[ccp4bb]: Re: Question about I to F conversion

[Jeff Taylor <jstaylor@duke.edu>]

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Michael John Theisen wrote:
> 
> Hello Jeffrey,
> Well, what value did Scalepack give for completeness with the -3 sigma cutoff
> (*before* you converted to amplitudes using Truncate)?
> Mike
> 
>  --


The  data from the -3 sigma cut in scalepack looks like this:

     Shell            I/Sigma in resolution shells:
  Lower Upper      % of reflections with I / Sigma less than
  limit limit     0     1     2     3     5    10    20   >20  total
  50.00  5.38   0.5   1.1   1.8   2.6   4.0   7.3  16.3  82.3   98.6
   5.38  4.27   1.6   2.6   3.7   4.5   6.6  11.4  25.5  74.4   99.9
   4.27  3.73   4.7   6.8   9.0  11.0  15.2  24.6  49.2  50.3   99.5
   3.73  3.39   8.5  11.7  14.5  17.2  22.5  37.2  71.6  27.8   99.4
   3.39  3.15   9.4  16.4  23.0  29.0  38.9  58.1  82.2  17.5   99.6
   3.15  2.96   9.0  19.9  31.2  40.9  55.5  76.1  93.4   6.3   99.7
   2.96  2.82  11.5  26.1  41.1  52.5  67.7  86.6  97.1   2.6   99.7
   2.82  2.69  15.9  36.1  54.3  66.7  80.5  93.5  98.6   1.0   99.6
   2.69  2.59  19.5  43.3  64.0  76.2  88.3  96.5  99.0   0.3   99.4
   2.59  2.50  23.4  51.7  73.1  84.0  92.9  98.2  99.4   0.1   99.5
 All hkl       10.3  21.4  31.4  38.2  46.9  58.6  72.9  26.5   99.5

I'm not surprise that the zero sigma cut has lower completeness.

Maybe I should restate my question:

I have a file of intensities, processed with a -3 sigma cut to preserve
the negative reflections.  If I convert this to amplitudes without any
Wilson scaling and then apply a 2 sigma cut I get 89% completeness.  If
I take the same starting file of intensities, convert it to amplitudes
with Wilson scaling and then apply a 2 sigma cut I get 97%
completeness.  

My problem is that I don't understand how the Wilson scaling works with
respect to the sigma values.  If a particular reflection is scaled up,
how is the corresponding sigma changed?  I'm sorry to bother everyone, I
could probably answer this question myself if I had the French and
Wilson paper, but I don't have easy access to the older Acta. journals
right now.  

- Jeff Taylor



-- 
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Dr. Jeffrey S. Taylor       Duke University Medical Center
Department of Biochemistry  Box 3711, Nanaline Duke Bld  
Phone (919) 681-5266        Durham, NC 27710