FirstGlance/Virus Capsids and Other Large Assemblies

Virus capsids and similarly large protein assemblies can be conveniently visualized and analyzed with FirstGlance in Jmol. Below some examples are explained and illustrated, but here is a quick start: polio virus capsid in FirstGlance (1pov).

FirstGlance in Jmol automatically constructs biological unit 1, thought to be the major functional quaternary assembly. Biological unit 1 is shown initially by default, and you can start separate sessions to show the asymmetric unit or other biological units when more than one are specified. When the resulting assembly is too large to work smoothly and efficiently in FirstGlance in Jmol (all Javascript), FirstGlance will automatically simplify the model to alpha carbons, or when necessary, to a subset of alpha carbons.

Polio Virus

Polio virus is small (among viruses pathogenic for humans) with an RNA genome inside a single-shell protein capsid. 1pov made up from 3 proteins, VP0, VP1 and VP3.

The polio capsid has an icosahedral construction with 12 vertices defining 20 triangular faces. Notice that the larger blue mesas protruding on the surface have 5-fold symmetry. These are pentagonal capsomeres at the vertices.

FirstGlance/How To Measure A Virus Capsid provides step by step instructions on how to view a slab of the capsid and measure distances.

In addition to assigning a distinct color to each group of sequence-identical chains, FirstGlance offers coloring by Help:Color_Keys#Rainbows:_N_to_C.2C_5.27_to_3.27 amino to carboxy rainbow, hydrophobic vs. polar, charge, and as illustrated below, evolutionary conservation.