garlic - molecular visualization program
garlic [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://www.zucic.org/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.
- -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.
The program is fully documented in the garlic-doc package
available on Debian GNU/Linux system.
There is also documentation online at
<URL:http://www.zucic.org/garlic/docs.html>.
garlic was written by Damir Zuci
<zucic@garlic.mefos.hr>, University of Osijek, Croatia, Europe. He
died in September 2007.
The original man page was written by zhaoway
<zw@debian.org>, for the Debian GNU system and later modified by
Damir Zuci.