Protonate parts of a model

[a.rohou@…]

From chimerax-users thread "addh to only parts of a model?":

Alexis (partial): 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).

Eric (partial): Probably the only feasible method for partially protonating a model would be to remember the initial protonation state of the model, add hydrogens, then remove any hydrogens that were added outside the target area.