Hi, at this purpose, what kind of range (positive - negative) should be used in order to visualize correctly the potential surface on a protein? Normally I used -10 to +10 but I am wondering how you behaves with this issue too.
Thanks in advance andrea 2006/11/23, D. Eric Dollins <d.e.doll...@gmail.com>:
Florian, I had the same problem and I couldnt get everything to work internally in pymol. I never got pymol to write the *.pqr files. I couldn't figure it out. However, you can give your pdb to the PDB2PQR server: http://agave.wustl.edu/pdb2pqr/server.html Strip the waters/ligands and load in your pdb. Choose that you want to create an APBS input file. You get 2 files: *.pqr and *.in. Rename without .txt extension (if the output has them. My mac put them on). You can load input pdb (the one with waters/ligands stripped). Change the temp file locations (temp.pqr, *.pdb, and APBS input file). Don't change the "pymol generated dx". Under main, choose "use another pqr". Choose "externally generated" pqr and browse for your x.pqr. Click "set grid". Click "run APBS". That will spit out a "pymol-generated.dx". In pymol type load_dx [file].dx. In APBS window, go to the visualization tab and choose "show mol. surface". Change levels and update. Perhaps not the best way to get this to work, but it will give you a surface to look at. Good luck, Eric On 11/22/06, Florian Schmitzberger <florian.schmitzber...@ki.se> wrote: > Dear All, > > I am having a small problem using the apbs plugin in pymol on my pdb (I am > using fink installed pymol and apbs versions on Mac OSX 10.4.8). > > When I try to run apbs I received the following message: > > "Unable to assign parameters for 100 atoms in the selection unassigned. > Please either remove these unassigned atoms and re-start ..." > > In principle, I think I understand the problem is that pdb2pqr cannot assign > charges to certain atoms, in my case posttranslationally modified cysteine > residues. > > My question would be what the best way to fare with those atoms is. Since > the modification introduces an acidic patch, if possible I would like to > leave the atoms in (rather than remove them) when calculating surface charge > representation, as this could be informative. > > So perhaps my question boils down to what the optimal way to manually assign > reasonable charges (in the pqr-file) for this oxidised cysteine (sulfinic > acid; O-S=O) is. > > I also noticed that I get the same error message with residues where > side-chain atoms have been removed (such as surface lysines), while leaving > the original residue name. But then I suppose there is no way around this. > > Thank you very much in advance for any comments! > > Best regards, > > Florian > > -------------------------------------------- > Florian Schmitzberger > Medical Biochemistry and Biophysics > Karolinska Institute > Scheeles vaeg 2 > SE-171 77 Stockholm, Sweden > Tel: +46-8-524-86875 > > > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > -- D. Eric Dollins C266 LSRC, Box 3813 Duke University Medical Center Durham, NC 27710 (919)681-1668 ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
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