Axes, planes, and centroids can be calculated from sets of atoms using the Axes/Planes/Centroids tool or the command define. Axes can be shown as cylinders, planes as disks, and centroids as spheres, and any of these can be used in distance and angle measurements.

For example, the figure shows the dopamine D3 receptor and bound inhibitor (PDB entry 3pbl) as modeled into the membrane in the OPM database. The planes of the inner and outer membrane boundaries are shown as transparent blue and red disks, respectively. The protein ribbon is rainbow-colored from blue at the N-terminus to red at the C-terminus, and the axis of each helix is shown as a cylinder of matching color. The axis of the red helix forms an angle of 15.1° with the membrane and comes within 3.5 Å of the inner boundary. The yellow and orange helices are nearly antiparallel (crossing angle 5.9°). The average (minimum, maximum) distance of inhibitor atoms from the outer boundary is 7.9 (5.1, 11.7) Å.

β-1,4-glycanase (gold, PDB 1exp) and cellobiohydrolase I (cyan, PDB 1cel) have similar glucose-binding sites but different folds. Ribbons were slimmed with Ribbon Style Editor and the title and captions were added with 2D Labels (see image how-to). (More samples...)