User:Eric Martz/Cavities tests: Difference between revisions

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Lower case PDB codes work in internal links, e.g. [[4cpa]], but upper case codes don't, e.g. [[4CPA]].
<StructureSection load='' size='350' side='right' caption='' scene=''>


Similarly, links to Proteopedia from outside have the same problem, e.g.
*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.
[http://proteopedia.org/wiki/index.php/4cpa http://proteopedia.org/wiki/index.php/4cpa] vs. [http://proteopedia.org/wiki/index.php/4CPA http://proteopedia.org/wiki/index.php/4CPA].
 
 
*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]])
 
 
*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])
 
 
*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.
 
*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>

Latest revision as of 18:59, 13 August 2020


  • 1 : simple surface on chain A of 1d66. Colored translucent green. This surface was generated with the representations tab of the SAT.


  • 2 (no isosurfaces). After clicking this standard SAT-generated green link, then

(From uploaded file http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl -- see File:6zgi-cavities.jvxl)


  • 3

(From uploaded file http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj -- see Image:6zgi-cavities.png)


  • 4 . SAT not involved. PNGJ file generated externally in the Jmol Java application, then uploaded to Proteopedia as for the previous item above.


  • 5 , 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.

  • 6 . 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.



Drag the structure with the mouse to rotate
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