FIGURE 4.

The secondary and tertiary structures of a fragment of gene 32 mRNA of bacteriophate T2. (A) The native secondary structure. (B) The native tertiary structure, data taken from the PDB databank (PDB 2tpk; http://www.wwpdb.org/). (C) The tertiary structure predicted by pk3D. Note that in both B and C, loops are shown in yellow dashed lines to illustrate chain connectivity and to facilitate structural comparison. The orange spheres show the position of the A8 nucleotide, which forms a short loop of length 1. All tertiary structures were drawn using PyMOL (http://pymol.org/).