User:Eric Martz/Cavities tests: Difference between revisions

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<span style="font-size:150%;background-color:#ffffb0;padding:5px;">'''See full explanation, and examples on how to use, at [[Help:Quiz]]'''.</span>
<StructureSection load='' size='350' side='right' caption='' scene=''>


*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.


<quiz display=simple>
{On a clear day at noon, what color is the sky?
|type="()"}
+ blue
|| The sky is blue when you look up.
- red
|| The sky is not red on a clear day at noon on Earth. Maybe on Mars?


{A defensive player is marking an offensive player with the disc. The defensive player gets to 'Five' in the stall count when the offensive player calls out 'disc space'. The defensive player agrees with the call and should :
*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
|type="()"}
<jmol>
- step back and continue counting from 'One'
<jmolButton>
+ step back and continue counting from 'Four'
<script>
- step back and continue counting from 'Five'
isosurface delete; isosurface "http://proteopedia.org/wiki/images/6/67/6zgi-cavities.jvxl";
- step back and continue counting from 'Six'
</script>
||see section XIV.B.3 and XIV.B.7 - ''"When a marking violation is called, play does not stop. The violation must be corrected before the marker can resume the stall count with the number last uttered before the call minus one".''
<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]])


{ 
|type="{}"}
Name a famous Greek philosopher.
{ Aristotle|Plato }


{Question
*3 <jmol>
|type="[]"}
<jmolButton>
+ First correct answer.
<script>
|| This optional feedback was added to the choice above. No optional feedback was supplied for the choices below.
load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
- First incorrect answer.
</script>
+ Second correct answer.
<text>Load .PNGJ file</text>
- Second incorrect answer.
</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])




{ Which of these structures are Complexed with Tacrine? }
*4 <jmol>
+ [[Image:1zgb.png|100px|1zgb]]
<jmolLink>
- [[Image:1stp.png|100px]]
<script>
+ [[Image:1acj.png|100px]]
load "http://proteopedia.org/wiki/images/c/c6/6zgi-cavities.pngj";
+ [[Image:1zgc.png|100px]]
</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.


</quiz>
 
*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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