Four Molecules in Two Protein Comparators

Multiple Explorer or Comparator windows can be run concurrently. Here, two Comparator windows were set up.
As you enter Explorer/Comparator, the screen which invites you to resize the window as desired contains a checkbox to put the molecule on the left (by default, it goes on the right). By using this option, you can arrange the two windows to have all four molecules adjacent to each other.
(The links in the snapshot don't work since this is just a snapshot.)