Re: [ccp4bb]: Alternate side chains..

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

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> I would object to that notion:
> 
> > > R and Rfree are not the most suitable statistics to judge the
> > > addition of a handful of scatterers since they are global
> 
> scatterers are added in real space LOCALLY thus affecting
> its Fourier transform, i.e. the structure factors, GLOBALLY,
> thus affecting R.

that's obvious, but besides the point. the point is that the addition of a few
scatterers will bring about changes that are within the noise of r/rfree, thus
invalidating their use for verification of such small, local changes. try
adding a single water to your model and recalculate rfree, then estimate the
error in rfree using the formula of brunger/cruickshank, and you'll see what i
mean. rfree can be used to judge global (or large-scale) changes to a model
that potentially produce changes that exceed the noise level (e.g., choice of
ncs model, choice of temperature factor model, addition of a large number of
scatterers). for validation of small (usually local) changes, statistics such
as real-space r-value or ditto correlation coefficient are beter suited.

--dvd


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                        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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