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Re: [ccp4bb]: contour ?

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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

- if you cut out maps around your molecule and then use
  them in O, the "sigma level" is recalculated by O. As
  a consequence, this level will almost always be lower
  than the sigma level in the asymmetric unit, and features
  will show up at deceptive levels (e.g., a "2-sigma"
  peak may be just a 1-sigma noise feature). [This problem
  does not occur when you use to good old map_* commands.]

- you want to be careful with going to too low a contour
  level. For an example of the dire consequences that
  can have, see Nature Structural Biology 8 (8), pp.
  663-664 ... [If you need convincing, check the real-space
  fit and the map for 1F83 (chain B and C) at the Uppsala
  Electron-Density Server, http://portray.bmc.uu.se/eds ]

--dvd


> The simple answer is that you want to contour at a level that gives the
> clearest view of the density. I normally contour 2Fo-Fc & Fo-Fc at 1 and 3
> sigma, respectively, but in some parts of the map you want to lower the
> contour level. Your density will most likely not be equally strong throughout
> the map due to variations in B-factor or missing strong low resolution terms,
> so you'll have to adjust contour levels. If you lower the contour level too
> much you'll be blinded by all the noise features. Just use your eyes to tell
> what works best.

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