  Structural disorder is present in almost all experimental measurements of
electronic transport through single molecules or molecular wires. To assess its
influence on the conductance is computationally demanding, because a large
number of conformations must be considered. Here we analyze an approximate
recursive layer Green function approach for the ballistic transport through
quasi one-dimensional nano-junctions. We find a rapid convergence of the method
with its control parameter, the layer thickness, and good agreement with
existing experimental and theoretical data. Because the computational effort
rises only linearly with system size, this method permits treatment of very
large systems. We investigate the conductance of gold- and silver wires of
different sizes and conformations. For weak electrode disorder and imperfect
coupling between electrode and wire we find conductance variations of
approximately 20%. Overall we find the conductance of silver junctions well
described by the immediate vicinity of narrowest point in the junction, a
result that may explain the observation of well-conserved conductance plateaus
in recent experiments on silver junctions. In an application to flexible
oligophene wires, we find that strongly distorted conformations that are
sterically forbidden at zero temperature, contribute significantly to the
observed average zero-bias conductance of the molecular wire.
