If you want to apply bands, you can drag them in a 2D area (parallel to screen), using x and y axis.
Their distance to the user stays the same as long as a "snapping point" (such as a backbone or sidechain edge) appears.
How about making the mouse-wheel affecting the bandpoint when dragging it instead of moving the puzzle?
This would make navigating within z-axis possible.
Everyone, who tried to apply bands corresponding to the guide, when the natural structure is known, should know what I am talking about.
As the guide is just a projection, band ending points don't snap to it, making it hard to apply bands in depth.
Or, if it is easier to implement:
When the user is dragging a band's endpoint, and he uses mousewheel, the puzzle moves in z-direction (as is does now already), but the band- endpoint does not move with the puzzle.
So, a user can push a band-point away by moving the puzzle towards him and vice versa.