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:
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.
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:
total score = 0.70(residue similarity score) + 0.30(secondary structure score) – gap penaltiesSetting the weight to 0% is not the same as turning the option off, however. The values in the secondary structure Scoring matrix (for all pairwise combinations of H helix, S strand, and O other) and the secondary-structure-specific Gap opening penalties can be adjusted. Reset secondary structure scoring parameters to defaults can be used to restore the default values of all secondary structure scoring parameters.
*When the fit has been restricted to selected residues, the unselected residues of matched chains will still appear in the alignment, but merely as a convenient compact representation; how they are aligned is not meaningful.
**These pairwise sequence alignments can be considered a by-product of superposition. Successful superposition only requires these alignments to be partly correct, as incorrect portions tend to be excluded from the fit during iteration. If the sequences are easy to align (highly similar), the sequence alignments are likely to be correct throughout. However, if the sequences are more distantly related, parts of the alignments may be incorrect even when a successful superposition is produced. In those cases, a structure-based alignment should be superior.
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.
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:
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: