On Wed, Feb 19, 2014 at 10:20 AM, Michaela Renner-Schneck <michaela.renner-schneck@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old job but unfortunately the pdb-interpretation option "stop_for_unknowns=False“ which I needed for this seems to be no longer valid.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