[phenixbb] Optimizing the Geometry Weight for a 2.76 A structure

Edward A. Berry BerryE at upstate.edu
Fri Apr 2 12:23:42 PDT 2010

Phil Jeffrey wrote:
> More pertinent to this example is the s.d. of the R-free itself, i.e.
> sigma(Rfree)/Rfree ~ 1/sqrt(Ntest)

I believe "~" here is read "proportional to", not "approximately".


Rfree can be seen* as an average of (|Fo-Fc|)/Fo weighted by Fo,
so variance should be proportional to sqr(N) like
the standard error of the mean. But SEM depends also on
the sigma for the individual observations, which I would
hope is less than 100%, so sigma(Rfree)/Rfree < 1/sqrt(Ntest)?

unweighted average: Sum(|Fo-Fc|/Fo)/N  = Sum(|Fo-Fc|/Fo)/Sum(1)

weighted by Fo:     Sum(Fo*|Fo-Fc|/Fo)/Sum(Fo)

                   = Sum(|Fo-Fc|)/Sum(Fo)

                   = R

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