I agree that it would certainly be bad if your model was inconsistent with the Wilson B. When I first ran into people who were worried about this I recommended that they calculate the Wilson B of their model, not look at the average B as a proxy. You can calculate structure factors from your model and feed those into a Wilson B calculator and get the proper value.
When you do this you find pretty quickly that a refinement program has to be screwed up pretty badly for it to create a model with even a small difference between the observed and calculated Wilson B. If your model is off only a little the R value shoots up! Other than when debugging refinement code, I have never seen a refined model where there was any significant difference between the calculated and observed Wilson B. This problem simply doesn't come up. Try it for yourself and see. When you see a difference between the Wilson B and the average of the B's in your model, all you are seeing is that you have a variety of B factors and that is not a surprise. I would be worried if all my B factors were equal! High B factors are not a problem to be fixed! Some atoms do move more than others. Why would you expect otherwise? Dale Tronrud On 10/14/2016 12:28 AM, Carlos CONTRERAS MARTEL wrote: > Sunanda, > > As "common people", ... "agreement" don't means for me "equals" ... > > So I hope I'm not so "incorrect" if I keep one mind the Wilson B as the > model > > refinement goes and the average B factor changes with different strategies. > > If you are still worry about your Bfactor, you could try TLS, using the > right approach could > > improve your results. > > All the best > > Carlos > > > > On 10/13/16 18:42, Dale Tronrud wrote: >> It seems to be common for people to make the incorrect assumption >> that the average of the atomic B factors in the PDB file should equal >> the Wilson B. The Wilson B is actually a weighted average of the >> individual B factors where the weighting is rather mysterious, but the >> small B factors have much higher weight than the larger ones. While the >> Wilson B is simply a property of your data set the average of the atomic >> B factors will also depend on choices you have made in building your >> model. >> >> In your case the core of your protein does have B factors that match >> your Wilson B. The fact that you have loops that have larger B's >> doesn't really mean there is a problem, because those atoms don't >> contribute much to the higher resolution reflections and don't come into >> the calculation of the Wilson B. >> >> The average of your B factors will increase if you choose to build >> model for more disordered regions, while the Wilson B will, of course, >> remain the same. The average B factor will be larger, for example, if >> you are more aggressive in building water molecules. This does not >> indicate a problem but is an unavoidable consequence of your choice to >> take more risks. >> >> Dale >> >> >> >> On 10/13/2016 12:16 AM, sunanda williams wrote: >>> Sorry for not making the problem clear! >>> The overall B factor for the 3.0 A structure is around 98.00 A*2. Most >>> of the deposited structures in the PDB site around this resolution >>> has an av B around 70 A*2.... >>> All other statistics looks fine. I got a warning message while trying to >>> upload the structure in PDB that 98 was higher than the norm! >>> The reason why the structure has such a high B factor could be due to >>> disordered loops... All the same I was wondering how acceptable this >>> structure would be to picky reviewers.. >>> And 'better the B factors' means bring them down...sorry couldn't phrase >>> it 'better'! I am going to try doing refinement with group B factors! >>> Would that help? >>> Thanks Robbie, I think this I need to make the best of the model I have. >>> Prof. Sekar will try PDB_redo..Thanks! >>> >>> >>> >>> On Thu, Oct 13, 2016 at 11:41 AM, Pavel Afonine <pafon...@gmail.com >>> <mailto:pafon...@gmail.com>> wrote: >>> >>> I fully agree with Dale in not understanding what the problem is. >>> Perhaps I have a better chance if you clearly explain what exactly >>> you mean by "is there any way to better the B factors". >>> Pavel >>> >>> >>> On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud >>> <de...@daletronrud.com <mailto:de...@daletronrud.com>> wrote: >>> >>> I'm sorry but I don't understand what your problem is. Do >>> you think >>> the B factors are too small for a 3A data set? A range of 70 to >>> 75 is a >>> little smaller than usual but probably not out of bounds. >>> >>> Dale Tronrud >>> >>> On 10/12/2016 7:59 PM, sunanda williams wrote: >>> > Hi all, >>> > I have a structure at 3.0 A and R/Rfree of 24/28. The mean B >>> value is >>> > around 98. The B value is especially high at the N terminus >>> and two loop >>> > regions (around 120-150 AA). >>> > The rest of the structure averaged around 70-75. Has anyone >>> faced such a >>> > scenario? How reliable is the structure and is there any way >>> to better >>> > the B factors. >>> > Any help is appreciated. >>> > Thank you!! >>> >>> >>> >
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