CSB Home | Search | Table of Contents | General Information

Electrostatics in PyMOL


Some  work has been done to add display of electrostatic potential surfaces to PyMOL. Michael Lerner at the University of Michigan has written some PyMOL add-ins that allow PyMOL to interface with the electrostatic calculation program APBS. One can set up an APBS calculation from within PyMOL, then display the resulting positive and negative isosurfaces.

To use this special version of Pymol in the Core on a Linux workstation, simply type:

setup pymol-electro
Then from the Wizard menu, select APBS Tools to set up an electrostatic model and calculation, and select Electrostatics to display and customize the results. Each of these wizards has a help button; in the case of the APBS Tools, the help display is actually useful.

An basic outline of how to proceed:

Disclaimer

Note that these tools are the result of someone's personal customizations of an obsolete version of PyMOL, tweaked to work in the Core. Note also that the APBS program is currently at release 0.3.1. All of this means that these tools are a rough work in progress. If it doesn't seem to be doing something right, it probably can't do it right. The Core staff cannot provide detailed help with these tools.

Return to the main PyMOL page.


CSB Home | Search | Table of Contents | General Information

Center for Structural Biology (www.csb.yale.edu), Yale University (www.yale.edu)
Contact: webadmin(at)mail^csb^yale^edu
Last Modified:Thursday, 15-Jul-2004 11:02:06 EDT by M. Strickler