Align positions the model(s) containing the specified atoms such that the two atoms lie along the Z axis (line of sight) at the center of the screen. Atom1 is positioned in the front and atom2 is in the back.
The atoms can be specified collectively using the word selected, sel, or picked if the current selection contains only the two atoms of interest; the order in which the atoms were selected (most likely picked) is used. When order information is lacking (for example, the atoms were selected simultaneously), there is no control over which atom will be placed in the front or back.