Hi Carsten,
A question about the riding Hydrogens and their B-factors. I noticed that at least with earlier versions of PHENIX the B-factor of the Hydrogens was not fixed to the B-factor of the bonded atoms.
I was not accurate when writing yesterday that the B-factor of a hydrogen in X-H bond is exactly equal to the B-factor of the atom it is bonded to, X. In fact, B(H) = B(X) * scale, where the scale in general may be from 1.0 to 1.5 (as described in SHELXL manual and in small molecule structural papers). phenix.refine uses scale=1.2. This scale is not a refinable parameter, but just a fixed value.
but during the course of the refinement and rebuilding they would start to diverge, sometimes drastically.
This was a possibility in very old versions of phenix.refine. I fixed this more than a year ago. So please make sure you are using a recent version. Pavel.