From PyMOLWiki
Jump to: navigation, search



Plugins are external modules that add functionality to PyMOL. Latest version of PyMOL came with two plugins already installed APBS and PDB_Loader_Service. Since version PyMOL also comes with a Plugin Manager, which can be used to conveniently install and uninstall plugins. You can find a list of several available PyMOL plugins on this page. If you are interested into writing your own plugin please read the Plugins_Tutorial.

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 or directly from the PyMOL wiki by providing the proper url (the name of the plugin's page at the PyMOL wiki).

Below you will find some more information that may be relevant when installing plugins and that is specific to different operating systems.

Plugins on Linux

On Linux, PyMOL is generally installed on a system's folder. Thus, if you want to install plugins you should launch PyMOL from a terminal using the command:

sudo pymol

Alternatively, if you launch PyMOL without administrators rights. The plugin manager will ask you if you want to install the plugin on the local folder


Plugins on OS X

Using MacPyMOL

The standard OS X Pymol application, does not run with the Tcl/Tk interface which is required for plugins to work. However, a quick renaming of the program from to makes the application run as an X11 application, and plugins are now available.

To rename the executable, right click (or control click) on MacPyMOL and choose "Get Info" in the Panel. Change the Name & Extension to This name can also be changed using the mv command in

Once this change is made, half of the program will show up under the X11 icon, and half will show up under the MacPyMOL icon.

Using a Package Manager

An alternative to renaming MacPyMOL is to download the PyMOL installation using a package manager such as Fink, MacPorts, or Homebrew.

fink install pymol-py27



Personal tools