The reason why phenix.refine allows B factors to grow until they fit the map is that it uses restraints that do not only require the similarity of B factors of covalently bonded atoms, but rather the similarity of B factors of atoms located within a sphere of radius R (around 5Å). This is to account for the fact that atomic B factors arise not only from atomic vibrations but also from other sources of motion, such as side chain librations and more. Additionally, atoms with higher B factors contribute less to the restraints target. This concept is encoded into the restraints formula 6 here:
https://journals.iucr.org/d/issues/2012/04/00/ba5180/index.html Other refinement programs may restrain the ΔB between bonded atoms to be as small as the data allows (Hirshfeld's rigid bond) or restrain these ΔB to match expected distributions (TNT). Regarding B factors versus ensembles: my understanding is that B factors model the spread of a single peak of density, whereas alternative conformations (ensembles) model distinct peaks of density. Essentially, the difference between B factors and occupancy is the size of the motion (disorder) you are trying to model. With this in mind, I'd question the validity of using an ensemble of point scatterers to model a single peak. Pavel On Tue, Jul 30, 2024 at 7:35 AM James Holton <jmhol...@lbl.gov> wrote: > 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 <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 > ######################################################################## 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/
