Hi Valesh,
in addition to the expected variance v=(Rfree)^2/(2T), where T is the size of your test set (Ian Tickle et al, https://doi.org/10.1107/S0907444999016868) it also matters whether you ran enough cycles to stabilise the refinement, i.e. the value of the target function should not drop any further. SHELXL prints the maximum shift, which is convenient, but with other programs, you may need to check the log-files to confirm. Did you consider this during you study? Cheers, Tim On Mon, 23 Jun 2025 14:55:36 +0000 "Oganesyan, Vaheh" <[email protected]> wrote: > Hi all, > > I’ve spent some time going through different flags for free > reflections for (somewhat stupid) reason to get lower Rfree. I made > sure all different flags were used only for each of sets of > refinement. I wanted to satisfy my inner belief that it doesn’t > matter which flag is used (between 0 and 19). To be short: I failed. > > Free reflections have been chosen “randomly”, no suspicion there. > However, there was clear difference at the end. The difference was > about 2-3% difference in Rfree value. This tells me that the > randomness has some sort of rule, which makes “random” choice not so > random. Having found this I also tried to see “a rule” that breaks > this randomness, like even numbers, odds, etc. I did not. Because > this was only on few cases I won’t even try to connect it to # of > molecules per AU, or SG. For each structure (I tried this for 2-3 > structures about 10 years ago) it was a different flag. I’m not sure > if DCC also is looking through different flags, but at the end it > finds the best, making these exercises unnecessary. Sorry, cannot > present a case. Was too long ago. > > Vaheh Oganesyan, Ph.D. > [cid:[email protected]] > R&D | Biologics Engineering > One Medimmune Way, Gaithersburg, MD 20878 > T: 301-398-5851 > [email protected]<mailto:[email protected]> > > > > From: CCP4 bulletin board <[email protected]> On Behalf Of Randy > John Read Sent: Monday, June 23, 2025 10:29 AM > To: [email protected] > Subject: Re: [ccp4bb] free R in shells > > Hi Ben, > > I would be very interested if you have a case where it makes a > difference to do this. At one point I was convinced that it had been > important when we were working on the structure of a Shiga-like toxin > bound to trisaccharide (1bos), with four pentamers in the asymmetric > unit. However, Pavel Afonine challenged me to show that the free set > was less biased when chosen in shells than when chosen randomly, and > even in that relatively extreme case I couldn’t see evidence of it. > So it’s probably not worth the bother. Also, if you select the free > set randomly, it’s distributed over the same resolutions as the > working data, which arguably is important when you’re using it to > calibrate the sigma(A) estimates for likelihood targets. > > Best wishes, > > Randy > > [...] > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building > Hills Road E-mail: [email protected]<mailto:[email protected]> > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<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<http://www.jiscmail.ac.uk/CCP4BB>, a > mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, > terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/<https://www.jiscmail.ac.uk/policyandsecurity/> > ________________________________ > > Confidentiality Notice: This message is private and may contain > confidential and proprietary information. If you have received this > message in error, please notify us and remove it from your system and > note that you must not copy, distribute or take any action in > reliance on it. 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