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 > 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. 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. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. ######################################################################## 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/
