Hi Martin, Re: Question 2: Are you wanting to calculate something similar to what Gerard Kleywegt called "effective resolution" and that he attributes the term and calculation method to a 1995 personal communication from Bart Hazes in a couple of his papers on good refinement practices and validation from 1997-2000. https://www.ebi.ac.uk/pdbe/docs/EMBO/Validation_XrayStructures_Gerard.pdf - 2000 - Acta D56, 249-265 https://hod.greeley.org/papers/ByAuthor/Kleywegt/gmrp.html - preprint of his 1997 Methods & Enzymology article?
Bart Hazes' sftools program can calculate this. See the "complete" command were it is called the "100% criterion" https://www.ccp4.ac.uk/html/sftools.html#checking-data-completeness (You could also get this 100% resolution for different I/sigI cutoffs by first selecting only those reflections above the desired threshold before calling the complete command -) Regards, Mitch On Tue, Nov 18, 2025 at 12:56 PM 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/
