  We present a set of benchmark calculations for the Kohn-Sham elastic
transmission function of five representative single-molecule junctions. The
transmission functions are calculated using two different density functional
theory (DFT) methods, namely an ultrasoft pseudopotential plane wave code in
combination with maximally localized Wannier functions, and the norm-conserving
pseudopotential code Siesta which applies an atomic orbital basis set. For all
systems we find that the Siesta transmission functions converge toward the
plane-wave result as the Siesta basis is enlarged. Overall, we find that an
atomic basis with double-zeta and polarization is sufficient (and in some cases
even necessary) to ensure quantitative agreement with the plane-wave
calculation. We observe a systematic down shift of the Siesta transmission
functions relative to the plane-wave results. The effect diminishes as the
atomic orbital basis is enlarged, however, the convergence can be rather slow.
