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pymol example.py # synchronous, in PyMOL module pymol -r example.py # synchronous in __main__ module

== Use of module include == The include module has been restricted to only accept pages from:

|type = Python Module

|type = module |module = psico.fitting

|module = psico.exporting

[[Category:Editing Module|H Fill]]

|type = module |module = psico.querying

|type = Python Module |module = psico.orientation

# use 'cmd' module if possible module = 'cmd'

[[Category:Input Output Module|Quit]]

|type = module |module = psico.orientation

[[Category:View Module|Move]]

[[Category:Editing Module|Redo]]

|module = psico.morphing

|type = module

|type = module

|module = psico.xtal

=== Import as a module === After importing the module, call the <code>set_colors()</code> function to add the colors to PyMOL's c

[[Category:View Module|Disable]]

pymol example.py # synchronous, in PyMOL module pymol -r example.py # synchronous in __main__ module

|type = module

|type = Python Module

|type = module

|module = psico.morphing

[[Category:View Module|View]]

|type = Python Module

|module = psico.minimizing

[[Category:View Module|Enable]]

|module = psico.helping

Section "Module"

|module = psico.editing

[[Category:Input Output Module]]

[[Category:View Module|Hide]]

...-like commands. The [[iterate]] commands by default expose the '''pymol''' module namespace as the [https://docs.python.org/2/library/functions.html#eval glo

[[Category:Editing Module]]

...n the global '''cmd''' module to '''_self''', or if using the '''pymol2''' module, an instance of '''pymol2.cmd2.Cmd'''. This wrapper allows running multiple This example provides a command help, does proper type conversion of arguments and would work with '''pymol2'''.

|module = psico.helping ###EXACT MATCH FOR: fit ==> try 'help fit' at the prompt.

[[Category:View Module|Orient]]

|type = Python Module

|type = Python Module help movie_color_fade

|module = psico.msms

A plugin is a Python module which uses PyMOL's API. The following entrypoints add functionality to PyMO * multiple files per plugin/module (see [[#More than one file per plugin]])

|module = psico.creating

|module = psico.importing

|module = psico.fitting

[[Category:Input Output Module|Save]]

[[Category:Editing Module|Protect]]

|type = module

|type = Python Module This script will help fade in and out settings in a movie. Just specify the setting, it's initial

|module = psico.fitting ...n, like, align, none or the name of an alignment object (see [[local_rms]] help for details) {default: align}

|type = Python Module [[psico]] is a python module which extends PyMOL with many commands. It was developed as an in-house scr

|module = psico.editing

[[Category:Editing Module|Fuse]]

|module = psico.mcsalign

|module = psico.fitting

[[Category:View Module|Get View]]

[[Category:Editing Module]]

|module = psico.querying#gyradius

[[Category:Editing Module|Undo]]

|type = Python Module The module '''quickdisplays''' is a package containing several functions for quick sta

[[Category:View Module|Set View]]

[[Category:View Module|Show]]

= string module = ....org/2/library/string.html#deprecated-string-functions <code>string</code> module functions are gone], use <code>str</code> methods instead.

Chempy is a python-importable module that can be used to write PyMOL-executable [[scripts]]. help(cpv)

[[Category:Editing Module|Create]]

This might be a bit tricky: In addition to scipy and numpy, you will need a module called tkintertable (http://code.google.com/p/tkintertable/). Download it a On my Mac I also had to install a new version of the Pmw module (for the GUI). You can get it here:

...nd which takes care of matching atom identifiers (requires the '''psico''' module)

The script can be [[run]], imported as a Python module, or installed with the [[Plugin Manager]].

1. Import '''request''' module

...-only Python variables. The global namespace by default is the '''pymol''' module namespace, and thus exposes objects like '''cmd''' and '''[[pymol.stored|st ...namespace, instead of evaluating the expression in the global '''pymol''' module namespace.

Install PyMOL and the Leap Python module from Anaconda Cloud:

Module for reading REMARK records from PDB files and in particular

* Pre-compiled ccealign.pyd python module: http://users.umassmed.edu/Shivender.Shandilya/pymol/cealign08/ccealign.zip # '''ccealign.so''' module into '''PYMOL/ext/lib/python2.4/site-packages'''

|type = Python Module

After importing the '''pymol''' module, PyMOL's event loop has to be started with a call to '''pymol.finish_launch

# Do install [https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads the current Microsoft Visua # First install "numpy" as an available module to Python. [http://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy Select appropr

[[Category:Input Output Module|Load]]

|type = Python Module

* Python module dependency

...between the ligand and a user specified protein using the 'show_contacts' module described below.

* [[psico]] is a python module which extends PyMOL with many commands

# using the array module for efficient arrays of numeric values