Interactive Chain Network

Chain-chain interfaces can be identified by buried surface areas and displayed as a network diagram with the interfaces command or the Molecule Display icon . In the diagram, nodes (circles) represent chains, larger for greater surface areas, and edges (lines) between nodes represent chain-chain interfaces (default ≥ 300 Ų buried area). Dotted lines represent interfaces smaller than half the size of the largest in the structure. Diagram context menus enable a variety of actions, such as “exploding” the structure by moving chains apart, hiding all but the chains in contact with a given chain, and showing a more detailed plot of the residues forming a given interface.

The structure is an HIV envelope glycoprotein trimer bound by three copies of a broadly neutralizing antibody (PDB 5v8m), with chain information shown in the Log. Glycosylations (not displayed) were included in the surface area calculations. For setup, see the command file trimer-network.cxc.

The architecture of the human ribosome has been determined at near-atomic resolution by electron microscopy (Anger et al., Nature 497:80 (2013)). The structure, comprising 82 proteins and five RNA molecules, is shown with shadows cast from all directions to accentuate depth. In the background are schematic representations of contacts between the component molecules.

See the image setup script card.cxc using the 'Tis the Season color palette (credit to MrsP). See also the RBVI holiday card gallery.

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