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/ | 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 | 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 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/
