Hi Jon, I guess you mean that for specific residues, you don't want the default result of negatively charged carboxylates in ASP and GLU sidechains. HIS is more complicated in that the default is to use the local environment to decide between delta-protonated neutral, epsilon-protonated neutral, or both sidechain nitrogens protonated (formal charge +1) sidechain states. To use the name-directed options, you would actually have to text-edit the residue name of the specific residue(s) in the input file to reflect the desired protonation state (e.g. change ASP to ASH) or in ChimeraX, use the setattr command to change the residue name, before you run "addh." Here is an example with a setattr command and then addh with the corresponding option: open 1zik show delete solvent label /B setattr /B:7 residues name ASH addh useAspName true ...of course you could change multiple residue names before adding the hydrogens, and use more addh settings including the other name-directed options. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/addh.html> I do not know how well this works with ISOLDE, however - let us know what you find out! Thanks! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 23, 2022, at 2:06 AM, Voss Jonathan Mark via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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

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