Does somebody have a .pdf of that French and Wilson paper?
Thanks in advance,
Jacob
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Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [log in to unmask]
*******************************************
----- Original Message -----
From: "Ethan Merritt" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Monday, September 08, 2008 3:03 PM
Subject: Re: [ccp4bb] truncate ignorance
> On Monday 08 September 2008 12:30:29 Phoebe Rice wrote:
>> Dear Experts,
>>
>> At the risk of exposing excess ignorance, truncate makes me
>> very nervous because I don't quite get exactly what it is
>> doing with my data and what its assumptions are.
>>
>> From the documentation:
>> ========================================================
>> ... the "truncate" procedure (keyword TRUNCATE YES, the
>> default) calculates a best estimate of F from I, sd(I), and
>> the distribution of intensities in resolution shells (see
>> below). This has the effect of forcing all negative
>> observations to be positive, and inflating the weakest
>> reflections (less than about 3 sd), because an observation
>> significantly smaller than the average intensity is likely
>> to be underestimated.
>> =========================================================
>>
>> But is it really true, with data from nice modern detectors,
>> that the weaklings are underestimated?
>
> It isn't really an issue of the detector per se, although in
> principle you could worry about non-linear response to the
> input rate of arriving photons.
>
> In practice the issue, now as it was in 1977 (French&Wilson),
> arises from the background estimation, profile fitting, and
> rescaling that are applied to the individual pixel contents
> before they are bundled up into a nice "Iobs".
>
> I will try to restate the original French & Wilson argument,
> avoiding the terminology of maximum likelihood and Bayesian statistics.
>
> 1) We know the true intensity cannot be negative.
> 2) The existence of Iobs<0 reflections in the data set means
> that whatever we are doing is producing some values of
> Iobs that are too low.
> 3) Assuming that all weak-ish reflections are being processed
> equivalently, then whatever we doing wrong for reflections with
> Iobs near zero on the negative side surely is also going wrong
> for their neighbors that happen to be near Iobs=0 on the positive
> side.
> 4) So if we "correct" the values of Iobs that went negative, for
> consistency we should also correct the values that are nearly
> the same but didn't quite tip over into the negative range.
>
>> Do I really want to inflate them?
>
> Yes.
>
>> Exactly what assumptions is it making about the expected
>> distributions?
>
> Primarily that
> 1) The histogram of true Iobs is smooth
> 2) No true Iobs are negative
>
>> How compatible are those assumptions with serious anisotropy
>> and the wierd Wilson plots that nucleic acids give?
>
> Not relevant
>
>> Note the original 1978 French and Wilson paper says:
>> "It is nevertheless important to validate this agreement for
>> each set of data independently, as the presence of atoms in
>> special positions or the existence of noncrystallographic
>> elements of symmetry (or pseudosymmetry) may abrogate the
>> application of these prior beliefs for some crystal
>> structures."
>
> It is true that such things matter when you get down to the
> nitty-gritty details of what to use as the "expected distribution".
> But *all* plausible expected distributions will be non-negative
> and smooth.
>
>
>>
>> Please help truncate my ignorance ...
>>
>> Phoebe
>>
>> ==========================================================
>> Phoebe A. Rice
>> Assoc. Prof., Dept. of Biochemistry & Molecular Biology
>> The University of Chicago
>> phone 773 834 1723
>> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
>>
>> RNA is really nifty
>> DNA is over fifty
>> We have put them
>> both in one book
>> Please do take a
>> really good look
>> http://www.rsc.org/shop/books/2008/9780854042722.asp
>>
>
>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center
> University of Washington, Seattle 98195-7742
>
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