FirstGlance/How To Measure A Virus Capsid - Revision history

Eric Martz at 16:18, 17 August 2022

Eric Martz — Wed, 17 Aug 2022 16:18:45 GMT

←Older revision		Revision as of 16:18, 17 August 2022
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	{{Template:EEEV}}		{{Template:EEEV}}

-	'''Quick Start''': [http://~~bioinformatics~~.org~~/firstglance/fgij4~~/fg.htm?mol=6mx4 Analyze the EEEV capsid 6mx4 in FirstGlance].	+	'''Quick Start''': [http://firstglance.jmol.org/fg.htm?mol=6mx4 Analyze the EEEV capsid 6mx4 in FirstGlance].

	[[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]].

Eric Martz at 16:14, 17 August 2022

Eric Martz — Wed, 17 Aug 2022 16:14:53 GMT

←Older revision		Revision as of 16:14, 17 August 2022
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	<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>
-
-	This page describes the use of version 4.0 of FirstGlance in Jmol. Its release is expected soon, but it is not yet publicly available. [[User:Eric Martz\|Eric Martz]] 22:25, 26 July 2022 (UTC)
-
-	</td></tr></table>
-
	{{Template:EEEV}}		{{Template:EEEV}}

Eric Martz at 19:44, 1 August 2022

Eric Martz — Mon, 01 Aug 2022 19:44:23 GMT

←Older revision		Revision as of 19:44, 1 August 2022
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	(total 720 protein chains).		(total 720 protein chains).

-	For more about the EEEV capsid, see [[Virus_Capsids_and_Other_Large_Assemblies#Eastern_Equine_Encephalitis_Virus\|Virus Capsids and Other Large Assemblies]].	+	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>

Eric Martz at 19:44, 1 August 2022

Eric Martz — Mon, 01 Aug 2022 19:44:03 GMT

←Older revision		Revision as of 19:44, 1 August 2022
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	</jmol>		</jmol>
	(total 720 protein chains).		(total 720 protein chains).
		+
		+	For more about the EEEV capsid, see [[Virus_Capsids_and_Other_Large_Assemblies#Eastern_Equine_Encephalitis_Virus\|Virus Capsids and Other Large Assemblies]].

	</StructureSection>		</StructureSection>

Eric Martz at 19:42, 1 August 2022

Eric Martz — Mon, 01 Aug 2022 19:42:04 GMT

←Older revision		Revision as of 19:42, 1 August 2022
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	</StructureSection>		</StructureSection>
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		+	==Reference==
		+	<references />

Eric Martz at 10:22, 1 August 2022

Eric Martz — Mon, 01 Aug 2022 10:22:15 GMT

←Older revision		Revision as of 10:22, 1 August 2022
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	<table style="background-color:#ffffa0;" class='wikitable'><tr><td>		<table style="background-color:#ffffa0;" class='wikitable'><tr><td>

-	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)	+	This page describes the use of version 4.0 of FirstGlance in Jmol. Its release is expected soon, but it is not yet publicly available. [[User:Eric Martz\|Eric Martz]] 22:25, 26 July 2022 (UTC)

	</td></tr></table>		</td></tr></table>

Eric Martz at 00:07, 28 July 2022

Eric Martz — Thu, 28 Jul 2022 00:07:21 GMT

←Older revision		Revision as of 00:07, 28 July 2022
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	==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''.

Eric Martz at 00:04, 28 July 2022

Eric Martz — Thu, 28 Jul 2022 00:04:59 GMT

←Older revision		Revision as of 00:04, 28 July 2022
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	{{Template:EEEV}}		{{Template:EEEV}}

-	Quick Start: [http://bioinformatics.org/firstglance/fgij4/fg.htm?mol=6mx4 Analyze the EEEV capsid 6mx4 in FirstGlance].	+	'''Quick Start''': [http://bioinformatics.org/firstglance/fgij4/fg.htm?mol=6mx4 Analyze the EEEV capsid 6mx4 in FirstGlance].

	[[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]].

Eric Martz at 00:04, 28 July 2022

Eric Martz — Thu, 28 Jul 2022 00:04:37 GMT

←Older revision		Revision as of 00:04, 28 July 2022
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	{{Template:EEEV}}		{{Template:EEEV}}
-
-	[[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]].

	Quick Start: [http://bioinformatics.org/firstglance/fgij4/fg.htm?mol=6mx4 Analyze the EEEV capsid 6mx4 in FirstGlance].		Quick Start: [http://bioinformatics.org/firstglance/fgij4/fg.htm?mol=6mx4 Analyze the EEEV capsid 6mx4 in FirstGlance].

		+	[[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]].

	==Slab of the Capsid==		==Slab of the Capsid==

Eric Martz at 00:04, 28 July 2022

Eric Martz — Thu, 28 Jul 2022 00:04:15 GMT

←Older revision		Revision as of 00:04, 28 July 2022
Line 9:		Line 9:

	[[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]].
		+
		+	Quick Start: [http://bioinformatics.org/firstglance/fgij4/fg.htm?mol=6mx4 Analyze the EEEV capsid 6mx4 in FirstGlance].
		+

	==Slab of the Capsid==		==Slab of the Capsid==