Just wanted to thank you for your remarkable contributions to this discussion.
These are a couple of articles that dive into the issue of unusually large B-factors: BMC Bioinformatics 2018 19 61 ( https://doi.org/10.1186/s12859-018-2083-8) & Zeit. Krist. 2018 234 73-77 ( https://doi.org/10.1515/zkri-2018-2057). Best, Oliviero Il giorno mar 4 mar 2025 alle ore 14:03 Frank von Delft < 0000bcb385fe5582-dmarc-requ...@jiscmail.ac.uk> ha scritto: > Interesting... > > Has this got onto the radar (or critical path) of the PDB's mmCIF working > group (or whatever it's called?) > > I'm assuming that's where this would go to next, if the downstream > developers are ever going to take it seriously. > > Frank > > > > On 04/03/2025 12:21, Alexandre Ourjoumtsev wrote: > > Dear all, > > Fully relevant to this discussion, you might noted that a couple of years > ago, we (Vladimir Lunin and myself) argued > > https://journals.iucr.org/m/issues/2022/06/00/tf5001/ > > that, when describing an atomic model, each atom should have one more > parameter, namely a local resolution with which it contributes to the map > from which it has been identified - or, in other words, with which value > its image should be calculated to reproduce the experimental map (and NOT > the density / potential itself) as a sum of atomic contributions (different > atoms may have different local resolution). > Indicating the local resolution large (and neither B-factors large > nor occupancy small) means exactly that one cannot localize it in this > given map; again in other words, that the map from which this part of the > model was constructed had not enough information. > > Naturally, cif-format has no obstacle to complete the model description by > the local resolution value associated to each individual atom. Moreover, > even the old good PDB format has a space for this; positions 67-72 have > been reserved :-) > > Going behind the current discussion, as you perfectly know, both B-factors > and resolution cut-off blur atomic images; however they do it in a > different way (Ezra already mentioned Fourier ripples). Considering this > new parameter allows one distingushing these two effects and even to > identify (fix?) some errors occured when using the current, conventional > procedures : see, for example, Lunin et al. in Current Research in > Structural Biology (2023) : > https://doi.org/10.1016/j.crstbi.2023.100102 > > There is a couple more of relevant articles, in Acta D and J.Appl.Cryst, > and there are works in progress. > > I hope, this helps... > > Have a nice day > > Sacha Urzhumtsev > > ------------------------------ > > 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 > ######################################################################## 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/
