Re: [ccp4bb]: Reducing the size of a FreeR-set

["M.D.Winn" <M.D.Winn@dl.ac.uk>]

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The problem is that the random number generator that generates
the free R column isn't random.... You need to run freerflag
with the SEED keyword to achieve this (or at least, a better
approximation to it). The program freerflag occurs 3 times
in the uniqueify script. Add the SEED keyword to the 2nd instance
and re-run it. 

"Works for me"

SEED isn't default because I seem to remember some people wanted
to be able to re-generate the same set of free R flags.

Martyn

> 
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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Dear all,
> 
> I'm trying to reduce the FreeR-set of one of my files from 10 % to 5 %.
> 
> To be politically correct and keep half of this original set for further 
> refinement my first idea was to generate a second FreeR-column with 
> 'uniqueify -p 0.5'. I thought that this should select half of my original 
> FreeR-reflections as double-flagged. A few conversion, grep and awk steps 
> should give me the desired new FreeR-set, I thought.
> 
> While I now have a script that is technically doing the steps described 
> above my initial assumption of getting half of the reflections 
> double-flagged turned out to be wrong. Of the original say 15000 FreeR 
> data, approx. 14300 got the double flag (0.00       0.00) and only 700 
> don't (0.00       1.00). I am obviously missing something 
> distribution-related here I think.
> 
> Does anybody know how to split a FreeR set? Is there a standard procedure 
> in CCP4 that I have overlooked?
> 
> 
> 
> Thanks in advance,
> 
> 
> 
> 
> Wulf
> 
> 
> -----------------
> Dr. Wulf Blankenfeldt
> 
> Structural Biology Group
> Biomolecular Sciences Building
> University of St. Andrews
> 
> North Haugh
> St. Andrews, Fife
> KY16 9ST
> UK
> 
> Tel:    +44 (0) 13 34 - 46 72 82
> Fax:    +44 (0) 13 34 - 46 25 95
> e-mail: wb6@st-andrews.ac.uk
> -----------------
> 
> 


-- 


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*                                                                        *
*                  Dr. Martyn Winn                                       *
*                                                                        *
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