Hi all

I am building a model in coot after aligning that model to my map in chimera.  However when I open the PDB and map in coot I notice the two are not at all aligned. 

I have tried:

• Open the map and pdb in chimera.  Fit the pdb into map. Save PDB.      
• Open map/pdb in chimera (pdb fits map on load).  Center map in box ("center" button in vol viewer").  Save map w/ new name.  Fit PDB into map.  Save PDB.  Re-open and confirm that pdb fits map on load and that map is centered in box.
• Opening PDB first in coot then MRC.   Then vice versa.
• Opening a "good" similar map and pdb in chimera that DO open together correctly in coot.   Open my "bad" map which does not align.  Fit the "bad" map into the "good" map and do vop resample.   Save the map.  Open it to confirm pdb fits map on load.  
• Open map/pdb in chimera (pdb fits map on load).  Use "vop cover ..." and save the output (reduced) map.