[phenixbb] Fix coordinates of one single residue

Pavel Afonine pafonine at lbl.gov
Fri Oct 28 00:25:34 PDT 2016

I agree, while technically it is possible to stop selected atoms from 
moving during refinement, it is much better to find out why refinement 
wants to move them (in a wrong place, as you seem to believe).

If you send me model (before and after refinement) and data files, and 
tell what residue you are looking at, then I might be able to tell 
what's going on..


On 10/27/16 21:19, Dale Tronrud wrote:
>     I think it would be better to understand why phenix.refine is pushing
> one conformer out of density while leaving the other in. There is likely
> some problem with the ideal geometry definition or with your description
> of the alternative conformations.  Forcing phenix.refine to accept your
> model, as is, prevents it from properly optimizing the side chain.
> Dale Tronrud
> On 10/27/2016 8:52 AM, ancacarl wrote:
>> Hi,
>> I'm working on the refinement of a protein mutated with an unnatural
>> amino acid that is present as two rotamers. Whenever I do refinements,
>> one of the rotamers moves away from the electron density map. I
>> therefore would like to
>> fix the coordinates for this amino acid only while continuing the
>> refinement of the rest of the protein. Is there a way in Phenix to do
>> this?  Any advice is welcome.
>> Best regards,
>> Anna-Carin

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