Re: [ccp4bb]: again rfree vs resolution (fwd)

["Gerard \"DVD\" Kleywegt" <gerard@xray.bmc.uu.se>]

dear members of the (ccp4 bulletin) board !

the appended message bounced earlier because of a
slight violation of the size limit for postings to
the ccp4bb. however, alun has kindly raised the
limit a wee bit so that it should get through this
time. i think the figure is of sufficient interest
to the community (if you don't agree, feel free
to complain to me directly, not to the list)

--gerard

---------- Forwarded message ----------
Date: Fri, 10 Aug 2001 23:37:34 +0200 (CEST)
From: Gerard "DVD" Kleywegt <gerard@xray.bmc.uu.se>
To: Bernhard Rupp <br@llnl.gov>
Cc: Gerard Kleywegt <gerard@xray.bmc.uu.se>, Ccp4 <ccp4bb@dl.ac.uk>
Subject: Re: [ccp4bb]: again rfree vs resolution

> I think I have pestered you already once with this question :
> Where was this elusive graph published of: 
> 
> statistical expectation value of rfree (or so) vs resolution ?

i suspect you may be refering to one of these two papers:

Tickle, I.J., Laskowski, R.A. & Moss, D.S. (1998). Rfree and the Rfree
ratio. I. Derivation of expected values of cross-validation residuals
used in macromolecular least-squares refinement. Acta Crystallogr. D54,
547-557.

Tickle, I.J., Laskowski, R.A. & Moss, D.S. (2000). Rfree and the Rfree
ratio. II. Calculation of the expected values and variances of
cross-validation statistics in macromolecular least-squares refinement.
Acta Crystallogr. D56, 442-450.

less likely (but a gripping yarn nonetheless ;-):

Kleywegt, G.J. & Brunger, A.T. (1996). Checking your imagination: 
applications of the free R value. Structure 4, 897-904.

i have attached a plot of rfree versus resolution based
on ~6500 pdb entries. this is a box plot - in every
resolution bin (from the bottom up) the 10th percentile,
25th, 50th (i.e. median), 75th and 90th percentile are
indicated; outliers below 10 and above 90 are shown
individually as small specks. the linear correlation
coefficient is +0.56. (figure from: gjk & ta jones,
to be published (2001, if i have time))

> A freeR of 20 for a 3.5 A structure is probably as unlikely as
> a freeR of 29 for a 1.2 A structure and both warrant some  
> explanantion....     

absolutely. this is also borne out by the attached plot

> And just to heat up the flames: I think freeR was probably the
> single most significant contribution to put an end to DreamWorks
> crystallography....almost.

well, producers of imaginary models can still publish in Nature
(cum suis) of course ... (and in fact they do)

--dvd

******************************************************************
                        Gerard J.  Kleywegt
    [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
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   The opinions in this message are fictional.  Any similarity
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rfree_vs_resolution.gif