Dear Gerard, A great remark! Thank you for starting this thread separately. I think that you are absolutely right in many of the points. However, it also raises several questions. Here are my favourite ones:
1) If STARANISO generally suggests "the same" resolution as PAIREF, there are fewer reflection in the final dataset because of the ellipsoidal cut in the worst diffraction direction. Is it good to avoid these data? 2) A very general one: Are we doing well when touching the experimental data with anisotropic scaling? Should we rather modify the model to fit the "raw" data? If so, how about to do it? I may be wrong, but would it be possible to refine the structure using all-atom based general anisotropic ADP (similar to TLS refinement)? Just a short comment to your table in the attachment. In case of BO from our publication, STARANISO resolution goes to 2.3, but our suggestion was to stop at the original resolution of 2.6 AA. The reason for that is sub-optimal refinement of the geometry. Once restrained in PAIREF, there is no improvement anymore. Best regards, Petr ________________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Gerard Bricogne <g...@globalphasing.com> Sent: Tuesday, October 4, 2022 6:01:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] PAIREF, Anisotropy and STARANISO Dear all, First of all, apologies for breaking the threads entitled "PAIREF - Warning - not enough free reflections in resolution bin" and "Anisotropy" by merging them into a new one, but it somehow felt rather against nature to keep them separate. Since the early days of the availability of STARANISO [1] (the actual starting year for the Web server [2] was 2016), we had a hunch that much of what was happening in the PAIREF procedure might simply be the detection of the existence of significant data beyond an initially chosen resolution cut-off not only as a result of an excessively conservative criterion having been applied in that initial choice, but as a consequence of anisotropy in the data. The latter would give rise to different diffraction limits in different directions, and the choice of a single value for "the resolution" at which the data were cut off would necessarily yield a compromise value between the best and the worse diffraction limits. This would imply that significant data would be excluded in the best diffracting directions, that would subsequently drive PAIREF towards increasing the estimated resolution compared to its compromise value. This "hunch" was validated by a detailed comparison carried out on the exact same examples that are considered in the 2020 paper by Maly et al., that is summarised in the attached PDF. In other words, whenever anisotropy is present in the data, PAIREF will tend to indicate a higher value for an isotropic cut-off than would have been estimated for the initial dataset. The problem with taking the PAIREF result as the final answer is that the higher cut-off it indicates is applied *isotropically*. The inclusion of the significant data thus reclaimed is therefore unavoidably accompanied by that of noisy data in the worst diffracting direction(s), resulting in alarmingly poor statistics in the outermost shell (as pointed out in Eleanor's message) that may cast doubts on the usefulness of the procedure. This consideration was the basis of the rationale for implementing an *anisotropic* cut-off surface in STARANISO, so that one could thus reclaim the significant data in the best-diffracting direction(s) while avoiding the simultaneous inclusion of the pure-noise measurements in the worse one(s). While this is clearly and extensively explained in the documentation provided on the STARANISO server [2], it seems to be far from having been assimilated. Of course this would be perfect material for a publication, but life is somehow too short, and our to-do list has remained too long, to leave us room for spending the necessary time to go through the process of putting a paper together. The truly important matter is to get our picture in front of the user community. Now that the combined topics of PAIREF and anisotropy are being brought to the foreground of the community's attention, this seems like the perfect opportunity to present our analysis and position: what PAIREF achieves in terms of an upward revision of an initial isotropic resolution cut-off is likely to be achieved more straightforwardly by submitting the same data to the STARANISO server (or using it within autoPROC [3]); and the STARANISO output will have the advantage of being devoid of the large extra amount of purely noisy, uninformative data that are retained in the output from PAIREF according to its revised isotropic cut-off. We would very much welcome feedback on this position: indeed we would like to *crowd-source* the validation (or refutation) of this conclusion. In our view, continuing to use the PAIREF procedure to revise an isotropic resolution cut off misses the point about the consequences of anisotropy. The only sensible use of a PAIREF-like procedure would be to adjust the cut-off threshold for the local average of I/sig(I) in STARANISO, whose default value is currently 1.2 but can be reset by the user through the Web server's GUI. We occasionally see datasets of very high quality for which the CC_1/2 value in the outermost shell stays above 0.6 or even 0.7, and it is quite plausible that further useful data could be rescued if the local I/sig(I) cut-off threshold were lowered below 1.2. Concerning Eleanor's view that noisy data can't hurt refinement because they are properly down-weighted by the consideration of e.g. Rfree values in resolution shells, we would point out that any criterion based on statistics in resolution shells will be polluted if the data are anisotropic and if the noisy data that STARANISO would reject are retained. That will result in excessive down-weighting of the significant data that STARANISO retains, hence in losing the information they contain. Perhaps this is a matter for later discussion, but the main idea is that retaining pure-noise data is not neutral in refinement, and that every "isotropic thinking habit" on which many views are based needs to be revisited. With best wishes, Clemens, Claus, Ian and Gerard. [1] Tickle, I.J., Flensburg, C., Keller, P., Paciorek, W., Sharff, A., Vonrhein, C., Bricogne, G. (2018). STARANISO. Cambridge, United Kingdom: Global Phasing Ltd. https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1806&L=CCP4BB&O=D&P=3971 [2] https://staraniso.globalphasing.org/ [3] https://doi.org/10.1107/s0907444911007773 https://www.globalphasing.com/autoproc/ ######################################################################## 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/ ######################################################################## 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/