[PyMOL] Display of electrostatic potential surfaces

[Roger D. <rb...@ca...>]

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