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 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/
