pymol(1) [debian man page]
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)
Check Out this Related Man Page
animate(1gv) Geomview Module animate(1gv) NAME
animate - animate a sequence of geomview files SYNOPSIS
animate [-p] [-b] [-s speed] [-o] [-S script] [-hide] [-f file1 file2 ...] DESCRIPTION
Animate is an interactive animation tool specifically designed to be used with Geomview. It provides several simple animation controls such as looping, bouncing, and single frame stepping, as well as adjustable speed playing. The program works by telling geomview to read in a sequence of geomview files and then telling geomview to display each frame of the sequence in order. There are two methods that Animate provides for specifying which frames one wants to have in the sequence being viewed. The first method is to enter the name of every frame into the text input box and press return or click on load. The name of each frame must correspond with the name of a geomview file existing in the file system. EXAMPLES pict1 pict2 pict3 pict4 pict* pic?? The second method of loading frames is to first create an animation script file outside of animate and then load the script in by typing its name in the input box and clicking on the script button. The advantage of this method is that you can more easily specify the exact order in which you want the frames to be shown. The format of the script file is a list of frame names each followed by a newline. Comments prepended by a # sign are allowed. EXAMPLE SCRIPT FILE # list of frames for # my rotating cube movie cube.02 cube.04 cube.03 # get rid of this frame later cube.01 . . . cube.90 Loading frames into memory may take a little time, especially if each frame is a particularly large file. Be sure the machine you're using has sufficient memory to load all the frames you desire. Once all frames have been loaded, an 'animate' object will appear in the geomview object browser. It is now possible to begin animating. Scrolling through frames can be accomplished in several different ways. The first, and most obvious way is by 'playing' the frames. Click- ing on the Play button causes animate to begin playing through the frames in order, starting with the first frame or whichever frame has been selected. The corresponding name of each frame being shown is shown in the pink text-entry box. Click on Stop to cease playing. Animation speed depends on the size and complexity of the object in each frame. Thus different sequences can have considerably different top playing speeds. Use the Speed slider to set an upper limit to the animation rate. You can also play slowly through the frames can also by clicking repeatedly on either step button. Press the Bounce button to enter bounce mode. While in bounce mode, direction of play reverses whenever the first or last frame is reached. Clicking on either Step button determines the playing direction. Clicking on Once puts animate in 'once' mode. While in this mode, upon reaching the first or last frame (depending on which direction you are going) of a specified sequence, animate will stop playing. Normal playing can be resumed by clicking on Once again to exit this mode. The Info button will bring up a short menu containing helpful hints for program usage. Clicking on the exit button will cause the program to exit. OPTIONS
-p Start playing through the frames right away upon startup. -b Go into bounce mode upon startup. -s speed Set the speed of play upon startup. The value of speed may be an integer between 0 and 100 which roughly signifies the percentage of top playing speed. -o Set animation to play through only once upon startup. -S script Specify name of script containing filenames for objects to be read in upon startup. Takes precedence over -f option if present. -hide Makes animate invisible upon startup. *Warning* all animate commands must be specified on the command line when this option is used since there is no way to access the main window. -f file1 file2 ... Specify names of files containing objects to be read in upon startup. BUGS
When loading sequences one after another, geomview will often not load a sequence on the first try. This can often be remedied by telling animate to load the sequence yet again. SEE ALSO
geomview(1) oogl(5) AUTHOR
Daeron Meyer The Geometry Center December 12, 1994 animate(1gv)