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       garlic - molecular visualization program


       garlic [true 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 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.

   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

       -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 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.


       The configuration file is searched in the following order:


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

       There        is        also        documentation        online       at


       garlic was written by Damir Zucic  <>,  University
       of Osijek, Croatia, Europe.

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

                                 June 7, 2007