Hi all,
As specified in the documentation, in command addh, "Hydrogens are added to
entire atomic model(s) even if only parts of models are specified."
Given how specifically this is stated, I'm guessing there was a good
rationale for doing it this way.
However I am facing a situation where I'd really, really like to add
hydrogens only to waters (which were added by Servalcat). For reasons that
I haven't got to the bottom of, addh adds hydrogens in the wrong places in
a ligand I'm working on (a peptide with a mixture of natural and
non-canonical amino acids, though I'm almost certain I've observed this
behavior with other, less exotic, ligands).
So: what is/was the rationale for not allowing users to add hydrogens to
only parts of a model? How would the developers feel about a pull request
adding an option to override this behavior and only add hydrogens to the
spec supplied by the user?
Cheers,
Alexis
