Alun, I agree completely with previously stated opinions (and your practice) that preservation of a single test set is very important for the refinement of similar structures. One complication that for spacegroups in which there is a potential axis-indexing ambiguity (e.g. certain trigonal and tetragonal cells), the same set of indices can refer to reflections with different intensities in the different datasets. That would be immediately apparent as a very high Rmerge if multiple, differently indexed dataset are merged, and may complicate transfer of a single test set among multiple, inconsistently indexed datasets for those spacegroups. Best regards, Mark
Mark A. Wilson Assistant Professor Department of Biochemistry/Redox Biology Center University of Nebraska N164 Beadle Center 1901 Vine Street Lincoln, NE 68588 (402) 472-3626 mwilso...@unl.edu "Borhani, David" <david.borh...@deshawresearch.com> Sent by: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> 12/18/08 02:38 PM Please respond to "Borhani, David" <david.borh...@deshawresearch.com> To CCP4BB@JISCMAIL.AC.UK cc Subject Re: [ccp4bb] Transferring a Free R set. Alun, Kay is right on target; I think there is no debate about that you must use one FreeR set for all (even marginally*) isomorphous crystals. Your colleagues who are not following this practice are not doing themselves any favors. If you don't keep the same FreeR set, R & Rfree for that 2nd crystal will be almost identical --- and low!, like the R from crystal 1. Best practice is to create an initial, master FreeR set that extends well beyond your current (first crystal) resolution...crystals usually get better as time spent on a project goes on, and extending the set correctly takes some careful neuronal work (admittedly, now a bit easier with the CCP4i GUI). Dave * I've not seen any arguments for why one *shouldn't* keep the same set, even as isomorphism fades away, due, e.g., to a slightly variable unit cell. Keeping the same set does no harm; calculating the potential harm due to switching sets seems not worth the bother (though I guess one of our more theoretically-inclined contributors will see an opportunity there!). > -----Original Message----- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On > Behalf Of Kay Diederichs > Sent: Thursday, December 18, 2008 3:05 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Transferring a Free R set. > > Alun R. Coker schrieb: > > Hi All, > > > > I have been in the habit of transferring my initial free R > assignments > > to any new data sets or to isomorphous data sets such as substrate > > complexes. Although theoretically this is necessary to > obtain a valid > > free R many of my colleagues maintain that this is completely > > unnecessary in practice. Does anyone on the list have a > view on this or > > has anyone tested to see if it makes any difference. > > > > Alun. > > > > Alun, > > I completely agree with you about the way how to treat R-free > reflections. If you want to have an unbiased R-free then you > need to set > these reflections aside for all refinement calculations of a project, > and this applies to all datasets you collect, as long as they are > isomorphous. > This is especially important for low resolution work where > the danger of > overfitting is highest. > > Kay >
