MAN page from OpenSuSE garlic-1.6-lp152.4.4.x86_64.rpm


Section: (1)


garlic - molecular visualization program 


garlic[true_garlic_options] [X11_options] [filename] 


This manual page briefly documents garlic, free molecular visualizationprogram. Extensive documentation in HTML format and sources may be foundat garlic home, Physical location: Schoolof Medicine, University of Osijek, Croatia, Europe. Precompiled packagesfor a number of GNU/Linux distributions are available. These includeDebian, SuSE, Mandriva, Linspire and a number of other distros. The HTMLdocumentation may be downloaded and unpacked for local use (recommendedusage). Here you can find a very short description of the program and thelist of command line options.

garlicis a molecular visualization program originally written for investigationof membrane proteins. Now it may be used to visualize and simple editingof all proteins and molecules. This version recognizes PDB format version2.1; see the source file pdb_atom.c for details about this format. 


Command line options may be divided in two groups: true (specific) garlicoptions and X11 options. Options may be given in any order. All optionsand hard-coded default values are listed in the table below. For eachparameter, the value defined through command line is used, if available.If not, the value defined in .garlicrc file is used. If .garlicrc file isnot available, or there is no corresponding entry in this file, thehard-coded default value is used. The sample .garlicrc file included inthe original package contains the values equal to hard-coded defaults.

garlic option:

-h, --help
Print help and exit.
-v, --version
Print version and exit.
-r, --register
Register garlic: inform author that your site has garlic installed andthat someone is going to use this program. By registering, you areencouraging author to continue development of garlic. You can also helpauthor to ensure support for further development. This option sends oneshort e-mail message, containing only the e-mail message header and theword 'Hi!',to Please execute garlic -r if you aregoing to use this program. If you are not connected to the Internet,consider sending a short message from some other system.
Hide the coordinate system icon (top left corner).
Hide the control window (upper right corner).
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: 2).
-fs number
Default number of color fading surfaces. Parallel planes, concentricspheres or concentric cylinders may be used as fading surfaces. Three RGBtriplets are assigned to each surface. Surfaces are evenly spaced; atleast one and at most eight should be defined. At least three colors(left, middle and right) are assigned to each visible atom. These threecolors are based on the position of a given atom relative to the nearestfading surface(s) and on colors assigned to these surfaces. Colors arecombined using linear weighting.
-lc<i> color
Left color at the i-th surface; i is between zero and seven. The colorstring should be compliant with X11R5. Blue, for example, may be definedas blue or as RGB:0000/0000/FFFF etc. For example -lc4 RGB:BBBB/8888/4444 defines the left color at the surface whose indexis 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.
Print cursor names to stdout and exit.
-log logfile
Write commands and messages to log file. The file will be created in thecurrent working directory. If this is not possible, log file will becreated in users home directory.

X11 option:

-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 theXC_ prefix.


The program is fully documented fully in theR garlic-docpackage available on Debian GNU system. 


garlicwas written by Damir Zucic (, University of Osijek,Croatia, Europe.

The original man page was written by zhaoway <>, forthe Debian GNU system and later modified by Damir Zucic. This man page was last modified on August 22, 2006.




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