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://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
