Use gemmi map mask instead of ccp4 map mask

[TJGorrie]

Example:

m = gemmi.read_ccp4_map('../tests/5i55_tiny.ccp4')
m.setup()
# edit these:? m.grid.spacegroup
# edit these:? m.grid.unit_cell
st = gemmi.read_structure('../tests/5i55.cif')
m.set_extent(st.calculate_fractional_box(margin=5))
m.write_ccp4_map('out.ccp4')

Workflow should allow for maps to be cut for each ligand and the aligned? Alternatively run through as a final pass...