The first thing you need to do is “Select” a species and a ribosomal subunit from the Species and Subunit menu. For this example, we will use E. coli.Further in this menu you may choose either the large subunit or small subunit. We will choose the large subunit. We select “Phylogeny-Structure” to continue.
Upon selecting the subunit, the secondary structure will load to the 2D panel in its default view, with the nucleotides colored by domain. The 1D Panel and the 3D Panel also show domain information. After a minute or two the 3D view of the Ribosome loads in the panel on the right. The default color scheme in the 3D panel differentiates the domains of ribosomal RNA.