<html> <head> <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 ========================================================================= </pre> <hr size="3"> </html>