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Re: [ccp4bb] significant drop in Rfree ?
 

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CCP4bb <-- 2008 <-- February 2008 <-- 24 February 2008
Previous message:
Subject: significant drop in Rfree ?
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2008-02-24 		Next message:
Subject: Re: significant drop in Rfree ?
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-25


Subject: Re: significant drop in Rfree ?
From: Ethan A Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-02-24
On Sunday 24 February 2008 20:33, Bernhard Rupp wrote:
>
> But I cannot use this error to judge whether
> something I do to the refinement is a significant improvement
> or not. Indirect proof through argumentum absurdum:
>
> Assume the su of Rfree is 0.008, and I build n waters. Rf drops
> from 24.4 to 13.9, by 0.005, less than the su. I build n+m waters,
> say drops by 1%. Larger than su. It seems nonsense to say that
> building n waters is insignificent, but n+m waters is.

There was once a fellow named Zeno who made a similar argument.
Aristotle was not convinced.

> Soooo...how can we quantify whether something gave a 'significant
> improvement in Rfree' or not? What constitutes an objective measure
> for a significant improvement in R-free? What test discriminates
> hypothesis A from B in terms of improvement of R-free?
>
> Any drop? Any drop until the gap exceeds the expected ratio?
>
> Or do I need a full blown Hamilton test (Acta 18:502 1965) to
> answer that?

Perhaps. But I am not sure that is correct either, because if you run the
test only on Rfree you are essentially ignoring the information from R itself.
I suspect you really want a likelihood ratio test that captures the
notion: "How likely is it that I would have gotten a decrease of
XX in R while only seeing a decrease of YY in Rfree?"

Ethan


> For a simple neutron case I once used the Himmelblau
> test, that worked (Ted Prince, ActaB 38:1099(1982) and does not need
> R-values.
>
> Maybe I missed such a discussion on BB before, leads welcome.
> Probably addressed in some Rf-ree paper?
>
> Thx, br
>
>
>
>
>
>
>

--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

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CCP4bb <-- 2008 <-- February 2008 <-- 24 February 2008
Previous message:
Subject: significant drop in Rfree ?
From: Bernhard Rupp bernhardrupp {- at -} SBCGLOBAL {- dot -} NET
Date: 2008-02-24 		Next message:
Subject: Re: significant drop in Rfree ?
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-25


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