On Saturday 04 October 2008 18:32:00 Engin Ozkan wrote: > Hi everyone, > > I was in the middle of creating a "Table 1" for a finished structure and > was puzzled by one number. It is the average B factor, especially in > the case of TLS-refined structures. In this case, the average reported > by refmac in the header is the average of the B factors in the pdb file, > which I assume is the residual B factors (right?) (A quick Baverage > confirmed the number is the average of numbers in the B column). If the > reported average is really for residual B factors, isn't this a bit > misleading? In this case, the average B was 17, but after I created > total B factors with TLSANL, average B was 25 A^2.
My current standard format for preparing "Table 1" explicitly lists the residues assigned to each TLS group, and reports B as follows: Mean B_{iso} + B_{TLS} protein atoms (Å^2): xxx Mean B_{iso} non-protein atoms: yyy > I think total B factors should be the one reported, but I am afraid that > might not have been the practice by many. It is such a petty point, but > with TLS becoming common, shouldn't users be warned more about such > issues? Or could Refmac report the average for total B factors? > > Engin > > P.S. I hate to bring up the controversy about the reporting of > TLS-refined B factors (residual vs. full anisotropic, or refmac vs > PHENIX), but it may come to that. I don't think any controversy is engendered by giving the formula for the quantity reported in Table 1. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742