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
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