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This page describes the use of FirstGlance in Jmol version 4.0. Its release is expected soon, but it is not yet publicly available. Eric Martz 22:25, 26 July 2022 (UTC)
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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 (UniProt P03300).
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 12 vertices.
Measuring Capsid Diameter
FirstGlance/How To Measure A Virus Capsid provides step by step instructions on how to view a slab of the capsid and measure distances.
(see caption). In addition to assigning a distinct color to each group of sequence-identical chains, FirstGlance offers coloring by amino to carboxy rainbow, hydrophobic vs. polar, charge, and as illustrated below, evolutionary conservation.
Hide and Isolate tools are provided in the Focus Box] of FirstGlance. Clicking on a chain offers to hide or isolate all sequence-identical chains. Here,
Similarly one can easily isolate
or
