[Chimera-users] Is it possible to change the protonation state of only one residue (histidine) of a protein ....

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 19 12:23:46 PST 2012

Hi Sergio,
You can specify how to protonate each ionizable residue using AddH, but it will add hydrogens to your whole structure.  After adding all hydrogens you can delete the ones you don't want, as mentioned below.  For histidine, use the dialog setting "Protonation states for [histidine]" and then check "Chosen individually" to specify the protonation for each histidine in your structure.

If you already have hydrogens you can still use AddH to add more, or if you just want to get rid of some hydrogens, delete them.

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

On Jan 19, 2012, at 12:08 PM, Sergio Garay wrote:

> Hi all
> I'd like to know if it is possible to change the protonatation state of only one particular residue (histidine) in my protein..
> I've been trying to do it using addh tool but with no success, I think it can only work with the protein as a whole, isn' it ? 
> Please, any suggestion is welcomed
> Sergio

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