It is a bit hard to understand why without looking at the structure..
One reason things get disordered is if the occupancies get misset so
they add up to a number > 1.0. In that case REFMAC decided this a a
"clash situation" and tries to remedy it ..
Could that have happened?
I build alternate conformations ifI can see them. Obviously they
exiist at every resolution, but like waters, it helps to position them
if the density is sharp.
Eleanor
Leonard Thomas wrote:
> I have been going over some structure for a group here. When the
> post-doc did the originally modeling a number of residues looked to
> have alternate conformations. The resolution of the structures are
> between 2.0 and 1.9 angstroms. My first question is when re-refining
> in with an updated version of Refmac the residues with the alternate
> conformations become highly disordered. The original version Refmac
> used was 5.2.0019 and the new version Refmac is 5.5.0088. I think the
> original ccp4 version was 6.0.2 and the latest version of ccp4 is now
> being used. All refine runs were done under OS X though on different
> processors. As far as I can tell all the input parameters are the
> same. Any ideas as to what is going on.
>
> As a followup question, at what point do you actually consider
> alternate conformations? The current resolution of these structures
> seem to be an a gray area from my perspective, the the density seems
> to indicate alternate conformations.
>
> Cheers,
>
> Leonard Thomas Ph.D.
> Macromolecular Crystallography Laboratory Manager
> University of Oklahoma
> Department of Chemistry and Biochemistry
> 620 Parrington Oval
> Norman, OK 73019
>
> [log in to unmask]
> http://barlywine.chem.ou.edu
> Office: (405)325-1126
> Lab: (405)325-7571
>
>
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