Provided by: garlic_1.6-3_amd64 bug


       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:>.   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

       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 <>. 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.


       The configuration file is searched in the following order:


       The program is fully documented in the garlic-doc package available  on  Debian  GNU/Linux

       There is also documentation online at <URL:>.


       garlic  was written by Damir Zucić <>, University of Osijek, Croatia,
       Europe. He died in September 2007.

       The original man page was written by zhaoway <>, for the  Debian  GNU  system
       and later modified by Damir Zucić.

                                           15 Feb 2008                                  GARLIC(1)