“pair_fit” fits matched sets of atom pairs between two objects.
pair_fit selection, selection, [ selection, selection [ … ]]
# superimpose protA residues 10-25 and 33-46 to protB residues 22-37 and 41-54: pair_fit protA/10-25+33-46/CA, protB/22-37+41-54/CA # superimpose ligA atoms C1, C2, and C4 to ligB atoms C8, C4, and C10, respectively: pair_fit ligA////C1, ligB////C8, ligA////C2, ligB////C4, ligA////C3, ligB////C10
So long as the atoms are stored in PyMOL with the same order internally, you can provide just two selections. Otherwise, you may need to specify each pair of atoms separately, two by two, as additional arguments to pair_fit.
Script files are usually recommended when using this command.