Re: [ccp4bb] unstable refinement

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

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Subject: Re: PDB protein strucutrues as screen saver
From: Jayashankar s {- dot -} jayashankar {- at -} GMAIL {- dot -} COM
Date: 2009-02-17

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Subject: Re: PDB protein strucutrues as screen saver
From: "Mark J {- dot -} van Raaij" mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2009-02-17

Subject: Re: unstable refinement
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-02-17

You dont say at which point in the refinement cycle you are..

The refinement algorithms are meant to reduce these parameters, and if
they diverge wildly there is probably something seriously wrong either
with the software or the model..
eg - different cell dimensions or space group for the coordinates and
reflections..

If you have some crazy clashes within the model that can disturb things..

If B factors go crazy then that usually indicates there are errors in
the model..

The causes you list can introduce problems but twinning causes
refinement to "stick" but not for the Rfactors to increase; anisotropy
should be catered for in the program scaling algorithms,

If the shifts are small things to consider are: FreeR set not carried
over from previous refinement regime, geometric restraints too tight/loose
Eleanor

John Bruning wrote:
> Hi,
>
> I would like to survey the group for causes and potential solutions to
> unstable refinement (the steady and upward drift of R and Rfree in each
> cycle of refinement). I am currently aware of the following potential
> causes: twinning (meohedral, pseduomerohedral, or epitaxial), anisotropy,
> pseudosymmetry, the lack of appropriately tight geometric constraints, and
> extraordinarily high b-factors. If anyone has run into any other causes of
> unstable refinement, I would like to hear about them.
>
>
> Thanks,
> John Bruning
>
>

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

Previous message:
Subject: Re: PDB protein strucutrues as screen saver
From: Jayashankar s {- dot -} jayashankar {- at -} GMAIL {- dot -} COM
Date: 2009-02-17

Next message:
Subject: Re: PDB protein strucutrues as screen saver
From: "Mark J {- dot -} van Raaij" mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2009-02-17