I've had good results with MolProbity (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.hed@bluewin.ch> 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.

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