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.
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.
From: firstname.lastname@example.org [mailto:email@example.com] On Behalf Of Roger Dodd
Sent: Thursday, December 18, 2003
Subject: [PyMOL] Display of
electrostatic potential surfaces
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.