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.
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