[Chimera-users] command line: how to add hydrogens to a phosphate group?

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 15 08:11:34 PDT 2021

Hi Sara,
You have to change the atom type of the O3- atoms to O3, and then add the hydrogens.  For example, commands:

setattr a idatmType O3 O3-

see details of the "setattr" command:

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

> On Jun 15, 2021, at 4:23 AM, Sara Luz Gomez Maya via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hi,
> I have a system consisting of a molecule intercalated into DNA. For a very specific application, I need to remove all the Sodium atoms from a PDB file and, in turn, add hydrogens to all the DNA phosphate groups (whatever the oxygen). Since for chimera that atom type is identified as O3- (possibly resonance-equivalent terminal oxygen on tetrahedral center (phosphate, sulfate, N-oxide), I have tried:
> labelopt info idatmType
> label #0
> addh spec O3-
> but it did not work.
> You can find attached herewith the pdb file. 
> Any help is appreciated.
> Regards,
> Sara
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