Hi Miguel,
Right, but why this happens only in the final bss step ? Why not in the first one?
It's arbitrary: one can do it every macro-cycle as well. The main idea is to have a total B-factor in ATOM records written out to a PDB file.
I have noticed the behaviour described by José when I refine in phenix a model previously refined in refmac5 _with_ TLS, so the ADPs in the model are actually 'residual' ADPs of refmac5 TLS refinement. In these cases, during the refinement in phenix, the ADPs seem to be kept at very low values all throughout until they abruptly go to the higher, more reasonable values, after the final bulk solvent correction step. There may be a good reason for this behaviour, but I don't see it. I would appreciate if you could elaborate.
Like I said, it is arbitrary. You can store the overall B-factor in overall anisotropic scale matrix (B_overall) or in individual atomic B-factors; in both cases the total model structure factor Fmodel = scale_overall * exp(-h*B_overall*ht) * (Fcalc + k_sol * exp(-B_sol*s^2) * Fmask)
will remain the same. Pavel.
