Hi Folmer,
Recently, some people have experienced problems with B-factor refinement in the official releases of PHENIX.
It seems to me that, generally speaking, the first suggestion is to use the nightly builds of phenix.
nightly build is a snapshot of today's current code, with all the latest and greatest bleeding edge features and bugs. Official release is a hand picked version that is more carefully checked to make sure it has less problems. My preference would be to use the latest nightly build for all routine work and fall back on an older version (aka official release) if a more recent one fails. You can have multiple Phenix installations.
With the current official releases, would I be better off using the nightly builds for refinement? (I have also seen some weird behavior with B-factor refinement).
Use the one that works for you. Typically, it would be the latest nightly build. A quick comment on "B-factor problem" recently brought to attention: in fact it is not a bug at all, but a conflict of philosophies. It all boils down to whether you want to keep meaningless bulk overall B-factor in ATOM records in your PDB file (current phenix.refine behavior) or you say it is junk and keep it in overall scale factors (previous behavior that many of you called a bug). Personally I would prefer to keep in overall scale factors. Pavel