Hi AndrĂ©,
As far as I know there is no way to do this with ChimeraX's command-line syntax, so I am going to assume you are asking how to do this in Python.  The following Python code will put the starting and ending backbone atom of each chain into a list named 'terminal_atoms':

from chimerax.atomic import all_atomic_structures, Residue
terminal_atoms = []
for s in all_atomic_structures(session):
        for chain in s.chains:
                ordered_bb_names = Residue.aa_min_ordered_backbone_names if chain.polymer_type == Residue.PT_AMINO \
                        else Residue.na_min_ordered_backbone_names
                existing_residues = chain.existing_residues
                terminals = []
                for terminal_residue, bb_names in [(existing_residues[0], ordered_bb_names),
                                (existing_residues[-1], reversed(ordered_bb_names))]:
                        for bb_name in bb_names:
                                a = terminal_residue.find_atom(bb_name)
                                if a:
                                        terminals.append(a)
                                        break
                        else:
                                print("No backbone atoms found in %s; skipping chain" % terminal_residue)
                                break
                else:
                        terminal_atoms.extend(terminals)

For your convenience, I've attached a file containing the above code.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab