Hello Pymol-users,
I have a problem mapping electrostatics on the surface of my pdb file
generated using the hhpred modelling method.
I load my pdb file and then do actions->generate ->vacuum
electrostatics->protein contact potential.
Pymol does a number of calculations and generates some objects, but then
finally ends up with an error message:
Fixing termini and assigning formal charges...
Util: Assigning Amber 99 charges and radii...
util.sum_formal_charges: sum = 15.0
util.sum_partial_charges: sum = 15.000
Util: Calculating electrostatic potential...
ObjectMap: Map created.
SelectorMapCoulomb: Total charge is 15.000 for 5455 points (5455 atoms).
SelectorMapCoulomb: Evaluating local Coulomb potential for grid
(shift=10.00)...
Executive: object "hhpred_531_879_mdl_060918_chain_e_pot" created.
Setting-Error: unknown color 'hhpred_531_879_mdl_060918_chain_e_pot'
I end up with a surface which has green, blue and red patches and not
the nice white,blue and red one that I see whenever I try this command
on other test pdb files. Does anybody know what is the problem?
-Pernille
--
Pernille Haste Andersen, M. Sc., Ph D. student
Immunological Bioinformatics group,
Center for Biological Sequence Analysis,
BioCentrum-DTU,Technical University of Denmark,
Bld. 208, DK-2800 LYNGBY, DENMARK
Tel:(+45) 45252472
E-mail : p...@cbs.dtu.dk
