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<mailto: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<mailto: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 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/
