Hi Phil, Just to make sure I got your point correctly... Are you suggesting to add Bcryst to the total ADP as well (so it is always included into isotropic B in ATOM record and anisotropic b in ANISOU record), similarly to what we already do with TLS contribution? If we do that: - all atoms will always have ANISOU (because Bcryst is anisotropic); - do you know how to convert Bcryst obtained in reciprocal space to the one in real space (so it can be added to individual ADP) (never thought about it - am I asking something stupid....?)? Thanks! Pavel. On 8/6/10 12:58 PM, Phil Jeffrey wrote:
Pavel Afonine wrote:
in summary, in that email I wrote that there are two ways of how you can handle the total B-factor and one of its components (Bcryst). You can subtract the trace of Bcryst and add it to individual ADPs (what CNS does, for example) or you can keep Bcryst as it is. Both ways do not change the Fmodel and therefore the R-factors. So I can't see how you conclude from this about refinement stability. These are purely formatting/convention things.
Strikes me that the convention should be that the B-factors associated with the atoms should be in the PDB B-factor field associated with those atoms, subject to the ability to represent the ADP model. Burying a constant isotropic offset in the PDB header - which might be of variable format depending on what program is used - seems like a good way to get the overall ADP of the model to be incorrectly assessed.
This would seem to be analogous to the difference between reporting the equivalent total B-iso in the isotropic B-factor field in TLS refinement (as phenix.refine does) versus reporting just the residual B (REFMAC default behavior). i.e. all the information is in the PDB file somewhere, but it's not necessarily where you expect it to be. I rather prefer the phenix.refine method for this.
Since most of the interest with Wilson B seems to be comparing Fmodel with the Fobs, it may make more sense to compare the Wilson B calculated from Fmodel with the Wilson B calculated with Fobs, which might at least cancel out some of the errors in the calculation. The underlying question seems to be "does the distribution of |Fmodel| with resolution match that of |Fobs|".
Phil Jeffrey Princeton