[phenixbb] stop_for_unknowns=False in new version ?

[Nathaniel Echols]

On Wed, Feb 19, 2014 at 10:20 AM, Michaela Renner-Schneck <
michaela.renner-schneck at uni-tuebingen.de> wrote:

> I haven't been running phenix.refine for a couple of weeks and meanwhile
> we have updated to the latest version.
> Now I need to re-run an old job but unfortunately the pdb-interpretation
> option "stop_for_unknowns=False" which I needed for this seems to be no
> longer valid.
> Is there a way to get this option work again ?
>

No, this was deliberately removed - it was actually a bug, since we never
intended this for use in refinement (but it was added by accident).  If you
are running on the command line, you can do this to get your job to run
anyway with the old parameter file:

phenix.refine params.eff --unused_ok

However, you will need to supply restraints for any non-standard molecules.

-Nat
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