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> I'm trying to refine structure generated by Cyana 2.1
> in Xplor-NIH but the E(BOND) dominates E(poten) in the
> first around of minimization, like E(BOND)=3125512
> while E(poten)=3144444. The structure blew out during
> refinement. As I read somewhere that Cyana 2.1 has
> changed the bond lengths, in calculation. I think this
> is how the unusual BOND violation arises. So the
> question is how I can fix this in either Cyana or
> Xplor?
>
you should look at the bond violations immediately after reading in the
coordinates using a line like:
xplor.command("print threshold=0.05 bond")
to see where the problem is,
regards--
Charles
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