Re: [ccp4bb] Does NCS bias a randomly-chosen test set (even if not enforced)?

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 09 February 2008

Previous message:
Subject: SLS proposals, new call and reminder, open call
From: heinz-josef {- dot -} weyer {- at -} PSI {- dot -} CH heinz-josef {- dot -} weyer {- at -} PSI {- dot -} CH
Date: 2008-02-09

Next message:
Subject: References for ligand flipping
From: Kendall Nettles knettles {- at -} SCRIPPS {- dot -} EDU
Date: 2008-02-09

Subject: Re: Does NCS bias a randomly-chosen test set (even if not enforced)?
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-09

> (I'm probably wrong, but I want someone to show me,and not with
> hand-waving
> arguments or invocation of crystallographic intuition or such)
>
> To convince me, someone needs to show that the expected value of the
> change
> in
Fo-Fc
at a test reflection upon a change in the model (a step of
> refinement)
> is negative, even in the absence of any real improvement in the model,
> simply because the change reduces
Fo-Fc
at a sym-related working
> reflection.

The problem is that a) the statistical drift will be very small, and b)
that this will be for *almost every* reflection in the test set. If it
were just a few, you'd be right, but not when it's all of them: then
your Rfree will not be informative.

That's in the absence of NCS restraints. In their presence, it's bad
anyway, because you're forcing Fc to be (almost) equal for both reflections.

phx.

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 09 February 2008

Next message:
Subject: References for ligand flipping
From: Kendall Nettles knettles {- at -} SCRIPPS {- dot -} EDU
Date: 2008-02-09