
First load the filtered map.
Check the header: Features tab > coordinates
Voxel size should be the sampling.
Origin index = 0.
Cell angles =90.

In volume viewer:  enable data display options, from Features tab.
Check "Show outline box using color"

Positioned pbd files (search ojbects) should at least be placed within the box, which defines 
the default unit cell.

To save the positioned pdb object:

Save the pdb file, relative to the map.

Then load them all in again (map and models) and check. The map could have moved while manipulating the pdb object.
