For 3jar_6351, a pseudo-helical reconstruction, we could only 
deduce reconstruction symmetry for the part of the map 
corresponding to deposited model (PDB entry 3jar), so we 
used the phenix.map_box tool to cut out a box of density 
around the region defined by the deposited model, 
analyzed this map, and at the conclusion of the process 
translated the automatically-generated models to match 
the deposited map.

The map used is 3jar_box.ccp4
The deposited pdb file, shifted to be in the box is 3jar_box.pdb
The symmetry from 3jar_box.pdb is 3jar_box_simple_ncs_from_pdb.ncs_spec
The model built from 3jar_box.ccp4 is map_to_model/map_to_model_original.pdb
The command applied to all the box pdb files to return them
to the original coordinate system of emd_6351 corresponds to:
  phenix.pdbtools translate="237.60 388.08 236.28" \
     box_file.pdb box_file_shifted.pdb
