Obviously no refined parameters can ever be completely error-free, it's just that for the co-ordinates we have very accurate geometric restraints so that the relative uncertainty in the refined co-ordinates is small (but try refining co-ordinates without restraints!). For the B factors we don't have accurate estimates (if any) for their restraints so their relative uncertainty after refinement is much greater.
-- Ian On Tue, Jul 30, 2024 at 6:57 PM Oganesyan, Vaheh < [email protected]> wrote: > Yes, it is and I like the definition of shared “trash bin”. It will have > more physical meaning if we can separate those contributions into separate > bins. > > > > Vaheh > > > > > > > > *From:* Pavel Afonine <[email protected]> > *Sent:* Tuesday, July 30, 2024 1:51 PM > *To:* Oganesyan, Vaheh <[email protected]> > *Cc:* [email protected] > *Subject:* Re: [ccp4bb] How high a B factor is too high to assume a loop > is in place, in the AlphaFold era? > > > > Vaheh, > > I think coordinates are no different from B factors, occupancies, f', or > f'' in this respect. Coordinates can play their "trash bin" role by > adjusting to the noise at the expense of violated geometry (bonds, angles, > planes, torsions, etc.). As I mentioned in my previous email, their trash > bin capacity is much smaller (but definitely not zero!) because the number > and strength (confidence) of geometry restraints are much greater than > those of ADP restraints. > > I agree that all refined parameters share this trash bin capacity, but to > varying degrees. Isn't this essentially what we call the error on the > refined parameter? All refined parameters have their error bars, which we > have referred to as the "trash bin" in this thread. > > Pavel > > > > On Tue, Jul 30, 2024 at 10:09 AM Oganesyan, Vaheh < > [email protected]> wrote: > > 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.* > > *R&D **| Biologics Engineering* > > One Medimmune Way, Gaithersburg, MD 20878 > > T: 301-398-5851 > > *[email protected] <[email protected]>* > > > > > > > > *From:* Pavel Afonine <[email protected]> > *Sent:* Tuesday, July 30, 2024 11:45 AM > *To:* Oganesyan, Vaheh <[email protected]> > *Cc:* [email protected] > *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 < > [email protected]> 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.* > > *R&D **| Biologics Engineering* > > One Medimmune Way, Gaithersburg, MD 20878 > > T: 301-398-5851 > > *[email protected] <[email protected]>* > > > > > > > > *From:* CCP4 bulletin board <[email protected]> *On Behalf Of *James > Holton > *Sent:* Tuesday, July 30, 2024 10:35 AM > *To:* [email protected] > *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 <[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 > > > ------------------------------ > > 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 > ######################################################################## 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/
