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