When we could use the original UI and we were not restricted to Selection UI, we could wiggle the ligand; now we can't? Is that acceptable?
Hmm, that's not right. You should be able to wiggle the ligand in Selection Interface.
If you have nothing selected and click Wiggle ('W'), then that should Wiggle everything that is not locked (including the ligand). This will Wiggle the ligand itself and may also move the ligand into or out of the binding pocket.
If you first select the ligand (by clicking anywhere on it) and then click Wiggle ('W'), then this will Wiggle the ligand itself and may also move the ligand into or out of the binding pocket.
Selecting the ligand should also bring up an extra button MMFF Wiggle ('M'). This button will Wiggle the ligand in place, but the ligand should not move into or out of the binding pocket.
Are you experiencing issues with one of these behaviors? Is there a different behavior that you'd like to see?
You definitely want to wiggle the ligand after changes.
But since the protein is fixed in the VHL puzzles, you can wiggle the ligand with the "Wiggle All" button.
If you did want to wiggle just the ligand, in the Selection interface you should be able to select just the ligand, then click the wiggle button. With residues selected, the wiggle button should change from a "Wiggle All" functionality to a "Wiggle selected" one. ("Select ligand, click the main Wiggle button" in Selection mode replaces the "Right click on ligand, select Wiggle from the pie menu" from the Original interface.)