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 <[email protected]> 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 <[email protected]> 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 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/
