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.
