Pair Fit
From PyMOLWiki
Pair_Fit fits a set of atom pairs between two models. Each atom in each pair must be specified individually, which can be tedious to enter manually. Script files are recommended when using this command.
USAGE
pair_fit (selection), (selection), [ (selection), (selection) [ ...] ]
USER EXAMPLES/COMMENTS
An description of selection caveats for these commands may be found at Intra_Rms.
