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Re: [ccp4bb] an over refined structure
 

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CCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008
Previous message:
Subject: Re: an over refined structure
From: Axel Brunger brunger {- at -} STANFORD {- dot -} EDU
Date: 2008-02-07 		Next message:
Subject: One small step for a crystallographer, one giant leap for mankind!
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-02-07


Subject: Re: an over refined structure
From: Edward Berry eaberry {- at -} LBL {- dot -} GOV
Date: 2008-02-07
Dean Madden wrote:
> Hi Dirk,
>
> I disagree with your final sentence. Even if you don't apply NCS
> restraints/constraints during refinement, there is a serious risk of NCS
> "contaminating" your Rfree. Consider the limiting case in which the
> "NCS" is produced simply by working in an artificially low symmetry
> space-group (e.g. P1, when the true symmetry is P2): in this case,
> putting one symmetry mate in the Rfree set, and one in the Rwork set
> will guarantee that Rfree tracks Rwork.
>

I don't think this is right- remember Rfree is not just based on Fc
but Fo-Fc. Working in your lower symmetry space group you will have
separate values for the Fo at the two "ncs-related" reflections.
Each observation will have its own random error, and like as not
the error will be in the opposite direction for the two reflections.

Hence a structural modification that improves Fo-Fc at one reflection
is equally likely to improve or worsen the fit at the related reflection.
The only way they are coupled is through the basic tenet of R-free:
If it makes the structure better, it is likely to improve the fit
at all reflections.

For sure R-free will go down when you apply NCS- but this is because
you drastically improve your data/parameters ratio.

Best,
Ed

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008
Previous message:
Subject: Re: an over refined structure
From: Axel Brunger brunger {- at -} STANFORD {- dot -} EDU
Date: 2008-02-07 		Next message:
Subject: One small step for a crystallographer, one giant leap for mankind!
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-02-07


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