User:Eric Martz/Sandbox 4: Difference between revisions

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Eric Martz (talk | contribs)
ConfirmAccount, Editor, Tester, Administrators
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Eric Martz (talk | contribs)
ConfirmAccount, Editor, Tester, Administrators
27,351 edits
No edit summary
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This green link is a <jmolLink> that directly loads an uploaded script (a modified state script).
This green link is a <jmolLink> that directly loads an uploaded script (a modified state script).
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.
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.
When this green link is clicked, an error is reported in the JSmol Javascript Console. I do not understand what causes this error.


<jmol>
<jmol>
Line 10: Line 8:
<script>
<script>
script /wiki/images/2/21/1sva-half-capsid-distance.spt;
script /wiki/images/2/21/1sva-half-capsid-distance.spt;
rotate y 90;
spin on;
spin on;
</script>
</script>
Line 17: Line 16:


The load command in the script loads a "frozen" uploaded PDB file [[Image:1sva-revdat2009.pdb.gz]].
The load command in the script loads a "frozen" uploaded PDB file [[Image:1sva-revdat2009.pdb.gz]].
When that command is run in the Proteopedia JSmol console, the virus capsid loads correctly.


Here is an extremely simplified script:
Here is an extremely simplified script:
Line 29: Line 27:


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.  
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.  
<!--
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
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).
-->


</StructureSection>
</StructureSection>

Revision as of 21:28, 25 July 2022


This green link is a <jmolLink> that directly loads an uploaded script (a modified state script). 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.

The load command in the script loads a "frozen" uploaded PDB file File:1sva-revdat2009.pdb.gz.

Here is an extremely simplified script: 

set autobond false;
load "https://proteopedia.org/wiki/images/2/29/1sva-revdat2009.pdb.gz" FILTER "*.CA;biomolecule 1;bmchains;/=5";
spacefill 4.0;
color chain;

When the above 4 commands are copied and pasted into the JSmol console and run, they work.

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.


Drag the structure with the mouse to rotate
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