Okay, thanks very much!
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: "William Scott" <[log in to unmask]>
To: "Jacob Keller" <[log in to unmask]>
Cc: <[log in to unmask]>
Sent: Monday, September 08, 2008 3:28 PM
Subject: Re: [ccp4bb] truncate ignorance
> 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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