Hi, I think it was Ian Tickle who worked out the statistical error in R-free that arises from taking different random samples, though I can’t track down the publication quickly. Anyway, the take-home from this is that you don’t expect all free sets to give the same R-free, and you shouldn’t over-interpret small differences in R-free.
Does anyone have the citation for this? Best wishes, Randy > On 23 Jun 2025, at 15:55, Oganesyan, Vaheh <[email protected]> > wrote: > > <!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; > panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 > 5 2 2 2 4 3 2 4;} @font-face {font-family:Aptos;} /* Style Definitions */ > p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0in; font-size:12.0pt; > font-family:"Aptos",sans-serif;} a:link, span.MsoHyperlink > {mso-style-priority:99; color:blue; text-decoration:underline;} > span.EmailStyle19 {mso-style-type:personal-reply; > font-family:"Aptos",sans-serif; color:windowtext;} .MsoChpDefault > {mso-style-type:export-only; font-size:10.0pt; mso-ligatures:none;} @page > WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;} > div.WordSection1 {page:WordSection1;} --> 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] > 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]> 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 > > > > This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a > > mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are > > available at 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] > 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 > > 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/ > > 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. > > > > > > > > > ----- 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] 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 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/
