id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
20109	Protonate parts of a model	a.rohou@…	Eric Pettersen	"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.
"	enhancement	assigned	moderate		Structure Editing				Elaine Meng				all	ChimeraX