While browsing the June 2019 issue of the RNA journal, I was surprised to see a cover image with familiar schematic representations:
The caption is as below:
Crystal structure of ykoY-mntP riboswitch chimera bound to cadmium (Protein Data Bank code: 6cc3; Bachas ST, Ferré-D’Amaré AR. 2018. Convergent use of heptacoordination for cation selectivity by RNA and protein metalloregulators. Cell Chem Biol 25: 962–973.e5). The RNA backbone is displayed as a red ribbon; bases are shown as blocks with NDB coloring: A—red, C—yellow, G—green, U—cyan; cadmium ions are shown as red spheres. The image was generated using 3DNA/blocview and PyMol software. Cover image provided by the Nucleic Acid Database (ndbserver.rutgers.edu).
In addition to the
blocview script distributed with 3DNA v2.x, the block-view has been integrated into DSSR via the
--blocview option. Notably, the DSSR-plugin introduces the
dssr_block command to PyMOL for interactive visualization of nucleic acid structures. See the DSSR User Manual for more information.