See the file examples/test_pdbfile.py. If you run
it, it creates tmp.single.pdb which I can read into
RasMol or PyMol. So it appears to be in a good
In my experience, I have found that the PDB files that pizza.py makes have numerical atom IDs where there would normally be the symbol of an element, and I have had to use awk or perl to fix that, at least so that the colors in AtomEye would display correctly.