1) The functions of Shift-drag and control-drag (in the background to change the view) seem to have been reversed: the former now pans while the latter now zooms.

2) The saturated pastel colour scheme for selected areas of the protein is hideous. Please change or provide an alternative.

3) The wiggle icon at the bottom left of the screen displays the number of selected residues. Great if you're working with a partial selection but if not it says No selection when it means All selected.

4) To invoke the move tool you need to select some residue when that shouldn't be necessary.

5) When bringing up a new menu e.g. View Options Menu, that menu is not necessarily bought to the front if it is already visible. The old original interface toggled menus: much less clutter.

6) This may sound trivial, but what's the purpose of all the exclamation marks in the tooltips? Surprise? Delight? I'm intrigued.