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garlic - molecular visualization program


garlic [true Garlic options] [X11 options] [filename]


This manual page briefly documents garlic, a free molecular visualization program.
Extensive documentation in HTML format and sources may be found at garlic home,
<URL: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.


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 options:
-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 <[email protected]>. 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).

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, 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

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.

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