Re: [ccp4bb]: I to F's

[Bart Hazes <bhazes@ualberta.ca>]

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> 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

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