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:warren@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-admin@lists.sourceforge.net [mailto:pymol-users-admin@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