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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: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU
Date: 2008-02-07 		Next message:
Subject: Re: an over refined structure
From: Dean Madden drm0001 {- at -} DARTMOUTH {- dot -} EDU
Date: 2008-02-07


Subject: Re: an over refined structure
From: Edward Berry eaberry {- at -} LBL {- dot -} GOV
Date: 2008-02-07
Actually the bottom lines below were my argument in the case
that you DO apply strict NCS (although the argument runs into
some questionable points if you follow it out).

In the case that you DO NOT apply NCS, there is a second
decoupling mechanism:
Not only the error in Fo may be opposite for the two reflections,
but also the change in Fc upon applying a non-symmetrical
modification to the structure is likely to be opposite. So there
is no way of predicting whether
Fo-Fc
will move in the same
direction for the two reflections. I completely agree with Dirk
(although I am willing to listen to anyone explain why I am wrong).

Ed


Edward Berry wrote:
> 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

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CCP4bb <-- 2008 <-- February 2008 <-- 07 February 2008
Previous message:
Subject: Re: an over refined structure
From: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU
Date: 2008-02-07 		Next message:
Subject: Re: an over refined structure
From: Dean Madden drm0001 {- at -} DARTMOUTH {- dot -} EDU
Date: 2008-02-07


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