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

From Proteopedia
Jump to navigationJump to search
← Older edit
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators
30,128 edits
No edit summary
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Print3D, Tester, Bureaucrats, journal, Administrators
30,128 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
<StructureSection load='' size='350' side='right' caption='' scene=''>
<StructureSection load='' size='350' side='right' caption='' scene=''>
<table style="background-color:#ffffa0;" class='wikitable'><tr><td>
{{Template:EEEV}}


This page describes the use of FirstGlance in Jmol version 4.0. Its release is expected soon, but it is not yet publicly available. [[User:Eric Martz|Eric Martz]] 22:25, 26 July 2022 (UTC)
'''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=6mx4 Analyze the EEEV capsid 6mx4 in FirstGlance].
 
</td></tr></table>
 
The
<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 three distinct protein sequences, and a total of 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]].
Line 23: Line 8:
==Slab of the Capsid==
==Slab of the Capsid==
In order to estimate the dimensions of the capsid, it is useful to "cut out a slab".
In order to estimate the dimensions of the capsid, it is useful to "cut out a slab".
<jmol>
{{Template:EEEV-slab}}
<jmolLink>
<script>
script /wiki/images/e/ee/Echo-loading.spt;
script /wiki/images/9/9f/6mx4-nohet-slab-distance.spt;
spin on;
</script>
<text>Here is a slab of the center of the capsid.</text>
</jmolLink>
</jmol>
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''.
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''.
Line 59: Line 34:
spin on;
spin on;
</script>
</script>
  <text>The capsid is made up of many copies of 3 protein sequences.
  <text>The capsid is made up of 240 copies of each of 3 protein sequences
</text>
</text>
  </jmolLink>
  </jmolLink>
</jmol>
</jmol>
(total 720 protein chains).
For more about the EEEV capsid, see [[FirstGlance/Virus_Capsids_and_Other_Large_Assemblies#Eastern_Equine_Encephalitis_Virus|Virus Capsids and Other Large Assemblies]].


</StructureSection>
</StructureSection>
==Reference==
<references />
Retrieved from "https://proteopedia.org/FirstGlance/How_To_Measure_A_Virus_Capsid"