Your point is taken, Pavel. However, despite resolution, you define coordinate of the atom as a geometric point with no width. Although coordinates are “refineable”, they have no capacity for “trash”. Their “trash” still goes into B-factor “trash bin”. At least this is how I see it.
Thank you. Vaheh Oganesyan, Ph.D. [cid:image001.png@01DAE281.A8E8D260] R&D | Biologics Engineering One Medimmune Way, Gaithersburg, MD 20878 T: 301-398-5851 vaheh.oganes...@astrazeneca.com<mailto:oganesy...@medimmune.com> From: Pavel Afonine <pafon...@gmail.com> Sent: Tuesday, July 30, 2024 11:45 AM To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com> Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era? From this perspective, all refinable atomic model parameters can be viewed as trash bins, with the size of these bins being proportional to the amount of prior information (restraints) imposed on these parameters. For example, coordinates have the most restraints and thus are the smallest trash bins, while B factors have the least restraints and thus are one of the largest bins. Pavel On Tue, Jul 30, 2024 at 8:25 AM Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com>> wrote: Early in my Crystallography life I was postdoc with Robert Huber in Munich. We had those gatherings once a week when in very informal way we can ask and answer questions. I remember my question about B factors: how is it possible to have high resolution structure and average B-factor of 100A2. I think it was Robert or Albrecht Messerschmidt who told that B-factor is a “trash can” that describes not only loosely positioned atoms but also all other problems that either you created during processing, harvesting or crystal had from the beginning. Vaheh Oganesyan, Ph.D. [cid:image001.png@01DAE281.A8E8D260] R&D | Biologics Engineering One Medimmune Way, Gaithersburg, MD 20878 T: 301-398-5851 vaheh.oganes...@astrazeneca.com<mailto:oganesy...@medimmune.com> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of James Holton Sent: Tuesday, July 30, 2024 10:35 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era? How high B factors can go depends on the refinement program you are using. In fact, my impression is that the division between the "let the B factors blow up" and "delete the unseen" camps is correlated to their preferred refinement program. You see, phenix.refine is relatively aggressive with B factor refinement, and will allow "missing" atoms to attain very high B factors. Refmac, on the other hand, has restraints that try to make B factor distributions look like those found in the PDB, and so tends to keep nearby B factors similar. As a result, you may get "red density" for disordered regions from refmac, inviting you to delete the offending atoms, but not from phenix, which will raise the B factor until the density fits. Then there are programs like VagaBond that don't formally have B factors, but rather let an ensemble of chains spread out in the loopy regions you are concerned about. This might be the way to go? You can also do ensemble refinement in the latest Amber. That is, you run an MD simulation of a unit cell (or more) and gradually increase structure factor restraints. This would probably result in the "fan" of loops you have in mind? -James Holton MAD Scientist On 7/28/2024 8:13 AM, Javier Gonzalez 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<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<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<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/
