User:Eric Martz/Cavities tests: Difference between revisions

(9 intermediate revisions by the same user not shown)

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*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>

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*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>

load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";

</script>

<text>Green link loading uploaded PNGJ file</text>

</jmolLink>

</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.

*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.

*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>

@@ 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>
 <jmolButton>
@@ 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>. SAT not involved. PNGJ file generated externally in the [[Jmol/Application|Jmol Java application]], then uploaded to Proteopedia as for the previous item above.
+*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.
-*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>