The axis align command moves the models containing any atoms of atom-spec onto the axis so that the principal axis of those atoms aligns with axis. The principal axis is the first eigenvector calculated from the coordinates of the atoms after subtracting the position of their collective centroid, and the principal axis is anchored at that centroid. If atom-spec is a single atom, then its model is simply translated so that the atom lies on axis.
The axis can be x, y, z or any of the other standard vector specifications. In addition it can be three or more atoms, in which cases the principal eigenvector of those atoms' coordinates will be used. See also: matchmaker, align, measure rotation, view zalignThe perModel option (default false) controls whether or not the models are treated as a unit or individually for positioning. If false, all atoms of atom-spec will be used to compute a principal axis, and the models containing those atoms will be repositioned together to align that principal axis onto axis. If true, each model contributing to atom-spec will have a principal axis computed based on the atoms it is contributing, and the model will be individually positioned to align that principal axis onto axis.
The bring option specifies one or more additional models to move along with the models being aligned. This option can only be used if perModel is false.