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This page describes PyMOL's plugin architechture since version

API Entry Points

A plugin is a Python module which uses PyMOL's API. The following entrypoints add functionality to PyMOL:

  1. pymol.cmd.extend(func) registers a function as a PyMOL command
  2. pymol.plugins.addmenuitemqt(label, callback) adds a plugin menu item, should be called inside __init_plugin__
  3. MyPlugin.__init_plugin__(app) is called during plugin initialization (if defined by the plugin)


A plugin can implement an __init_plugin__(app) function (previously __init__, deprecated) which is called during plugin initialization. It is passed an object which is compatible with the legacy PMGApp instance and provides access to the Tkinter parent (app.root).

Example for a PyQt5 GUI (PyMOL 2.x)

See also the Plugins Tutorial

def __init_plugin__(app=None):
    from pymol.plugins import addmenuitemqt
    addmenuitemqt('My Qt Plugin', myqtdialog)

def myqtdialog():
    from pymol.Qt import QtWidgets
    QtWidgets.QMessageBox.information(None, 'My Plugin Title', 'Hello World')

Example for a legacy Tkinter GUI (PyMOL 1.x)

It is important that all Tkinter objects are created with the app.root parent, otherwise legacy plugins won't work in PyMOL 2.0.

def __init_plugin__(app):
    app.menuBar.addmenuitem('Plugin', 'command',
        label='My Tk Plugin',
        command=lambda: mytkdialog(app.root))

def mytkdialog(parent):
        import tkMessageBox  # Python 2
    except ImportError:
        import tkinter.messagebox as tkMessageBox  # Python 3
    tkMessageBox.showinfo(parent=parent, title='My Plugin Title', message='Hello World')

More than one file per plugin

Plugins can be either a single Python file, or a directory with an file.

Single file layout: (defines "__init_plugin__(app=None)" function)

Directory layout:

├── data
   ├── datasheet.txt
   └── image.png
└── (defines "__init_plugin__(app=None)" function)

They can be zipped (.zip) for distribution, the Plugin Manager handles the unzipping during installation.

zip -r MyPlugin

Config files

PyMOL offers a basic API to store custom settings in ~/ Only basic types (str, int, float, list, tuple, dict, etc.) are suppored (those who produce executable code with repr()).


pymol.plugins.pref_set(key, value)

# needed if pymol.plugins.pref_get("instantsave") == False


value = pymol.plugins.pref_get(key, default=None)


apbsbinary = pymol.plugins.pref_get("APBS_BINARY_LOCATION", "/usr/bin/apbs")

PyMOL OS Fellowship Project 2011/2012

Thomas Holder was working on the new plugin system as part of his 2011-2012 Fellowship. The improvements were incorporated into PyMOL

  • graphical Plugin Manager
  • multiple files per plugin/module (see #More than one file per plugin)
  • user plugin directory
  • rarely used plugins can be disabled for better performance and enabled on demand
  • metadata support (version, author, description, citation, tags, ...)
  • install from online repositories
  • settings API for plugins (see #Config files)

See Also