Fig. 3

Different visualizations of nucleic acid secondary structure features. The atom coordinates and annotations of A and B are taken from PDB 6ZYB [39]. For C they are taken from PDB 4P5J [40]. Green lines/cuboids denote canonical base pairs, while blue lines/cuboids denote non-canonical base pairs. The base pairs were elucidated using base_pairs(). A Visualization of base pairing interactions with Pymol. Red cuboids indicate unpaired bases. B Visualization of base pairing interactions and their Leontis-Westhof annotations using plot_nucleotide_secondary_structure(). The first letter of the paired base annotations indicates the relative orientation of the glycosidic bonds (c - cis, t - trans), while the second letter encodes the interacting edges (S - Sugar, W - Watson-Crick, H - Hoogsteen/C-H). The relative glycosidic bond orientations and interacting edges were elucidated using base_pairs_glycosidic_bonds() and base_pairs_edge() respectively. C Visualization of base pairing interactions as an arc diagram created with Matplotlib. The dot-bracket-letter notation was generated with dot_bracket(). Solid arcs indicate pseudoknot order zero, dashed arcs pseudoknot order one, and dotted arcs pseudoknot order two. Capital letters represent canonical bases, while lowercase letters represent non-canonical bases mapped to the canonical base indicated by the respective one-letter-code. The bases were mapped using map_nucleotide()