Re: [ccp4bb]: ccp4bb

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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syed ibrahim wrote:
> Dear All,
> 
> I am using ccp4-4.2.2 version. I have been asked to calculate patterson 
> vectors. I want to know the extent of map, and exclusion of reflection. 
> Is these columns have to be filled with specific number? And please let 
> me know how to interpret the peaks file after running the program.
> 
> Thanks in advance
> 
>  
> 


  You seem to be talking about calculating a Patterson map?
You do not say for what.. If you want to look at any difference 
Patterson map, eg between a native and a derivative, or betwen anomalous 
pairs you need to exclude the outliers. If you are using the GUI , run 
scale and Analyse under the experimental phasing and look at the Log 
Graphs given as a function of resolution. These show the average and 
maximum differences. If there are huge spikes - large diffs which may 
well be in error, you should exclude them. ( A large spurious 
difference, squared become a VERY large term.. ) So I usually exclude on 
F1 and F2 < 3 Sigma, and on the DIFF > ~ 4* mean.
Resolution you must decide for yourself. In general to find heavy atom 
position 3.5 to 4A is enough..

  Eleanor

>  
> 
>  
> 
> -----------------------------------------------------------------------------------------------------------------------
> 
> B. Syed Ibrahim,
> 
> Dept. Of Crystallography and Biophysics, University of Madras, 
> Chennai-600 025
> 
>  
> 
> 
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