Superimposing Structures

There are several ways to superimpose structures in Chimera:

• MatchMaker (or command 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.

The figure shows five distantly related proteins (pairwise sequence identities < 25%) from the SCOP WD40 repeat-like superfamily before and after MatchMaker superposition with default parameters.

• Structures can be matched using a pre-existing sequence alignment shown in Multalign Viewer.
  
  
• 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.

For the special case of an ensemble, which contains multiple sets of coordinates for exactly the same atoms, see also: Ensemble Match, MD Movie (RMSD analysis)

A multiple sequence alignment can be generated from a set of superimposed structures using Match -> Align.

See also: matrixcopy, measure rotation, rmsd, measures of structural similarity

MatchMaker vs. Match

Usually MatchMaker (or command matchmaker) provides the easier route to superimposing related proteins or nucleic acids. Unlike match, it does not require the user to specify which atoms should be used. On the other hand, it:

• takes more time due to the sequence alignment step (determining residue pairing)
• offers less control over which atoms are used for fitting: always uses one point per residue
• recomputes protein secondary structure assignments; this promotes consistency in assignments between structures and can improve how they are superimposed, but the option to reassign secondary structure should be turned off if one would rather use the assignments in the input files