[phenixbb] XYZ refinement vs individual sites refinement

Kendall Nettles knettles at scripps.edu
Sun Mar 13 13:56:39 PDT 2011

Yuri, I don't think this is a good idea.    I would suggest running the refinement with the residue in the different positions. I would also make an alternate conformer and refine occupancy. Lastly I would refine after deleting the side chain.

Kendall Nettles

On Mar 13, 2011, at 1:38 PM, "Yuri" <yuri.pompeu at ufl.edu> wrote:

> I am new to phenix and I am trying to probe two residues that are 
> putative H-bond partners, after refinement they seem to be put in 
> orientations that would make it impossible for them to be interacting 
> with a ligand. My SA composite omit map may suggest that one of the Asn 
> could be in a different position.
> My question: If I manually change its conformation is it wise to keep 
> its position fixed during refinement to see what the new maps would 
> look like? If so where would I do that under the real space or 
> individual sites tab on GUI phenix? I am not sure what these 2 tasks 
> accomplish exactly.
> Any guidance would be appreciated.
> Thanks
> Yuri Pompeu
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