Roger,
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.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Roger Dodd
Sent: Thursday, December 18, 2003 3:53 AM
To: pymol-users@lists.sourceforge.net
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.
cmd.set("coulomb_dielectric",80.0)
cmd.map_new("e_pot","coulomb",1.0,"pept",5)
cmd.ramp_new("e_lvl","e_pot",[-3.6,-1.6,0.4])
cmd.set("surface_color","e_lvl","pept")
cmd.refresh()
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
--
Roger Dodd
CIMR
Addenbrooke's Hospital
Cambridge
