[phenixbb] --unused_ok, .def, documentation,...

[Ralf W. Grosse-Kunstleve]

> [ phenix v1.4 rel. tag 3 cctbx tag: 2008_12_07_1353 ]
>
> using an old .def w/ "latest devel. rel" phenix (but not nightly)
>
> i used --unused_ok b/c it looks like that's what its for.

I'm going to retire that option when I get a chance since it causes
too much confusion. Please try this:

  Using phenix.refine 1.4-3:
    phenix.refine --diff-params your.def > your.dif

  Using new release:
    phenix.refine your.dif

If that fails because of unused parameters, review and edit your.dif
and try again.
It is not as convenient as --unused-ok, but should rule out surprises.

> i am expecting an "updated" .def to write after the job - yes?... if so, 
> it reads slightly differently than the documentation.. hard to give an 
> example...  things look ok in general, but ought i to have a new .def?
>
> -bryan
>
> p.s:
>
> does phenix write version/release info in the .def (i can't find it)?

Nope. Maybe we'll change it in the future, so that the new phenix.refine
can do the diff with the old phenix.refine version automatically
(if you still have it installed).

Ralf