PYMOL(1)							   User commands							  PYMOL(1)

NAME

       pymol - free and flexible molecular graphics and modelling package

SYNOPSIS

       pymol [options] [files]

DESCRIPTION

       Over the years, PyMOL has become a capable molecular viewer with support for animations, high-quality rendering, crystallography, and other
       common molecular graphics activities. It has been adopted by many hundreds (perhaps even thousands) of scientists spread over thirty  coun-
       tries. However, PyMOL is still very much a work in progress, with development expected to continue for years to come.

OPTIONS

       These options are currently supported:

       -2     Start in two-button mouse mode.

       -c     Command line mode, no GUI.  For batch opeations.

       -d string
	      Run pymol command string upon startup.

       -e     Start in full-screen mode.

       -f #line
	      Controls display of commands and feedback in OpenGL (0=off).

       -g file.png
	      Write a PNG file (after evaluating previous arguments)

       -i     Disable the internal OpenGL GUI (object list, menus, etc.)

       -l file.py
	      Spawn a python program in new thread.

       -o     Disable security protections for session files.

       -p     Listen for commands on standard input.

       -q     Quiet launch. Suppress splash screen & other chatter.

       -r file.py
	      Run a Python program (in __main__) on startup.

       -s script
	      Save commands to this PyMOL script or program file.

       -t     Use Tcl/Tk based external GUI module (pmg_tk).

       -u script
	      Load and append to this PyMOL script or program file.

       -x     Disable the external GUI module.

       -B     Enable blue-line stereo signal (for Mac stereo)

       -G     Start in Game mode.

       -M     Force mono even when hardware stereo is present.

       -R     Launch Greg Landrum's XMLRPC listener.

       -S     Force and launch in stereo, if possible.

       -X int -Y int -W int -H int -V int
	      Adjust window geometry.

       All files provided will be loaded or run after PyMOL starts.  They can have one of the following extensions:

       .pml	       PyMOL command script to be run on startup
       .py[cm]	       Python program to be run on startup
       .pdb	       Protein Data Bank format file to be loaded on startup
       .mmod	       Macromodel format to be loaded on startup
       .mol	       MDL MOL file to be loaded on startup
       .sdf	       MDL SD file to be parsed and loaded on startup
       .xplor	       X-PLOR Map file (ASCII) to be loaded on startup
       .ccp4	       CCP4 map file (BINARY) to be loaded on startup
       .cc[12]	       ChemDraw 3D cartesian coordinate file
       .pkl	       Pickled ChemPy Model (class "chempy.model.Indexed")
       .r3d	       Raster3D file
       .cex	       CEX file (Metaphorics)
       .top	       AMBER topology file
       .crd	       AMBER coordinate file
       .rst	       AMBER restart file
       .trj	       AMBER trajectory
       .pse	       PyMOL session file
       .phi	       Delphi/Grasp Electrostatic Potential Map

       For a list of options, you can also enter the following in the command line of pymol:

	      help launching

COMMANDS

       Please refer to PyMols online documentation at http://www.pymolwiki.org/index.php/Category:Commands or its internal help for a command ref-
       erence.

AUTHOR

       This manpage was written by Daniel Leidert <daniel.leidert@wgdd.de> for the Debian distribution (but may be used by others).

								    2008-05-06								  PYMOL(1)