Anytime you have a section displayed on the main display you can go to Display->Energies Viewer and the 3D energies viewer window will pop up. This is essentially a 3D representation of the Main Display energy data, and selection and highlighting here has a 1-1 correspondence with the 2D main display.
When you do you'll be greeted by a rotated graph, arranged as follows:
- X-Axis: Position
- Y-Axis: Window-size
- Z-Axis: Energy
Thus, x corresponds to x on the main display, y to y, and z to the main display's color. The colors should be the same for each structure as well. You can move your mouse to highlight individual structures and click to select them, which sends it through the pipeline for rendering.