Hi Ken, Here's what's going on. You have BIOMT matrices in your PDB file that specify the rotations and translations that operate in the coordinate system of the EM map. This is just what the Chimera "sym" command expects. The multiscale model tool though assumes that the BIOMT matrices act in the coordinate system of the PDB atoms. It knows nothing about the volume. The trouble is that you've moved the PDB model relative to the map using "Fit model in map". So the coordinate frame for the PDB atoms is no longer aligned with the coordinate frame of the EM map. In some cases this is what you want. For example if your BIOMT matrices said how to make an icosahedral virus from a monomeric subunit, you'd want it still to make the correct icosahedron if you first fit the monomer into a density map. But in your case it isn't so nice since your BIOMT matrices are defined relative to the map coordinates. Here's the fix. Fit your PDB model into the map, then use File / Save PDB..., turn on the "Save relative to mymap.mrc" option and save the new PDB. Put the BIOMT matrices in that PDB file that has already been fit into the map and multiscale will work with it. Tom