Jmol/Electrostatic potential - Revision history

Karsten Theis at 01:37, 11 October 2020

Karsten Theis — Sun, 11 Oct 2020 01:37:21 GMT

←Older revision		Revision as of 01:37, 11 October 2020
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked>		<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked>
-	<scriptWhenchecked>select all; isosurface molecular map mep; color isosurface range -0.05 0.05	+	<scriptWhenchecked>select all; isosurface molecular map mep; color isosurface range -0.05 0.05; color isosurface translucent
	</scriptWhenchecked>		</scriptWhenchecked>
	<checked>false</checked>		<checked>false</checked>

Karsten Theis — Sun, 11 Oct 2020 01:32:30 GMT

←Older revision		Revision as of 01:32, 11 October 2020
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked>		<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked>
-	<scriptWhenchecked>select all; isosurface molecular map mep color ~~translucent~~</scriptWhenchecked>	+	<scriptWhenchecked>select all; isosurface molecular map mep; color isosurface range -0.05 0.05
		+	</scriptWhenchecked>
	<checked>false</checked>		<checked>false</checked>
	<text>potential map</text>		<text>potential map</text>

Karsten Theis — Sat, 10 Oct 2020 15:16:38 GMT

←Older revision		Revision as of 15:16, 10 October 2020
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	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked>		<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked>
-	<scriptWhenchecked>select all; isosurface JVXL "http://proteopedia.org/wiki/images/2/2c/1F36.jvxl" ~~color translucent~~</scriptWhenchecked>	+	<scriptWhenchecked>select all; isosurface JVXL "http://proteopedia.org/wiki/images/2/2c/1F36.jvxl"</scriptWhenchecked>
	<checked>false</checked>		<checked>false</checked>
	<text>potential map</text>		<text>potential map</text>

Karsten Theis — Sat, 10 Oct 2020 15:08:57 GMT

←Older revision		Revision as of 15:08, 10 October 2020
Line 62:		Line 62:
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked>		<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked>
-	<scriptWhenchecked>select all; isosurface JVXL "http://proteopedia.org/wiki/images/2/2c/1F36.jvxl"</scriptWhenchecked>	+	<scriptWhenchecked>select all; isosurface JVXL "http://proteopedia.org/wiki/images/2/2c/1F36.jvxl" color translucent</scriptWhenchecked>
	<checked>false</checked>		<checked>false</checked>
	<text>potential map</text>		<text>potential map</text>

Karsten Theis — Sat, 10 Oct 2020 15:07:56 GMT

←Older revision		Revision as of 15:07, 10 October 2020
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	DNA-binding (and DNA-bending) of <scene name='86/864093/Fis/1'>FIS</scene> is believed to be mostly electrostatic, explaining the low sequence-specificity and the high sensitive of interactions to ionic strength of the solvent.		DNA-binding (and DNA-bending) of <scene name='86/864093/Fis/1'>FIS</scene> is believed to be mostly electrostatic, explaining the low sequence-specificity and the high sensitive of interactions to ionic strength of the solvent.
		+
		+	Use this checkbox to toggle the potential on and off:
		+	<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked>
		+	<scriptWhenchecked>select all; isosurface JVXL "http://proteopedia.org/wiki/images/2/2c/1F36.jvxl"</scriptWhenchecked>
		+	<checked>false</checked>
		+	<text>potential map</text>
		+	</jmolCheckbox>
		+	</jmol>
		+
	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Karsten Theis — Sat, 10 Oct 2020 14:59:56 GMT

←Older revision		Revision as of 14:59, 10 October 2020
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	===Example 2: the DNA-binding protein FIS===		===Example 2: the DNA-binding protein FIS===

		+	DNA-binding (and DNA-bending) of <scene name='86/864093/Fis/1'>FIS</scene> is believed to be mostly electrostatic, explaining the low sequence-specificity and the high sensitive of interactions to ionic strength of the solvent.
	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>

Karsten Theis — Sat, 10 Oct 2020 14:06:28 GMT

←Older revision		Revision as of 14:06, 10 October 2020
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	===Example 1: water===		===Example 1: water===
	Electrostatic potential of <scene name='86/864093/Water/1'>water</scene> based on partial charges calculated in molcalc.org.		Electrostatic potential of <scene name='86/864093/Water/1'>water</scene> based on partial charges calculated in molcalc.org.
		+
		+	Use this checkbox to toggle the potential on and off:
		+	<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenUnChecked>isosurface off</scriptWhenUnChecked>
		+	<scriptWhenchecked>select all; isosurface molecular map mep color translucent</scriptWhenchecked>
		+	<checked>false</checked>
		+	<text>potential map</text>
		+	</jmolCheckbox>
		+	</jmol>

	After loading the .smol file, the following command was used to show the potential:		After loading the .smol file, the following command was used to show the potential:

Karsten Theis — Sat, 10 Oct 2020 14:03:14 GMT

←Older revision		Revision as of 14:03, 10 October 2020
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	molcalc.org, e.g. http://molcalc.org/calculation/cc11a07f2bb4579391c1e0603665f673#/solvation		molcalc.org, e.g. http://molcalc.org/calculation/cc11a07f2bb4579391c1e0603665f673#/solvation

-		+	Some theory on the Poisson Boltzmann equation: DOI:10.1002/jmr.577

	<StructureSection load='1F36' size='340' side='right' caption='' scene=''>		<StructureSection load='1F36' size='340' side='right' caption='' scene=''>
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	===Example 1: water===		===Example 1: water===
-	Electrostatic potential of water based on partial charges calculated in molcalc.org.	+	Electrostatic potential of <scene name='86/864093/Water/1'>water</scene> based on partial charges calculated in molcalc.org.

	After loading the .smol file, the following command was used to show the potential:		After loading the .smol file, the following command was used to show the potential:

Karsten Theis — Sat, 10 Oct 2020 14:01:41 GMT

←Older revision		Revision as of 14:01, 10 October 2020
Line 38:		Line 38:

	===Example 1: water===		===Example 1: water===
		+	Electrostatic potential of water based on partial charges calculated in molcalc.org.
		+
		+	After loading the .smol file, the following command was used to show the potential:
		+	<nowiki>isosurface molecular map mep color translucent</nowiki>

Karsten Theis — Sat, 10 Oct 2020 13:55:09 GMT

←Older revision		Revision as of 13:55, 10 October 2020
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	<StructureSection load='1F36' size='340' side='right' caption='' scene=''>		<StructureSection load='1F36' size='340' side='right' caption='' scene=''>
-	~~This is a default text for your page '''Jmol/Electrostatic potential'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.~~	+

	===Example 1: water===		===Example 1: water===