Hi Edward This is because taking a naive straight arithmetic average of the B factors as all the programs do is nonsense! To simplify your argument say we have just 2 atoms with B = 10 and 1000. What's the average B? Answer: not 505 but very close to 10 because the atom with B=1000 most likely isn't there. So you need an average weighted by the contribution to the scattering over the resolution range. This is effectively what the Wilson plot is doing: it is certainly not performing a naive arithmetic average. So if you're going to compare it, at least compare it with the right quantity, though I'm not claiming that this will give you better agreement between the weighted average & Wilson Bs, for reasons mentioned by others.
For a possible solution see: Acta Cryst. <http://journals.iucr.org/d> (1998). D*54* <http://journals.iucr.org/d/contents/backissues.html>, 243-252 (shameless plug). Cheers -- Ian On Tue, 12 Mar 2019 at 21:24, Edward A. Berry <ber...@upstate.edu> wrote: > What if you have one domain with many B-factors aroun 70 and above, and > another domain with B-factors around 20? The atoms with high B-factor will > make essentially no contribution to the intensty of spots beyond 3 A, and > so have no effect on the slope of the Wilson plot byond that. But they will > contribute mightily to the average atomic B. Or so it seems to me. > eab > > On 03/12/2019 04:39 PM, DUMAS Philippe (IGBMC) wrote: > > > > Le Mardi 12 Mars 2019 19:55 CET, Dale Tronrud <de...@daletronrud.com> a > écrit: > > > > Dale > > Good to have the opportunity of going back to the crystallography of the > fifties in these post-modern times... > > There is an essential argumentation that should be recalled. The only > reason for the fact that one ignores low-resolution data in a Wilson plot > is that a Wilson plot is based precisely upon Wilson statistics, which > assumes that the atoms are cast randomly in the unit cell. > > This assumption obviously does not hold at low resolution and there is > no reason to obtain a straight line that stems from the latter assumption. > > Therefore, I do not think one may say that a Wilson plot tends to ignore > atoms with high B values. > > Consequence: if one has data at rather low resolution, a Wilson plot is > inherently inaccurate, but if one has data at very high resolution, the > Wilson plot should give a very decent estimate of the average B and any > significant discrepancy should ring the bell. > > Philippe Dumas > > > > > >> The numeric average of the B factors of the atoms in your model only > >> roughly corresponds to the calculation of the Wilson B. While I always > >> expect the average B to be larger than the Wilson B, how much larger > > > >> depends on many factors, making it a fairly useless criteria for judging > >> the correctness of a model. > >> > >> While it is pretty easy to understand the average of the B factors > in > >> your model, the Wilson B is more difficult. Since it is calculated by > >> drawing a line though the (Log of) the intensity of your structure > >> factors as a function of the square of sin theta over lambda, it is > >> rather removed from the atomic B factors. When drawing the line the low > >> resolution data are ignored because those data don't fall on a straight > >> line, and this means that the large B factor atoms in your model are > > > >> ignored in the Wilson B calculation. > >> > >> The Wilson B is (sort of) a weighted average of the B factors of > your > >> model, with the smallest B's given the largest weight. The actually > > > >> weighting factor is a little obscure so I don't know how to simulate it > >> to adjust the averaging of atomic B's to come out a match. The easiest > >> way to compare your model to the Wilson B is to calculate structure > >> factors from it and calculate the Calculated Wilson B. No one does this > >> because it will always come out as a match. If your calculated Wilson B > >> doesn't match the observed Wilson B your R values are guaranteed to be > >> unacceptable and your refinement program will have to be malfunctioning > >> to create such a model. > >> > >> If all the B factors in your model are equal to each other, your > >> refined model will have an average B that matches the Wilson B, because > >> weighting doesn't matter in that situation. If you allow the B's to > > > >> vary, the difference between the average and the Wilson B will depend on > >> how high of an individual B factor you are willing to tolerate. If you > >> are a person who likes to build chain into weak loops of density, or > > > >> build side chains where there is little to no density, then your average > >> B will be much larger than the Wilson B. This does not mean there is an > >> error, it is simply a reflection of the Wilson B's insensitivity to > >> atoms with large B. > >> > >> I do not believe comparing the average B to the Wilson B has any > >> utility at all. > >> > >> Dale Tronrud > >> > >> On 3/12/2019 11:34 AM, Eze Chivi wrote: > >>> Dear CCP4bb community, > >>> > >>> > >>> The average B-factor (calculated from model) of my protein is 65, > >>> whereas the Wilson B is 52. I have read in this BB that "it is expected > >>> that average B does not deviate strongly from the Wilson B". How I can > >>> evaluate if the difference calculated for my data is razonable or not? > >>> > >>> > >>> Thank you in advance > >>> > >>> > >>> Ezequiel > >>> > >>> > >>> > ------------------------------------------------------------------------ > >>> > >>> To unsubscribe from the CCP4BB list, click the following link: > >>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=ogn2iPkgF7TkVSicOVBfKg&r=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA&m=-fTd4oA6kyxvaBzbNTV3k0NgBmWBjYlUUtlEH_QD8p4&s=bqGH09vp_sRJZT2kklSy0UXYuG2cMiVrDn8w4KP4u7U&e= > >>> > >> > >> ######################################################################## > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=ogn2iPkgF7TkVSicOVBfKg&r=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA&m=-fTd4oA6kyxvaBzbNTV3k0NgBmWBjYlUUtlEH_QD8p4&s=bqGH09vp_sRJZT2kklSy0UXYuG2cMiVrDn8w4KP4u7U&e= > > > > > > > > > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=ogn2iPkgF7TkVSicOVBfKg&r=cFgyH4s-peZ6Pfyh0zB379rxK2XG5oHu7VblrALfYPA&m=-fTd4oA6kyxvaBzbNTV3k0NgBmWBjYlUUtlEH_QD8p4&s=bqGH09vp_sRJZT2kklSy0UXYuG2cMiVrDn8w4KP4u7U&e= > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
