Superimposing Structures

There are several ways to superimpose structures in Chimera:

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.
Except for manual matching, the methods allow iterative exclusion of poorly superimposed atoms from the fit.

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:

Of course, match would be the preferred method for superimposing sets of atoms representing known local similarities within globally dissimilar structures such as proteins of different folds.

UCSF Computer Graphics Laboratory / March 2010