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I agree.<br>
<br>
At least I would try both: with and without NCS, carefully inspect the
results and follow whatever works better. <br>
<br>
Pavel.<br>
<br>
<br>
On 4/22/2008 2:05 PM, Francis E Reyes wrote:
<blockquote cite="mid:CC62A2DE-44A2-4604-834B-59477343DE35@colorado.edu"
type="cite">
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">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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<pre wrap=""><!---->
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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