PyMOL Plugins

PyMOL Plugins are user-developed modules that extend PyMOL's capabilities via the Tcl/Tk user interface. In order to use them, you'll need an Tcl/Tk-based version of PyMOL (on Macs, this means either the Fink or X11/Hybrid versions -- not the Aqua-based MacPyMOL).

• pynmr (Leigh Willard and Stephane Gagne)
  Features loading of multiple pdb files, dihedral restraints checks, NOE restraints checks, and superposition routines.
   
CAVER (Martin Petrek)
For identifying and visualizing access routes to protein cavities.
 
• PDB Loader Service (Charles Moad)
  This plugin allows you to download a PDB file straight into PyMOL simply by entering the PDB code.
   
• APBS Tools (Michael Lerner)
  An easy interface for performing APBS electrostatics calculations from within PyMOL (requires APBS).
   
• DivScore (Kaushik Raha)
  A plugin for use with Amber ($$$ for commercial usage) and DivCon ($$$ for all usage) that is designed to perform modeling tasks involving proteins and small molecules.
   
• GPSSpyMOL (Andrew Binkowski)
  A plugin for visualizing surfaces and voids using the CASTp algorithm. This plugin replaces CASTpyMOL. (Updated March 3, 2006)
   

PyMOL 0.97 and 0.98 can install plugins into the correct directory automatically, via the "Install Plugin..." menu item. Some early versions of 0.98 weren't able to install plugins, so download the latest 0.98 release if you're having trouble (http://delsci.com/rel/0_98.

PyMOL Plugins need to be installed in the following directory:

   $PYMOL_PATH/modules/pmg_tk/startup
   (or /usr/lib/python2.X/site-packages/pmg_tk/startup for distutils-based installs)

On Windows, this is usually:

   C:\Program Files\DeLano Scientific\PyMOL\modules\pmg_tk\startup

On Macintosh, with the X11/Hybrid version, you need to right-click and "Show Package Contents" on the PyMOLX11Hybrid bundle and copy the plugin into:

   PYMOLX11Hybrid.app/pymol/modules/pmg_tk/startup

If you're unsure where PyMOL is located, then launch PyMOL, type "cd $PYMOL_PATH", and then "pwd"

Some plugins may require that additional programs or files be installed elsewhere, so please check the instructions available with each individual plugin.

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