[phenixbb] phenix.rosetta_refine on OS X?

Nathaniel Echols nechols at lbl.gov
Thu Dec 19 07:16:50 PST 2013

On Thu, Dec 19, 2013 at 7:08 AM, Scott Horowitz <horowsah at umich.edu> wrote:

> Well, while we're on this topic, I was just starting to try phenix-rosetta
> on a mac, and after following the instructions online I get this error
> message:
> ...
>   File
> "//Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/cctbx_project/cctbx/xray/structure_factors/manager.py",
> line 234, in __init__
>     assert xray_structure.space_group() == miller_set.space_group()
> AssertionError

Your PDB file and your data file have different space groups - usually this
means that either the PDB file is missing symmetry entirely and gets
treated as a P1 box, or the PDB file specifies the screw axes while the
data file only specifies the point group (for instance, P212121 versus
P222).  This is something we normally try to handle more automatically but
the input handler for the Rosetta refinement is somewhat less flexible at
the moment.  I'll fix this, but it should run okay if you ensure that the
space group is unambiguously specified in both files.

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