Dear ChimeraX users!

I have a question about the protonation of ligands in the complex. When I protonate only a ligand (using addh :LIG) I see in the log that it takes into account the hydrogen bonds.

Does it mean that it defines the protonation state of each titratable group based on its local chemical environment of binding pocket? If so, is it possible to manually define the total charge of the ligand (and protonate it according to it)?

Many thanks in advance!

Enrico