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PDB protein crystal structures most of the time lack hydrogen atoms. Usually I use PyMOL (h_add) but it does not always seem to be giving the correct result. What can I use for accurate hydrogen addition?

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I've used Reduce before, which is excellent. I'm not sure what you mean by ' does not always seem to be giving the correct result', though? Perhaps you could file a bug report with the PyMOL team if you think there is a bug in h_add.

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    $\begingroup$ Indeed, I think the PyMOL team would be highly interested in knowing about bugs in hydrogen addition from a PDB crystal structure. $\endgroup$ – Geoff Hutchison Jun 1 '15 at 14:54
  • $\begingroup$ @GeoffHutchison : True. Actually, it wouldn't be so hard to run h_add and Reduce over some subset of the pdb (small, high-res structures?) to see what differences there are - if any. $\endgroup$ – gilleain Jun 1 '15 at 16:22
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Olex2 (free, available for Windows, MacOS, Linux) can also be used to add hydrogens to any structure with the similar to PyMOL's command hadd. Example: hemoglobin PDB without H-atoms loaded in Olex2:

enter image description here

Executing hadd command adds hydrogens to all atoms where it is appropriate (taking hybridization into account), chemdraw assigns proper bonds order:

enter image description here

Alternatively, one can only populate certain atom types with hydrogens by selecting them first, e.g. for carbons: sel $C, then hadd. Also, one can hide/show added hydrogens by pressing Ctrl+H.

To save the file, type file name_of_protein.xyz. Saving in PDB also works, but the metadata/header is going to be lost, and sometimes the PDB file cannot be read properly by third-party software. So XYZ is the most safe option here.

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There are many software packages that do what you request. PHENIX, Schrodinger, SCWRL4. It depends on how accurate you want, and options for pH etc.

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