To answer your question regarding ISOLDE: yes, if you change the protonation state of an acid or histidine residue then it will be treated as (un)charged accordingly. If you just want to protonate a single acid, you could select the relevant oxygen and then do ISOLDE/Model Building/Add Hydrogen. For a histidine, select any atom in the residue, then use the command "isolde mod his sel {ND|NE|both}" (or "isolde shorthand" once, then "ht {ND|NE|both}" from then on), where "ND", "NE" or "both" refer to the nitrogen(s) to be protonated.

-- Tristan

From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Voss Jonathan Mark via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: 23 March 2022 09:06
To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] addh

Hello,

I would like to protonate ASP, GLU, and HIS side chains throughout a model. I'm a little confused about the syntax of the useAspName, useGluName, etc. option. I've looked around but haven't found any examples. Could you provide one?

Furthermore, once a side chain is protonated, will ISOLDE recognize that site as being charged? Or does this need to be specified somehow?

Best

-Jon