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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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The
(EEEV) consists of three distinct protein sequences, and a total of 720 chains. It has nearly 2 million non-hydrogen atoms (so about 3.6 million atoms including hydrogen). The structure 6mx4 determined by electron microscopy (4.4 Å resolution) has 12 chains, with instructions for constructing the entire capsid using 60 copies of the asymmetric unit.
FirstGlance in Jmol automatically constructs the capsid, and simplifies it to a subset of alpha carbon atoms small enough (not more than 25,000) to be analyzed efficiently in the FirstGlance and JSmol, both of which run in the Javascript of the web browser. FirstGlance offers a number of useful color schemes, including distance from center, colors that distinguish sequence-identical groups of chains, and amino-to-carboxy rainbow. When the structure is small enough that all alpha carbons can be displayed (not more than 250,000 alpha carbons; EEEV has 242,340), it can also be colored by charge, hydrophobic vs. polar, or evolutionary conservation.
Slab of the Capsid
In order to estimate the dimensions of the capsid, it is useful to "cut out a slab".
Immediately you can see that this is a double-layered capsid, with outer and inner shells. Between the shells are transmembrane alpha helical "spikes" or "posts" embedded in a lipid bilayer (not represented by any atoms here).
To obtain this slab in FirstGlance, you simply depress a Slab button. By default, the thickness of the slab is 10% of the diameter of the capsid (but this is adjustable). Here is a snapshot of the Views tab of FirstGlance. After the initial view of the capsid appears, getting this slab takes 3 clicks indicated by the red arrows: Click on the Views tab, depress the Slab button, and check Rotate slab.
Measuring the Slab
In FirstGlance (and JSmol), distances are measured by double-clicking on first one, then the second of the two relevant atoms.
