Command Line Options - Revision history

Cchem: 1 revision

2017-06-26T04:31:24Z

1 revision

Speleo3: pymol --help 1.8.6

2017-05-31T06:43:24Z

pymol --help 1.8.6

Pyadmin: 8 revisions

2014-03-28T01:43:27Z

8 revisions

Jaredsampson: fixed typos

2013-08-02T15:46:53Z

fixed typos

New page

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 =
{| width="45%"
|+ style="font-weight:bold; text-align:center; font-size:150%;" | PyMOL Command line Options
! Option !! What it Does
|-
||'''-c''' || Command line mode, no GUI. For batch operations.
|-
||'''-b''' || Runs benchmark.
|-
||'''-i''' || Disable the internal OpenGL GUI (object list, menus, etc.)
|-
||'''-k''' || Suppress the use of the .pymolrc file.
|-
||'''-x''' || Disable the external GUI module.
|-
||'''-t''' || Use Tcl/Tk-based external GUI module (pmg_tk).
|-
||'''-q''' || Quiet launch. Suppress splash screen & other chatter.
|-
||'''-p''' || Listen for commands on standard input.
|-
||'''-e''' || Start in full-screen mode.
|-
||'''-2''' || Start in two-button mouse mode.
|-
||'''-o''' || Disable security protections for session files.
|-
||'''-R''' || Launch Greg Landrum's XMLRPC listener.
|-
||'''-B''' || Enable blue-line stereo signal (for Mac stereo)
|-
||'''-G''' || Start in Game mode.
|-
||'''-S''' || Force and launch in stereo, if possible.
|-
||'''-M''' || Force mono even when hardware stereo is present.
|-
||'''-X <int> -Y <int> -W <int> -H <int> -V <int>''' || Adjust window geometry.
|-
||'''-f <# line>''' || Controls display of commands and feedback in OpenGL (0=off).
|-
||'''-r <file.py> ''' || Run a Python program (in __main__) on startup.
|-
||'''-l <file.py> ''' || Spawn a python program in new thread.
|-
||'''-d <string> ''' || Run pymol command string upon startup.
|-
||'''-u <script> ''' || Load and append to this PyMOL script or program file.
|-
||'''-s <script> ''' || Save commands to this PyMOL script or program file.
|-
||'''-g <file.png> ''' || Write a PNG file (after evaluating previous arguments)
|}

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

{| width="45%"
|+ style="font-weight:bold; text-align:center; font-size:150%;" | 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 =
<source lang="bash">
# 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
</source>

[[Category:Launching]]

Desastre at 13:22, 15 January 2009

2009-01-15T13:22:07Z

New page

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 =
{| width="45%"
|+ style="font-weight:bold; text-align:center; font-size:150%;" | PyMOL Command line Options
! Option !! What it Does
|-
||'''-c''' || Command line mode, no GUI. For batch opeations.
|-
||'''-b''' || Runs benchmark.
|-
||'''-i''' || Disable the internal OpenGL GUI (object list, menus, etc.)
|-
||'''-k''' || Supress the use of the .pymolrc file.
|-
||'''-x''' || Disable the external GUI module.
|-
||'''-t''' || Use Tcl/Tk based external GUI module (pmg_tk).
|-
||'''-q''' || Quiet launch. Suppress splash screen & other chatter.
|-
||'''-p''' || Listen for commands on standard input.
|-
||'''-e''' || Start in full-screen mode.
|-
||'''-2''' || Start in two-button mouse mode.
|-
||'''-o''' || Disable security protections for session files.
|-
||'''-R''' || Launch Greg Landrum's XMLRPC listener.
|-
||'''-B''' || Enable blue-line stereo signal (for Mac stereo)
|-
||'''-G''' || Start in Game mode.
|-
||'''-S''' || Force and launch in stereo, if possible.
|-
||'''-M''' || Force mono even when hardware stereo is present.
|-
||'''-X <int> -Y <int> -W <int> -H <int> -V <int>''' || Adjust window geometry.
|-
||'''-f <# line>''' || Controls display of commands and feedback in OpenGL (0=off).
|-
||'''-r <file.py> ''' || Run a Python program (in __main__) on startup.
|-
||'''-l <file.py> ''' || Spawn a python program in new thread.
|-
||'''-d <string> ''' || Run pymol command string upon startup.
|-
||'''-u <script> ''' || Load and append to this PyMOL script or program file.
|-
||'''-s <script> ''' || Save commands to this PyMOL script or program file.
|-
||'''-g <file.png> ''' || Write a PNG file (after evaluating previous arguments)
|}

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

{| width="45%"
|+ style="font-weight:bold; text-align:center; font-size:150%;" | 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 =
<source lang="bash">
# 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
</source>

Jcorn: /* Command Line Options */

2005-02-17T20:22:45Z

Command Line Options

Jcorn: /* Command Line Options /*

2005-02-17T20:22:31Z

/* Command Line Options /*

New page

== Command Line Options ==
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.

PyMOL COMMAND LINE OPTIONS

-c Command line mode, no GUI. For batch opeations.
-i Disable the internal OpenGL GUI (object list, menus, etc.)
-x Disable the external GUI module.
-t Use Tcl/Tk based external GUI module (pmg_tk).
-q Quiet launch. Suppress splash screen & other chatter.
-p Listen for commands on standard input.
-e Start in full-screen mode.
-2 Start in two-button mouse mode.
-o Disable security protections for session files.
-R Launch Greg Landrum's XMLRPC listener.
-B Enable blue-line stereo signal (for Mac stereo)
-G Start in Game mode.
-S Force and launch in stereo, if possible.
-M Force mono even when hardware stereo is present.

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

-f <# line> Controls display of commands and feedback in OpenGL (0=off).
-r <file.py> Run a Python program (in __main__) on startup.
-l <file.py> Spawn a python program in new thread.
-d <string> Run pymol command string upon startup.
-u <script> Load and append to this PyMOL script or program file.
-s <script> Save commands to this PyMOL script or program file.
-g <file.png> Write a PNG file (after evaluating previous arguments)

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

.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

@@ Line 2: / Line 2: @@
 = Command Line Options =
-{| width="45%"
-|+ style="font-weight:bold; text-align:center; font-size:150%;" | PyMOL Command line Options
+ shell> pymol --help
-! Option !! What it Does
-|-
+ PyMOL 1.8.6.0 Incentive Product
-||'''-c''' ||  Command line mode, no GUI.  For batch operations.
+ Copyright (C) Schrodinger, LLC
-|-
-||'''-b''' ||  Runs benchmark.
+ Usage: pymol [OPTIONS]... [FILES]... [-- CUSTOM SCRIPT ARGUMENTS]
-|-
-||'''-i''' ||  Disable the internal OpenGL GUI (object list, menus, etc.)
+  Options
-|-
-||'''-k''' ||  Suppress the use of the .pymolrc file.
+   --help    display this help and exit
-|-
+   --version display PyMOL version and exit
-||'''-x''' ||  Disable the external GUI module.
+   --retina  use retina resolution (MacPyMOL) and set display_scale_factor=2
-|-
-||'''-t''' ||  Use Tcl/Tk-based external GUI module (pmg_tk).
+   -1        config_mouse one_button
-|-
+   -2        config_mouse two_button
-||'''-q''' ||  Quiet launch. Suppress splash screen & other chatter.
+   -a N      alias for -A
-|-
+   -A N      application configuration:
-||'''-p''' ||  Listen for commands on standard input.
+     -A1     simple viewer window          (-qxiF -X 68 -Y 100)
-|-
+     -A3     internal GUI only, no splash  (-qx -X 68 -Y 100)
-||'''-e''' ||  Start in full-screen mode.
+     -A4     used by PYMOLVIEWER           (-X 68 -Y 100)
-|-
+     -A5     helper application            (-QxiICUF -X 68 -Y 100)
-||'''-2''' ||  Start in two-button mouse mode.
+     -A6     full screen presentation      (-qxieICUPF)
-|-
+   -b[N]     benchmark wizard
-||'''-o''' ||  Disable security protections for session files.
+   -B        (DEPRECATED)
-|-
+   -c        launch in command-line only mode for batch processing
-||'''-R''' ||  Launch Greg Landrum's XMLRPC listener.
+   -C        don't terminate on Ctrl-C
-|-
+   -d cmd    execute PyMOL command
-||'''-B''' ||  Enable blue-line stereo signal (for Mac stereo)
+   -D N      defer_builds_mode=N
-|-
+   -e        full screen
-||'''-G''' ||  Start in Game mode.
+   -E N      multisampling (GL_MULTISAMPLE_ARB)
-|-
+   -f N      internal_feedback=N
-||'''-S''' ||  Force and launch in stereo, if possible.
+   -F        internal_feedback=0
-|-
+   -g file   save image (png) or movie (mpg)
-||'''-M''' ||  Force mono even when hardware stereo is present.
+   -G        game mode (DEPRECATED)
-|-
+   -h        generic helper application (no controls, no feedback)
-||'''-X <int> -Y <int> -W <int> -H <int> -V <int>''' || Adjust window geometry.
+   -H N      window height in pixels
-|-
+   -i        internal_gui=0
-||'''-f <# line>''' || Controls display of commands and feedback in OpenGL (0=off).
+   -I        auto_reinitialize=1 (Mac only)
-|-
+   -j        side-by-side stereo (stereo_mode=4)
-||'''-r <file.py> ''' || Run a Python program (in __main__) on startup.
+   -J        cd to user's home directory
-|-
+   -k        don't load pymolrc or plugins
-||'''-l <file.py> ''' || Spawn a python program in new thread.
+   -K        keep alive: when running without a GUI, don't quit after the input
-|-
+             is exhausted
-||'''-d <string> ''' || Run pymol command string upon startup.
+   -l file   run python script in thread (spawn)
-|-
+   -L file   load file after everything else (only if something was loaded before)
-||'''-u <script> ''' || Load and append to this PyMOL script or program file.
+   -m        INTERNAL - do not use (mac external GUI)
-|-
+   -M        force mono
-||'''-s <script> ''' || Save commands to this PyMOL script or program file.
+   -n        INTERNAL - do not use (incentive_product=1)
-|-
+   -N name   UNSUPPORTED - external gui type (default: pmg_tk) (same as -w)
-||'''-g <file.png> ''' || Write a PNG file (after evaluating previous arguments)
+   -o        disable security protections
-|}
+   -O N      sphere_mode=N
 = Supported File Formats  =

← Older revision		Revision as of 20:22, 17 February 2005
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−	~~== Command Line Options ==~~
	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.		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.

← Older revision	Revision as of 04:31, 26 June 2017
(No difference)

← Older revision	Revision as of 01:43, 28 March 2014
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