Agreed. I was not entirely serious but just trying to present a diametrically opposed
viewpoint. A middle of the road approach would be to say the additional reflections could
benefit either refinement or ML (and maybe the two are not really separate since
ML guides the refinement), and so continue to apportion them at the same rate
between
free and working sets.
Mark van Raaij wrote:
But at higher resolution you would like to release the restraints and introduce
more
parameters in refinement, such as anisotropic Bs - ideally keeping the
observation/parameter ration more or less constant...
On 3 Nov 2013, at 12:50, Edward Berry wrote:
Looking at it from the other side- suppose we say for a robust refinement we
need a
certain number of reflections- say 4 times the number of atoms, maybe less, I
don't
know. Any more than that is not really going to affect the structure, So if you
have
high resolution you can afford to use a large percentage of free reflections,
and the
cross-validation and maximum liklihood will go really well, even with thin
shells. On
the other hand at low resolution, well, sorry, you really can't spare any
reflections
for cross-validation. (I have no idea whether this makes sense or not, but it
would be
another way of looking at it).
>>> Mark van Raaij <mjvanra...@cnb.csic.es <mailto:mjvanra...@cnb.csic.es>>
11/01/13
7:39 PM >>>
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.
>
> Pavel
>
> 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: n...@salk.edu <mailto:n...@salk.edu> <mailto:n...@salk.edu>
>>
>> Publications & Citations:
>> http://scholar.google.com/citations?user=xiL1lscAAAAJ
>>
>> Homepage Salk: http://www.salk.edu/faculty/noel.html
>> Homepage HHMI: http://hhmi.org/research/investigators/noel.html
>>
______________________________________________________________________________________
>>
>>
>>
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