Re: [ccp4bb] difference of R work and R free as a function of resolution

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

Previous message:
Subject: difference of R work and R free as a function of resolution
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2007-11-15

Next message:
Subject: Re: difference of R work and R free as a function of resolution
From: "Miller, Mitchell D {- dot -} " mmiller {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-11-15

Subject: Re: difference of R work and R free as a function of resolution
From: "Santarsiero, Bernard D {- dot -} " bds {- at -} UIC {- dot -} EDU
Date: 2007-11-15

One of the major problems with any R-factor is that it's a function of the
denominator, and therefore I, F^2, or F. Depending on how you "push" to
higher resolution, the R's will very likely increase due to the dominance
of the denominator over the numerator. It's good to also monitor on
evaluation functions that follow the numerator, like chi^2 in
scaling/averaging, and the figure-of-merit (rho-calc vs. rho-obs), and
goodness-of-fit.

Bernie Santarsiero

On Thu, November 15, 2007 10:41 am, Kay Diederichs wrote:
> Dear crystallographers,
>
> today I explained to a student that I believe that the difference of
> R_work and R_free should decrease as a function of resolution, because
> at high resolution there is less danger of overfitting, whereas at low
> resolution one is always overfitting to some extent. I'd say this should
> be true at least in absolute terms, but probably even in relative terms:
> for example, for a 1.5A structure I'd expect R_work/R_free= 14%/16%,
> whereas at 3A I'd expect 28%/35%.
>
> I believe that I saw plots (maybe in a link given in a posting on
> CCP4BB) obtained for structures from the PDB, which confirmed this
> hypothesis. But I've been googling and searching through postings now
> for quite some while, and cannot seem to find anything to that effect.
>
> Does anybody have a pointer to an analysis of this effect?
>
> thanks,
>
> Kay
>
> P.S. Would be good to put this into the CCP4 Wiki article on R-factors
> --
> Kay Diederichs http://strucbio.biologie.uni-konstanz.de
> email: Kay.Diederichs@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183
> Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
>

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

Previous message:
Subject: difference of R work and R free as a function of resolution
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2007-11-15