Both structures, the reference first, are expected as command line arguments. The fitted structure is written to standard output in PDB format. Other atoms can be chosen with -sel .
Possible choices are ca , cb , cab , and heavy .
Examples lsqfit.pl 1vii.xray.pdb 1vii.xray.min.pdb performs a least squares fit of 1vii.xray.min.pdb with respect to the reference structure in 1vii.xray.pdb . Only C-alpha atoms are used for the fit.