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.
[cid:22581c74-c780-4454-8ae6-83da9d0e8114] 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<mailto: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 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/
