[phenixbb] Cross-validation when test set is miniscule

Derek Logan derek.logan at biochemistry.lu.se
Fri Dec 19 03:18:37 PST 2014

Hi everyone,

Right now we have one of those very difficult Rfree situations where it's impossible to generate a single meaningful Rfree set. Since we're in a bit of a hurry with this structure it would be good if someone could point me in the right direction. We have crystals with 1542 non-H atoms in the asymmetric unit that diffract to only 3.6 Å in P65, which gives us a whopping 2300 reflections in total. 5% of this is only about 100 reflections. Luckily the protein is only a single point mutation of a wild type that has been solved to much better resolution, so we know what it should look like and I simply want to investigate the effect of different levels of conservatism in the refinement, e.g. NCS in xyz and B, group B-factors, reference model, Ramachandran restraints etc. However since the quality criterion for this is Rfree I'm not able to do this.

I believe the correct approach is k-fold statistical cross-validation, but can someone remind me of the correct way to do this? I've done a bit of Googling without finding anything very helpful.

Derek Logan                                         tel: +46 46 222 1443
Associate Professor                                 mob: +46 76 8585 707
Dept. of Biochemistry and Structural Biology              www.cmps.lu.se<http://www.cmps.lu.se>
Centre for Molecular Protein Science            www.maxlab.lu.se/crystal
Lund University, Box 124, 221 00 Lund, Sweden           www.saromics.com

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