[phenixbb] XYZ refinement vs individual sites refinement
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.
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.
> Yuri Pompeu
> phenixbb mailing list
> phenixbb at phenix-online.org
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