|
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)
|
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. The empty capsid is made up from 4 proteins, VP1, VP2, VP3, VP4. All these are products of the proteolysis of a single large polyprotein.
