cealign SEL1, SEL2where SEL1 is the first selection to align, and SEL2 is the second selection. Any PyMol selection should be valid. For example all of the following are syntactically valid:
# align two proteins cealign 1ggz, 1cll # align residue ranges on two proteins cealign 1cbs and i. 6-55, 1hmt and i. 6-90 # align certain chains on two proteins cealign 1OKE and c. A, 1S6N