[phenixbb] NCS problem

Bobby Huether bhuether at hwi.buffalo.edu
Tue Apr 22 06:42:28 PDT 2008


My structure contains 2 protein molecules in the asymmetric unit, and they
are related by 2-fold rotational NCS to form a dimer. The  refinement is
nearing completion (1.7 A) and the solvent molecules are now being included.
A blob of density has been tentatively identified as being occupied by
glycerol, which was present as the cryo-protectant. The issue is that this
blob of density lies on the 2-fold NCS rotation axis, and so we need to use
2 glycerol molecules within this density, each at 0.5 occupancy, to conform
to the NCS symmetry. This blob of density lies in a surface pocket formed by
residues from both NCS-related proteins.

When we build in the 2 glycerol molecules and then use phenix.refine, the
two glycerols are pushed out of density. Presumably this is because
phenix.refine is interpreting this situation as two glycerol molecules
sitting on top of on another rather than interpreting it as being a model
for a disordered ligand.

Can phenix.refine handle this situation?


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