Dear Christoph,
Does sound a bit strange. I could think of some reasonable explanations,
but I'd need to know more about the details before I could comment. We
cannot guarantee the same behaviour as any one dynamics program - they
have different data and a different situation - but, depending on what is
happening, we might improve the documentation (or maybe the program?).
Could you send us:
What are the actual constraints in the restraint list?
What is the corresponding peak assignment?
What other restraints do you have involving HEa and Heb?
What are the actual distances HE2-HA and HE3-HA?
How do the various averaged distances come out in XPLOR and Analysis?
Thanks,
Rasmus
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Dr. Rasmus H. Fogh Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
On Fri, 20 Apr 2007, Christoph Brockmann wrote:
> Hi there,
>
> I am aware that the way Analysis handles violations is still fairly
> experimental and since it doesn't support ensembles still a bit
> meaningless anyway. Nevertheless I try to understand how things like the
> problem depicted below can occur. I have a constraint for 6A, the
> calculated distances are ~4.9A (NOE sum) and ~5.0A (min Dist). Analysis
> reports a violation of 0.7A that it could only derive if it takes the
> HE2-HA distance (from a Ha-Hea assignment).
>
> Since Xplor-NIH doesn't think this is violated I think this is a case
> where there is something going on within Analysis that should probably
> made more transparent to the users...
>
> Anyway in my opinion the assignment software should be faithful to the
> ways the structure calculation software handles this, since there is no
> way to enforce restraints that don't come up as violated during the
> calculations.
>
> Or is there a better explanation?
>
> Christoph
>
> --
> ---------------------------------------------------------
> Dr. Christoph Brockmann
> Division of Structural Studies
> MRC Laboratory of Molecular Biology
> Hills Road
> Cambridge, CB2 2QH
> phone: +44-1223-40-2261 or +44-1223-40-2068
> e-mail: [log in to unmask]
> ---------------------------------------------------------
>
>
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