Ubuntu Manpage: garlic - molecular visualization program

NAME

       garlic - molecular visualization program

SYNOPSIS

       garlic [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://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.

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

AUTHOR