[phenixbb] Official release vs nightly builds

Folmer Fredslund folmerf at gmail.com
Sat Apr 6 02:15:53 PDT 2013

Hi Pavel,

Thank you for the quick response!

2013/4/6 Pavel Afonine <pafonine at lbl.gov>

> 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,

> Pavel
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Folmer Fredslund
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