From Linux Man Pages
garlic [true_garlic_options] [X11_options] [filename]
GARLIC
garlic - molecular visualization program
DESCRIPTION
This manual page briefly documents garlic, free molecular visualization program. Extensive documentation in HTML
format and sources may be found at garlic home, http://garlic.mefos.hr/garlic. Physical location: School of
Medicine, University of Osijek, Croatia, Europe. Precompiled packages for a number of GNU/Linux distributions are
available. These include Debian, SuSE, Mandriva, Linspire and a number of other distros. The HTML documentation
may be downloaded and unpacked for local use (recommended usage). Here you can find a very short description of
the program and the list of command line options.
garlic is a molecular visualization program originally written for investigation of membrane proteins. Now it
may be used to visualize and simple editing of all proteins and molecules. This version recognizes PDB format
version 2.1; see the source file pdb_atom.c for details about this format.
OPTIONS
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 val-
ues 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 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 one short e-mail message,
containing only the e-mail message header and the word 'Hi!',to zucic@garlic.mefos.hr. Please execute
garlic -r if you are going to use this program. If you are not connected to the Internet, consider
sending a short message 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: 2).
-fs number
Default number of color fading surfaces. Parallel planes, concentric spheres or concentric 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 defined 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:
-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.
RELATED
The program is fully documented fully in the R garlic-doc package available on Debian GNU system.
CATEGORY