On a design puzzle it would be good to have a "view sidechains" option that meant that only the mutable sidechains are shown.

The "colour mutated segments" option would be of more use if it were possible to reset it after each mutate run, so that it can show the changes on each run, rather than every change from the start.

Additionally, on these very large protiens, the ability to "highlight" one or more segments so that you can keep a visual track on them while moving the protien about, would be something I would find useful.
I appreciate you can use "freeze", but that then affects things if you want to do any action on the protein.