By right-clicking on a molecule table or on a molecule plot, its properties can be accessed from the bottom of the menu. For the table, an extra tab (shown below) will appear to the right in the table properties. Here, the user can change from viewing molecules in 2D to 3D (if 3D information is available in the imported data file). It is also possible to show the atom numbering and to choose if atoms of different types should be colored differently.

In addition to the tab above, accessing the molecule plot properties by right-clicking on the plot will show a second tab with some additional settings. The user can turn on/off "Depth-cuing", which changes the feel of depth of the rendered molecule. With this setting turned on, atoms are rendered with a gradient perpendicular to the plot. The user can also change the background color of the plot.