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Tool: Matchmaker

The Matchmaker tool superimposes protein or nucleic acid structures by first creating a pairwise sequence alignment, then fitting the aligned residue pairs. It is also implemented as the matchmaker command.

Residue types and/or protein secondary structure information can be used to align the sequences, and the pairwise alignment can be shown in the Sequence Viewer. Fitting uses one point per residue: CA in amino acid residues and C4' in nucleic acid residues. 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. To use a different set of atoms, including those not in biopolymer chains, see the align command instead. See also: Fit in Map, morph, view, dssp, measure rotation, save PDB

The method was originally implemented in Chimera, as described in:

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.

Matchmaker can be opened from the Structure Analysis section of the Tools menu and manipulated like other panels (more...). It contains three tabbed sections, explained in detail below:

The following three buttons relate to the preferences, and there is a checkbox option as to whether they should apply to all three tabbed sections or only the one that is currently shown:

Clicking OK or Apply will start the calculations with or without closing the dialog, respectively. Close simply closes the dialog, while Help opens this page in the Help Viewer.

Sequence alignment scores, parameter values, and root-mean-square deviations (RMSD values) will be reported in the Log (see also verbose logging). 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.

Chain Pairing

The chain-pairing method dictates what choices of structure are available in the top section of the dialog.

Also restrict to 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.


Sequence alignment scores may include contributions from residue similarity, secondary structure, 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.

UCSF Resource for Biocomputing, Visualization, and Informatics / April 2023