Re: [ccp4bb]: contour ?

["Leslie A." <andrew@mrc-lmb.cam.ac.uk>]

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"Gerard \"DVD\" Kleywegt" writes:
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 > 
 > 
 > Some remarks:
 > 
 > - 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.


          Andrew Leslie