illustrate_backbone_alignment ()

backbone_atom_pairs ( atoms )

center_of_atoms ( atoms )

In object coordinates. Assume they are all from same model.

align_backbones_using_selected_atoms ()

Align two molecules using selected atoms. Two selected atoms are paired if one is from each molecule, they have the same chain identifier, residue number, residue name, and atom name, and the atom name is CA or P (ie. backbone only). Selected atoms which are not paired are not used in the alignment. The model with the higher model id number is moved to align it with the one with the lower id number. The RMSD and the rotation angle are printed to the reply log and status line.

transform_square ( xform,  center )

paired_alignment_atoms ( atoms )

atom_molecules ( atoms )

transform_schematic (
        xform,
        center,
        from_rgba,
        to_rgba,
        )

Create a surface model showing two squares, the second being the transformed version of the first. The first should pass through the center point. The two squares should have a common edge (rotation axis).