Hi all, I always appreciate detailed discussions on this bulletin board—the specific topic almost doesn’t matter! Thank you for engaging in such thoughtful conversation.
To clarify, if I had any intention of misconduct, I certainly wouldn’t be posting my questions here. Likewise, my concern is not with the absolute values of Rwork and Rfree, but with the difference between these two measures, which I believe is more critical. When I see a button in a GUI, I assume it serves an important function. With minimal explanation, it’s natural to be curious and want to experiment or explore. A brief note about the selection of reflections: During data processing, we apply certain criteria to filter out incorrectly measured reflections, and the advantages of this are clear and uncontroversial. The approach is sufficiently robust to avoid excluding weak reflections in low-resolution shells or strong reflections in high-resolution shells. However, when it comes to free sets, I have some doubts. For instance, what if a strong, well-measured reflection at high resolution is randomly selected for the free set and therefore excluded from refinement? While it contributes nothing to the electron density map, its relatively high intensity could artificially inflate the Rfree value. Is my understanding correct? Additionally, I recall a recommendation from a 1990s publication (though I can’t recall which) that suggested selecting approximately 1,000 reflections for the free set irrespective of data resolution. With an average of 20 resolution shells, that corresponds to about 50 free reflections per shell. My question is: Would it be sensible to select, for each shell, around 50 reflections whose intensities are close to the median value? Thank you. 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 Robbie Joosten Sent: Wednesday, June 25, 2025 4:20 AM To: [email protected] Subject: Re: [ccp4bb] free R in shells I have tested this a lot and I get the same result in the sense that after extensive refinement there is no evidence of bias. That is, the R-free from previously used test sets is not systematically lower than that of the original 'free' test set. I used REFMAC for that. In the context of PDB-REDO, I reset the B-factor to a flat value related to the Wilson B-factor and then do many cycles of refinement. That would be whatever I used before in PDB-REDO given the kind of refinement needed for the model + 40 (see 10.1107/S0907444911054515). I only add coordinate noise for cases where the model already has a flat B-factor (very low resolution cases mostly), but very little (gemmi set --noise 0.05). Adding too much noise makes a mess and to be honest haven't really seen that the noise adds that much except that some referees are particularly keen on it. Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board > <[email protected]<mailto:[email protected]>> On Behalf Of Tim > Gruene > Sent: Wednesday, June 25, 2025 09:49 > To: [email protected]<mailto:[email protected]> > Subject: Re: [ccp4bb] free R in shells > > On Tue, 24 Jun 2025 22:54:28 +0100 > Martin Malý <[email protected]<mailto:[email protected]>> wrote: > > > Actually I would be quite interested what is your best practise when > > you want to reset a structure model to not be biased towards any test > > reflection set. > Dear Martin, > > according to Ian Tickle, the idea or 'resetting' the structure is the wrong > understanding, and if you notice model bias, there was a mistake in the > approach. You can safely build your model and refine against all data all the > way to the end. When you are interested in Rfree, you pick any random set > and refine to convergence, i.e. until the target function does not drop any > further. Refinement removes bias. (see Ian's emails on this topic, quite some > years back) > > 'shaking' the model coordinates and/or adps is no good. I remember in one > case when I worked on Rcomplete, there was a side chain the flipped into a > different rotamer from shaking. This is a different model, and you cannot > average R-values from different models (see sections "Effect of Parameter > Perturbation." and "Influence of Parameter Perturbation on Convergence > Rate" and Figures S4 /S5 in > https://doi.org/10.1073/pnas.1502136112<https://doi.org/10.1073/pnas.1502136112> > / > https://www.pnas.org/doi/suppl/10.1073/pnas.1502136112/suppl_file/pnas<https://www.pnas.org/doi/suppl/10.1073/pnas.1502136112/suppl_file/pnas>. > 1502136112.sapp.pdf > > Best, > Tim > > > > -- > -- > Tim Gruene > Head of the Core Facility Crystal Structure Analysis Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > https://ccsa.univie.ac.at<https://ccsa.univie.ac.at> > > GPG Key ID = A46BEE1A > > ############################################################### > ######### > > 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> ######################################################################## 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. 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