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