User:Karsten Theis/Sandbox 4

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<scene name='88/886517/Cobalamin/1'>Cobalamin example</scene>
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<StructureSection size='350' side='right' 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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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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==Beta sheet saved with different quality settings==
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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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<StructureSection load='1lys' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''>
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<scene name='88/886517/Hiq/1'>High quality scene</scene>
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<jmol>
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<jmolLink>
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<script>
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load wiki/images/2/21/1sva-half-capsid-distance_shorter.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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<scene name='88/886517/Loq/1'>Low quality scene</scene>
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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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When that command is run in the Proteopedia JSmol console, the virus capsid loads correctly.
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<scene name='88/886517/Hiq/2'>High quality scene with fancy cartoon</scene>
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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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<!--
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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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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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-->
</StructureSection>
</StructureSection>

Revision as of 00:47, 25 July 2022

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Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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