Dear Warren and Martin,

Thank you for your answers.

I'm using the free version 0.99rc6, so the function "matrix_copy" is not available. 

However, I performed my alignment, saved my pdb file and redid the process PBD2PQR+ABPS. After that, I'm able to load the PQR files and the corresponding maps into PyMol and it's perfect for me.

Best regards,
Romain


Am 20.03.2009 um 18:16 schrieb Romain Studer:

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.

The electrostatic maps loaded into pymol aren't moved together with your protein. You can do the alignment first (in pymol) and then write out pdb/pqr files. After processing these with apbs, you can load the maps with files again.

Hope this helps.

Best
Martin


Le 20 mars 09 à 20:16, Warren DeLano a écrit :

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.studer@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
 
Swiss Institute of Bioinformatics
Evolutionary Bioinformatics Group - FBM / DEE
 
 
 
------------------------
 

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

--



-----
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