Re: [PyMOL] Adding Hydrogens

[Martin H. <ma...@bl...>]

Dear all, thanks for the feedback, I'll definitely give it a try.





On 16.03.11 16:50, Michael Lerner wrote:
> I've had good results with MolProbity 
> (http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18c&eventID=15 
> <http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18c&eventID=15>) 
> in the past.
>
> I had a script that would let me cycle through all of the HIS 
> residues, add hydrogens, and cycle between states. It's broken at the 
> moment. The trick was that PyMOL doesn't care about the name of the 
> residue, so you have to manually cycle the valences.
>
> On Wed, Mar 16, 2011 at 11:22 AM, Martin Hediger <ma...@bl... 
> <mailto:ma...@bl...>> wrote:
>
>     Dear All
>     I would like to ask if the PyMOL function to add hydrogens to an
>     entire
>     protein also has options, meaning is it possible to set the
>     protonation
>     state of individual residues specifically? Like in a list or
>     something?
>     h_add, His202:+1 or so?
>     And, it can be relevant at what atom a residue gets protonated:
>     His can
>     be protonated at Nd, or Ne or both. Is there a way to control this?
>
>     On a more general note: what other smart hydrogen adding tools are
>     there
>     out there anyway? Does anyone know a really smart tool for this? I
>     know
>     OpenBabel has a pH parameter. But on the other hand OpenBabel just
>     appends the hydrogens to the PDB file, whereas PyMOL really writes
>     them
>     within the block of atoms corresponding to one residue.
>     Also, AutoDock can add hydrogens and it even has an option for the
>     protonation state of histidine, but it doesn't seem to work in my
>     case.
>
>     Thanks for your answers and input.
>     martin
>
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> -- 
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
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