Comparison between multipole and rmsd distances ( Case 1 ). The distance matrices between aligned portions of proteins in the multipolar (a) and Cartesian coordinate (b) representations. Multipoles up to order four are retained in (a). The rmsd distances are calculated after prior spatial superimposition. The shading is in both cases proportional to the distance, however the scale is normalized to the entire range of values taken in each case. The order of the 31 proteins along the two axis is as described in the text and the same as in Figure 1.