Examples of ribbon diagrams as seen in modern molecular visualization programs are shown in Figure 1. Richardson had described aligning ribbons with the axes of the helices and hydrogen bonds of the beta sheets ( Richardson (1985)), which is reflected in Carson and Bugg’s choice to align the normals of the ribbons with that of the peptide plane. One of the first computer algorithms for reproducing these diagrams was described by Carson and Bugg (1986), and utilized in several early programs ( Carson and Bugg (1988), Carson (1991), Carson (1997)). These diagrams also guided the form that future diagrams would take, with the secondary structure motifs of helices and beta sheets appearing as wide flat ribbons, in contrast to the cylindrical tubes of the intervening backbone. Starting from a trace of the experimentally determined positions of the alpha carbons, subjective decisions were made to smooth the final curves such that they clearly conveyed the structures in question ( Richardson (1985)). These diagrams were first and foremost tasked with conveying the three dimensional structure of proteins upon the two-dimensional page. This culminated in the production of diagrams for all 75 protein structures currently determined, by Richardson (1981, 2000). The ribbon diagrams used to visualize protein secondary structure can trace their origins to hand-drawn illustrations. We illustrate the utility of this algorithm by using it to visualize iMD-VR (interactive molecular dynamics in virtual reality) simulations of the secondary structure of the SARS-CoV-2 main protease (Mpro), which is being investigated as a potential target for COVID drug therapies. This yields diagrams which are well suited for viewing dynamic simulations, such as those used for interactive molecular dynamics. Here we outline a new method which prevents this artifact by morphing between consecutive cross sections instead of rotating. However, most algorithms used to generate these diagrams do not maintain visual continuity when viewing a molecular trajectory, with certain sections of ribbons flipping between clockwise and counterclockwise twists. Ribbon diagrams are important for protein visualization, used to convey the secondary structure in a clear and concise manner.
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