NAME
garlic - molecular visualization program
SYNOPSIS
garlic [true Garlic options] [X11 options] [filename]
DESCRIPTION
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.
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 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
<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.
FILES
The configuration file is searched in the following order:
./.garlicrc
${HOME}/.garlicrc
${HOME}/garlic/.garlicrc
/usr/share/garlic/.garlicrc
/etc/garlicrc
/usr/local/lib/garlic/.garlicrc
/usr/lib/garlic/.garlicrc
SEE ALSO
The program is fully documented in the garlic-doc package available on
Debian GNU/Linux system.
There is also documentation online at
<URL:http://garlic.mefos.hr/garlic/docs.html>
AUTHOR
garlic was written by Damir Zucic <zucic@garlic.mefos.hr>, University
of Osijek, Croatia, Europe.
The original man page was written by zhaoway <zw@debian.org>, for the
Debian GNU system and later modified by Damir Zucic.
June 7, 2007