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Re: [ccp4bb]: contour ?

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i seriously disagree with your seriously disagreeing.
assume that the sigma level at the end of a refinement
is 0.0001 e/A3. then a 10-sigma feature is noise. my point
is that the "number of sigmas" of a feature in an fo-fc
map is meaningless - the absolute sigma level is not, of
course (but this assumes that you calculate your maps on
an absolute scale to begin with !).

--gerard

>  > - the sigma level of an Fo-Fc is meaningless. In the early
>  >   stages (poor and incomplete model), a 2-sigma feature
>  >   may be genuine, whereas near the end of the refinement
>  >   process (when the difference map is hopefully flat
>  >   except for noise) even a 5-sigma peak need not be
> 
>    I seriously disagree with this remark. The sigma level in an Fo-Fc
> map does indeed give an indication of the noise level of the map, and
> one would certainly hope that this noise level, in absolute terms,
> would go down as refinement proceeds. However, this certainly does NOT
> mean that a 5 sigma peak in a difference map near the end of
> refinement is not suggesting an error in the model in that region.
> Whether or not one can interpret the feature is a different matter, as
> very often they arise from multiple conformations/disorder that is
> very difficult if not impossible to model correctly.

--gerard

******************************************************************
                        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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