MatchMaker MatchMaker icon

MatchMaker superimposes protein or nucleic acid structures by first creating pairwise sequence alignments, then fitting the aligned residue pairs. Residue types and/or secondary structure information can be used to create the initial sequence alignments. Fitting uses one point per residue. Optionally, a structure-based multiple sequence alignment can be computed after the structures have been superimposed.

Note: if it is already known which residue numbers in one structure should be paired with which residue numbers in the other, another possibility is to use the command match. See superimposing structures for a discussion of the different methods available in Chimera. See also: Match -> Align, Multalign Viewer, Align Chain Sequences, the Superpositions and Alignments tutorial, and

Tools for integrated sequence-structure analysis with UCSF Chimera. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. BMC Bioinformatics. 2006 Jul 12;7:339.

There are several ways to start MatchMaker, a tool in the Structure Comparison category. MatchMaker is also implemented as the command mmaker (or matchmaker).

The MatchMaker dialog is organized by the main steps to be performed:

  1. generating pairwise sequence alignments
  2. matching, i.e., superimposing the structures according to those pairwise alignments
  3. optionally, creating a multiple sequence alignment from the structural superposition
Save settings writes the current MatchMaker parameters to the preferences file. Reset to defaults resets the dialog to the factory default parameter settings without changing any preferences.

Clicking OK or Apply will start the calculations with or without closing the dialog, respectively. Sequence alignment scores, parameter values, and structure RMSDs will be reported in the Reply Log. If the fit is iterated, the final RMSD over all residue pairs (columns in the sequence alignment) will be reported along with the RMSD over the pruned set of pairs.

Cancel simply closes the dialog, while Help opens this manual page in a browser window.

Initial Pairwise Sequence Alignments

Further restrict matching to current selection allows ignoring residues of the reference and/or match structures that are not selected. In general, restriction should only be used in specific cases to suppress results that would otherwise be obtained. For example, two chains that would otherwise align on their N-terminal domains can be forced to align on their C-terminal domains by selecting the C-terminal domains and using the restriction option. Otherwise, restriction is not recommended, because full-length alignments tend to be of higher quality, and iteration already serves to exclude poorly superimposed regions from the final fit. Although unselected parts of matched chains will appear in the resulting sequence alignment (if shown), they have simply been added back in as “filler,” without consideration of how the characters align, after alignment and matching of only the selected residues.

Chain pairing options:

Alignment algorithm: Sequence alignment scoring can include a residue similarity term, a secondary structure term, and gap penalties.


Fitting uses one point per residue: CA atoms in amino acids and C4' atoms in nucleic acids. If a nucleic acid residue lacks a C4' atom (some lower-resolution structures are P traces), its P atom will be paired with the P atom of the aligned residue.

Iterate by pruning long atom pairs until no pair exceeds [x] angstroms (default on and x=2.0) - whether to iteratively remove far-apart residue pairs from the “match list” used to superimpose the structures. This does not change the initial sequence alignment, but restricts which columns of that alignment will be used in the final fit. Otherwise, all of the columns containing both sequences (i.e. without a gap) will be used. In each cycle of iteration, atom pairs are removed from the match list and the remaining pairs are fitted, until no matched pair is more than x Å apart. The atom pairs removed are either the 10% farthest apart of all pairs or the 50% farthest apart of all pairs exceeding the cutoff, whichever is the lesser number of pairs. Iteration tends to exclude sequence-aligned but conformationally dissimilar regions such as flexible loops, allowing a tighter fit of the best-matching "core" regions.
Regardless of which chain(s) in a model to be matched are aligned in sequence to the reference, the entire model will be reoriented.

Final Structure-Based Sequence Alignment

If MatchMaker is used simply to superimpose structures, this step can be omitted. However, if one also wants a corresponding structure-based sequence alignment, this step is recommended, especially if the sequences are dissimilar.

After superposition, compute structure-based multiple sequence alignment (default off) - call Match -> Align to generate a sequence alignment consistent with the superposition. If not called with this option, Match -> Align can still be started later independently.
Calculating a structure-based alignment can take several minutes, depending on the number of structures, but there are advantages: The output sequence alignment is automatically shown in Multalign Viewer and can be saved to a file from that tool. The fully populated columns are highlighted as a region (colored boxes). Clicking the region will select the corresponding parts of the structures, in effect their common cores. The “RMSD: caheader shows the spatial variation per column.


Meaning of 0% secondary structure score. Turning off Include secondary structure score is not the same as moving the slider to zero with the option turned on. When the option is on:

UCSF Computer Graphics Laboratory / December 2015