MatchMaker MatchMaker icon

MatchMaker superimposes structures with similar sequences 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.

There are several ways to start MatchMaker, a tool in the Homology and Utilities categories. MatchMaker is also implemented as the command mmaker (or matchmaker).

The Chain pairing options are mutually exclusive and control which chain sequences are used to construct each reference-match alignment:

Regardless of which chain(s) in a model to be matched are aligned in sequence to the reference, the entire model will be reoriented.

The sequence alignment algorithm can be Smith-Waterman (local) or Needleman-Wunsch (global). Several scoring matrices are available (various BLOSUM, DNA, various PAM), and the gap opening penalty and gap extension penalty are adjustable. The default gap parameter settings are not necessarily optimal, so it is reasonable to try different values when the desired results have not been obtained.

Sequence alignment scores and match RMSD values are reported in the status line and Reply Log. When show alignment(s) in Multalign Viewer is checked, each pairwise reference-match sequence alignment will be shown in a separate window.

OK performs the aligning/matching and dismisses the dialog, whereas Apply performs the operations without dismissing the dialog. Cancel simply dismisses the dialog. Help opens this manual page in a browser window.


UCSF Computer Graphics Laboratory / December 2004