This is also known as “Map and molecule (coordinates) display control”. Here you can select which maps and molecules you can see and how they are drawn 1. The “Display” and “Active” are toggle buttons, either depressed (active) or undepressed (inactive). The “Display” buttons control whether a molecule (or map) is drawn and the “Active” button controls if the molecule is clickable 2 (i.e. if the molecule's atoms can be labeled).
The "Scroll" radio buttons sets which map is has its contour level changed by scrolling the mouse scroll wheel.
By default, the path names of the files are not displayed in the Display Manager. To turn them on:
(set-show-paths-in-display-manager 1)
If you pull across the horizontal scrollbar in a Molecule view, you will see the “Render as” menu. You can use this to change between normal “Bonds (Colour by Atom)”,“Bonds (Colour by Chain)” and “C\alpha” representation There is also available “No Waters” and “C\alpha + ligands” representations.