[chimerax-users] addh

[Voss Jonathan Mark]

Hi Elaine,


Thank you for the detailed example. It is exactly what I was looking for! As you recommended, I will use the setattr command to change the states of residues throughout my structure.


Thank you again,


Jon

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, March 23, 2022 3:57:07 AM
To: Voss Jonathan Mark
Cc: chimerax-users at cgl.ucsf.edu
Subject: Re: [chimerax-users] addh

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 at 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

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