As pointed out by a reviewer recently, this has been object of study in
the past when Gerard K. and Axel B. found that actually 500-700
reflections should suffice to monitor Rfree with sufficient precision.
I guess everybody will agree on that we want to have the best refined
structure and this entails not setting aside valuable reflections
unnecessarily.
Kleywegt GJ, Brünger AT. _Checking your imagination: applications of the
free R value._ <http://www.ncbi.nlm.nih.gov/pubmed/8805582>Structure.
1996; 4:897-904.
Brünger AT. _Free R value: cross-validation in crystallography._
<http://www.ncbi.nlm.nih.gov/pubmed/18488318>Methods Enzymol.
1997;277:366-96
As to the convenience of carrying over a test set to another dataset,
Eleanor made a suggestion to circumvent this necessity some time ago:
pass your coordinates through pdbset and add some noise before refinement:
pdbset xyzin xx.pdb xyzout yy.pdb <<eof
noise 0.4
eof
Xavier
On 20/11/14 11:43 PM, Keller, Jacob wrote:
Dear Crystallographers,
I thought that for reliable values for Rfree, one needs only to satisfy
counting statistics, and therefore using at most a couple thousand reflections
should always be sufficient. Almost always, however, some seemingly-arbitrary
percentage of reflections is used, say 5%. Is there any rationale for using a
percentage rather than some absolute number like 1000?
All the best,
Jacob
*******************************************
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
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