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
