On top, there is the Toolbar window, which regroups frequently used centering and measuring tools, and also where the software provides useful instant feedback about atoms.

The next window shows information about each Layer (structures) loaded into the workspace and allows to alter their individual display preferences.

In the middle, there is the main window, where you can manipulate your molecules in real time, measures distances and angles, make mutations and compare structures.

On the right side, you've got a control Panel, that provides a convenient way to select and manipulate the attriubutes of individual groups.

On the bottom of your screen lays a window that shows the alignment of your proteins, gives some feedback informations and permit to thread a sequence onto a reference in order to submit an homology modelling request to Swiss-Model.