There are several ways to superimpose structures in Chimera:
•  MatchMaker performs a fit after automatically identifying which residues should be paired. Pairing uses both sequence and secondary structure, allowing similar structures to be superimposed even when their sequence similarity is low to undetectable.
The figure shows five distantly related proteins (pairwise sequence identities <25%) from the SCOP WD40 superfamily before and after MatchMaker superposition with default parameters.
•  Structures can be matched using a pre-existing sequence alignment.
•  The exact atoms to pair can be specified with the match command. This works on any type of structure, while the preceding methods apply only to peptide and nucleotide chains.
•  Structures can be superimposed manually by activating/deactivating them for motion and using the mouse.

The image shows tetramers of influenza neuraminidase (Protein Data Bank entry 3k3a) styled as flowers. Three tetramers are colored pink, with a central metal ion in white and nearby residues in yellow, and a fourth tetramer is colored green to resemble leaves. Each monomer or “petal” is a six-bladed β-propeller. (More samples...)