Command Line Options

PyMOL has lots of options for controlling it immediately from startup. Run 'help launching' from the command line for detailed listings of options for your current version of PyMol. Here is a sample output which should be pretty consistent for recent versions.

Command Line Options

shell> pymol --help

PyMOL 1.8.6.0 Incentive Product
Copyright (C) Schrodinger, LLC

Usage: pymol [OPTIONS]... [FILES]... [-- CUSTOM SCRIPT ARGUMENTS]

Options

  --help    display this help and exit
  --version display PyMOL version and exit
  --retina  use retina resolution (MacPyMOL) and set display_scale_factor=2

  -1        config_mouse one_button
  -2        config_mouse two_button
  -a N      alias for -A
  -A N      application configuration:
    -A1     simple viewer window          (-qxiF -X 68 -Y 100)
    -A3     internal GUI only, no splash  (-qx -X 68 -Y 100)
    -A4     used by PYMOLVIEWER           (-X 68 -Y 100)
    -A5     helper application            (-QxiICUF -X 68 -Y 100)
    -A6     full screen presentation      (-qxieICUPF)
  -b[N]     benchmark wizard
  -B        (DEPRECATED)
  -c        launch in command-line only mode for batch processing
  -C        don't terminate on Ctrl-C
  -d cmd    execute PyMOL command
  -D N      defer_builds_mode=N
  -e        full screen
  -E N      multisampling (GL_MULTISAMPLE_ARB)
  -f N      internal_feedback=N
  -F        internal_feedback=0
  -g file   save image (png) or movie (mpg)
  -G        game mode (DEPRECATED)
  -h        generic helper application (no controls, no feedback)
  -H N      window height in pixels
  -i        internal_gui=0
  -I        auto_reinitialize=1 (Mac only)
  -j        side-by-side stereo (stereo_mode=4)
  -J        cd to user's home directory
  -k        don't load pymolrc or plugins
  -K        keep alive: when running without a GUI, don't quit after the input
            is exhausted
  -l file   run python script in thread (spawn)
  -L file   load file after everything else (only if something was loaded before)
  -m        INTERNAL - do not use (mac external GUI)
  -M        force mono
  -n        INTERNAL - do not use (incentive_product=1)
  -N name   UNSUPPORTED - external gui type (default: pmg_tk) (same as -w)
  -o        disable security protections
  -O N      sphere_mode=N
  -p        read commands from STDIN
  -P        handle scenes as if the session were opened in presentation mode
  -q        supress startup message
  -Q        quiet, suppress all text output
  -r file   run python script
  -R        launch RPC Server
  -s file   log to file
  -S        force stereo
  -t N      stereo_mode=N
  -T name   UNSUPPORTED - Tcl/Tk GUI skin
  -u file   resume log file (execute existing content and append new log output)
  -U        UNSUPPORTED reuse the helper application
  -v        UNUSED
  -V N      external GUI window height in pixels
  -w name   UNSUPPORTED - external gui type (default: pmg_tk) (same as -N)
  -W N      window width in pixels
  -x        no external gui
  -X N      window x position on screen
  -y        exit on error
  -Y N      window y position on screen
  -z N      window_visible=N
  -Z N      zoom_mode=N

Supported File Formats

<file> can have one of the following extensions, and all files provided will be loaded or run after PyMOL starts.

PyMOL Supported File Formats

Extension	Format
.pml	PyMOL command script to be run on startup
.py, .pym, .pyc	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
.cc1, .cc2	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

Examples

# load the 3 pdb files and execte the following commands
pymol mol1.pdb mol2.pdb mol3.pdb -d 'as ribbon;spectrum count;set seq_view'

# load the 3 pdbs and run the script
pymol mol1.pdb mol2.pdb mol3.pdb my_script.pml

# Run my_program using PyMOL as the Python interpreter
# passing the 3 pdb files to my_program.py
pymol my_program.py -- mol1.pdb mol2.pdb mol3.pdb