Re: [ccp4bb] What is an aceptable spread in ADP values?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Strange problem running cpp4i over nx - job reported as failed even though it succeeds-log file has nx errors
From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
Date: 2010-02-04

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Subject: Fwd: Strange problem running cpp4i over nx - job reported as failed even though it succeeds-log file has nx errors
From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
Date: 2010-02-04

Subject: Re: What is an aceptable spread in ADP values?
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-02-04

Pavel Afonine wrote:
> Dear Ed,
>
>> Tightly restrained refinement will be equivalent to
>> torsion angle parametrization, since bonds and angles are essentially
>> fixed (but dihedrals are not).
>
> Simply not true. Think why -:) Hint: in restrained refinement the weight
> applies to all terms - bonds, angles, torsions, etc... So if you choose
> tight weight in such refinement the torsions will be restrained as
> tightly as other terms (at least as it would be in CNS or
> phenix.refine). In torsion angle refinement (which is, in fact, a
> constrained rigid-body refinement) you still have weights, and you can
> make your torsion angle refinement as tight as you like.

However, many refinement programs allow you to adjust the weights of
different terms differently. So, if you were to make the bond length and
angle terms sufficiently tight, but leave the torsion restraints loose,
you can indeed end up with something very similar to torsion angle
refinement.

So why use torsion angle refinement? Because in the scheme I've outlined
above the target function can have vastly different curvatures along
different directions in parameter space. This presents a problem for the
minimiser - without a good deal of second order information the
refinement steps have to be incredibly small (step size related to the
sharpest curvature) and minimisation process becomes impossibly slow.

However, it is seems possible to me that a sufficiently good minimiser
with a carefully constructed sparse curvature matrix may be able to
deliver the same benefits as torsion refinement while working in
Cartesian space.

Kevin

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