Part 1: lower window, including the 3D viewer.
Part 2: upper window, including menus, buttons, and text.
Basic Mouse Controls
Part 1: rotation, translation, and zooming using left, middle, and right drag.
Part 2: centering by middle-clicking and releasing.
Part 3: clipping using the scroll wheel.
Part 1: left-clicking to select, and coloring a selection.
Part 2: the default selection, (sele).
Part 3: renaming selections to save them.
Part 1: measuring distances.
Part 2: measuring distances (continued).
Part 3: measuring angles.
Part 4: measuring dihedrals.