Dear All,
I would argue that there are very few situations where it is
necessary to use R-free as a criterion for optimization (as opposed
to R-work). In any case where the parameterization is fixed and we
are simply looking for the best set, R-work will do just fine. It is
only situations such as deciding what type of NCS restraints to
use, and in which the parameterization changes and R might not be
comparable in the various cases, where Rfree might be useful. As
long as only a very few decisions of this kind are made on the basis
of R-free, it will remain essentially unbiased.
The case that Gerard Kleywegt mentions of generating many models in
many ways and using R-sleep for evaluation is an interesting
possibility. I would agree that if a very large set of structures is
to be created and ranked based on R-free, then the R-sleep idea is
useful. However I would argue that it would be simpler and perhaps
just as effective to only use R-work and real-space criteria to
evaluate the structures and reserve R-free as we do now.
At 12:27 PM 10/1/2007, William Scott wrote:
If R-sleep is to be the "real" validation R-factor, why not just sequester
each of R-sleep and the current R-free, each as a randomly-chosen (but
mutually exclusive) set of reflections, and then proceed as normally with
the other (eg) 80% of the data until the very end of the refinement, using
the R-free set to optimize weightings for geometries, NCS symmetry
averaging, and so forth, and then simply add those back in at the
penultimate step of refinement. In the end, you have R-sleep and the
Rfactor corresponding to the rest of the data, just like before, and you
can have the additional statistic reporting the difference between R-sleep
and and R-free, which we could call something like the R-i-didn't-peak.
Peter Adrian Meyer wrote:
> This raises a slightly tangential question though - how do we know how
> what obs/param ratio is good enough?
Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: [EMAIL PROTECTED]
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web
site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
