[phenixbb] local refinement of target weights?

Yarrow Madrona amadrona at uci.edu
Tue Oct 4 14:32:47 PDT 2011

Thanks Pavel

I hadn't considered the issues you brought up.

I have heard of people doing this with CNS but I am not sure how it is
done or how well it worked.


> Hi Yarrow,
>> I am wondering if there is a way to restrain geometry target weights for
>> a
>> ligand seperate from the rest of the molecule. I would like to impose
>> higher restraints for the ligand than that of the protein in the same
>> refinement run.  Thanks for your help.
> currently you can only do it by editing the corresponding esds in ligand
> CIF file. By making the esds smaller you will make the corresponding
> restraints stronger.
> But in general it is dangerous to do, and normally is not recommended.
> If you make the esds too small, that means the corresponding
> contribution to overall restraints target arising from that ligand will
> be overwhelmingly large, so the restraints from other atoms will be
> negligibly small. In practice this means you will get a model with
> distorted geometry.
> This is exactly why often the CIF files created by PRODRG do not work
> well with phenix.refine (since it sometimes puts very small esds, which
> explodes refinement).
> Pavel
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Yarrow Madrona

Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697

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