FirstGlance/How To Measure A Virus Capsid: Difference between revisions

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The
{{Template:EEEV}}
<jmol>
<jmolLink>
<script>
script /wiki/images/e/ee/Echo-loading.spt;
script /wiki/images/5/56/6mx4-capsid-nohet-distance.spt;
spin on;
</script>
<text>capsid of Eastern Equine Encephalitis Virus</text>
</jmolLink>
</jmol>
(EEEV) consists of 240 copies of each of three distinct protein sequences, totaling 720 [[chains]]. It has nearly 2 million non-hydrogen atoms (so about 3.8 million atoms including hydrogen). The structure [[6mx4]] determined by electron microscopy (4.4 &Aring; 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 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 [[Help:Color_Keys#Rainbows:_N_to_C.2C_5.27_to_3.27|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]].
[[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 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 [[Help:Color_Keys#Rainbows:_N_to_C.2C_5.27_to_3.27|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]].
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