Hi Pavel,
Thank you for the quick response!
2013/4/6 Pavel Afonine
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.
OK, that makes sense.
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.
Thank you for the clarification. I think we should not start a discussion (people have better things to do in the weekend, I think) about what is best to do. I was not aware that there this was the difference between the official and nightly builds. Best regards, Folmer
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-- Folmer Fredslund