramachandran plot, in the bottom right corner of the main window. The current position in the Ramachandran plot may be recognized as the small, yellow square with red outline. The favorable regions are colored blue, with the more favorable regions colored dark blue. Two dark blue squares represent the positions of alpha helix and beta strand. Note that these conformations may be unfavorable in some cases (pre-proline in alpha helix, for example). There are four different types of auxiliary Ramachandran plot, describing residues with different steric constraints:

glycine proline pre-proline residues all other residues

Be sure to read something about the revision of Ramachandran steric constrains: http://xray.bmc.uu.se/~gerard/rama/ramarev.html

EDIT OMEGA
Change the angle omega. Click here for detailed definitions of dihedral angles. Most of residues in a protein are in trans conformation, with omega value of about 180 degrees. A small fraction of residues may be found in cis conformation, with omega value of about 0 degrees. The cis conformation is typical for proline. The auxiliary plot at the bottom of the main window shows the current omega value (yellow vertical line with red outline) and the statistical distribution of omega values, across the range between -180 degrees and +180 degrees. The blue peaks represent the most probable values. Note that -180 degrees is equivalent to +180 degrees; two prominent peaks in the auxiliary plot are actually two parts of the same (trans) peak. The central (cis) peak is almost invisible.



EDIT PHI
Change dihedral angle phi. Click here for detailed definitions of dihedral angles. The angle phi may be changed by using the keys 7 and 9 on numeric keypad. The operation will be done for every selected residue. A residue is treated as selected if the first atom of this residue is selected. An auxiliary Ramachandran plot (described above in EDIT MAIN section) will be visible in the bottom right corner.

EDIT PSI
Change dihedral angle psi. Click here for detailed definitions of dihedral angles. The angle psi may be changed by using the keys 7 and 9 on numeric keypad. The operation will be done for every selected residue. A residue is treated as selected if the first atom of this residue is selected. An auxiliary Ramachandran plot (described above in EDIT MAIN section) will be visible in the bottom right corner.

EDIT SIDE
Edit the side chain dihedral angles chi1 and chi2. Four numeric keys are used to change dihedral angles: 4 and 6 to change chi1 and 2 and 8 to change chi2. The command EDI SID (EDIT SIDE) is suitable for asparagine, aspartic acid, histidine, isoleucine, leucine, phenylalanine, proline, tyrosine and tryptophan.

NOTES
(1) The commands REPLACE, CREATE, LOAD, DISCARD, CATCH, SELECT, ADD and RESTRICT are switching program to default editing mode (no editing).

RELATED COMMANDS
The command SET may be used to set dihedral angles directly. It is more precise than the command EDIT. The commands ADD, RESTRICT and SELECT (short forms: ADD, RES and SEL) may be used to select one or more residues for editing. As it will be difficult to combine script execution and interactive rotational controls (numeric keys), the command ROTATE (short form: ROT) may be used to change dihedral angles in scripts, after executing the command EDIT. BONDS REFRESH may be used to fix bad bonds, which may sometimes be generated after executing the command CREATE.

garlic-1.6/commands/cen.html0000644000000000000000000000355110345613351016020 0ustar rootroot00000000000000 CEN, center

CEN, center

NAME
CEN, center - change the origin of the internal coordinate system.

SYNOPSIS
CEN
center

DESCRIPTION
An internal coordinate system is assigned to each structure. The command CEN (center) redefines the position of this origin. A new origin will be equal to the geometric center position calculated for selected atoms. This may be quite useful if working with a large structure. By selecting a small portion of the structure, or even a single atom, the internal system origin may be set to a place which contains the most interesting part of the structure. Rotations, slab changes and color changes will be done with respect to new origin. This will keep the interesting part in the same part of the screen. It is recommended to hide the uninteresting part of the structure, to make rotations and other transformations faster. When you load the structure the geometric center of the whole structure is used as the internal system origin. If you displaced the origin but now you want to move it back to the original position, just execute the following commands:

sel all
cen

This command is applied to the structure which is currently hangled, i.e. the one to which the command CATCH was applied last.

NOTES
(1) The command CEN (center) does not move the structure to the screen center. To do this, use the command POS (POSITION).

RELATED COMMANDS
POS sets the origin of the internal system to the specified position in the main (global) coordinate system.

garlic-1.6/commands/ato.html0000644000000000000000000001166710357045321016044 0ustar rootroot00000000000000 ATO, ATOMS

ATO, ATOMS

NAME
ATO, ATOMS - change drawing style for atoms.

SYNOPSIS
ATO style
ATOMS style

DESCRIPTION
Change drawing style for atoms. Atom style is defined separately from bond style. For BALLS, BA2, BIG, BI2, COVALENT, CO2, SMALL, SM2, SPACEFILL and SP2 style, atomic radii are read from .garlicrc file. If this file is not available, hard-coded defaults are used. The styles listed above may be used to produce nice output but require more CPU time than other styles. The list of realistic, nice styles, sorted by size, from the smallest to the largest:
(1) SMALL and SM2;
(2) COVALENT and CO2;
(3) SPACEFILL and SP2;
(4) BIG and BI2.

Note that BALLS and BA2 style are not included in this list. All atoms drawn using this style will have the same physical size.

The second version of a given style has more enhanced contrast and more specular look than the first version (BA2 vs. BALL, BI2 vs. BIG etc). See the image at the bottom of this page to understand this difference.

STYLE DESCRIPTION size
0 Invisible atoms. Fixed size.
1 A single pixel. Fixed size.
2 3x3 cross (5 pixels). Fixed size.
3 3x3 square (9 pixels). Fixed size.
4 5x5 circle (21 pixel). Fixed size.
5 7x7 square (37 pixels). Fixed size.
6 9x9 circle (61 pixel). Fixed size.
7 11x11 circle (109 pixels). Fixed size.
bal
balls 		Balls (suitable to draw balls and sticks). Proportional.
ba2 Balls with enhanced contrast. Proportional.
sma
small 		Small style (default: 70% of covalent radius). Proportional.
sm2 Small style, enhanced contrast. Proportional.
cov
covalent 		Covalent style (default: covalent radius). Proportional.
co2 Covalent style, enhanced contrast. Proportional.
spa
spacefill 		Spacefill style (default: 70% of van der Waals radius). Proportional.
sp2 Spacefill style, enhanced contrast. Proportional.
big Big style (default: van der Waals radius). Proportional.
bi2 Big style, enhanced contrast. Proportional.

EXAMPLES
The image below shows all drawing styles for atoms. To reproduce this image, execute the script atoms.script; the file trp.pdb (tryptophan) is required as input.



NOTES
(1) Invisible atoms (style 0) are not treated as hidden - they are just invisible.

(2) A good performance and fairly good contrast may be achieved choosing atom drawing style 0 (no pixels) and bond drawing style 2 (line width of three pixels).

(3) The ATOM keywords SMALL, SM2, COVALENT, CO2, SPACEFILL, SP2, BIG and BI2 may be combined with the command BONDS NICE to produce very nice images. All other atomic styles (0 - 7, BALL, BA2) will not work with BONDS NICE.

RELATED COMMANDS
The command BAL (BALLS) is used to change the ball radius. BON (BONDS) is used to change drawing style for bonds. PRO (PROBE) is used to change the bond probe radius (this probe is used to draw nice bonds).

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ANG, ANGLE

NAME
ANG, ANGLE - set angle.

SYNOPSIS
ANG value
ANGLE value

DESCRIPTION
Set the rotation angle between adjacent residues. This angle is stored as an internal variable and used to draw helical wheel or hydrophobic moment plot. The value should be specified in degrees. Default value is 100 degrees, which corresponds to alpha helix rotation angle. To prepare helical wheel or hydrophobic moment plot you have to make the assumption about the secondary structure. The assumption is made by setting the rotation angle for adjacent residues. The table below lists the common structural motifs and the corresponding angles.

STRUCTURAL
MOTIF 		RESIDUES
PER TURN 		ANGLE
(DEGREES)
alpha helix 3.6 100
3-10 helix 3 120
beta strand 2.3 160

3-10 helices are usually short, but if you assume that more than three residues fold into 3-10 helix, modify the angle used to draw the helical wheel. If you use the realistic angle (120 degrees), some residues will be obscured (hidden behind the residues which are drawn later). Use 115 or 125 instead of 120 degrees, to avoid overlapping of residues.

RELATED COMMANDS
WHEEL draws the helical wheel. PLOT draws the hydrophobic moment plot.

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Garlic Controls

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
The image in the main window is controled by CONTROLS and by COMMANDS . This page contains description of garlic controls.

Garlic controls are reserved keys, which may be used to rotate and translate the structure, to rotate bonds, to shift selected atoms and to change the position of slab surfaces and to change the way color depends on distance from the observer. At present, the reserved keys are numeric keypad keys and four function keys (F1, F2, F3 and F4).

Some desktop environments are reserving function keys for some special purposes. This means that some function keys will fail to work properly with garlic. To avoid this problem, you can use mouse to click on dummy buttons in control window. Another solution will be to change your desktop environment settings.

Numeric keypad Function keys

For each control, five steps are available: normal, large, very large, small and very small. If you press the control without holding a modifier key (shift, alt or control), the normal step will be used.

Modifier keys may be used in combination with reserved keys to select large, very large, small or very small step. Here is the table of modifier keys:

MODIFIER KEYS STEP EXAMPLE
none Normal
shift Large
alt_shift Very large
control Small
shift_control Very small

Be sure to avoid ctrl_alt combinations, because some of these combinations may have a very interesting effect (try, for example, ctrl_alt_del or ctrl_alt_F1).

The table below contains the list of controls and the corresponding default actions upon the structure which is currently handled (held, catched). These default actions will be active in default editing mode (no editing at all, just viewing the structure). If editing atoms or bonds some of the controls will have different role. The table refers to PC (101/102) keyboard. There are slight differences between PC and terminal keyboard; three terminal keys are listed in the table (KP_F2, KP_F3, KP_Separator). If you have some exotic keyboard, use the program xshowkey to check the mapping of keys and send this list to the author: zucic@mefos.hr

KEY LOCATION ACTION
0 Numeric keypad Translate structure along z in negative direction.
1 Numeric keypad Move back (distant) slab surface along z in positive direction.
2 Numeric keypad Rotate structure clockwise around x.
3 Numeric keypad Move back (distant) slab surface along z in negative direction.
4 Numeric keypad Rotate structure clockwise around y.
5 Numeric keypad Translate structure along z in positive direction.
6 Numeric keypad Rotate structure counterclockwise around y.
7 Numeric keypad Rotate structure counterclockwise around z.
8 Numeric keypad Rotate structure counterclockwise around x.
9 Numeric keypad Rotate structure clockwise around z.
delete Numeric keypad Move front (close) slab surface along z in positive direction.
enter Numeric keypad Move front (close) slab surface along z in negative direction.
/ (slash)
KP_F2 		Numeric keypad Translate structure left.
* (asterisk)
KP_F3 		Numeric keypad Translate structure right.
- (minus) Numeric keypad Translate structure up.
+ (plus)
KP_Separator 		Numeric keypad Translate structure down.
F1 Function keys Move back (distant) color surface along z in positive direction.
F2 Function keys Move back (distant) color surface along z in negative direction.
F3 Function keys Move front (close) color surface along z in positive direction.
F4 Function keys Move front (close) color surface along z in negative direction.
Num Lock Numeric keypad Unused key.
Escape Top left corner Return to the main drawing mode (display structure).


Here are the illustrations:

PC
keyboard 		Terminal
keyboard
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Garlic Cookbook
(Garlic HOWTO's)

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This page contains a collection of garlic recipes. These recipes have nothing to do with a real garlic (@@pisum sativum). Instead, these are HOWTO's for a molecular visualization program called garlic. If you have reached this page while searching for real garlic recipes, I am sorry for this inconvenience.
Why should I consider using garlic, a command-driven Unix/Linux program?
@@
garlic-1.6/cookbook/garlic_recipe1.html0000644000000000000000000000206210361663423020130 0ustar rootroot00000000000000 Garlic Recipe #1

Garlic Recipe #1

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This page explains why you should consider using garlic, free molecular visualization program written for unix and unix compatible machines.
INGREDIENTS
(1) Some computer running Unix, Linux or some other Unix compatible system.
(2) Self-respect (arbitrary quantity, more is better).
(3) Curiosity (here too, more is better).
(4) garlic, free molecular visualization program, any version.
(5) A couple of PDB files, with data about some biologically important molecules.
RECIPE
(1) @@
(2) @@
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_\!& GNU Free Documentation License, Version 1.2, November 2002 


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If a section in the Document is Entitled "Acknowledgements",
"Dedications", or "History", the requirement (section 4) to Preserve
its Title (section 1) will typically require changing the actual
title.


9. TERMINATION

You may not copy, modify, sublicense, or distribute the Document except
as expressly provided for under this License.  Any other attempt to
copy, modify, sublicense or distribute the Document is void, and will
automatically terminate your rights under this License.  However,
parties who have received copies, or rights, from you under this
License will not have their licenses terminated so long as such
parties remain in full compliance.


10. FUTURE REVISIONS OF THIS LICENSE

The Free Software Foundation may publish new, revised versions
of the GNU Free Documentation License from time to time.  Such new
versions will be similar in spirit to the present version, but may
differ in detail to address new problems or concerns.  See
http://www.gnu.org/copyleft/.

Each version of the License is given a distinguishing version number.
If the Document specifies that a particular numbered version of this
License "or any later version" applies to it, you have the option of
following the terms and conditions either of that specified version or
of any later version that has been published (not as a draft) by the
Free Software Foundation.  If the Document does not specify a version
number of this License, you may choose any version ever published (not
as a draft) by the Free Software Foundation.


ADDENDUM: How to use this License for your documents

To use this License in a document you have written, include a copy of
the License in the document and put the following copyright and
license notices just after the title page:

    Copyright (c)  YEAR  YOUR NAME.
    Permission is granted to copy, distribute and/or modify this document
    under the terms of the GNU Free Documentation License, Version 1.2
    or any later version published by the Free Software Foundation;
    with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
    A copy of the license is included in the section entitled "GNU
    Free Documentation License".

If you have Invariant Sections, Front-Cover Texts and Back-Cover Texts,
replace the "with...Texts." line with this:

    with the Invariant Sections being LIST THEIR TITLES, with the
    Front-Cover Texts being LIST, and with the Back-Cover Texts being LIST.

If you have Invariant Sections without Cover Texts, or some other
combination of the three, merge those two alternatives to suit the
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If your document contains nontrivial examples of program code, we
recommend releasing these examples in parallel under your choice of
free software license, such as the GNU General Public License,
to permit their use in free software.
garlic-1.6/future-docs.html0000644000000000000000000000442710361656073015723 0ustar rootroot00000000000000 Garlic Documentation

Garlic Documentation

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
Garlic documentation is written in html format. The sections are listed below, with a brief description. Newbies are recommended to read at least parts of each section.
Garlic Features An overview of garlic features.
Controls Reserved keys: rotations, translations, slab and color.
Commands Detailed description of garlic commands.
Mouse Usage Mouse tricks specific for garlic.
Reference Card A quick reminder, both for newbies and experienced users.
Tutorial A collection of lessons and demonstration scripts.
Garlic Cookbook A collection of garlic recipes (garlic HOWTO's).
Options Command line options.
Configuration File Configuration file for garlic, called .garlicrc (for experts).
Environment Variables Environment variables recognized by garlic.
Molecular Structures Proteins, nucleic acids and hetero compounds.
garlic-1.6/features/0000755000000000000000000000000010403105234014365 5ustar rootroot00000000000000garlic-1.6/features/favicon.ico0000644000000000000000000000047607063421763016535 0ustar rootroot00000000000000(( garlic-1.6/features/index.html0000644000000000000000000000537510361665760016416 0ustar rootroot00000000000000 Garlic Features

Garlic Features

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This page describes the most important features of garlic, free molecular visualization program.

Garlic is free. The source code is available to everyone.
With garlic, you will be able to replace residues, to create new structures and to adjust bond angles.
Atoms may be drawn as spheres of different sizes. Bonds may be drawn as cylindrical sticks, conical sticks or as curved surfaces.
Five types of slab are available: planar, spherical, semi-spherical, cylindrical and semi-cylindrical.
The slab position and thickness are visible in a small window.
Atomic bonds as well as atoms are treated as independent drawable objects.
The atomic and bond colors depend on position. Five mapping modes are available (as for slab).
Garlic is capable to display stereo image.
Garlic is capable to display other geometric objects, like membrane, for example.
In addition to standard chemical elements, garlic allows the usage of two imaginary elements, called "jellium" (J) and "quarkonium" (Q). These elements may be used to draw some special objects. Jellium never forms any bonds, while quarkonium binds to neighboring atoms in the list (so it forms no bond, one bond or two bonds at most). Imaginary atoms may be used to adapt garlic for medical imaging, for example.
Atomic information is available for atom covered by the mouse pointer. No click required, just move the mouse pointer over the structure!
Garlic is capable to load more than one structure.
It will be possible to color the residues according to hydrophobicity and other properties.
Garlic is capable to draw Ramachandran plot, helical wheel, Venn diagram, averaged hydrophobicity, hydrophobic moment plot and sequence comparison plot.
The command prompt is available at the bottom of the main window. It is capable to display one error message and one command string.
garlic-1.6/features/garlic.gif0000644000000000000000000000465007012505402016325 0ustar rootroot00000000000000GIF87aFFɲ̻ոտĻ®ȹ@]^\ @ @P @@x((]VVP(PdVd dd\?).]@vP]dD(r?V @, @()$V@@]\ @lVi(rV@@l,( ]V) @@H]@\]@HiH(\VL @(PVd @X(,Vdd*[H\L( Vh𤝂pDPD]HxM x @(IVd( Vddx(/VrP d^ @F FR<_Pd?.@2_<  @F Fn(VGR (@,FF @PÇ#Jl8  %jܸ1A$

_\!& Bug Fixes

Bug Fixes

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This page contains the list of bugs and bug fixes.

BUG DESCRIPTION STATUS
200601071910: Some bad bonds be generated after the command REPLACE.
This happens if a new side chain falls close to neighboring chain.
Fixed by introducing the keyword REFRESH (BONDS REFRESH). 		Fixed 2006/01/04
garlic-1.6/bugfixes/garlic.gif0000644000000000000000000000465007066653377016353 0ustar rootroot00000000000000GIF87aFFɲ̻ոտĻ®ȹ@]^\ @ @P @@x((]VVP(PdVd dd\?).]@vP]dD(r?V @, @()$V@@]\ @lVi(rV@@l,( ]V) @@H]@\]@HiH(\VL @(PVd @X(,Vdd*[H\L( Vh𤝂pDPD]HxM x @(IVd( Vddx(/VrP d^ @F FR<_Pd?.@2_<  @F Fn(VGR (@,FF @PÇ#Jl8  %jܸ1A$

_\!& Lesson 10

Garlic Tutorial

Lesson 10 - The Semitransparent Plane

This lesson explains how to control the plane associated with the structure. More precisely, you will learn how to show, hide or move the plane and how to change the plane properties. The plane may be used to divide the structure in two parts, for selection and to model the cellular membrane.

It might be good idea to read the text about the command PLANE before you start with this lesson.

Step 1 - start garlic (if not started already):

garlic

Step 2 - load some the structure. In this lesson the papain structure is used, but you can use any other structure.

load 9PAP.pdb

Step 3 - make the plane visible:

pla

Now you should see an ellipsa which represents the plane. If you have not rotated the structure before making the plane visible, the ellipsa will be blue. The near edge will be bright, while the far edge will be dark.

Step 4 - rotate both the structure and the plane about x axis:

Hold the [shift] key and press 8 on numeric keypad.

Note the change of the ellipsa color: now you see another face of the plane. The blue face is treated as the upper side, while the orange-red face is treated as bottom side.

Step 5 - change the plane radius.

pla rad 20

Step 6 - Change the plane transparency (make it opaque):

pla tra 0

Step 7 - select all atoms above the plane:

sel above

Step 8 - change color for the current selection:

color cold

Step 9 - attach movement controls to the plane:

mov pla

Step 10 - rotate the plane, leaving the structure in its current orientation:

Use numeric keypad (keys 2, 8, 4 and 6) and modifier keys (shift, alt, control) to rotate the plane.

Step 11 - attach controls to both structure and plane:

mov all

Step 12 - hide the plane:

pla off

Step 13 - discard the structure:

dis all

garlic-1.6/tutorial/lesson11.html0000644000000000000000000000224310345621162016756 0ustar rootroot00000000000000 Lesson 11

Garlic Tutorial

Lesson 11 - Creating Small Structure

In this lesson you will learn how to create a short alpha helix. The structure created using the method described here may be saved as any other structure.

Before starting with this lesson, read something about the command CREATE .

Step 1 - start garlic (if not started already):

garlic

Step 2 - prepare a short sequence (polyalanine, eight residues):

seq = ala ala ala ala ala ala ala ala

Step 3 - initialize the secondary structure (let's play with an alpha helix):

str = hhhh hhhh

Step 4 - create a short alpha helix:

create

Step 5 - save your structure:

save test.pdb

Step 6 - discard the structure:

dis all

That's all!

garlic-1.6/tutorial/lesson12.html0000644000000000000000000000234410345621132016756 0ustar rootroot00000000000000 Lesson 12

Garlic Tutorial

Lesson 12 - Replace Selected Residues

In this lesson you will learn how to replace selected residues. The structure used in this example will be 1HUC.pdb, but you can use any other protein structure.

Before starting with this lesson, read something about the command REPLACE .

Step 1 - start garlic (if not started already):

garlic

Step 2 - load the structure:

load 1HUC.pdb

Step 3 - change color:

color cold

Step 4 - select the residue 26 in the chain A:

sel a/26/*/*

Step 5 - define the replacement for this residue:

seq = ser

Step 6 - replace CYS 26 by SER:

replace

Move the residue 26 closer to check the replacement (use numeric keys).

Step 7 - discard structure:

dis all

garlic-1.6/tutorial/index.html0000644000000000000000000000515610361664343016434 0ustar rootroot00000000000000 Garlic Tutorial

Garlic Tutorial

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.

Lessons

These lessons should help you to learn how to use garlic. Command are given in lowercase, in a short form, but you can use the long form as well as the uppercase letters. File names should be specified in the correct case.

RECOMMENDED USAGE: Print lessons.

In addition, you should read the pages describing garlic commands and controls !

Lesson 1 - Get familiar with garlic
Lesson 2 - Load a small structure
Lesson 3 - Playing with two structures
Lesson 4 - Drawing styles and color schemes
Lesson 5 - How to select atoms
Lesson 6 - Ramachandran plot
Lesson 7 - Helical wheel plot
Lesson 8 - Plot averaged hydrophobicity and hydrophobic moment
Lesson 9 - Venn diagram
Lesson 10 - Semitransparent plane
Lesson 11 - Create small structure
Lesson 12 - Replace selected residues

Scripts

The scripts listed below may be used to demonstrate the available drawing styles for atoms and bonds, as well as some predefined color schemes. These scripts were included into the garlic source package 28. March 2000. If you have an older package, copy these scripts to your local host. How to save the script? Go to the page which contains the script you selected. Mark and copy the script. Paste it into a local file. Recommended file names: 1: atoms.script, 2: bonds.script, 3: colors.script, 4: dance.script .

Script 1 - Drawing styles for atoms
Script 2 - Drawing styles for bonds
Script 3 - Predefined (hard-coded) color schemes
Script 4 - Dancing tryptophan
garlic-1.6/tutorial/lesson1.html0000644000000000000000000000170110345621067016677 0ustar rootroot00000000000000 Lesson 1

Garlic Tutorial

Lesson 1 - Get Familiar with Garlic

In this lesson, you will execute only one command at garlic prompt: exit, to quit the garlic session.

Start your X session. Use the terminal window to start garlic:

garlic

If garlic is in the path searched by your shell, the garlic window will appear on your screen. Try to remember what are the parts of the entire garlic window. The input window will be empty, but the image below is adapted to show the area reserved for error messages and the area reserved for commands.



When you have learned what are the main parts of the garlic window, quit your garlic session by typing exit or quit (exi or qui):

exit

garlic-1.6/tutorial/lesson2.html0000644000000000000000000000542610357045470016711 0ustar rootroot00000000000000 Lesson 2

Garlic Tutorial

Lesson 2 - Load a Small Structure

In this lesson, you will learn how to load a PDB file and how to move the structure.

Step 1 - start garlic (if not started already):

garlic

Step 2 - load tryptophan (it should be included in the source package). This command should be executed at garlic prompt:

loa trp.pdb

Step 3 - how to use the pointing device (mouse):

Move the mouse pointer over atoms and bonds and read the text which appears in the output window (bottom right corner). Note that half of each bond is assigned to each of two atoms involved in bond formation.

Step 4 - use garlic controls (i.e. the keys on numeric keypad) to rotate the structure (just a single amino acid):

First play for a while with keys 4 and 6, then with 2 and 8, and finally with 7 and 9. Try the same while holding shift (alone), control (alone), alt and shift (simultaneously) and control and shift (simultaneously). Do not try control-alt combinations, unless you are very experienced with unix and X.

Step 5 - use garlic controls (numeric keypad) to translate the structure:

PC keyboard: use /, *, -, +, 5 and 0.
Terminal keyboard: use PF2, PF3, -, comma, 5 and 0.
Repeat while holding modifier keys (alone or in combination).

Step 6 - move the structure to the screen center again:

pos 0 0 0

Step 7 - rotate and translate the structure using commands instead of controls. Try the following set of commands:

rot x 90
tra x 4
tra y -4
tra z -50
rot y 180

Step 8 - move the color surfaces. As your structure is very small, be sure to hold the control key while pressing functions keys:

Hold control key and press F1.
Hold control key and press F4.
Note that color is changing.
Hold control key and play with F1, F2, F3 and F4 for a while.

Step 9 - move the slab surfaces. As your structure is very small, be sure to hold the control key:

Hold control key and 3 (numeric keypad). Repeat until some atoms and bonds disappear.
Hold control key and play with 1, 3, decimal separator (next to 0) and enter for a while. Note that (in control window) visible atoms are red and invisible atoms are dark cyan.

Step 10 - discard loaded structure:

dis all

garlic-1.6/tutorial/lesson3.html0000644000000000000000000000346110345621044016701 0ustar rootroot00000000000000 Lesson 3

Garlic Tutorial

Lesson 3 - Playing with Two Structures

In this lesson, you will learn how to work with two or more structures. The original source package contains two PDB files: trp.pdb and phe.pdb. Each contains a single amino acid: trp.pdb = tryptophan, phe.pdb = phenylalanine. In this lesson, tryptophan will be colored blue, while phenylalanine will be colored red. Note the role of the command cat (catch).

Step 1 - start garlic (if necessary):

garlic

Step 2 - load trypthophan:

loa trp.pdb

Step 3 - change TRP color to blue:

col blue

Step 4 - load phenylalanine:

loa phe.pdb

Step 5 - change PHE color to red:

col red

Two structures will be distinguished by color and by the identifier: tryptophan is treated as structure number 1, and phenylalanine is treated as structure number 2. Two structures are now overlapping.
Step 6 - move tryptophan to the left:

cat 1
pos -5 0 0

Step 7 - move phenylalanine to the right:

cat 2
pos 5 0 0

Step 8 etc. - use the command cat (catch) to rotate structures one by one:

Use cat 1 and cat 2 to catch and rotate structures, one by one.
Translate both structures to the position where they will be overlapped, but do not use keyword pos!

When finished, discard loaded structures:

dis all
garlic-1.6/tutorial/lesson4.html0000644000000000000000000000522610357045506016711 0ustar rootroot00000000000000 Lesson 4

Garlic Tutorial

Lesson 4 - Drawing Styles and Color Schemes

In this lesson, you will learn different drawing styles, used for atoms and bonds. Note that garlic uses separate styles for atoms and bonds. You will also try some predefined color schemes. Use the X server which offers 24 bits per pixel, if possible.

As you will often reuse some commands, just with a different argument, note that garlic has a history buffer, where commands which were previously used are stored. The arrow keys may be used to recall one of these commands.

Use the "UP" arrow to scan the history buffer backwards, "DOWN" arrow to scan it upwards, "LEFT" arrow to move the insertion mark left and "RIGHT" arrow to move the insertion mark to the right (if possible, of course). Backspace (or delete, if you have some unusual keyboard mapping) may be used to remove characters.

Step 1 - start garlic (if this wasn't done before):

garlic

Step 2 - load trypthophan and bring it closer to you:

loa trp.pdb
pos 0 0 -150

Step 3 - make bonds invisible (i.e. set bond thickness to zero):

bon 0

Step 4 - learn which drawing styles are available for atoms.
Hint: use the arrow key "UP" to call the previous command.

ato 1
ato 2
ato 3
ato 4
ato 5
ato 6
ato 7
ato bal
ato ba2
ato big
ato bi2
ato spa
ato sp2

Step 5 - hide atoms:

ato 0

Step 6 - learn which drawing styles are available for bonds.
Hint: use the arrow key "UP" to call the previous command.

bon 1
bon 2
bon 3
bon 4
bon 5

Step 7 - learn how to draw balls and sticks:

bon 4
ato bal

Step 8 - try some predefined color schemes.
Hint: use the arrow key "UP" to call the previous command.
Warning: Always use the full color scheme name (do not abbreviate)!

col red
col green
col blue
col yellow
col cyan
col magenta
col white
col yellow-green
col cyan-green
col cyan-blue
col magenta-blue
col magenta-red
col orange
col hot
col cold
col cpk

Step 9 - discard loaded structure:

dis all

garlic-1.6/tutorial/lesson5.html0000644000000000000000000000476010345621025016705 0ustar rootroot00000000000000 Lesson 5

Garlic Tutorial

Lesson 5 - How to Select Atoms

In this lesson, you will learn how to select atoms. The command select (or whatever command plays this role) is one of the most important commands in every molecular visualization program.

For this lesson, you will need a true protein structure, not just a single amino acid as in previous lessons.

Step 1 - obtain the protein structure:

Use you web browser to access The Protein Data Bank (www.rcsb.org) .
Type 1HUC into the small search field. Start the search and wait for the answer.
Choose the option "Download/Display File".
Finally, choose file format "PDB", compression "none" in the section "Download the Structure File" and wait.

Step 2 - start garlic (if necessary):

garlic

Step 3 - load the structure. You should have the file 1HUC.pdb somewhere in the path searched by garlic (if you defined the environment variable MOL_PATH), or in your current working directory.

loa 1HUC.pdb

Step 4 - draw backbone, to simplify the picture:

bac

Step 5 - use different colors for different chains:

col chain

Step 6 - select chain A, draw balls and sticks and change color scheme to CPK:

sel a/*/*/*
bac off
bon 4
ato bal
col cpk

Step 7 - redefine the internal system origin (the rotation center) and move chain A to the screen center:

cen
pos 0 0 0

Step 8 - restrict the selection to aliphatic amino acids and change color to yellow (chain A):

res ali
col yellow

Step 9 - select all, make it visible, show only backbone but reduce the backbone thickness:

sel *
sho
bac 3

Step 10 - hide side chains:

Step 10 - select cysteine residues, but only for chains A and C; make them visible, use spacefill style:

sel a,c/*/cys/*
show
ato spa

Step 11 - discard loaded structure:

dis all

garlic-1.6/tutorial/lesson6.html0000644000000000000000000000315010345621016016676 0ustar rootroot00000000000000 Lesson 6

Garlic Tutorial

Lesson 6 - Draw Ramachandran Plot

In this lesson, you will learn how to prepare Ramachandran plot. This plot shows the pairs of dihedral angles phi and psi. You can find more details here .

You can use any protein structure for this lesson. Here we are going to use 1HUC.pdb, retrieved in the previous lesson.

Step 1 - start garlic (if not started already):

garlic

Step 2 - load the structure. You should have the file 1HUC.pdb somewhere in the path searched by garlic (if you defined the environment variable MOL_PATH), or in your current working directory.

loa 1HUC.pdb

Step 3 - prepare Ramachandran plot.

rama

Step 4 - Identify some residues.

Use mouse (pointing device) to identify individual residues. Just move the pointer over the choosen residue symbol and you will see the residue name, serial number and dihedral angles in the output window.

Step 5 - draw Ramachandran plot for glycines.

sel gly
rama sel

Step 6 - return to the main drawing mode. You can either type the command rama off or hit the escape key.

rama off

Step 7 - discard loaded structure:

dis all

garlic-1.6/tutorial/lesson7.html0000644000000000000000000000761410345621007016710 0ustar rootroot00000000000000 Lesson 7

Garlic Tutorial

Lesson 7 - Draw Helical Wheel

In this lesson, you will learn how to prepare the helical wheel plot. This plot may be used to identify amphipatic segments in a protein sequence, i.e. the amphipatic helices. In this lesson, the solved structure will be used for demonstration. For more details, read this (WHEEL command description).

You can use any protein structure for this lesson. In this example 1HUC.pdb is used, though you can use any protein structure.

Step 1 - start garlic (if not started already):

garlic

Step 2 - load the structure. You should have your PDB file (here 1HUC.pdb) somewhere in the search path (if you defined the environment variable MOL_PATH), or in your current working directory.

loa 1HUC.pdb

Step 3 - select all atoms except hetero atoms. If this is not done the hetero "residues" (i.e., solvent molecules) will corrupt the helical wheel plot. The trick is to select hetero residues, and then to select complement. You don't have to hide hetero residues, so you can skip the command hide.

sel het
hide
sel com

Step 4 - check the number of chains in human cathepsin B. If there are two or more chains, the residue serial number should not be used as unique residue identifier.

color chain

Step 5 - there are obviously four chains. Hide all chains except B. Hide everything, after that select only the chain B and make it visible. Hetero residues will not be included into selection, so the step 3 was in fact unnecessary.

sel all
hide
sel b/*/*/*
show

Step 6 - try to find one helix at the chain B surface. Helices may be easily recognized if using backbone representation of the protein. It is also practical to use the geometric center of the chain B as the rotation center, and to move it to the screen center.

bac
cen
pos 0 0 0

Step 7 - play with the chain B to find this helix:
76 77 78 79 80 81 82 83 84 85 86
PRO ALA GLU ALA TRP ASN PHE TRP THR ARG LYS

Step 8 - copy the sequence of the chain B to the main sequence buffer. Note that the helical wheel plot uses the sequence which is stored in the main sequence buffer. Right now this buffer is empty!

seq from 1

Step 9 - draw helical wheel for residues from 76 to 86:

wheel 76-86

Step 10 - return to the main drawing mode. Hit the escape key or type the following command:

whe off

Step 11 - discard loaded structure:

dis all

Step 12 - clear the main sequence buffer:

seq reset

Do not forget that for helical wheel plot, the main sequence buffer should be initialized!
garlic-1.6/tutorial/lesson8.html0000644000000000000000000000411710345620777016721 0ustar rootroot00000000000000 Lesson 8

Garlic Tutorial

Lesson 8 - Draw Averaged Hydrophobicity and Hydrophobic Moment

In this lesson, you will learn how to draw the averaged hydrophobicity and hydrophobic moment for the sequence which is stored in the main sequence buffer.

In this lesson no atomic coordinates will be used. The only information available will be the sample protein sequence stored in FASTA format. The sample sequence may be found in the original garlic package. Save this sequence as ASCII text, not as html.

In this example, mouse may be used to identify residues and their imminent sequence neighborhood. The residue information will be visible in the output window (bottom right corner), while the neighboring residues will be listed in the upper part of the main window. The central residue (the one choosen by the mouse) will be enclosed in a small rectangle.

Step 1 - start garlic (if not started already):

garlic

Step 2 - load the sequence.

seq load sample.fasta

Step 3 - plot the averaged hydrophobicity. Use mouse to identify the residues in the plot. The residue information will be visible in the output window (bottom right corner).

plot hyd

Step 4 - plot the hydrophobic moment. Use mouse to identify residues.

plot mom

Step 5 - plot both averaged hydrophobicity and hydrophobic moment. Note that the numeric value in the output window will be equal to the hydrophobic moment in this case!

plot hyd mom

Step 6 - return to the main drawing mode. You can either type the command plot off or hit the escape key.

plot off

Step 7 - clear the sequence buffer. You can skip this step, it is not very important.

seq reset

garlic-1.6/tutorial/lesson9.html0000644000000000000000000000317210345621117016707 0ustar rootroot00000000000000 Lesson 9

Garlic Tutorial

Lesson 9 - Venn Diagram

In this simple lesson, you will learn how to prepare the Venn diagram with some residue counts. There is nothing special in this routine and experts will not find it very useful. It is primarily intended for students and other newbies, which are interested in the residue composition of the given protein.

The only information required to prepare the Venn diagram is the protein sequence. In this example, the sequence will be extracted from PDB data. Another approach will be to load the sequence from some FASTA file. The PDB file used here is 1HUC.pdb, but you can replace it with any PDB file which contains the protein structure.

Step 1 - start garlic (if not started already):

garlic

Step 2 - load the structure.

load 1HUC.pdb

Step 3 - discard all hetero atoms:

sel het
sel com

Step 4 - restrict your selection to chains A and B:

res a,b/*/*/*

Step 5 - extract sequence:

seq from 1

Step 6 - draw Venn diagram with residue counts:

venn

Step 7 - discard the structure:

dis all

Step 8 - clear the sequence buffer. You can omit this command.

seq reset

garlic-1.6/tutorial/script1.html0000644000000000000000000000426610361664430016710 0ustar rootroot00000000000000 Script 1

Garlic Tutorial

Script 1 (atoms.script) - Drawing styles for atoms

This script shows the available drawing styles for atoms. Note that nothing is visible for style "0" (row one, column one)! The file trp.pdb is required as input. You can mark, copy and paste this script to your local host (create the file atoms.script).

Type the following command at garlic prompt:

exe atoms.script

The sample image is at the bottom of this page. 

# Show all drawing styles used to draw atoms. Bonds are hidden!
# This script requires garlic version 1.2 or later!

# Atom style 0:
load trp.pdb
pos -24 -15 0
ato 0
bon 0
tag "0"

# Now inform user that refreshing is off:
title 1 50 50 "Please be patient ..."

# Switch refreshing off:
refresh off

# Atom style 1:
load trp.pdb
pos -12 -15 0
ato 1
bon 0
tag "1"

# Atom style 2:
load trp.pdb
pos 0 -15 0
ato 2
bon 0
tag "2"

# Atom style 3:
load trp.pdb
pos 12 -15 0
ato 3
bon 0
tag "3"

# Atom style 4:
load trp.pdb
pos 24 -15 0
ato 4
bon 0
tag "4"

# Atom style 5:
load trp.pdb
pos -24 -5 0
ato 5
bon 0
tag "5"

# Atom style 6:
load trp.pdb
pos -12 -5 0
ato 6
bon 0
tag "6"

# Atom style 7:
load trp.pdb
pos 0 -5 0
ato 7
bon 0
tag "7"

# Atom style bal:
load trp.pdb
pos 12 -5 0
ato bal
bon 0
tag "bal (ball)"

# Atom style ba2:
load trp.pdb
pos 24 -5 0
ato ba2
bon 0
tag "ba2"

#Atom style small:
load trp.pdb
pos -24 5 0
ato sma
bon 0
tag "sma (small)"

# Atom style sm2:
load trp.pdb
pos -12 5 0
ato sm2
bon 0
tag "sm2"

# Atom style covalent:
load trp.pdb
pos 0 5 0
ato cov
bon 0
tag "cov (covalent)"

#Atom style co2:
load trp.pdb
pos 12 5 0
ato co2
bon 0
tag "co2"

#Atom style spacefill:
load trp.pdb
pos -24 15 0
ato spa 
bon 0
tag "spa (spacefill)"

#Atom style sp2:
load trp.pdb
pos -12 15 0
ato sp2
bon 0
tag "sp2"

#Atom style big:
load trp.pdb
pos 0 15 0
ato big
bon 0
tag "big"

#Atom style bi2:
load trp.pdb
pos 12 15 0
ato bi2
bon 0
tag "bi2"

# Hide the title:
title 1 off

# Switch refreshing on:
refresh
garlic-1.6/tutorial/script2.html0000644000000000000000000000261510361664416016711 0ustar rootroot00000000000000 Script 2

Garlic Tutorial

Script 2 (bonds.script) - Drawing styles for bonds

This script shows the available drawing styles for bonds. The file trp.pdb is required as input. You can mark, copy and paste this script to your local host (create the file bonds.script).

Type the following command at garlic prompt:

exe bonds.script

The sample image is at the bottom of this page. 

# Show all drawing styles used to draw bonds. Atoms are hidden,
# except for nice bonds!
# This script will work if you use default .garlicrc script.
# This script requires garlic version 1.2 or later!

# Bond style 1:
load trp.pdb
pos -12 -6 -40
ato 0
bon 1
tag "1"

# Now inform user that refreshing is off:
title 1 50 50 "Please be patient ..."

# Switch refreshing off:
refresh off

# Bond style 2:
load trp.pdb
pos 0 -6 -40
ato 0
bon 2
tag "2"

# Bond style 3:
load trp.pdb
pos 12 -6 -40
ato 0
bon 3
tag "3"

# Bond style 4:
load trp.pdb
pos -12 6 -40
ato 0
bon 4
tag "4"

# Bond style 5:
load trp.pdb
pos 0 6 -40
ato 0
bon 5
tag "5"

# Bond style nice:
load trp.pdb
pos 12 6 -40
ato co2
bon nice
tag "nic (nice)"

# Hide the title:
title 1 off

# Switch refreshing on:
refresh
garlic-1.6/tutorial/script3.html0000644000000000000000000000362210361664403016705 0ustar rootroot00000000000000 Script 3

Garlic Tutorial

Script 3 (colors.script) - Predefined color schemes

This script shows some selected color schemes. All schemes shown here are hard-coded in the program. The file trp.pdb is used. You can mark, copy and paste this script to your local host (create the file colors.script).

Type the following command at garlic prompt:

exe colors.script

The sample image is at the bottom of this page. 

# Show predefined color schemes, version 1.2 and later versions.
# This script will work if you use default .garlicrc script.
# This script requires garlic version 1.2 or later!

load trp.pdb
pos -18 -15 0
ato sp2
bon nice
color red

# Now inform user that refreshing is off:
title 1 50 50 "Please be patient ..."

# Switch refreshing off:
refresh off

load trp.pdb
pos -6 -15 0
ato sp2
bon nice
color green

load trp.pdb
pos 6 -15 0
ato sp2
bon nice
color blue

load trp.pdb
pos 18 -15 0
ato sp2
bon nice
color yellow

load trp.pdb
pos -18 -5 0
ato sp2
bon nice
color cyan

load trp.pdb
pos -6 -5 0
ato sp2
bon nice
color magenta

load trp.pdb
pos 6 -5 0
ato sp2
bon nice
color white

load trp.pdb
pos 18 -5 0
ato sp2
bon nice
color yellow-green

load trp.pdb
pos -18 5 0
ato sp2
bon nice
color cyan-green

load trp.pdb
pos -6 5 0
ato sp2
bon nice
color cyan-blue

load trp.pdb
pos 6 5 0
ato sp2
bon nice
color magenta-blue

load trp.pdb
pos 18 5 0
ato sp2
bon nice
color magenta-red

load trp.pdb
pos -18 15 0
ato sp2
bon nice
color orange

load trp.pdb
pos -6 15 0
ato sp2
bon nice
color hot

load trp.pdb
pos 6 15 0
ato sp2
bon nice
color cold

load trp.pdb
pos 18 15 0
ato sp2
bon nice
color cpk

# Hide the title:
title 1 off

# Switch refreshing on:
refresh
garlic-1.6/tutorial/script4.html0000644000000000000000000000147510361664370016715 0ustar rootroot00000000000000 Script 4

Garlic Tutorial

Script 4 - Dancing tryphophan

Just try it!

Type the following command at garlic prompt:

exe dance.script 

load trp.pdb
bon 4
pos 0 0 1000
tra z -50
rot y 20
tra z -50
rot y -20
tra z -50
rot y 20
tra z -50
rot y -20
tra z -50
rot y 20
tra z -50
rot y -20
tra z -50
rot y 20
tra z -50
rot y -20
tra z -50
rot y 20
tra z -50
rot y -20
tra z -50
rot y 20
tra z -50
rot y -20
tra z -50
rot y 20
tra z -50
rot y -20
tra z -50
rot y 20
tra z -50
rot y -20
tra z -50
rot y 20
tra z -50
rot y -20
tra z -50
rot y 20
tra z -50
rot y -20
tra z -50
rot y 20
tra z -50
rot y -20
tra z -50
rot y 20
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What is Garlic?

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
Garlic is a free molecular viewer and editor written for Unix and Unix clones, like GNU/Linux.
Garlic was born September 30, 1998. At that time I needed a good molecular visualization program and almost the only thing at hand was RasMol. I had some hard time with RasMol so I tryed to adapt it to my needs. However, I realized that it is very hard to read and change RasMol source code, so I decided to write my own molecular visualization program.

Further, I decided to learn programming for the X window system, and this is my first serious program written for X11.

Since 1997 I use GNU/Linux software, so I concluded that it would be fair to add something useful and modern to the existing collection of free software because this software significantly improved my working conditions.

Garlic was forgotten few times, for months, as I had some other things to do, but now it is finaly operative.

Though the version number of the current version (1.6) is not very high, the program is very stable and robust, at least on systems which were available for testing here at University of Osijek, Croatia.
The name garlic was choosen because my original intention was to write a modular program, which will be capable to call a number of modules via system calls. In fact, I did the opposite thing: garlic now consists of a single unit which integrates all functions. Anyway, back in 1998 I thought that this program will be similar to garlic - a small core with a number of units packed around this core. I also like garlic.

Later, I reallized that program name may be reinterpreted as follows:
G stands for GNU (license),
AR for analysis and rendering,
LI for Linux,
C for C (the computer language).

Who might be interested to use this program?

Students
As garlic is free and open, students may find it interesting as a learning tool. Garlic may be installed on a cheap, no-name PC (running a free Linux distribution) or even on a laptop (very handy!).

University assistents and professors
It is somewhat delicate to use commercial software for lectures and seminars (assignments). In their later carrier students may be boosted toward the software which they used during their study just because they have some experience with it. Universities should not influence the software market by choosing certain commercial product just because it is cheap or for some other reason suitable for university assignments.

Professionals
Many professionals would like to use some molecular visualization program at home or on a portable computer. Some others may be interested to adapt the program to their own needs. Software makers are unwilling to give the source code and to allow modification of their product. They also try to drain as much money as possible for additional (home) copies. Anyone wishing to cut the rope is invited to use and modify garlic, but the final product has to remain free and open, in agreement with the GNU General Public License .

Others
Anyone interested to learn something about proteins, DNA and some other molecules may find garlic useful.

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Free Molecular Visualization Programs
for Unix and/or Linux

free molecular visualization programs, free molecular viewers, list of molecular visualization programs, list of molecular viewers, molecular rendering, protein visualization tools, molecular visualization resources, download page, download source, download executable, download binary, AMMP, B, Bodil, BRAGI, Cn3D, Deep View Swiss-PDBViever, DINO, Flex, garlic, gdpc, Ghemical, gOpenMol, Grasp, ICMlite, Jmol, Kinemage, mdxvu, Mercury, MOIL-View, MOLDEN, MOLEKEL, MOLMOL, MolScript, Moviemol, NAMOT, QMOL, PREPI, PyMOL, RasMol, Raster3D, spock, VEGA, Viewmol, WinMGM, VMD, XMakemol, XmMol, XMol, Ymol, biological macromolecule, protein structure, DNA structure, PDB, Unix, Linux, free software download, open source software, Damir Zucic.
This page contains the list of free molecular visualization programs, complete with links. Only freely available programs which run on Unix or Unix compatible platform are listed. Some of these programs are available only as binary code for some specific platform(s).

Most programs were found using AltaVista, Lycos and Google, while some others were suggested by readers of this list. Thanks to all of them!

Some of the programs listed below have a very limited license. Be sure to read the license before using such program!

The time-limited trial versions of commercial programs were omitted from the list.

The programs listed here were not evaluated and no comparison was made.

If you have your own free molecular visualization program for Unix or Linux, or if you know for such program which is not included in the list below, please send an e-mail message to Damir Zucic (zucic@mefos.hr) . Please send corrections and changes to the same address.
Last updated: June 10, 2003.

The information contained here was valid before that day. As developing is going on, it is likely that some additional libraries may become necessary for some of the programs listed here. However, it is almost certain that libraries listed here will be required in future versions too.
PROGRAM LIBRARIES REQUIRED PROGRAM TYPE / LICENSE
AMMP libc, libm, libX11, libXt, libXext, libXmu,
libXm, libSM, libICE, libNoVersion 		Stand alone program,
modified GNU GPL license.
B
(where is it now?) 		Java based package. Your browser should support
Java Virtual Machine.
Bodil libc, libm, libstdc++, libgcc_s, libqt,
libX11, libXext + some other libraries
which are shipped with the program. 		Stand alone program,
free for academic use.
BRAGI It seems that this program
is still under development. 		The license has to be negotiated.
Chimera Needs Python, Tcl/Tk, Tix, Togl, PIL,
Numeric, Grail, Pmw, msms, VRML,
JPEG, Info-ZIP, TR, ScientificPython;
still under development. 		Stand alone program,
online registration required.
Requires many libraries.
Cn3D libc, libm, libX11, libXt, libXext,
libXmu, libXp 		Both browser plug-in
and stand alone program.
Deep View
Swiss-PdbViewer 		libc, libm, libX11, libXt, libXext,
libXmu, libXi, libXp, libMesaGL,
libMesaGLU, libpthread, libz 		Stand alone program,
IRIX or Linux required.
DINO libc, libm, libX11, libXt, libXext,
libXmu, libXi, libgdbm, libGL, libGLU 		Stand alone program.
Flex libc, libm, libX11,
libxview, libolgx, xlibflexdraw 		Stand alone, binaries for
DEC/alpha, DEC/MIPS,
IBM RS, SGI, Sun.
garlic libc, libm, libX11 Stand alone program,
GNU GPL license.
Ghemical requires g++ compiler, f2c compiler, glut,
GNOME, gtkglarea, mpich, MPQC ... 		Stand alone program,
GNU GPL license.
gdpc libc, libm, libX11, libXext, libXi,
libgtk, libgdk, libgmodule, libglib,
libdl, libpthread 		Stand alone program.
gOpenMol libc, libm, libX11, libXt, libXext,
libXmu, libXi, libdl, libXaw, Tcl/Tk,
+ Mesa or Open GL libraries 		Graphics interface to the
OpenMol set of programs;
GNU GPL license.
Grasp This program has been written
for Silicon Graphics computers. 		Under special circumstances,
the $500 fee will be waived.
ICMlite Binaries: SGI, DEC Alpha, SUN, Linux;
libc, libm, libX11, libXt, libXext,
libXmu, libSM, libICE, libpthread 		Stand alone program,
free for academic use.
Jmol Java-based application. Stand alone program
(Java-based application).
Kinemage libc, libm, libX11,
libXt, libXm 		Stand alone program.
mdxvu libc, libm, libX11,
precompiled for some systems 		Stand alone program.
Mercury libc, libm, libX11, libXt, libXext, libXmu,
libXi, libXft, libXRender, libMesaGLU,
libMesaGL, libSM, libICE, libjpeg,
libpng, libmng, libdialogs, libwidgets,
libqt, libqtspecific, libguiindep,
libtoolkit, libcsd, libCif, libKCC-eh,
libz, libfreetype, liblcms 		Stand alone program, read
conditions of use carefully.
MOIL-View FORTRAN program, binaries available
for Silicon Graphics workstations. 		Stand alone program,
registration expected.
MOLDEN FORTRAN 77,
libc, libm, libX11 		Stand alone,
free for academic use.
MOLEKEL libc, libm, libX11, libXext, libXmu, libXi,
libMesaGL, libMesaGLU, libtiff, libjpeg 		Precompiled for SGI IRIX,
Linux PC and SunOS,
registration required.
MOLMOL libc, libm, libX11, libXt, libXext, libXm,
libGL, libGLU, libGLcore, libC, libgen,
libgen, libpng, libz 		Stand alone, binaries for
DEC/MIPS, DEC/alpha,
SGI, SPARC and RS/6000.
MolScript libc, libm, libX11, libXt, libXext, libXmu,
libGL, libGLU, libGLcore, libmedia, libC,
libgen, libvice, libjpeg, libpng, libz 		Stand alone, online
registration required.
Moviemol libc, libm, libX11, libXext,
libYgl or OpenGL
Stand alone program.
NAMOT libc, libm, libX11,
libxview, libolgx 		Stand alone program.
QMOL libc, libm, libX11, libXt, libXext,
libXm, libGLw, libMesaGL, libMesaGLU,
libstdc++, libSM, libICE 		Stand alone program.
PREPI Precompiled binary for
Silicon Graphics IRIX. 		Stand alone, registration
required (written agreement).
PyMOL libc, X libs, libpng, zlib, python, Mesa Requires Python, an intepreted
programming language.
RasMol libc, libm, libX11
libXext, libXi 		Stand alone program.
Raster3D Mixed FORTRAN 77 and C code,
requires both compilers. 		Stand alone program.
spock libc, libm, libX11, libXt, libXext, libXmu,
libXm, libXi, libXpm, libMesaGL,
libMesaGLU, libSM, libICE, libjpeg,
libtiff, libcrypt, libz, libNoVersion 		Stand alone program,
free for some users,
registration required.
VEGA libc, libm, libz, liblocale No OpenGL support
for Linux version.
Viewmol libc, libm, libX11, libXt, libXext, libXm,
libXi, libXp, libGL, libGLU, libtiff,
libtiff, libpthread, libdb, libdl, libutil 		Graphical front end for
comp. chemistry programs,
GNU GPL license.
WinMGM libc, libm, libMesaGL, libsubplex,
libchelpers, libmgmcalctools,
libmolecules, libmolenergy 		Stand alone, some custom
libraries required.
VMD Statically linked binaries for AIX,
HPUX, IRIX, Linux, Solaris and TRU64. 		Stand alone, online
registration required.
XMakemol libc, libm, libX11, libXt,
libXm, libXpm, libGL, libGLU 		Stand alone program,
GNU GPL license.
XmMol libc, libm, libX11, libXt, libXext,
libXm, libXp, libSM, libICE;
Motif or openMotif required. 		Free for academic use,
registration required
(written agreement).
XMol Precompiled binaries for SGI,
Sun-3, Sun-4 and RS/6000. 		Some other binaries may be
found in some other archives;
development seems to be halted.
Ymol libc, libm, libX11,
libXext 		Stand alone program.
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_\!& Garlic Versions

Garlic Versions

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, unix, linux, free software download, open source software, Damir Zucic.
This page contains a list of garlic versions, with links.
1.0 March 2000.
1.1 February 2001.
1.2 September 2002.
1.3 April 2003.
1.4 October 2004.
1.5 January 2006.
1.6 Under development, initiated 2006/01/21.
garlic-1.6/options/0000755000000000000000000000000010403105234014242 5ustar rootroot00000000000000garlic-1.6/options/favicon.ico0000644000000000000000000000047607064164573016416 0ustar rootroot00000000000000(( garlic-1.6/options/index.html0000644000000000000000000002347710361662326016271 0ustar rootroot00000000000000 Garlic Command Line Options

Garlic Command Line Options

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This page explains the command line options. To see this list, type one of the following commands:

garlic -h
garlic -h | less 

=========================================================================
               Garlic - free molecular viewer and editor
=========================================================================

Garlic  was written by  Damir Zucic  (zucic@mefos.hr)  as a complement to
other molecular  visualization  programs,  like rasmol  (by Roger Sayle).
It was written to simplify  the analysis of membrane proteins, but it can
be used as general purpose molecular visualization program, provided that
molecular coordinates are available in  PDB format, version 2.1 or older.
Garlic may also be used to analyze protein sequences.

Some of the  features, which  distinguish this program from  others, are:
(1) Coordinates, labels and  other data are  automatically displayed  for
    the atom nearest to the current pointer (mouse) position.
(2) Additional numeric data,  like  hydrophobicity, may be associated  to
    each amino acid. The  whole  structure  may be  colored  according to
    these values.
(3) Selection mechanism is different.
(4) Two bonds at different distance from  observer have different colors.
-------------------------------------------------------------------------
Usage:              garlic [true_garlic_options] [X11_options] [filename]
-------------------------------------------------------------------------
Command line options may be divided in two groups: true (specific) garlic
options and X11 options.  Options may be given in any order.  All options
and hard-coded  default values are listed  in the table  below.  For each
parameter, the value defined through command line is used,  if available.
If not, the value defined in .garlicrc file is used. If .garlicrc file is
not  available,  or there is  no corresponding  entry in  this file,  the
hard-coded default value is used.  The sample  .garlicrc file included in
the original package contains  the values equal to  hard-coded  defaults.
-------------------------------------------------------------------------
garlic option:        Description:
-------------------------------------------------------------------------
-h, --help            Print help and exit.
-v, --version         Print version and exit.
-r, --register        Register garlic:  inform author that  your site has
                        garlic installed and that someone is going to use
                        this program. By registering, you are encouraging
                        author to continue development of garlic. You can
                        also help  author to  ensure support  for further
                        development. This option sends an e-mail message,
                        containing only the e-mail message header and the
                        word 'Hi!', to zucic@garlic.mefos.hr. Please type
                        garlic -r   if you are going to use this program.
                        If your system is  not connected to the Internet,
                        you can send short e-mail from some other system.
-nosys                Hide the coordinate system icon  (top left corner).
-no-control           Hide the control window (upper right corner).
-stereo               Display stereo image.
-slab mode            Default slab mode.  Available slab modes are:  off,
                        planar (default),  sphere, half-sphere,  cylinder
                        and half cylinder.
-fading mode          Default color fading mode.  Available  modes:  off,
                        planar (default),  sphere, half-sphere,  cylinder
                        and half cylinder.
-as number            Default atom drawing style (hard-coded default: 2).
-bs number            Default bond drawing style (hard-coded default: 3).
-fs number            Default number of  color fading surfaces.  Parallel
                        planes, concentric spheres or conc. cylinders may
                        be used as  fading surfaces.  Three  RGB triplets
                        are assigned to each surface. Surfaces are evenly
                        spaced;  at least one and at most eight should be
                        defined. At least three colors  (left, middle and
                        right) are assigned to  each visible atom.  These
                        three colors are based on the position of a given
                        atom  relative to  the nearest  fading surface(s)
                        and on colors assigned to these surfaces.  Colors
                        are combined using linear weighting.
-lc[i] color          Left color at the  i-th surface;  i is between zero
                        and seven.  The color string should be  compliant
                        with X11R5.  Blue, for example,  may be specified
                        as blue or as RGB:0000/0000/FFFF etc. For example
                        -lc4 RGB:BBBB/8888/4444  defines  the left  color
                        at the surface whose index is equal to four.
-mc[i] color          Middle color at the i-th surface.
-rc[i] color          Right color at the i-th surface.
-pc, --print-config   Print configuration data and exit.
-pcn                  Print cursor names to stdout and exit.
-log logfile          Write commands and messages to  log file.  The file
                        will be created in the current working directory.
                        If this is not possible, log file will be created
                        in users home directory.
-------------------------------------------------------------------------
X11 option:           Description:
-------------------------------------------------------------------------
-display displayname  X server to contact.
-geometry geom        Window geometry (default: almost the whole screen).
-bg color             Main window background color (default is black).
-fg color             Main window foreground color (default: white).
-fn fontname          Text font; (default is 10x20).
-tbg color            Text background color (default is black).
-tfg color            Text color (default is white).
-cursor cursorname    Cursor name; see  /usr/include/X11/cursorfont.h for
                         names; remove the XC_ prefix.
-------------------------------------------------------------------------
filename:             The input file name.  Full pathname may be used. If
                      filename does not contain the path, garlic will try
                      to find  the specified file in  the current working
                      directory.  If the first attempt  to open  the file
                      fails,  the filename  is appended to the content of
                      the environment  variable  MOL_DIR  for  the second
                      attempt.  If this fails too, garlic will search all
                      directories  specified in  the environment variable
                      MOL_PATH.
-------------------------------------------------------------------------
Personal initializations may be written to .garlicrc file. Normally, this
file should be kept in users home directory.  Note that this is  not  the
first directory to be searched for  .garlicrc file! Up to seven pathnames
are tryed in the following order:

.garlicrc                       .garlicrc  in current  working directory.
$HOME/.garlicrc                 .garlicrc in home directory.  This is the
                                   recommended location.
$HOME/garlic/.garlicrc          ./garlicrc,  subdirectory garlic of users
                                   home directory.
/usr/share/garlic/.garlicrc     ./garlicrc in  /usr/share/garlic (Linux).
/etc/garlicrc                   garlicrc in /etc, Debian Linux; note that
                                   file name is  garlicrc  in  this case!
/usr/local/lib/garlic/.garlicrc .garlicrc  in  /usr/local/lib/garlic dir.
/usr/lib/garlic/.garlicrc       .garlicrc in /usr/lib/garlic; this is the
                                   last attempt; if it failes, hard-coded
                                   default values will be used.
-------------------------------------------------------------------------
Environment variables:
-------------------------------------------------------------------------
MOL_DIR               Defines where to look for the specified file if not
                         found in the current working directory.
MOL_PATH              The list of directories to be searched.  It is used
                         if attempt with MOL_DIR failes  or if MOL_DIR is
                         not defined. Use space  or colon (:) to separate
                         directory names. MOL_PATH is quite useful; it is
                         recommended to define  this environment variable
                         through  .login,  .bashrc or  some other script.
                         MOL_PATH  is more useful  than  MOL_DIR so it is
                         recommended  to define only  MOL_PATH  variable.
DISPLAY               X server to which  the program should be connected.
-------------------------------------------------------------------------
garlic home page:                           http://garlic.mefos.hr/garlic
Damir Zucic home page:                      http://garlic.mefos.hr/zucic
E-mail:                                     zucic@mefos.hr
=========================================================================
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Compiling Garlic on Apple McIntosh

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
Here you can read how to compile garlic for Apple MacIntosh running Xtools from Tenon . I would like to thank Chris from Macinchem for this contribution. Chris is also porting other chemistry related programs to Apple MaxIntosh. Please visit his Macinchem site:
http://www.macinchem.fsnet.co.uk/macosx.htm
If you don't have access to Chris site, here is the important part: 

... This was my first port, it requires X-Tools from Tenon.
Minor modifications of the Makefile allow compilation ...

        CC = gcc 

        CCOPT = -O -I/usr/X11R6/include

        #CCOPT = -O3

        #CCOPT = -ansi -pedantic -O -Wall -Wstrict-prototypes -g3

        headERS = defines.h typedefs.h

        LIBPATH = -L/usr/X11R6/lib

        LINKOPT = -lX11 -lm
garlic-1.6/install/index.html0000644000000000000000000001501110364510740016220 0ustar rootroot00000000000000 Garlic Installation

Garlic Installation

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
Package maintainers, please read this text first!
Garlic is the most portable molecular viewer/editor in the Unix world, because the only libraries required by this program are the standard C library (libc), the standard math library (libm) and the standard X library (libX11). All other molecular visualization programs require some additional libraries.

Before starting the installation, you might be interested to check the technical requirements . Most contemporary Unix and Unix-like systems (like Linux) meet these requirements without need to change the configuration, so you can skip this text if you are impatient.

If you have Apple McIntosh running Xtools from Tenon, please read these hints , contributed by Chris from Macinchem.

To compile and install garlic, follow these instructions:

(1) Put garlic package (garlic-1.6.tar.gz) into some empty directory.
(2) Uncompress and unpack the package:
gzip -d garlic-1.6.tar.gz
tar xf garlic-1.6.tar
(3) Change your working directory:
cd garlic-1.6
(4) Check which C compiler is available on your system.
If you don't know how to find this information, try this:
man -k compiler
to obtain the list of available compilers.
(5) If gcc (GNU C) compiler is not available on your system,
use your favorite editor to edit Makefile. Replace gcc in:
CC = gcc
line with the name of your compiler (this may be cc, for example).
If gcc is available on your system, do not change the CC line.
(6) Find a directory which contains the Xlib library. Try this:
cd /
find . -name libX11\*
Check where is the file libX11.so (sharable library - prefered)
or libX11.a (static library - reserve option).
If your directory is different from /usr/X11R6/lib, modify the line:
LIBPATH = -L/usr/X11R6/lib
in Makefile. For example, if libX11.so is stored in /usr/shlib
directory on your system, the LIBPATH should be changed to:
LIBPATH = -L/usr/shlib
(7) Compile the package - just type:
make
and wait, it will take some time.
(8) If everything worked fine, copy the executable to a choosen directory.
/usr/local/bin may be a good choice. This job should be done by root
(system administrator):
cp garlic /usr/local/bin
If you don't have root privileges, ask your local administrator to install
garlic, or just leave it in one of your directories.
(9) Now the .garlicrc configuration file and the file which contains the
template residues should be copied to a directory where these files
will be accessible to everyone. If this is not done, garlic will work
anyway, using hard-coded default configuration, but you will be unable
to replace residues and to create peptides.
The recommended directory is /usr/share/garlic (since January 2006).
This directory and two default files should be should be prepared by
the system administrator or by the "sudoer":
mkdir /usr/share/garlic
cp .garlicrc /usr/share/garlic
cp residues.pdb /usr/share/garlic
(10) It may be good idea to copy the configuration file to your home directory
or to the subdirectory garlic of your home directory. The same may be
done with the file residues.pdb. If you do this, you will be able to
personalize your garlic sessions, because your private files will override
the system-wide defaults. Of course, you don't need root privileges
to do this:
cp .garlicrc $HOME
cp residues.pdb $HOME
or:
mkdir $HOME/garlic
cp .garlicrc $HOME/garlic
cp residues.pdb $HOME/garlic
(11) It is recommended to set the environment variable MOL_PATH, so garlic
will search all directories listed in this variable to find the specified
file. Click here for detailed instructions.
(12) Clean up the mess (sources and .o files). Be sure to leave all .pdb files
for later practice. Leave also the files with the extension .script, these
are some garlic tutorial scripts.

If garlic refuses to work because it fails to get the TrueColor visual, try to execute
xdpyinfo and xwininfo (click into the root window); check the list of supported visuals
and the current color depth. Choose the color depth for which the TrueColor visual
is available. If you have the SGI Octane workstation, please read this text ,
contributed by Randal R. Ketchem. If you have IBM RS6000 with AIX, read this
hint, contributed by Nicolas Ferre.

The list of sites with proteins, nucleic acids and hetero compounds is here .

If you can't compile, install or run garlic, write to me (Damir Zucic),
my address is zucic@mefos.hr .
garlic-1.6/install/octane.html0000644000000000000000000000256010361663116016372 0ustar rootroot00000000000000 Setting the Color Depth on SGI Octane

Setting the Color Depth on SGI Octane

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
Some people are using SGI Octane in 8 bits per pixel mode. The TrueColor visual is not available at this color depth on this system. If you have such system, think of using it at its full power. I have no access to SGI Octane, so I had no idea how to change the color depth. I would like to thank Mr. Randal R. Ketchem for contributing the answer to this question.

Edit /usr/lib/X11/xdm/Xservers and change the argument list passed to /usr/bin/X11/X.

e.g.
To change the default configuration from the 8-bit pseudomap visual to the 24-bit TrueColor visual, change the single line:
:0 secure /usr/bin/X11/X -bs -nobitscale -c -pseudomap 4sight -solidroot sgilightblue -cursorFG red -cursorBG white

to a single line with:
:0 secure /usr/bin/X11/X -bs -nobitscale -c -class TrueColor -depth 24 -solidroot sgilightblue -cursorFG red -cursorBG white

garlic-1.6/install/mol_path.html0000644000000000000000000000470110361663116016723 0ustar rootroot00000000000000 Environment Varible MOL_PATH

Environment Variable MOL_PATH

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
The environment varible MOL_PATH may be used to define the list of directories which should be searched when you are trying to load certain PDB file. It is not mandatory to define this environment variable, but it is very practical.

MOL_PATH is not the only environment variable recognized by garlic. There is also MOL_DIR, but it is capable to specify only one directory, so it is not recommended.

The exact procedure which should be used to define the environment variable MOL_PATH depends on the shell you use. The procedure is described here for some commonly used shells.

If you don't know what is you shell, execute these commands:

echo $shell
echo $SHELL

Bourne Shell

If you are using the Bourne shell (sh) or the GNU clone called Bourne-again shell (bash), use the example bellow to create your own MOL_PATH variable. Use colon ( : ) to separate directories. It is important to export the variable! You should define this variable through your .bash_profile or .bashrc resource file in your home directory. Don't forget to replace the user name and directories.

MOL_PATH="/home/zucic/pdb:/home/zucic/glob:/home/zucic/memb"
export MOL_PATH

C Shell

If you are using the C shell (csh) or it's clone tcsh, use the command setenv to define the environment variable MOL_PATH. Use colon ( : ) to separate directories. You should define this variable through your .cshrc, .tcshrc or .login resource file in your home directory. The user name and directories should be replaced, of course.

setenv MOL_PATH /home/zucic/pdb:/home/zucic/glob:/home/zucic/memb

Other Shells

For other shells, read the manual page to learn how to define the environment variable MOL_PATH. In most cases, the method is similar to one of the methods described above.
garlic-1.6/install/garlic.gif0000644000000000000000000000465007061730474016172 0ustar rootroot00000000000000GIF87aFFɲ̻ոտĻ®ȹ@]^\ @ @P @@x((]VVP(PdVd dd\?).]@vP]dD(r?V @, @()$V@@]\ @lVi(rV@@l,( ]V) @@H]@\]@HiH(\VL @(PVd @X(,Vdd*[H\L( Vh𤝂pDPD]HxM x @(IVd( Vddx(/VrP d^ @F FR<_Pd?.@2_<  @F Fn(VGR (@,FF @PÇ#Jl8  %jܸ1A$

_\!& Setting the Color Depth on IBM RS6000 with AIX4.3

Setting the Color Depth on IBM RS6000 with AIX4.3

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
To use the X window system with 24 bits per pixel, run the following command:

xinit -- -x dbe -x abx -layer 0 -d 24 -cc TrueColor

I would like to thank Mr. Nicolas Ferre (Nancy, France) for this hint.
garlic-1.6/changes/0000755000000000000000000000000010403105234014157 5ustar rootroot00000000000000garlic-1.6/changes/favicon.ico0000644000000000000000000000047607070106602016315 0ustar rootroot00000000000000(( garlic-1.6/changes/index.html0000644000000000000000000000345110345612612016167 0ustar rootroot00000000000000 Changes

Changes

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, unix, linux, free software download, open source software, Damir Zucic.
This page contains the list of changes. Bug fixes are not included here!

DATE CHANGE
2000/03/28 Five scripts included into garlic source package.
2000/04/10 Version 1.0 released (see below for changes)
2000/04/10 The keyword ALL may be used with the command DISCARD,
to discard all structures.
2000/04/10 The history buffer is now capable to store the commands
executed from the script.
2000/04/10 The command TAG added. With this command, a short
text may be associated with a structure. Tag is
bound to the structure, so it moves along with it.
2000/04/10 Color handling sligthly improved.
2000/04/10 Mouse clicks may be used for translations and rotations
as well as for slab and color adjustment. Click on a
selected button in a control window (top right).
2000/04/10 A simple startup logo (text) added.
garlic-1.6/changes/garlic.gif0000644000000000000000000000465007070106602016122 0ustar rootroot00000000000000GIF87aFFɲ̻ոտĻ®ȹ@]^\ @ @P @@x((]VVP(PdVd dd\?).]@vP]dD(r?V @, @()$V@@]\ @lVi(rV@@l,( ]V) @@H]@\]@HiH(\VL @(PVd @X(,Vdd*[H\L( Vh𤝂pDPD]HxM x @(IVd( Vddx(/VrP d^ @F FR<_Pd?.@2_<  @F Fn(VGR (@,FF @PÇ#Jl8  %jܸ1A$

_\!&