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 > > > ------------------------------------------------------- > This SF.net email is sponsored by: IT Product Guide on ITManagersJournal > Use IT products in your business? Tell us what you think of them. Give us > Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more > http://productguide.itmanagersjournal.com/guidepromo.tmpl > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
