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

[Eric Pettersen]

Elaine is correct, but the command she suggests will protonate every phosphate oxygen, whereas you likely only want to protonate one per phosphate group.  Assuming the phosphate oxygens are named OP1 and OP2, you could protonate all the OP2s with:

	setattr a idatmType O3 @OP2
	addh

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jun 15, 2021, at 8:11 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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-
> addh
> 
> see details of the "setattr" command:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> 
> I hope this helps,
> Elaine
> -----
> 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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