Thanks! Don’t know why I couldn’t find them… Randy
> On 23 Jun 2025, at 16:38, Gerard Bricogne <[email protected]> wrote: > > Dear Randy, > > Might it be these? > > https://doi.org/10.1107/S0907444997013875 > > https://doi.org/10.1107/S0907444999016868 > > > Best wishes, > > Gerard > > -- > On Mon, Jun 23, 2025 at 03:33:36PM +0000, Randy John Read wrote: >> 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 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/ >>> >>> 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 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/
