Hi Martin, if I correctly understood your 2nd question, here are a couple of papers that may be helpful:
https://doi.org/10.1107/S0907444913016673 https://doi.org/10.1107/S1600576715001648 Re your 1st question, how reflections are split into bins depends on what this is done for, for example: - estimation of parameters of ML targets require certain number of free reflections in each bin and those bins has to be sufficiently thin, - monitoring of bulk-solvnet modeling requires a closer look at low-res reflections and this log scaling of resolution is best for binning, - .... etc etc etc. This doesn’t really answer your question, I know. - ;) However, I am having a hard time finding meaningful arguments for the utility of splitting reflection data into 20 bins with the same number of reflections in each bin (sorry, I failed to catch this from your original email!). Pavel On Tue, Nov 18, 2025 at 10:55 AM Martin Moche < [email protected]> wrote: > Dear colleagues, > > > > *Question 1:* > > > > Is there already a way? or possible to add a second option in how AIMLESS? > divide reflections into 20 bins where the second option is to put an equal > number of reflections in each bin (like STARANISO does). > > > > I like to use REFMAC5 for refinement, and STARANISO for data processing, > but the way the reflections are divided into bins in AIMLESS make REFMAC5 > refinement after STARANISO data processing, less compatible. > > > > As we all know STARANISO selects the best ellipse, instead of sphere, when > integrating reflections. > > > > In my experience this is good because > > > > 1. Crystals generally diffract better in some directions than others > 2. The electron density maps look better after STARANISO elliptical > data truncation, as compared to spherical data truncation in XDS, XDSAPP3, > DIALS etc. so it becomes easier and faster to build a model and refine a > structure. > > > > To my understanding AIMLESS assumes 100 % completeness when creating its > 20 bins, and elliptically truncated data has extremely low completeness in > the highest resolution shells, so Table 1 is looking very odd with > extremely low completeness in the highest resolution shell when using > REFMAC5 after STARANISO. > > > > *Question 2:* > > > > Are there software or online servers that given space group and cell > parameters and number of your measured reflections calculate the “efficient > resolution” assuming 100% completeness in each shell? > > > > Perhaps a better estimate of resolution in a single number than today’s > practice as: > > > > 1. Spherical integration, XDS and DIALS, integrating reflections that > are not present > 2. Staraniso integration, having a few percent of reflections in the > highest resolution shell, making statements of resolution in a single > number impossible > > > > Best regards, > > Martin > > > > Head of Macromolecular X-ray Crystallography <https://ki.se/en/mbb/psf-mx> > | Protein Science Facility <https://ki.se/en/mbb/protein-science-facility> > > Medical Biochemistry and Biophysics > <https://ki.se/en/mbb/department-of-medical-biochemistry-and-biophysics> > > 171 65 Solna | Solnavägen 9 > > +46 8 524 868 43 | +46 73 322 93 27 > > [email protected] | ki.se > > ______________________________________ > > <https://ki.se/psf> <https://gu.se/pps> <https://ki.se/> > > > > > > > > *När du skickar e-post till Karolinska Institutet (KI) innebär detta att > KI kommer att behandla dina personuppgifter. *Här finns information om > hur KI behandlar personuppgifter > <https://ki.se/om-ki/integritetsskyddspolicy>. > > > *Sending email to Karolinska Institutet (KI) will result in KI processing > your personal data.* You can read more about KI’s processing of personal > data here <https://staff.ki.se/data-protection-policy>. > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
