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User:Eric Martz/Cavities tests
From Proteopedia
< User:Eric Martz(Difference between revisions)
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| - | + | <StructureSection load='' size='350' side='right' caption='' scene=''> | |
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| + | *1 <scene name='31/319439/Surface_test/1'>Surface test 1</scene>: simple surface on chain A of 1d66. Colored translucent green. This surface was generated with the '''representations''' tab of the SAT. | ||
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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 standard SAT-generated green link, then | ||
| + | <jmol> | ||
| + | <jmolButton> | ||
| + | <script> | ||
| + | isosurface delete; isosurface "http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl"; | ||
| + | </script> | ||
| + | <text>Load isosurface cavities</text> | ||
| + | </jmolButton> | ||
| + | </jmol> | ||
| + | (From uploaded file http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl -- see [[Image:6zgi-cavities.jvxl]]) | ||
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| + | *3 <jmol> | ||
| + | <jmolButton> | ||
| + | <script> | ||
| + | load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj"; | ||
| + | </script> | ||
| + | <text>Load .PNGJ file</text> | ||
| + | </jmolButton> | ||
| + | </jmol> | ||
| + | (From uploaded file http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj -- see [http://proteopedia.org/wiki/index.php/Image:6zgi-cavities.pngj Image:6zgi-cavities.png]) | ||
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| + | *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. | ||
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| + | *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.) | ||
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| + | Tested in Firefox (current version) on macOS Mojave, mid-2014 MacBook Pro, 2.2 GHz Intel Core i7. | ||
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| + | *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. | ||
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| + | </StructureSection> | ||
Current revision
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