User:Eric Martz/Cavities tests - Revision history

Eric Martz at 15:59, 13 August 2020

Eric Martz — Thu, 13 Aug 2020 15:59:25 GMT

←Older revision		Revision as of 15:59, 13 August 2020
Line 34:		Line 34:
	<text>Green link loading uploaded PNGJ file</text>		<text>Green link loading uploaded PNGJ file</text>
	</jmolLink>		</jmolLink>
-	</jmol>. SAT not involved. PNGJ file generated externally in the [[Jmol/Application\|Jmol Java application]].	+	</jmol>. SAT not involved. PNGJ file generated externally in the [[Jmol/Application\|Jmol Java application]], then uploaded to Proteopedia as for the previous item above.

Eric Martz: User:Eric Martz/Sandbox 4 moved to User:Eric Martz/Cavities tests

Eric Martz — Wed, 12 Aug 2020 23:00:43 GMT

User:Eric Martz/Sandbox 4 moved to User:Eric Martz/Cavities tests

←Older revision

Revision as of 23:00, 12 August 2020

Eric Martz at 22:48, 12 August 2020

Eric Martz — Wed, 12 Aug 2020 22:48:06 GMT

←Older revision		Revision as of 22:48, 12 August 2020
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	load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";		load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
	</script>		</script>
-	<text>Green link loading uploaded PNGJ file</text>.	+	<text>Green link loading uploaded PNGJ file</text>
	</jmolLink>		</jmolLink>
-	</jmol> SAT not involved. PNGJ file generated externally in the [[Jmol/Application\|Jmol Java application]].	+	</jmol>. SAT not involved. PNGJ file generated externally in the [[Jmol/Application\|Jmol Java application]].

Eric Martz at 22:47, 12 August 2020

Eric Martz — Wed, 12 Aug 2020 22:47:25 GMT

←Older revision		Revision as of 22:47, 12 August 2020
Line 34:		Line 34:
	<text>Green link loading uploaded PNGJ file</text>.		<text>Green link loading uploaded PNGJ file</text>.
	</jmolLink>		</jmolLink>
-	</jmol> SAT not involved. PNGJ file generated externally in the [[Jmol/Application Jmol Java application]].	+	</jmol> SAT not involved. PNGJ file generated externally in the [[Jmol/Application\|Jmol Java application]].

Eric Martz at 22:47, 12 August 2020

Eric Martz — Wed, 12 Aug 2020 22:47:02 GMT

←Older revision		Revision as of 22:47, 12 August 2020
Line 35:		Line 35:
	</jmolLink>		</jmolLink>
	</jmol> SAT not involved. PNGJ file generated externally in the [[Jmol/Application Jmol Java application]].		</jmol> SAT not involved. PNGJ file generated externally in the [[Jmol/Application Jmol Java application]].
		+

	*5 <scene name='31/319439/6zgi_cavities_from_pngj/1'>Test dropping pngj with cavities into SAT</scene>, then saving scene. (No molecule loaded with the SAT "load molecule" tab.)		*5 <scene name='31/319439/6zgi_cavities_from_pngj/1'>Test dropping pngj with cavities into SAT</scene>, then saving scene. (No molecule loaded with the SAT "load molecule" tab.)

Eric Martz at 22:46, 12 August 2020

Eric Martz — Wed, 12 Aug 2020 22:46:50 GMT

←Older revision		Revision as of 22:46, 12 August 2020
Line 34:		Line 34:
	<text>Green link loading uploaded PNGJ file</text>.		<text>Green link loading uploaded PNGJ file</text>.
	</jmolLink>		</jmolLink>
-	</jmol>	+	</jmol> SAT not involved. PNGJ file generated externally in the [[Jmol/Application Jmol Java application]].
-	SAT not involved. PNGJ file generated in the [[Jmol/Application Jmol Java application]].	+

	*5 <scene name='31/319439/6zgi_cavities_from_pngj/1'>Test dropping pngj with cavities into SAT</scene>, then saving scene. (No molecule loaded with the SAT "load molecule" tab.)		*5 <scene name='31/319439/6zgi_cavities_from_pngj/1'>Test dropping pngj with cavities into SAT</scene>, then saving scene. (No molecule loaded with the SAT "load molecule" tab.)

Eric Martz at 22:46, 12 August 2020

Eric Martz — Wed, 12 Aug 2020 22:46:12 GMT

←Older revision		Revision as of 22:46, 12 August 2020
Line 32:		Line 32:
	load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";		load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
	</script>		</script>
-	<text>Green link loading uploaded PNGJ file</text>~~. SAT not involved. PNGJ file generated in the [[Jmol/Application Jmol Java application]]~~.	+	<text>Green link loading uploaded PNGJ file</text>.
	</jmolLink>		</jmolLink>
	</jmol>		</jmol>
-		+	SAT not involved. PNGJ file generated in the [[Jmol/Application Jmol Java application]].

	*5 <scene name='31/319439/6zgi_cavities_from_pngj/1'>Test dropping pngj with cavities into SAT</scene>, then saving scene. (No molecule loaded with the SAT "load molecule" tab.)		*5 <scene name='31/319439/6zgi_cavities_from_pngj/1'>Test dropping pngj with cavities into SAT</scene>, then saving scene. (No molecule loaded with the SAT "load molecule" tab.)

Eric Martz at 22:45, 12 August 2020

Eric Martz — Wed, 12 Aug 2020 22:45:39 GMT

←Older revision		Revision as of 22:45, 12 August 2020
Line 32:		Line 32:
	load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";		load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
	</script>		</script>
-	<text>Green link loading uploaded PNGJ file</text>.	+	<text>Green link loading uploaded PNGJ file</text>. SAT not involved. PNGJ file generated in the [[Jmol/Application Jmol Java application]].
	</jmolLink>		</jmolLink>
	</jmol>		</jmol>

Eric Martz at 22:43, 12 August 2020

Eric Martz — Wed, 12 Aug 2020 22:43:37 GMT

←Older revision		Revision as of 22:43, 12 August 2020
Line 4:		Line 4:


-	*2 <scene name='31/319439/6zgi_translucen_backbone/1'>6zgi as translucent backbone, chain colors</scene> (no isosurfaces). After clicking this green link, then	+	*2 <scene name='31/319439/6zgi_translucen_backbone/1'>6zgi as translucent backbone, chain colors</scene> (no isosurfaces). After clicking this standard SAT-generated green link, then
	<jmol>		<jmol>
	<jmolButton>		<jmolButton>

Eric Martz at 22:42, 12 August 2020

Eric Martz — Wed, 12 Aug 2020 22:42:32 GMT

←Older revision		Revision as of 22:42, 12 August 2020
Line 27:		Line 27:


-	*4 <scene name='31/319439/6zgi_cavities_from_pngj/1'>Test dropping pngj with cavities into SAT</scene>, then saving scene. (No molecule loaded with the SAT "load molecule" tab.)	+	*4 <jmol>
		+	<jmolLink>
		+	<script>
		+	load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
		+	</script>
		+	<text>Green link loading uploaded PNGJ file</text>.
		+	</jmolLink>
		+	</jmol>
		+
		+
		+	*5 <scene name='31/319439/6zgi_cavities_from_pngj/1'>Test dropping pngj with cavities into SAT</scene>, then saving scene. (No molecule loaded with the SAT "load molecule" tab.)


	Tested in Firefox (current version) on macOS Mojave, mid-2014 MacBook Pro, 2.2 GHz Intel Core i7.		Tested in Firefox (current version) on macOS Mojave, mid-2014 MacBook Pro, 2.2 GHz Intel Core i7.

-	*5 <scene name='31/319439/6zgi_cavities/1'>Cavities in coronavirus spike protein 6zgi</scene>. It took 8.5 min to generate the cavity isosurfaces after I entered the command "isosurface minset 100 interior cavity 3.0 10.0" into the command slot in the SAT. (This command takes ~45 sec in the Jmol Java app which is therefore 11-fold faster for this operation.) After clicking this green link, I waited 11 min and the scene still did not appear. So I think the isosurfaces are being generated again when the green link is clicked.	+	*6 <scene name='31/319439/6zgi_cavities/1'>Cavities in coronavirus spike protein 6zgi</scene>. It took 8.5 min to generate the cavity isosurfaces after I entered the command "isosurface minset 100 interior cavity 3.0 10.0" into the command slot in the SAT. (This command takes ~45 sec in the Jmol Java app which is therefore 11-fold faster for this operation.) After clicking this green link, I waited 11 min and the scene still did not appear. So I think the isosurfaces are being generated again when the green link is clicked.



	</StructureSection>		</StructureSection>