Avogadro has many good qualities but I can't seem to find a way to display ligands differently to macromolecules in the same view window. Frankly I can't seem to find a way to display any two things differently (like one as ball and stick, another as ribbons, or w/e) to one another in the same view. It seems like in a given view window everything has to be displayed the same way, there's no room for making one part displayed one way and another part displayed another way.
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