Display markers include labels, distance markers, hydrogen bonds and steric clash indicators. Once they are created, they can be manipulated individually using the display marker manager, which is available through Appearance -> Manage display markers menu. This component lists all markers by category and allows several actions on each of them: hide, show and delete. If a marker is hidden, it's denoted by an empty circle in the tree display. Otherwise, the circle is filled.

In addition to common operations, labels can be edited to change their font size, color, as well as text (which converts a label into a custom marker).

The manager is associated with the structure viewer and is updated in real time. For example, when an atom with a label is hidden, the label is removed from the display and the manager is updated to reflect the change. Moreover, if structures are being moved or a substructure is being rotated around a bond with dynamic steric clash tracking, the clashes are shown in the manager in real time reflecting the current set of steric interactions.