Hi Jon, generally I agree that the accuracy of the data is inversely related to the danger of overfitting, and that selection in shells is not necessary. But if twinning is suspected, as here, and/or a choice between high and low symmetry spacegroup has to be made, one has to make sure that potentially symmetry-related reflections are _either_ labelled as test _or_ as work; a mixture will artificially down-bias Rfree.
Selecting the test set in the highest possible symmetry (which is what Phenix does) is a good solution. This test set should be symmetry-expanded when trying the low-symmetry spacegroup (if one wants to compare R values). The latter is not necessary when working with thin shells - but that has other disadvantages. best wishes, Kay On Sun, 29 Aug 2021 14:32:34 +0000, Jon Cooper <jon.b.coo...@protonmail.com> wrote: >Hello Engin, we discussed this a year or two ago in relation to NCS when Ian >Tickle convinced me that since overfitting is due errors in the data, there is >no reason to expect these errors to be correlated by NCS and picking the >R-free set uniformally or in shells doesn't matter. No doubt my incompetence, >but I can't see why twinning would be different. > >Cheers, Jon.C. > >Sent from ProtonMail mobile > >-------- Original Message -------- >On 29 Aug 2021, 05:32, Engin Özkan wrote: > >> Hi, >> >> I believe this is taken care of automatically if you use phenix to pick >> your free reflections. >> >> From http://www.phenix-online.org/documentation/tutorials/twinning.html >> >> "When a test set is designed, care must be taken that free and work >> reflections are not related by a twin law. The R-free set assignment in >> phenix.refine and phenix.reflection_file_converter is designed with this >> in mind: the free reflections are chosen to obey the highest possible >> symmetry of the lattice." >> >> I believe this applies to all datasets, just in case there may be twinning. >> >> Engin >> ... ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
