Re: [ccp4bb] How many reflections for Rfree?

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

Previous message:
Subject: Re: How many reflections for Rfree?
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-06-16

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Subject: Call for proposals: Australian Synchrotron.
From: Tom Caradoc-Davies Tom {- dot -} Caradoc-Davies {- at -} SYNCHROTRON {- dot -} ORG {- dot -} AU
Date: 2008-06-17

Subject: Re: How many reflections for Rfree?
From: "Michael S {- dot -} Chapman" chapmami {- at -} OHSU {- dot -} EDU
Date: 2008-06-16

Mark et al.
Rfree can be calculated with as few as 150 reflections, depending on the
desired precision of Rfree.
The real issue is scaling. Many programs scale vs. the test set
independently, which becomes unstable with a small test set, and this is the
main cause of error in Rfree. The topic and remedy are discussed in:
Chen, Z., E. Blanc, et al. (1999). "Improved free R-factors for the
cross-validation of structures." Acta Crystallographica D55: 219-24.
Good luck. Michael.

Michael S. Chapman, R.T. Jones Professor of Structural Biology
Dept. Biochemistry & Molecular Biology; School of Medicine, Mail Code L224
Oregon Health & Science University
3181 Sam Jackson Park Road; Portland, OR 97239-3098
chapmami@ohsu.edu / (503) 494-1025; http://xtal.ohsu.edu/

> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Mark J. van Raaij
> Sent: Monday, June 16, 2008 11:22 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] How many reflections for Rfree?
>
> Dear All,
>
> It has recently been put to me that 5-10% of reflections should always
> be set aside for calculation of Rfree. However, when one has, say, 200
> 000 reflections (high resolution and/or large asymmetric unit), that
> seems to me to be a waste, because it would mean removing 10 000 to 20
> 000 reflections from the refinement target.
>
> My opinion is based on discussions with a particular knowledgeable
> crystallographer and a meeting report (
> http://journals.iucr.org/d/issues/1996/01/00/li0216/li0216.pdf
> ), in which 1000 reflections is said to be enough (i.e.
> statistically valid). As a result, I always take 1000-1500
> reflections, independently of the number of total reflections,
> adjusting the percentage or the width of the thin shells (in case of
> NCS) accordingly.
>
> What is the opinion of the community? And, if you agree with me, how
> should we try to get this opinion (more) generally accepted?
>
> On a related note, how to refine a structure with only 5000
> reflections, which could happen when you have a small a.u. and modest
> resolution? Could, exceptionally, a lower absolute amount of
> reflections be used for Rfree, say 500?
>
> Greetings,
>
> Mark
>
>
> Mark J. van Raaij
> Dpto de Bioquímica, Facultad de Farmacia
> Universidad de Santiago
> 15782 Santiago de Compostela
> Spain
> http://web.usc.es/~vanraaij/

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

Previous message:
Subject: Re: How many reflections for Rfree?
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-06-16

Next message:
Subject: Call for proposals: Australian Synchrotron.
From: Tom Caradoc-Davies Tom {- dot -} Caradoc-Davies {- at -} SYNCHROTRON {- dot -} ORG {- dot -} AU
Date: 2008-06-17