Garlic Command Line Options

garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic.
This page explains the command line options. To see this list, type one of the following commands:

garlic -h
garlic -h | less

               Garlic - free molecular viewer and editor

Garlic  was written by  Damir Zucic  (  as a complement to
other molecular  visualization  programs,  like rasmol  (by Roger Sayle).
It was written to simplify  the analysis of membrane proteins, but it can
be used as general purpose molecular visualization program, provided that
molecular coordinates are available in  PDB format, version 2.1 or older.
Garlic may also be used to analyze protein sequences.

Some of the  features, which  distinguish this program from  others, are:
(1) Coordinates, labels and  other data are  automatically displayed  for
    the atom nearest to the current pointer (mouse) position.
(2) Additional numeric data,  like  hydrophobicity, may be associated  to
    each amino acid. The  whole  structure  may be  colored  according to
    these values.
(3) Selection mechanism is different.
(4) Two bonds at different distance from  observer have different colors.
Usage:              garlic [true_garlic_options] [X11_options] [filename]
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 option:        Description:
-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 an e-mail message,
                        containing only the e-mail message header and the
                        word 'Hi!', to Please type
                        garlic -r   if you are going to use this program.
                        If your system is  not connected to the Internet,
                        you can send short e-mail 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: 3).
-fs number            Default number of  color fading surfaces.  Parallel
                        planes, concentric spheres or conc. 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 specified
                        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:           Description:
-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.
filename:             The input file name.  Full pathname may be used. If
                      filename does not contain the path, garlic will try
                      to find  the specified file in  the current working
                      directory.  If the first attempt  to open  the file
                      fails,  the filename  is appended to the content of
                      the environment  variable  MOL_DIR  for  the second
                      attempt.  If this fails too, garlic will search all
                      directories  specified in  the environment variable
Personal initializations may be written to .garlicrc file. Normally, this
file should be kept in users home directory.  Note that this is  not  the
first directory to be searched for  .garlicrc file! Up to seven pathnames
are tryed in the following order:

.garlicrc                       .garlicrc  in current  working directory.
$HOME/.garlicrc                 .garlicrc in home directory.  This is the
                                   recommended location.
$HOME/garlic/.garlicrc          ./garlicrc,  subdirectory garlic of users
                                   home directory.
/usr/share/garlic/.garlicrc     ./garlicrc in  /usr/share/garlic (Linux).
/etc/garlicrc                   garlicrc in /etc, Debian Linux; note that
                                   file name is  garlicrc  in  this case!
/usr/local/lib/garlic/.garlicrc .garlicrc  in  /usr/local/lib/garlic dir.
/usr/lib/garlic/.garlicrc       .garlicrc in /usr/lib/garlic; this is the
                                   last attempt; if it failes, hard-coded
                                   default values will be used.
Environment variables:
MOL_DIR               Defines where to look for the specified file if not
                         found in the current working directory.
MOL_PATH              The list of directories to be searched.  It is used
                         if attempt with MOL_DIR failes  or if MOL_DIR is
                         not defined. Use space  or colon (:) to separate
                         directory names. MOL_PATH is quite useful; it is
                         recommended to define  this environment variable
                         through  .login,  .bashrc or  some other script.
                         MOL_PATH  is more useful  than  MOL_DIR so it is
                         recommended  to define only  MOL_PATH  variable.
DISPLAY               X server to which  the program should be connected.
garlic home page:                 
Damir Zucic home page: