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*To*: Bart Hazes <bhazes@ualberta.ca>*Subject*: Re: [ccp4bb]: I to F's*From*: Ronado Nagem <nagem@lnls.br>*Date*: Tue, 14 Nov 2000 19:53:20 -0200*CC*: Phraenquex VD <loretta@scripps.edu>, ccp4 <ccp4bb@dl.ac.uk>*References*: <Pine.A41.4.10.10011141515091.42740-100000@gpu5.srv.ualberta.ca>*Sender*: owner-ccp4bb@dl.ac.uk

Bart Hazes wrote:

> 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.

Thanks for the answers but I guess we are just in the beginning....

There is no mention to I(+) and I(-)...?!?!?!

I guess truncate will do that but let's suppose a simple case where I do not use

the TRUNCATE YES keyword. My questions still holds! How standard deviations for

F(+), F(-), and also DANO and SIGDANO are calculated?

How I(+), I(-), SIGI(+) and SIGI(-), which are all that we get from a difraction pattern,

are combined (in a formula) to generate Imean, SIGIMean, F(+),

F(-), DANO and SIGDANO ?

For example; in CNS

if I >= 0 and sigI < I: F = sqrt(I) sigF = F - sqrt(I - sigI) if I >= 0 and sigI >= I: F = sqrt(I) sigF = F if I < 0: F = 0 sigF = 0

In CNS F(+) and F(-) are treated separetelly and we do not have DANO and SIGDANO.

In CCP4 we have DANO and SIGDANO.... So how do we obtain them ?

I hope this discussion could help us all to understand that !!!

Best regards

Nagem.

-- ______________________________________________________________________ Ronaldo A. P. Nagem | Protein Crystallography Group | E-mail: nagem@lnls.br LNLS Laboratorio Nacional de Luz Sincrotron | Phone: 55-019-2874520 Rua Giuseppe Maximo Scolfaro, 10.000 Guara | Fax: 55-019-2877110 CEP 13084-971 Campinas SP Brasil | Website: www.lnls.br

**Follow-Ups**:**Re: [ccp4bb]: I to F's***From:*Bart Hazes <bhazes@ualberta.ca>

**References**:**Re: [ccp4bb]: I to F's***From:*Bart Hazes <bhazes@ualberta.ca>

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