How to display ligands as ball and stick and macromolecules as cartoons (if protein) / rings (if nucleic acids) in Avogadro?
This was also asked on the Avogadro discussion forum

It's possible in Avogadro 1.x and discussed in the documentation


Select part of the molecule
Click on the "options" button for a particular display type (e.g. "ball and stick")
Click on the button to only show the selected atoms