Hi,
Did you get an answer to this already? I've been swamped recently, so I
haven't answered many PyMOL/APBS questions. Anyway ..
I don't know anything about MSMS data and plotting surfaces, but I know a
bit about PyMOL + APBS. APBS calculations (like a lot of other
electrostatics calculations) require a PQR file. This is just a PDB file
that also has information about the charge and radius of each atom. There
are good sets of standard parameters for generating PQR files for standard
amino acids, so PyMOL can automatically generate PQR files most proteins.
However, it can't automatically generate PQR files for non-standard
protein residues. It also can't generate PQR files for non-proteins.
From your question, I think you already know this, which brings me to the
little bit of help that I might be able to provide:
I don't know how you do your electrostatics calculataions, but if you
generate a PQR file somewhere along the way, you can tell the APBS plugin
to use that PQR file (and then you can use the APBS plugin to do your
electrostatics calculations and show the results with the APBS plugin,
etc.).
If you don't use PQR files, or if you don't want to use APBS to do your
electrostatics calculations, you can still probably convert your results
to a format that PyMOL understands. The DX format is a particularly easy
one to read and write .. you can find some documentation here
http://agave.wustl.edu/apbs/doc/html/user-guide/x2539.html
and I can probably help you out with it if that's not enough. If you can
convert things to a PyMOL readable format, you can use the APBS plugin to
show the electrostatic potential (or you can just use the built-in PyMOL
commands like isosurf, isomesh, etc.).
I get the feeling that I've said a lot, none of which will actually be
useful .. sorry about that if it's true!
thanks,
-michael
--
This isn't a democracy;|_ |Michael Lerner
it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
-Torrence, Bring It On| - against HTML email X | Biophysics
| / \ | mler...@umich
On Sat, 16 Oct 2004, Alan Wilter Sousa da Silva wrote:
Hi List!
I was wondering why PyMol does not do the same as VMD about importing data
from MSMS and plotting surfaces. So, I would not have problems anylonger
about making surface of drugs or ligands that are not based in residues.
Moreover, I finally could use apbs plugin to draw electrostatic surface of
some drugs that we have been studied here.
How about it?
Or is there another alternative?
Thanks in advance for any commentary.
Cheers,
--
--
Alan Wilter Sousa da Silva
--
D.Sc. - IBCCF/UFRJ
Projeto BioPAUA - HP/LNCC
Petrópolis (RJ), Brasil
www.lncc.br/~alan
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