Re: [PyMOL] apbs plugin in pymol

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...@gm...>:
> 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 <Flo...@ki...> 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 a=
ssign
> > charges to certain atoms, in my case posttranslationally modified cyste=
ine
> > residues.
> >
> > My question would be what the best way to fare with those atoms is. Sin=
ce
> > the modification introduces an acidic patch, if possible I would like t=
o
> > leave the atoms in (rather than remove them) when calculating surface c=
harge
> > representation, as this could be informative.
> >
> > So perhaps my question boils down to what the optimal way to manually a=
ssign
> > reasonable charges (in the pqr-file) for this oxidised cysteine (sulfin=
ic
> > acid; O-S=3DO) 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 lea=
ving
> > the original residue name. But then I suppose there is no way around th=
is.
> >
> > 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
> >
> >
> >
> >
> > -----------------------------------------------------------------------=
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> >
> >
>
>
> --
> D. Eric Dollins
> C266 LSRC, Box 3813
> Duke University Medical Center
> Durham, NC 27710
> (919)681-1668
>
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