It is A34: 517
http://journals.iucr.org/a/contents/backissues.html
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Sep 8, 2008, at 1:19 PM, Jacob Keller wrote:
> Does somebody have a .pdf of that French and Wilson paper?
>
> Thanks in advance,
>
> Jacob
>
> *******************************************
> 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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