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
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
Subject: [PyMOL] How to manipulate
different proteins with electrostaticmaps?
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
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?
of Ecology and Evolution
University of Lausanne,
+41 21 692 4221 Fax: +41 21 692 4165
Institute of Bioinformatics
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
ramp_new ramp1, pdbset_1, [ -3, 0, 3]
ramp_new ramp3, pdbset_3, [ -3, 0, 3]
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).