You may want to drop the symmetry to see what is happening with the loop.
James
On Jun 10, 2014, at 11:48 AM, Nicholas Keep <[log in to unmask]> wrote:
> Am refining a structure in P3(1)21 with three copies in the ASU. It is pretty close to completion R/Rfree 18/21 with 2A data.
> However in one copy a section that is clear in the other two is poor as it meets itself on a two fold.
>
> My interpretation is that one copy of the loop is in a visible conformation that is on the two fold axis and the symmetry related copy is disordered so it does not clash. Presumably close to half the time the ordered copy is from one side and the rest from the other to give the symmetric density.
>
>
> If you push the structure into the density then the symmetry related copy clashes.
>
> Is this conformation refineable in refmac5 or phenix if the occupancy is set to zero?
>
> Should I allow clashes to push both copies either side of the density as is currently happening?
>
> Any tips on dealing with this?
>
> Best wishes
> Nick
>
> --
> Prof Nicholas H. Keep
> Executive Dean of School of Science
> Professor of Biomolecular Science
> Crystallography, Institute for Structural and Molecular Biology,
> Department of Biological Sciences
> Birkbeck, University of London,
> Malet Street,
> Bloomsbury
> LONDON
> WC1E 7HX
>
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