Back to FreeR factors - Phenix, and I believe FreeRflag now select FreeRs in the highest possible symmetry for the crystal class - eh P6/mmm for a trigonal crystal, and expand the set to fill the actual space group. This means the Free R assignment is suitable if later the crystal symmetry is reassigned. But this was not always done in the past so if you are trying to reuse free/work assignments from an old project there are possibilities of not getting this. Maybe the best solution is to just generate a new Free R set ? Eleanor
On Mon, 30 Aug 2021 at 16:59, Andrew Leslie - MRC LMB < and...@mrc-lmb.cam.ac.uk> wrote: > Dear Kay and Jon, > > I cannot remember Ian Tickles original posting on this (assuming that it > was made to the bulletin board), but surely the resolution of the data is > also a very important factor in the danger of over-fitting. The lower the > resolution, the worse the experimental data to refined parameter ratio > becomes, and the more likely it is to obtain an overfitted model, > regardless of how accurate that data might be. Perhaps this is why Kay said > “generally I agree that the accuracy of the data is inversely related to > the danger of overfitting”, or did you have something else in mind Kay? > > Cheers, > > Andrew > > > On 30 Aug 2021, at 13:59, Kay Diederichs <kay.diederi...@uni-konstanz.de> > wrote: > > > > 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/ > > ######################################################################## > > 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/ > ######################################################################## 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/
