Align rotates and translates the view to place two atoms, the centroids of two sets of atoms, or the axis of a geometrical object along the line of sight at the center of the Chimera window.
When two atoms are to be aligned, atom-spec must specify only those two atoms. The order of specification is important, as the first will be placed in front and the second behind. 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 in front or back, but the view can be flipped afterwards as described below.
If two atom-specification strings separated by a space are supplied (atom-spec1 and atom-spec2), the centroids of the two sets of atoms will be aligned, with the first in front and the second behind.
Alternatively, instead of atoms, an axis or plane object created with define or Axes/Planes/Centroids can be specified by ID (for example, a4 or p1). An axis object will be aligned along the line of sight at the center of the Chimera window, as will the normal axis of a plane object (the plane object will be in the plane of the screen). There is no control over which end of the axis will be in front, but the view can be flipped 180° with the command:
turn y 180 center viewIt may still be necessary to adjust the scale and/or clipping plane positions to obtain the desired view, for example with focus or window.