The problem with computing electrostatic maps in PyMOL currently is that the Coulomb equation assumes a uniform dielectric and thus doesn’t give you correct potentials for macromolecules.  It is much better to use an external tool such as Grasp, MEAD, APBS, or Delphi, which can apply a different dielectric constant to the inside of the protein than to the surrounding solvent.


            Yes, PyMOL can compute a Coulombic map using the approach you’ve outlined if partial charges have been assigned – but there isn’t a good way to do that in PyMOL just yet.




Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax   (650)-593-4020

-----Original Message-----
From: [] On Behalf Of Roger Dodd
Sent: Thursday, December 18, 2003 3:53 AM
Subject: [PyMOL] Display of electrostatic potential surfaces


Dear PyMOL users,


I would like to generate a figure of my protein where the surface electrostatic potential is displayed. PyMOL now comes with a demo function for display of such a surface. However, when I apply the commands used in this demo, i.e.




to the model from my pdb file, I get a uniformly blue surface. I believe this must be due to the lack of assignment of partial/formal charges to the atoms in the pdb file. So, my questions are:


1. Is it possible to automatically assign the correct charges to atoms within PyMOL

2. If not, is there a program that will do this and if so can the output from this program be understood by PyMOL in some way.


Thanks for your help





Roger Dodd


Addenbrooke's Hospital