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Hello Michael--
Sorry for the slow response. We've been out of town, or having babies.
> I get much fewer NOE, CDIH and VDW violations. Though, I still don't have it
> down to zero. As you can see from the attached "sa.stats" file, the RMSDs for
> all the violations are very low. Do people think that this is an acceptable
> number of violations?
The number and size of the NOE violations seem unacceptible to me. The
fact that the NOE rmsd is low indicates that the number of NOE's is very
large. right?
> At the moment my biggest concern is with the large RMSD for the final ensemble
> of fitted structures. When I include only the ordered residues (excluding
> unstructured N and C termini), I still only have about a 2.5 Ang RMSD for
> backbone atoms. I am surprised it is so large.
that seems large to me. I expect that there still is some issue with
the conversion of your NOE restraints.
> For comparison, and to remind
> you from my previous post, I originally assigned all these NOEs using
> NOEASSIGN (formerly known as CANDID) in CYANA. The final ensemble of
> structures from CYANA were very tight, around 0.5 Ang RMSD for backbone
> atoms. Granted, I suspect they were TOO tight, due to overly restrictive NOE
> distance restraints. However, I didn't expect for the structures to become
> this loose in Xplor-NIH after loosening the NOEs, especially because I added
> NH RDC restraints, some HBDA (h-bond) restraints and used the RAMA potential
> term. Additionally, I am concerned because the secondary structure elements
> are not "well-formed", i.e. the beta-strands and the alpha-helices are not
> fully formed and regular. The final CYANA output structures had better formed
> backbone secondary structure.
> encouraging. However, the HNCO and NCO RDCs do not agree at all. I think I
> scaled them correctly (approximately 3-fold for HNCO and 8-fold for NCO
> relative to NH).
If you use the scale_toNH, you do not need to scale the data.
best regards--
Charles
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