True and the “more faulty” those reflections are the bigger is their influence. Would then it make sense to flag possibly “faulty” reflections not to be used in the free set? I think it is a logical conclusion, however, recognizing the faultiness may not be as straightforward, in my opinion.
Thank you for your comments. Vaheh From: Jeroen Mesters <[email protected]> Sent: Monday, June 23, 2025 12:39 PM To: Oganesyan, Vaheh <[email protected]> Subject: Re: [ccp4bb] free R in shells Hi, with 5% of the reflections randomly flagged by numbers 0 to 19, any of these Rfree sets is 19x smaller than the working set of reflections. The impact of a few really faulty reflections in terms of Intensity will therefore be much larger on the Rfree set than on the Rwork. Regards, Jeroen __ Dr. math. et dis. nat. Jeroen R. Mesters Biological Safety Officer (BBS) Deputy, Lecturer, Program Coordinator Infection Biology Visiting Professorship in Biophysics - University South Bohemia [cid:[email protected]] University of Lübeck Center for Structural and Cell Biology in Medicine Institute of Biochemistry Ratzeburger Allee 160 23562 Lübeck Tel +49 451 3101 3105 https://orcid.org/0000-0001-8532-6699<https://orcid.org/0000-0001-8532-6699> Am 23.06.2025 um 16:55 schrieb Oganesyan, Vaheh <[email protected]<mailto:[email protected]>>: 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. <image001.png> 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]<mailto:[email protected]>> On Behalf Of Randy John Read Sent: Monday, June 23, 2025 10:29 AM To: [email protected]<mailto:[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 > On 23 Jun 2025, at 12:35, Ben Bax > <[email protected]<mailto:[email protected]>> wrote: > > Hi, > How do you select R-free in shells with CCP4? > Thanks, Ben Bax > > ######################################################################## > > 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 > http://www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing > list hosted by http://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> ----- Randy J. 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