Figure 2.
Genus traces for RNA structure—a large ribosomal unit from Haloarcula marismortui (PDB code: 4v9fo)—together with some other data shown in the database. Genus traces, for various types of base pairs in the Leontis–Westhof classification (17,18) (denoted cWW, tHS, tWH, etc., as also explained in the main text below), are shown in the main diagram (in the left)—the bottom plot (in orange) is the genus trace calculated by taking into account only canonical cWW base pairs; each other consecutive plot includes non-canonical base pairs of an additional type, in the order given in (2); for each genus trace, the genus value for a choice of a residue on the horizontal axis is shown in the colored box. In the top, the PDB ID and the name/title of the structure are shown. Apart from the genus data, one can also view chain information, and a list of similar chains (as indicated by the tabs in the figure). Also the JSmol visualization is shown in the database (right). In the bottom of the figure, some other options and files that can be downloaded, available in the database, are shown.