[phenixbb] NCS problem

Francis E Reyes Francis.Reyes at Colorado.EDU
Tue Apr 22 14:05:27 PDT 2008

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:

> 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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Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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