Romain,
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. Cheers, Warren ________________________________ From: Romain Studer [mailto:romain.stu...@unil.ch] Sent: Friday, March 20, 2009 10:21 AM To: pymol-users@lists.sourceforge.net 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 ----- 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 http://bioinfo.unil.ch/ Swiss Institute of Bioinformatics Evolutionary Bioinformatics Group - FBM / DEE http://www.isb-sib.ch/ ------------------------ Youzhong, 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 directly: 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). Cheers, Warren --
