[phenixbb] Official release vs nightly builds

Pavel Afonine pafonine at lbl.gov
Sat Apr 6 02:00:00 PDT 2013

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 

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.


More information about the phenixbb mailing list