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Re: [ccp4bb]: I to F's

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
 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