MatchMaker

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:

• specific reference chain(s) with specific chain(s) in match structure - One or more reference chains should be chosen from the list. Individual chains or blocks of chains can be chosen with the left mouse button; Ctrl-click toggles the status of an individual chain. For each reference chain chosen, one chain to be matched should be chosen from the corresponding pulldown menu. If multiple chains are to be matched to the same reference chain, it is necessary to match them in separate steps (by choosing the chain to match and then clicking Apply). A given chain cannot be matched to two different reference chains simultaneously, and chains from the same structure (molecule model) cannot simultaneously serve as a reference chain and a chain to match.
• specific reference chain with best-aligning chain in match structure - One reference chain and one or more structures to match should be chosen. For each structure to be matched, the chain that aligns to the reference chain with the highest sequence alignment score will be used.
• best-aligning pair of chains between reference and match structure - One reference structure and one or more structures to match should be chosen. For each structure to be matched, the reference-match pair of chains with the highest sequence alignment score will be used.

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.