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*To*: Phraenquex VD <loretta@scripps.edu>*Subject*: Re: [ccp4bb]: I to F's*From*: Bart Hazes <bhazes@ualberta.ca>*Date*: Tue, 14 Nov 2000 15:27:07 -0700 (MST)*cc*: Ronado Nagem <nagem@lnls.br>, ccp4 <ccp4bb@dl.ac.uk>*In-Reply-To*: <Pine.SGI.3.96.1001114134550.24052A-100000@patterson>*Sender*: owner-ccp4bb@dl.ac.uk

*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html *** > Scalepack2mtz does not convert I to F, it merely writes I, sigmaI into mtz > format. Then TRUNCATE does the conversion. Basically: F = sqrt(I), but > the reference is in the truncate manual. Well truncate is a bit more sophisticated than that. It considers the probability distribution of I as a normal distribution with an aveage of Imean and standard deviation of SigImean but with the restriction that I must be positive. Therefore it truncates (I guess that's where the name came from) the left tail of the distribution at I=0. It then calculates I as the weighted average over this truncated distribution and takes the square root of the result. For moderate and strong reflections the probability of I < 0 is so small that almost nothing gets truncated and F is just sqrt(I). However, for the weak, or even slightly negative, reflections the truncation is significant. The result is that F for weak reflections gets increased a bit compared to a straight sqrt(I). One of the nice features is that truncate can also handle negative reflections this way, unlike sqrt(I) which fails for negative numbers. I believe truncate does not accept very negative intensities but it is long ago that I read the paper. I recommend you read it as well to get the details. I guess the reference is in the TRUNCATE man page. Bart Hazes =============================================================================== Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta, T6G 2H7, Canada phone: 1-780-492-0042 fax: 1-780-492-7521 ===============================================================================

**Follow-Ups**:**Re: [ccp4bb]: I to F's***From:*Ronado Nagem <nagem@lnls.br>

**Re: [ccp4bb]: I to F's***From:*Edward Berry <eaberry@lbl.gov>

**References**:**Re: [ccp4bb]: I to F's***From:*Phraenquex VD <loretta@scripps.edu>

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