Hi Matthew, One thing to consider is that B factors model "small-scale" atomic vibrations within the harmonic approximation, while occupancies are used to model larger-scale disorder. From your description, it sounds like occupancies may be a better descriptor in your case.
See page 21 here, which I use to illustrate what I just wrote when giving talks on this topic: https://phenix-online.org/phenixwebsite_static/mainsite/files/user_meeting/2024_07_ACA/3_refinement_Xray_PVA.pdf All the best! Pavel On Wed, Mar 5, 2025 at 11:18 AM Matthew Snee < matthew.sne...@manchester.ac.uk> wrote: > Thankyou for those links > > One of those papers seems to basically say that atoms that accumulate > stratospheric B factors are "speculative", but Im working on an example > with a Wilson B factor of over 100 where some of the weaker features have > enormous B values. > > > > The crystal is very atypical, very high solvent, and a very wide range of > flexibility where whole domains can move almost freely in solvent > channels, but are still observed. > The features that have obtained super high B factors are the glycans. The > general shape of the core Glycan can be seen clearly, but the conformation > is not constrained by any contacts, so the density is extremely diffuse. > > The "answer" is obviously that there is an ensemble of conformations (for > these features and also a whole domain), which would exist at low occupancy > but would also accrue a lower B factor, but I think it is more appropriate > to model a single favourable conformer that fits the density. > > > This is certainly the first X-ray structure that I ever worked on that was > quite like this, so id like to hear peoples opinions on how I should handle > it. The values out of context would certainly raise eyebrows! > > I work quite a bit on EM and it appears really similar to some EM examples > with resolution ranges between 2.8-6A. > > I am certain that the features with the very high values are much more > than speculative, and the model is more accurate when complete, but the B > factors are certainly not describing the relationship between the model and > the data in a useful way! > > Best wishes > > Matthew. > > > > > > > > > > > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Italo > Carugo Oliviero <olivieroitalo.car...@unipv.it> > *Sent:* 05 March 2025 16:21 > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject:* Re: [ccp4bb] IDS in PDB > > > 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 > [doi.org] > <https://urldefense.com/v3/__https://doi.org/10.1186/s12859-018-2083-8__;!!PDiH4ENfjr2_Jw!GvXajeqHyc78oG7fUDHacPe5o0b-HFbzBJLEkYOApVm5CM5RsNpkyhm68SnJnELJZ8zxhNWbJBcraWaoE7qkEaKzveL3tjJenPIJ8Wkn7A$>) > & Zeit. Krist. 2018 234 73-77 (https://doi.org/10.1515/zkri-2018-2057 > [doi.org] > <https://urldefense.com/v3/__https://doi.org/10.1515/zkri-2018-2057__;!!PDiH4ENfjr2_Jw!GvXajeqHyc78oG7fUDHacPe5o0b-HFbzBJLEkYOApVm5CM5RsNpkyhm68SnJnELJZ8zxhNWbJBcraWaoE7qkEaKzveL3tjJenPIIucbmag$> > ). > > 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/ [journals.iucr.org] > <https://urldefense.com/v3/__https://journals.iucr.org/m/issues/2022/06/00/tf5001/__;!!PDiH4ENfjr2_Jw!GvXajeqHyc78oG7fUDHacPe5o0b-HFbzBJLEkYOApVm5CM5RsNpkyhm68SnJnELJZ8zxhNWbJBcraWaoE7qkEaKzveL3tjJenPJrQbXHqQ$> > > that, when describing an atomic model, each atom should have one more > parameter, namely a local resolution with which it contributes to the map > from which it has been identified - or, in other words, with which value > its image should be calculated to reproduce the experimental map (and NOT > the density / potential itself) as a sum of atomic contributions (different > atoms may have different local resolution). > Indicating the local resolution large (and neither B-factors large > nor occupancy small) means exactly that one cannot localize it in this > given map; again in other words, that the map from which this part of the > model was constructed had not enough information. > > Naturally, cif-format has no obstacle to complete the model description by > the local resolution value associated to each individual atom. Moreover, > even the old good PDB format has a space for this; positions 67-72 have > been reserved :-) > > Going behind the current discussion, as you perfectly know, both B-factors > and resolution cut-off blur atomic images; however they do it in a > different way (Ezra already mentioned Fourier ripples). Considering this > new parameter allows one distingushing these two effects and even to > identify (fix?) some errors occured when using the current, conventional > procedures : see, for example, Lunin et al. in Current Research in > Structural Biology (2023) : > https://doi.org/10.1016/j.crstbi.2023.100102 [doi.org] > <https://urldefense.com/v3/__https://doi.org/10.1016/j.crstbi.2023.100102__;!!PDiH4ENfjr2_Jw!GvXajeqHyc78oG7fUDHacPe5o0b-HFbzBJLEkYOApVm5CM5RsNpkyhm68SnJnELJZ8zxhNWbJBcraWaoE7qkEaKzveL3tjJenPJqf5yqcw$> > > 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 > [jiscmail.ac.uk] > <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!GvXajeqHyc78oG7fUDHacPe5o0b-HFbzBJLEkYOApVm5CM5RsNpkyhm68SnJnELJZ8zxhNWbJBcraWaoE7qkEaKzveL3tjJenPIr_83TBw$> > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > [jiscmail.ac.uk] > <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!GvXajeqHyc78oG7fUDHacPe5o0b-HFbzBJLEkYOApVm5CM5RsNpkyhm68SnJnELJZ8zxhNWbJBcraWaoE7qkEaKzveL3tjJenPIr_83TBw$> > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > [jiscmail.ac.uk] > <https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!GvXajeqHyc78oG7fUDHacPe5o0b-HFbzBJLEkYOApVm5CM5RsNpkyhm68SnJnELJZ8zxhNWbJBcraWaoE7qkEaKzveL3tjJenPIr_83TBw$> > > ------------------------------ > > 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/
