Although it is technically possible to drag maps along after their structures using the matrix_copy command, my advice is to pre-align all of the structures you wish to compare and then save them back out prior to performing the electrostatics calculations.


If that does not meet your intended purpose, then use matrix_copy as follows, to bring the maps into alignment with the transformed objects:


matrix_copy source_name, target_name


Where source_name is the transformed molecule and target_name is the transformed map (or mesh, or surface) object


PyMOL isn’t yet sophisticated enough to do this automatically, or interactively…though the need is apparently there.






From: Romain Studer []
Sent: Friday, March 20, 2009 10:21 AM
Subject: [PyMOL] How to manipulate different proteins with electrostaticmaps?


Dear all,


I'm working with PyMol-X11Hybrid on MacOSX.


I have 5 different homologous proteins.


I used pdb2pqr to convert all my proteins.


For each protein, I applied APBS in command line to get the electrostatic maps.


I am able to load all proteins (.pdb) in PyMol and the corresponding electrostatic maps (.dx).


But I can't manipulate them. If I align all to one structure, if I rotate them and if I made translations, 

the electrostatic map doesn't stay on the structure.


I followed the insctrutions gived by Warren in July 2008 (see at the end of my email), but it still doesn't work. I can't view two or more structure with electrostatic map in the same window in PyMol.


I would to know if it is possible to fix the electrostatic map (ie colours blue and red) onto the surface of the protein?


Thank you in advance.



Best regards,




Romain Studer

Department of Ecology and Evolution

Biophore, University of Lausanne

CH-1015 Lausanne, Switzerland.

Tel: +41 21 692 4221    Fax: +41 21 692 4165


Swiss Institute of Bioinformatics

Evolutionary Bioinformatics Group - FBM / DEE







If you're still having trouble getting what you want with Michael's APBS
Plugin, here's how I might display two such maps using PyMOL commands

load pdbset1.pqr
load pdbset_1.dx

load pdbset3.pqr
load pdbset_3.dx

ramp_new ramp1, pdbset_1, [ -3, 0, 3]
ramp_new ramp3, pdbset_3, [ -3, 0, 3]

show surface

set surface_ramp_above_mode

set surface_color, ramp1, pdbset1
set surface_color, ramp3, pdbset3

Note that the surface_ramp_above_mode setting colors surfaces based on the
potential that would be felt by an atom in contact with the surface, as
opposed to the potential at the molecular surface itself (which is less
meaningful, since no atom could ever feel such a potential).