[phenixbb] high average b-factor vs. Wilson B - EXPLANATION

Sue Roberts suer at email.arizona.edu
Fri Aug 6 09:58:41 PDT 2010


I'm a little confused about Pavel's response.  Perhaps I'm not understanding it correctly.

I don't understand why you say this is nothing to worry about.  It seems to me that it means that the refinement strategy isn't stable or optimal - the contributions from the overall Baniso and the individual B factors are not being (and prossibly can not be) separated properly - maybe they can't be because  the overall anisotropy is so large that it swamps the anisotropic B or perhaps the resolution is not sufficient to refine anisotropic Bs for individual atoms.  In these cases shouldn't either (1) the anisotopic B be refined and then fixed rather than be allowed to creep up or (2) anisotropic Bs for individual atoms not be refined?

Can this problem be debugged by looking at the anisotropic Bs in coot?  If the anisotropic scale is being incorporated improperly into the atomic anisotropic Bs then would all the thermal ellipsoids have almost the same shape and orientation and only differ in magnitude?


On Aug 6, 2010, at 9:15 AM, Pavel Afonine wrote:

> Hi Geoffrey,
> thanks for sending me the data and model - this helped me to find out what happens in your and other similar repeatedly reported cases.
> Have a quick look at the total model structure factor formula that is used in all phenix.refine, phenix.model_vs_data, phenix.maps and many other similar tools:
> see page 6 here:
> http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf
> and glance through the page 29, PHENIX Newsletter:
> http://www.phenix-online.org/newsletter/CCN_2010_07.pdf
> As you see there is  overall anisotropic scale matrix Ucryst (see Acta Cryst. (2005). D61, 850-855 and references therein for deeper level of     details). In refinement, the trace of this matrix is subtracted from it and added to individual ADPs and Bsol, making Fmodel invariant under this manipulation. Most of the time, this is a small value, but sometimes it is relatively large.
> Now, let's see what happens in your particular case.
> The Wilson B-factor is 27.
> If we reset all B-factors to 27 and repeat the refinement until convergence using two scenarios:
> 1) we add the trace of Ucryst to individual ADPs,
> 2) we do not add the trace of Ucryst to individual ADPs,
> we will get the following:
> 1) R-work = 0.1728, R-free = 0.2177
> Bcryst (Ucryst reported as B) = (-10.42,-11.48,21.90,-0.00,0.00,0.00); trace/3= 0.00
> ksol= 0.33   Bsol= 54.75
> Average ADP = 43.56
> 2) R-work = 0.1744, R-free = 0.2171
> Bcryst (Ucryst reported as B) = (4.42,3.35,36.58,0.00,0.00,0.00); trace/3= 14.78
> ksol= 0.32   Bsol= 40.00
> Average ADP = 29.03
> Clearly, in case "2)" you get almost exact match of Wilson B and Average ADP (27 and 29), while in case "1)" the B-factors are higher. Note, the R-factors in both cases are "identical" (negligibly different given the resolution and the R-factor value).
> So I guess everything is more or less consistent and clear. It depends where and how you keep different contributions to the total ADP, and which values you use to compute mean ADP.
> Answering your very original question "Should I be concerned about this?": the answer is no. But I had a quick look at your maps: and     this is what I would spend some more time: you have a lot of positive and negative peaks, some of them are very strong: larger than 6sigma! I guess you are missing some ions, and alternative conformations may need some more attention. This is normal, it just needs some care and time to be spent before your structure is ready to go (to PDB). 
> Pavel.
> PS> I'm sending you the results of these two runs off list.
> On 8/3/10 10:20 PM, Geoffrey Feld wrote:
>> Dear PhenixBBers,
>> I'm working on a 1.45 A structure I solved using MR (phaser) and I'm pretty close to finishing, just plopping in waters and fixing rotamers. Rw = 19.8 Rfree= 22.8. I am a little concerned because my Wilson B is 27.00 while my average B for macromolecule is more like 43, and for solvent is 48. I have enough data to use anisotropic ADP refinement, which was a big help in bringing down the Rfree, but the average B hasn't really moved much. Should I be concerned about this? Should I try adjusting the wxu, or some other parameter? 
>> Thanks!
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Dr. Sue A. Roberts
Dept. of Chemistry and Biochemistry
University of Arizona
1041 E. Lowell St.,  Tucson, AZ 85721
Phone: 520 621 8171
suer at email.arizona.edu

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