[phenixbb] Implementation of French & Wilson data correction?

Joseph Noel noel at salk.edu
Fri Feb 25 10:38:48 PST 2011

I'll give it a go! I know Otwinowski well and we have had many discussions about negative intensities. Do you know if Scala/Truncate resets negative intensities to 0?

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Joseph P. Noel, Ph.D.
Investigator, Howard Hughes Medical Institute
Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
The Salk Institute for Biological Studies
10010 North Torrey Pines Road
La Jolla, CA  92037 USA

Phone: (858) 453-4100 extension 1442
Cell: (858) 349-4700
Fax: (858) 597-0855
E-mail: noel at salk.edu

On Feb 25, 2011, at 10:05 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Joe,
> the main motivation to implement F&W based conversion of Iobs to Fobs was the community driven suggestion that this is a better way of converting Iobs to Fobs, compared to simple
> if(Iobs >= 0):
> Fobs = sqrt(Iobs)
> else:
> Fobs = 0
> that phenix.refine uses.
> I'm not aware of any systematic and conclusive study demonstrating that one way is better or worse than the other one. Since now we have both options available in PHENIX this opens a good opportunity (for whoever who has enough of enthusiasm and time) to study this some more within one software framework.
> Some good discussion on related subjects can be found here:
> "Structure refinement: some background theory and practical strategies".
> David Watkin.
> J. Appl. Cryst. (2008). 41, 491–522
> Pavel.
> On 2/25/11 8:56 AM, Joseph Noel wrote:
>> Hi All,
>> Any pointers on implementing the new option in the latest build for French & Wilson correction? Does scala output negative intensities so that a proper scaling with this new option can be used? Also, what column labels should be used particularly for proper treatment of anomalous data? Can one use the labels output by scala?
>> Joe

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