Thank you all for your thoughtful answers. I'll stick to the crystallographic data and model as much as I can with reasonable occupancy and B factors, even if the result is a truncated model.
I don't believe in the zero occupancy trick either. I just thought the PDB was more flexible these days, since the community of structural biologists seems to have accepted the highly accurate and highly imprecise coordinates of AF-generated noodle-like loops in the UniProt database. It sounds like the PDB-DEV database is the right place to deposit those hybrid models I had in mind, and leave the genuine crystallographic models for the PDB. Best wishes, Javier On Sun, Jul 28, 2024 at 2:52 PM Guillaume Gaullier < guillaume.gaull...@kemi.uu.se> wrote: > Hello Javier, > > Placing atoms implies that you know they are present somewhere (possibly > with some uncertainty on exactly where), but setting their occupancies to > zero implies that you know they are nowhere at all. This is a paradox. > > I think atoms with zero occupancy make no sense in a final deposited model > (they could be useful as a working intermediate to exclude the bulk solvent > model, but this is unrelated to what you describe). > So in this particular case, partial occupancies only make sense for > multiple conformations (and should add up to 1), as Pavel describes. > > If you can’t resolve more than one conformation, maybe a better approach > is to fix the coordinates to what AlphaFold suggested (which is often > reasonable, but check their pLDDT to assess this) and refine to let the > B-factors of these atoms rise. This will convey the large uncertainty on > their positions. I think it is a valid approach because you know these > residues are there somewhere (in other words, to me you would need evidence > of their absence to justify truncating these loops: SDS-PAGE showing that > the protein is cleaved, for example). > > I hope this helps, > > Guillaume > > On 28 Jul 2024, at 17:32, Pavel Afonine <pafon...@gmail.com> wrote: > > > > Javier, > > Flexible loops may be better modeled with ensembles of N models, meaning > the occupancy of each-one would be 1/N, and the map contours to visualize > them should be chosen as 1/N sigma (not 1 sigma). While model prediction > tools such as AlphaFold are helpful, they don't suddenly lift the > requirement for the atomic model you release to the world to fit the > experimental data! With this premise in mind, the approaches to validate > your model geometry and model-to-data fit quality have not changed before > and after the AlphaFold era. > > Whether you truncate residue side chains/loops that you don't see or keep > them with zero occupancy is a perennial question on this list that has been > coming up for decades, and I have yet to see an answer that everyone agrees > on! > > All the best, > Pavel > > > On Sun, Jul 28, 2024 at 8:13 AM Javier Gonzalez <bio...@gmail.com> wrote: > >> >> >> Dear CCP4bb, >> >> I'm refining the ~3A crystal structure of a big protein, largely composed >> of alpha helices connected by poorly-resolved loops. >> In the old pre-AlphaFold (AF) days I used to simply remove those >> loops/regions with too high B factors, because there was little to none >> density at 1 sigma in a 2Fo-Fc map. >> However, considering that the quality of a readily-computable AF model is >> comparable to a 3A experimental structure, and that the UniProt database is >> flooded with noodle-like AF models, I was considering depositing a combined >> model in the PDB. >> Once R/Rfree reach a minimum for the model truncated in poorly resolved >> loops, I would calculate an augmented model with AF calculated missing >> regions (provided they have an acceptable pLDDT value), assign them zero >> occupancy, and run only one cycle of refinement to calculate the formal >> refinement statistics. >> Would that be acceptable? Has anyone tried a similar approach? >> I'd rather do that instead of depositing a counterintuitive model with >> truncated regions that few people would find useful!! >> >> Thank you for your comments, >> >> Javier >> >> -- >> Dr. Javier M. González >> Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET) >> Universidad Nacional de Santiago del Estero (UNSE) >> RN9, Km 1125. Villa El Zanjón. (G4206XCP) >> Santiago del Estero. Argentina >> Tel: +54-(0385)-4238352 >> Email <bio...@gmail.com> Twitter <https://twitter.com/_biojmg> >> >> >> ------------------------------ >> >> 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 > > > VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner > igen avsändaren och vet att innehållet är säkert. > CAUTION: Do not click on links or open attachments unless you recognise > the sender and know the content is safe. > > > > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör > det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal > data. For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/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 > -- Dr. Javier M. González Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET) Universidad Nacional de Santiago del Estero (UNSE) RN9, Km 1125. Villa El Zanjón. (G4206XCP) Santiago del Estero. Argentina Tel: +54-(0385)-4238352 Email <bio...@gmail.com> Twitter <https://twitter.com/_biojmg> ######################################################################## 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/
