garlic - molecular visualization program

garlic was written by DamirZucić <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 DamirZucić.

                                                   15 Feb 2008                                         GARLIC(1)

       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.

       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

       garlic - molecular visualization program

       Command line options may be divided in two groups:  true(specific)garlicoptions  and  X11options.
       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.

   garlicoptions:-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.

       -slabmode
              Default slab mode. Available slab modes are: off, planar (default), sphere, half-sphere,  cylinder
              and half cylinder.

       -fadingmode
              Default  color  fading mode. Available modes: off, planar (default), sphere, half-sphere, cylinder
              and half cylinder.

       -asnumber
              Default atom drawing style (hard-coded default: 2).

       -bsnumber
              Default bond drawing style (hard-coded default: 2).

       -fsnumber
              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.

       -loglogfile
              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.

   X11option:-displaydisplayname
              X server to contact.

       -geometrygeom
              Window geometry (default: almost the whole screen).

       -bgcolor
              Main window background color (default is black).

       -fgcolor
              Main window foreground color (default: white).

       -fnfontname
              Text font; (default is 10x20).

       -tbgcolor
              Text background color (default is black).

       -tfgcolor
              Text color (default is white).

       -cursorcursorname
              Cursor name; see /usr/include/X11/cursorfont.h for names; remove the XC_ prefix.

       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 [Garlicoptions] [X11options] [filename]