Hi Charlie, There is not a standard molecule deep copy routine in Chimera. The "split" command python code (in __init__.py) contains about 80 lines of code to copy atoms of a chain as a separate molecule, preserving most of the display style (ribbon, sphere, coloring, ...). It does not preserve everything, for example, if you change atom radii or bond linewidth, I didn't copy these attributes. Why not? Laziness. Two other Chimera tools, Unit Cell and Multiscale Models, also copy molecules and they use other code (written by me): share/PDBmatrices/copymolecule.py This is even a more basic copying (36 lines of code) that copies only the data (atom names, connectivity, residue numbers) but not the display attributes like colors, ribbon display, atom style (sphere, ball and stick, ...). We probably should have a copy routine that copies everything but it hasn't been a pressing need so far. Tom