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Yes SFTOOLS can select reflections in thin shells but I must admit I'm
not overly enthusiastic about this approach myself and would only use it
for high symmetry NCS cases. The problem is that to get a reasonable
number of shells covering the full resolution range, they need to be
very thin. This puts nearly every RFREE reflection at the edge of the
shell. The NCS-related reciprocal space position of an RFREE reflection
at the edge of the shell is likely going to be correlated to non-RFREE
reflections just outside the shell. I believe one person (Ian Tickle???)
suggested to use just 3 or so thick shells which is the more purist
approach but I'm not sure refinement programs can derive proper Sigmaa
weights for ML refinement when many resolution bins don't include any
RFREE reflections.
I've started long ago on an algorithm to select Rfree islands but never
completed it. Basically, you select your first Rfree reflection at
random and then flag reflections in a small NCS-related reciprocal
volume as a "no-take zone" for future Rfree reflection picks. With more
complex NCS relationships and the complexities of asymmetric unit
definitions this gets real messy real quick. However, now that NCS is
becoming so common maybe I should revisit that idea.
Bart
PS: Although the Rfree-bias problem is real, high NCS itself is also a
powerful means to reduce overfitting with properly applied restraints
and by NCS averaging of maps prior to visual inspection. So high NCS
represents both a problem and a solution.
Dean Madden wrote:
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Actually, one can use SFTOOLS, which is part of CCP4. However, the
selection of a test set can only be done using the stand-alone version
of the program. The "RFREE frac SHELL" command is not currently
available through ccp4i.
Dean
Jan Abendroth wrote:
A way to avoid biasing Rfree values is to choose the test set in
thin resolution shells whenever NCS is present. Currently, this
precaution is often ignored. It should become a de facto standard
for publication of structures containing NCS.
Hi all,
btw - it would be fantastic and certainly would encourage us to use
it more often if the assignment of free reflections in resolution
shells was incorporated in a ccp4 program. Yes, one can for instance
go through shelxpro, however if one wants to go back to ccp4 this
route is a bit painful.
Cheers
Jan
