Usage:
[ mmaker | matchmaker ] refstruct matchstruct options

Mmaker (or matchmaker) is the command-line implementation of MatchMaker, which superimposes structures with similar sequences. A sequence alignment is constructed, and then residues aligned in sequence are spatially superimposed with a least-squares fit.

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.

Unlike the keywords of most commands, option keywords for mmaker (matchmaker) can be truncated to unique strings. In addition, keyword case does not matter.

A vertical bar "|" designates mutually exclusive options, of which the default is indicated in 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 (default) - a specific chain in the reference model with a specific chain in the model to match; refstruct and matchstruct should each specify a chain
• 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 - 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

matrix scoring-matrix
The scoring-matrix can be any of those listed in the MatchMaker graphical interface; BLOSUM-62 is the default.

gapOpen opening-penalty
The opening-penalty is subtracted from the alignment score when a gap is opened (12 by default).

gapExtend extension-penalty
The extension-penalty is subtracted from the alignment score for each increment in gap length (2 by default).

showAlignment true|false
Whether to show the resulting sequence alignment in Multalign Viewer