Fig. 1.

Representations of an RNA molecule. (A) The secondary structure of tRNA with each base-paired segment differently colored and simplified as a cylinder (of radius 11 Å) shown in three-dimensions (B). A reference helix (black) is arbitrarily chosen to define a reference coordinate system. The other helices are color-coded. (C) Each helix axis is projected on the reference coordinate system to give two angles (θ_h and ϕ_h). The vector pointing from the origin of the reference helix to the helix origin (defined as position closest to the junction) is also projected giving θ_o and ϕ_o. Each projection can be represented as x, y, and z-axes scaled direction cosines (labeled l_x, l_y, and l_z for the helix orientation projection). These scaled direction cosines and the origin coordinates, were used as the clustering metric.