[phenixbb] Appropriate number of reflections for FreeR
Mark van Raaij
mjvanraaij at cnb.csic.es
Fri Nov 1 16:38:29 PDT 2013
the limit of 2000 reflections I guess is just because it would be a waste to "throw away" more reflections for refinement, once the statistical minima for calculating a reliable Rfree have been met. I.e. if you have 100.000 reflections, it would be a waste to use 5 or 10% of the reflections instead of just 2%. I'd rather use as many as possible reflections for refinement.
On 31 Oct 2013, at 20:21, Pavel Afonine wrote:
> Hi Joe,
> flags should be selected such that there is enough of them in each relatively thin resolution shell (thin enough so ML target parameters can be considered constant in each such shell). Lower end is about 50 reflections per shell. All in all this usually translates into about 10% overall.
> Yes, there is a limit parameter set to 2000 by default. I don't know what's the rationale for having it, may be someone can explain.
> On 10/31/13 12:10 PM, Joseph Noel wrote:
>> Hi All. I think I have asked this before but forgot. Old age. What is
>> the appropriate number / percentage of reflections to flag for a
>> statistically appropriate Free-R calculation? If I am correct, the
>> reflection file editor in Phenix chooses by default either 10% of the
>> measured reflections or 2000 whichever comes first.
>> Joseph P. Noel, Ph.D.
>> Arthur and Julie Woodrow Chair
>> 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 <mailto:noel at salk.edu>
>> Publications & Citations:
>> Homepage Salk: http://www.salk.edu/faculty/noel.html
>> Homepage HHMI: http://hhmi.org/research/investigators/noel.html
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> phenixbb mailing list
> phenixbb at phenix-online.org
More information about the phenixbb