User:Karsten Theis/Sandbox 4

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Current revision (03:29, 6 August 2022) (edit) (undo)
 
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<StructureSection size='350' side='right' scene='88/886517/Test/1'>
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<StructureSection load='' size='350' frame='true' height='500' side='right' caption='' scene='91/919062/Blue_adamantane/1'>
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==Receptor ligand interaction==
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<scene name='88/886517/Test/1'>Initial scene reload</scene>
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<scene name='88/886517/Overall/3'>First scene</scene>
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This green link is a &lt;jmolLink&gt; that directly loads an uploaded script (a modified state script).
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<scene name='88/886517/Pocket/1'>Second scene
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When the script is dropped into Jmol.jar 14.31.8 (current main version in Proteopedia) it works (3 unrecognized but harmless set commands) even though the script was written from JSmol 14.32.64.
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</scene>
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When this green link is clicked, an error is reported in the JSmol Javascript Console. I do not understand what causes this error.
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==Adamantane==
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<jmol>
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<scene name='91/919062/Blue_adamantane_2/1'>not working
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<jmolLink>
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</scene>91/919062/Blue_adamantane_2/1 atoms are loaded, not displayed
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<script>
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load /wiki/images/2/21/1sva-half-capsid-distance.spt
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</script>
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<text>1sva half capsid colored by distance</text>
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</jmolLink>
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</jmol>
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<jmol>
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<scene name='88/886517/Blue_adamantane_2/1'>working</scene>: 88/886517/Blue_adamantane_2/1
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<jmolLink>
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<script>script /scripts/37/376372/Overall/3.spt; hide water; set zshade off; spin off;</script>
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<text>lyso</text>
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</jmolLink>
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</jmol>
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The load command in the script loads a "frozen" uploaded PDB file [[Image:1sva-revdat2009.pdb.gz]].
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<scene name='91/919062/Blue_adamantane/1'>does not load atoms, but displays them</scene>: 91/919062/Blue_adamantane/1
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When that command is run in the Proteopedia JSmol console, the virus capsid loads correctly.
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Here is an extremely simplified script:
 
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<small><pre>
 
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set autobond false;
 
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load "https://proteopedia.org/wiki/images/2/29/1sva-revdat2009.pdb.gz" FILTER "*.CA;biomolecule 1;bmchains;/=5";
 
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spacefill 4.0;
 
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color chain;
 
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</pre></small>
 
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When the above 4 commands are copied and pasted into the JSmol console and run, they work.
 
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However, when a .spt file containing those commands is dropped into JSmol, the capsid loads, but the spacefill and color commands do not execute. I don't know why they fail.
 
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</StructureSection>
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<!--
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==all about adamantane==
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OBSOLETE - FAILS TO LOAD: <scene name='85/859610/Half_capsid_spt_minus_props/1'>Half Capsid by Script</scene>: Scene created by dropping half-capsid-nodata.spt into JSmol after first loading 1sva. State script load command modified to
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testing here
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load "" FILTER "*.CA;biomolecule 1;bmchains;/=5"; and function _setDataState() made an empty function {} (previously it assigned distances from center to each of ~25,000 alpha carbons).
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-->
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</StructureSection>
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<StructureSection load='' size='350' side='right' caption='Insert caption here' scene='91/919062/Blue_adamantane/1'>
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<Structure load='https://proteopedia.org/wiki/images/8/80/Initial_scene.spt' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
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this is a test
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An example of using unaltered PNGJ files, <jmol><jmolLink>
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<script>
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load /wiki/images/a/a0/Histamine_-_Copy.png
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</script>
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<text>click here to see</text>
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</jmolLink></jmol> how it looks.
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==Your Heading Here (maybe something like 'Structure')==
 
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<StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''>
 
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Anything in this section will appear adjacent to the 3D structure and will be scrollable.
 
</StructureSection>
</StructureSection>
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== References ==
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<references/>

Current revision

Drag the structure with the mouse to rotate

all about adamantane

testing here

Insert caption here

Drag the structure with the mouse to rotate



References

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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