The Matchmaker
tool (or
matchmaker
command) is convenient for superimposing related structures
without having to worry about numbering or missing residues.
It superimposes proteins or nucleic acids by creating a pairwise
sequence alignment, then matching the sequence-aligned residues in 3D.
Secondary structure helps guide the sequence alignment
for better performance on more distantly related proteins with
harder-to-align sequences.
By default, the fit is iterated to exclude structurally dissimilar regions
and superimpose the most similar parts more closely.
The resulting sequence alignments can be displayed, as in
this example of three pectate lyases: PDB
1jta,
1bn8, and
2pec (see the
command file peclyases.cxc).
In the sequence alignments, residues
used in the final fit iteration are enclosed in light orange boxes.
RMSD values and other fit statistics are reported
in the Log.
More features...