The meaning of B-factor is the (scaled) sum of all positional uncertainties, and not just its one contributor, the Atomic Displacement Parameter that describes the relative displacement of an atom in the crystal lattice by a Gaussian function. That meaning (the sum of all contributions) comes from the procedure that calculates the B-factor in all PDB X-ray deposits, and not from an arbitrary decision by a committee. All programs that refine B-factors calculate an estimate of positional uncertainty, where contributors can be both Gaussian and non-Gaussian. For a non-Gaussian contributor, e.g. multiple occupancy, the exact numerical contribution is rather a complex function, but conceptually it is still an uncertainty estimate. Given the resolution of the typical data, we do not have a procedure to decouple Gaussian and non-Gaussian contributors, so we have to live with the B-factor being defined by the refinement procedure. However, we should still improve the estimates of the B-factor, e.g. by changing the restraints. In my experience, the Refmac's default restraints on B-factors in side chains are too tight and I adjust them. Still, my preference would be to have harmonic restraints on U (square root of B) rather than on Bs themselves. It is not we who cram too many meanings on the B-factor, it is the quite fundamental limitation of crystallographic refinement.
Zbyszek Otwinowski > The fundamental problem remains: we're cramming too many meanings into one number [B factor]. This the PDB could indeed solve, by giving us another column. (He said airily, blithely launching a totally new flame war.) > phx. >
