Center models for mmCIF output.

The trajectories here are multimodel PDB files, which have already
been centered, so it makes sense to center the mmCIF output to match.
This used to happen automatically, but this behavior changed in PMI
as of salilab/pmi@f87844. Relates ihmwg/IHMCIF#30.

scripts/nup84.isd.modeling.py

@@ -276,6 +276,9 @@
                                     localization_densities=den,
                                     ensemble_file=f)
         m = po.add_model(c.model_group)
+        # Center the mmCIF model so that it's consistent with our
+        # PDB trajectories, which are centered in the same way
+        m.transform = IMP.algebra.Transformation3D(-m.geometric_center)
         m.name = 'Best scoring model'
         m.stats = s