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<title>
Garlic Command Line Options
</title>
</head>
<h1 align=center>
Garlic Command Line Options
</h1>
<hr size="3">
<font size="-1" color="red">
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.
</font>
<hr size="3">
This page explains the command line options. To see this list, type one of
the following commands:
<br><br>
garlic -h
<br>
garlic -h | less
<br><br>
<hr size="3">
<pre>
=========================================================================
Garlic - free molecular viewer and editor
=========================================================================
Garlic was written by Damir Zucic (zucic@mefos.hr) 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 zucic@garlic.mefos.hr. 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
MOL_PATH.
-------------------------------------------------------------------------
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: http://garlic.mefos.hr/garlic
Damir Zucic home page: http://garlic.mefos.hr/zucic
E-mail: zucic@mefos.hr
=========================================================================
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