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.

[Eric Pettersen]

addh now accepts an atom spec instead of a model spec and only protonates atoms in the atom spec

[a.rohou@…]

Thanks Eric!

On Tue, Jun 16, 2026 at 11:41 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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[a.rohou@…]

Hi Eric,

If Claude summarized your fix correctly to me, I think your implementation
will have undesirable side effects. Suppose for example that I have an
already-protonated ligand, which I place into a protein that isn't yet
protonated. I then want to use "addh #1 & ~ligand" to protonate the protein
but leave the ligand alone. Claude reckons that addh would actually strip
hydrogens off of my ligand. I think this is undesirable behavior. The
command is called "addh" - it should add zero or more hydrogens, not remove
any...

#20109: Protonate parts of a model
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[Eric Pettersen]

That diabolical Claude is correct. I have committed a fix.