Mmaker (or matchmaker) is the command-line implementation of MatchMaker, which superimposes structures by first constructing a sequence alignment and then performing a least-squares fit to superimpose the aligned residue pairs. The sequence alignment is based on some combination of residue identity/similarity and secondary structure correspondence. 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.
If residue number correspondences between the structures are already known, however, they can be specified directly with the match command, which executes more quickly because it does not include a sequence alignment step.
A reference structure (refstruct) and a structure to match (matchstruct) must be specified. The pairing mode determines whether chains or models should be specified. Specifying any part of a model suffices to specify the whole model. If a specification includes any spaces, it must be enclosed in single or double quote marks. The reference structure and structure to match must correspond to two different models.
mm #0 #1 show true(example structures: pectate lyases 1jta, 1bn8)
mmaker #0:.a #1 pair sb alg sw matrix PAM-150 ss false iter 5.0(example structures: mouse and human phosphoserine phosphatases 1j97, 1nnl)
mm #0:.a:.b #1:.c:.d pair ss show true(example structures: insulin 1b17, 1ben open as models 0 and 1, respectively)
Sequence alignment scores, parameter values, and final match RMSDs are reported in the Reply Log.
Option keywords for mmaker (matchmaker) can be truncated to unique strings and their case does not matter. A vertical bar "|" designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.
pairing mode
The mode controls which chain sequences are used to construct the reference-match alignment:
- ss - specific chain(s) in the reference model with specific chain(s) in the model to match; refstruct and matchstruct should specify equal numbers of chains
- sb - a specific chain in the reference model with whichever chain in the match model gives the highest alignment score; refstruct should specify a chain, matchstruct a model or part of a model
- bb (default) - whichever pair of chains, one from the reference model and one from the match model, gives the highest alignment score; refstruct and matchstruct should each specify a model or part of a model
alg alignment-algorithm
The alignment-algorithm can be:
- nw (or needle; default) - Needleman-Wunsch
- sw (or smith) - Smith-Waterman
showAlignment true|false
Whether to show the resulting sequence alignment in Multalign Viewer. When fit iteration is employed, the pairs used in the final fit will be shown in the alignment as a region named matched residues. The header named RMSD is automatically shown and other headers hidden. This line shows the spatial variation among residues associated with a column. In the pairwise case, the value is simply the distance between atoms in the two residues associated with a column.*Note: The main purpose of matchmaker is to superimpose related structures; the sequence alignments are just a by-product. Successful superposition only requires a partially correct sequence alignment, as incorrect portions tend to be omitted during fit iteration. If the sequences are easy to align, the matchmaker sequence alignment is likely to be correct from beginning to end. However, if they are more distantly related, parts of the sequence alignment may be incorrect even when the resulting iterated match looks very good. If the goal is to obtain not just a structural superposition but also an alignment of dissimilar sequences, Match -> Align is recommended for generating a structurally verified sequence alignment after the structures have been superimposed. Furthermore, matching the structures (again) using this structurally verified sequence alignment, while having little effect on the superposition, will provide better statistics for describing structural similarity (RMSD, etc.) because more columns will be aligned correctly.
iterate cutoff|false
Whether to iteratively fit the structures, and the cutoff for excluding residue pairs from the fit. An iterative fit will be performed unless this option is set to false. The sequence alignment is not changed, but residue pairs in the alignment can be removed from the "match list" used to superimpose the structures. In each cycle, pairs of atoms are removed from the match list and the remaining pairs are fitted, until no matched pair is more than cutoff angstroms apart (2.0 by default). 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. The result is that the best-matching "core" regions are maximally superimposed; conformationally dissimilar regions such as flexible loops are not included in the final fit, even though they may be aligned in the sequence alignment.
matrix similarity-matrix
The similarity-matrix can be any of those listed in the MatchMaker graphical interface (case is important): BLOSUM-30, BLOSUM-35, BLOSUM-40, BLOSUM-45, BLOSUM-50, BLOSUM-55, BLOSUM-60, BLOSUM-62 (default), BLOSUM-65, BLOSUM-70, BLOSUM-75, BLOSUM-80, BLOSUM-85, BLOSUM-90, BLOSUM-100, BLOSUM-N, Nucleic, PAM-40, PAM-120, PAM-150, and PAM-250. Matrix files reside in the share/SmithWaterman/matrices/ directory of a Chimera installation.If an amino acid matrix (any except Nucleic) is chosen, only peptide chains will be aligned; if the Nucleic matrix is chosen, only nucleic acid chains will be aligned. An error message will appear if there are no reference-match pairs of the appropriate type.
gapOpen opening-penalty
When secondary structure scoring is not being used, the opening-penalty is subtracted from the score for each gap opened (12 by default). When secondary structure scoring is used, secondary-structure-specific gap opening penalties (see hgap, sgap, and ogap) are used instead.
gapExtend extension-penalty
The extension-penalty is subtracted from the score for each increment in gap length (1 by default).
ssFraction fraction|false
Sequence alignment scores can include a residue identity/similarity term, a secondary structure term, and gap penalties. Fraction is the relative weight of the secondary structure term and can range from 0 to 1 (default 0.3). Unless the option is set to false, a secondary structure term will be included with a weight of ssfract and the residue similarity term will be given a weight of (1-ssfract).
computeSS true|false
When secondary structure scoring is used, whether to first identify helices and strands with the ksdssp algorithm. This will override any pre-existing secondary structure assignments. When secondary structure scoring is not being used, this option is ignored and secondary structure assignments are not computed.
hgap intrahelix-penalty
When secondary structure scoring is used, the intrahelix-penalty is subtracted from the score for each gap opened within a helix (18 by default). When secondary structure scoring is not being used, a generic gap penalty (see gapOpen) is used instead.
sgap intrastrand-penalty
When secondary structure scoring is used, the intrastrand-penalty is subtracted from the score for each gap opened within a strand (18 by default). When secondary structure scoring is not being used, a generic gap penalty (see gapOpen) is used instead.
ogap other-penalty
When secondary structure scoring is used, the other-penalty is subtracted from the score for each gap opened that is not within a helix or strand (6 by default). When secondary structure scoring is not being used, a generic gap penalty (see gapOpen) is used instead.
matHH helix-helix-score
When secondary structure scoring is used, helix-helix-score is the value added to the secondary structure term for aligning a residue in a helix with a residue in a helix (default 6).
matSS strand-strand-score
When secondary structure scoring is used, strand-strand-score is the value added to the secondary structure term for aligning a residue in a strand with a residue in a strand (default 6).
matOO other-other-score
When secondary structure scoring is used, other-other-score is the value added to the secondary structure term for aligning a non-helix, non-strand residue with a non-helix, non-strand residue (default 4).
matHS helix-strand-score
When secondary structure scoring is used, helix-strand-score is the value added to the secondary structure term for aligning a residue in a helix with a residue in a strand (default -9).
matHO helix-other-score
When secondary structure scoring is used, helix-other-score is the value added to the secondary structure term for aligning a residue in a helix with a non-helix, non-strand residue (default -6).
matSO strand-other-score
When secondary structure scoring is used, strand-other-score is the value added to the secondary structure term for aligning a residue in a strand with a non-helix, non-strand residue (default -6).
See also: match, rmsd, ksdssp, matrixcopy, MatchMaker, Match -> Align, Ensemble Match