[phenixbb] NCS problem
pafonine at lbl.gov
Tue Apr 22 14:13:00 PDT 2008
At least I would try both: with and without NCS, carefully inspect the
results and follow whatever works better.
On 4/22/2008 2:05 PM, Francis E Reyes wrote:
> 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.
> On Apr 22, 2008, at 7:42 AM, Bobby Huether wrote:
>> 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
>> 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
>> 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
>> for a disordered ligand.
>> Can phenix.refine handle this situation?
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
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