Chimera Commands Index

Usage:
( mmaker | matchmaker ) refstruct matchstruct options

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 CA atoms of amino acid residues (C4' atoms of nucleic acid residues) are matched. The sequence alignment is based on some combination of residue identity/similarity and secondary structure correspondence.

If it is already known which residue numbers in each structure should be used for matching, however, the match command is a faster alternative (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.

Examples:

mm #0 #1 show true iter 5.0
- compute secondary structure assignments with the ksdssp algorithm, then match the best-scoring chain pair (one from model 0 and one from model 1) using the Needleman-Wunsch algorithm with the BLOSUM-62 residue similarity matrix (weight 0.7) and secondary structure scoring (weight 0.3); show the resulting sequence alignment with Multalign Viewer; iteratively fit the structures using a cutoff of 5.0 angstroms
mmaker #0:.a #1:.a pair ss alg sw matrix PAM-150 ss false
- match chain A in model 0 to chain A in model 1 (specific chains) using the Smith-Waterman algorithm with the PAM-150 residue similarity matrix and no secondary structure scoring; iteratively fit the structures using a cutoff of 2.0 angstroms

Sequence alignment scores, parameter values, and final match RMSDs are reported in the Reply Log.

Options

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:
alg alignment-algorithm
The alignment-algorithm can be:
showAlignment true|false
Whether to show the resulting sequence alignment in Multalign Viewer
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, atom pairs (CA-CA for amino acids, C4'-C4' for nucleic acids) 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 are kept in the share/SmithWaterman/matrices/ directory of a Chimera installation.
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, matrixcopy, MatchMaker, Match -> Align