Not an answer but another question: What reason would you be keeping NCS with a moderately complete model at 1.7A? I would guess that keeping NCS restraints at such a high resolution and completeness would count against you, if not the solvent exposed side chains having different conformations among the molecules in the asu then it would be different solvent configurations around each molecule in the asu. Or maybe you have a super symmetric assembly, but even then in a case where I have three molecules in the ASU, adding NCS seemed to hurt refinement statistics when I had most (90% or better) residues built. Curious. FR On Apr 22, 2008, at 7:42 AM, Bobby Huether wrote:
Hello,
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?
Thanks, Robert
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