Dear all,
Augustine, "Confessions", Book 11 Chap. XIV, has it:
"If no one ask of me, I know; if I wish to explain to him who asks, I
know not."
With best wishes,
Gerard.
--
On Tue, Oct 26, 2010 at 01:30:11PM -0500, Phoebe Rice wrote:
> Another issue with these statistics is that the PDB insists on a single value of "resolution" no matter how anisotropic the data. Especially in the outermost bins, Rmerge could be ridiculously high simply because the data only exist in one out of 3 directions.
> Phoebe
>
> =====================================
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>
>
> ---- Original message ----
> >Date: Tue, 26 Oct 2010 09:46:46 -0700
> >From: CCP4 bulletin board <[log in to unmask]> (on behalf of "Bernhard Rupp (Hofkristallrat a.D.)" <[log in to unmask]>)
> >Subject: [ccp4bb] Against Method (R)
> >To: [log in to unmask]
> >
> >Hi Folks,
> >
> >Please allow me a few biased reflections/opinions on the numeRology of the
> >R-value (not R-factor, because it is neither a factor itself nor does it
> >factor in anything but ill-posed reviewer's critique. Historically the term
> >originated from small molecule crystallography, but it is only a
> >'Residual-value')
> >
> >a) The R-value itself - based on the linear residuals and of apparent
> >intuitive meaning - is statistically peculiar to say the least. I could not
> >find it in any common statistics text. So doing proper statistics with R
> >becomes difficult.
> >
> >b) rules of thumb (as much as they conveniently obviate the need for
> >detailed explanations, satisfy student's desire for quick answers, and
> >allow superficial review of manuscripts) become less valuable if they have a
> >case-dependent large variance, topped with an unknown parent distribution.
> >Combined with an odd statistic, that has great potential for misguidance and
> >unnecessarily lost sleep.
> >
> >c) Ian has (once again) explained that for example the Rf-R depends on the
> >exact knowledge of the restraints and their individual weighting, which we
> >generally do not have. Caution is advised.
> >
> >d) The answer which model is better - which is actually what you want to
> >know - becomes a question of model selection or hypothesis testing, which,
> >given the obscurity of R cannot be derived with some nice plug-in method. As
> >Ian said the models to be compared must also be based on the same and
> >identical data.
> >
> >e) One measure available that is statistically at least defensible is the
> >log-likelihood. So what you can do is form a log-likelihood ratio (or Bayes
> >factor (there is the darn factor again, it’s a ratio)) and see where this
> >falls - and the answers are pretty soft and, probably because of that,
> >correspondingly realistic. This also makes - based on statistics alone -
> >deciding between different overall parameterizations difficult.
> >
> >http://en.wikipedia.org/wiki/Bayes_factor
> >
> >f) so having said that, what really remains is that the model that fits the
> >primary evidence (minimally biased electron density) best and is at the same
> >time physically meaningful, is the best model, i. e., all plausibly
> >accountable electron density (and not more) is modeled. You can convince
> >yourself of this by taking the most interesting part of the model out (say a
> >ligand or a binding pocket) and look at the R-values or do a model selection
> >test - the result will be indecisive. Poof goes the global rule of thumb.
> >
> >g) in other words: global measures in general are entirely inadequate to
> >judge local model quality (noted many times over already by Jones, Kleywegt,
> >others, in the dark ages of crystallography when poorly restrained
> >crystallographers used to passionately whack each other over the head with
> >unfree R-values).
> >
> >Best, BR
> >-----------------------------------------------------------------
> >Bernhard Rupp, Hofkristallrat a.D.
> >001 (925) 209-7429
> >+43 (676) 571-0536
> >[log in to unmask]
> >[log in to unmask]
> >http://www.ruppweb.org/
> >------------------------------------------------------------------
> >Und wieder ein chillout-mix aus der Hofkristall-lounge
> >------------------------------------------------------------------
--
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* Gerard Bricogne [log in to unmask] *
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* Global Phasing Ltd. *
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