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Plugins are external modules that add functionality to PyMOL.

Plugins can be single Python files (*.py) or directories with an file (see PluginArchitecture).

Looking for available Plugins? Browse the plugins category.

Installing Plugins

To install a plugin, open PyMOL and then go to

Plugin > Plugin Manager > Install new plugin

You will have the option to install from a file on your computer (*.py, *.zip) or directly from the PyMOLWiki by providing the wiki page url.

Plugin manager install new.png

Writing Plugins

See the Plugins Tutorial.

Legacy Notes

Version 3.0

Currently, support for plugins written in Tkinter is considered deprecated with full expectation of removal by PyMOL 4.0. Plugin developers should consider migrating legacy plugins to PyQt.

Before Version 2.0

Plugins written with PyQt5 do not run in PyMOL 1.x.

PyMOL 2.x has a legacy layer for Tkinter to support old plugins, but the preferred toolkit for new plguins is PyQt5.

Before Version

Before PyMOL's Plugin Manager was added in version, plugins could not be installed per user, the plugin search path was a single directory inside the PyMOL installation: $PYMOL_PATH/modules/pmg_tk/startup

Plugins were limited to single Python files, directories were not supported yet.


MacPyMOL was the native macOS version of PyMOL before version 2.0. It supported Plugins only in the X11 Hybrid mode.

See Also