[Chimera-users] Change the formal charge of amino acid side chains

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 21 09:32:27 PDT 2020

Dear Friederike,
I don't know if Chimera is the best approach, but if I absolutely had to do it in Chimera these would be my steps:

(1) text-edit PDB file to change residue names to signify the neutral state: GLU -> GLH,  ASP -> ASH, LYS -> LYN, and HIS -> HIE or HID.  HIE means neutral with epsilon nitrogen protonated, whereas HID means neutral with delta nitrogen protonated.  There is no option in Chimera to intelligently choose between only these two based on each residue's local environment (the automatic-choice approach could make some of them positively charged).  There is no option for ARG so you will have to deal with that later.

(2) open the edited PDB file in Chimera, add hydrogens using command: addh useGluName true useAspName true useLysName true useHisName true

(3) In Chimera decide which hydrogen you are going to delete from each arginine. I'm thinking it would be HE (the one on the non-terminal nitrogen) but you should check the chemical diagram to make sure that's the one you want to get rid of.  To delete HE on all arginines, command: delete :arg at he

(4) Save PDB from Chimera.  Depending on what you need this for, after that you probably have to text-edit the residue names back to normal ones (the reverse of the changes in step 1).

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 21, 2020, at 6:09 AM, Friederike Leßmöllmann <friederike.lessmoellmann at ufz.de> wrote:
> Dear Chimera users,
> I need to change the formal charges of all charged AA side chains in a protein to be neutral and all open valencies to be filled with explicid hydrogen. I am very new to Chimera and I basically downloaded it in hope to find a solution to my problem. I know, it is not common to change the charge of a side chain and shouldn't be done usually. Does anybody have an idea how to do this anyway?
> Thanks a lot in advance!
> With kind regards
> Friederike

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