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