Align rotates and translates the view to place two atoms (specified with atom-spec) or the centroids of two sets of atoms (specified with atom-spec1 and atom-spec2) along the line of sight at the center of the screen. The first is placed in front and the second behind. It may still be necessary to adjust the clipping plane positions and/or scale to get a good view of the specified atoms, for example with focus or window.
When two atoms are to be aligned, atom-spec must specify only those two atoms. The order of specification is important; for example, :12@ca@cb and :12@cb@ca will produce the opposite orientations. If the two atoms are selected, they can be specified collectively with the word selected, sel, or picked, and the order in which they were selected will be 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.