To reproduce use matplotlib>=1.5.0 and try to plot a 3D system with site_size set to something. Verify that in the resulting figure fig.axes[0].collections[0].transforms have a shape (N,), and not (N, 3, 3), as would be expected by matplotlib. This results in a failure to plot inside a notebook with an inline backend.

Looking at the source code, I see that transforms get reshaped over here; my guess that's where the problem originates from.

In an interactive backend setting the sizes doesn't seem to have any effect at all (which may or may not be a separate bug).