User:Eric Martz/Sandbox 4: Difference between revisions

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ConfirmAccount, Editor, Tester, Administrators
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==Your Heading Here (maybe something like 'Structure')==
<StructureSection size='350' side='right' scene=''>
<StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''>


Anything in this section will appear adjacent to the 3D structure and will be scrollable.
==Running State Script==
This green link is a &lt;jmolLink&gt; 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.


</StructureSection>Test again
<jmol>
<jmolLink>
<script>
script /wiki/images/e/ee/Echo-loading.spt;
script /wiki/images/2/21/1sva-half-capsid-distance.spt;
rotate y 90;
spin on;
</script>
<text>1sva half capsid colored by distance</text>
</jmolLink>
</jmol>


Here is another test
The load command in the script loads a "frozen" uploaded PDB file [[Image:1sva-revdat2009.pdb.gz]].
More added now
 
<jmol>
<jmolLink>
<script>
script /wiki/images/e/ee/Echo-loading.spt;
script /wiki/images/7/75/1sva-half-capsid-distance3.spt;
spin on;
</script>
<text>1sva half capsid colored by distance WITH CAPTION</text>
</jmolLink>
</jmol>
Changes to the state script:
# load command should load frozen uploaded .pdb.gz file, for example [https://proteopedia.org/wiki/index.php/Image:1sva-revdat2009.pdb.gz Image:1sva-revdat2009.pdb.gz].
# Optional: delete the DATA block in _setDataState()
# Caption in _setState(), see [https://proteopedia.org/wiki/images/7/75/1sva-half-capsid-distance3.spt 1sva-half-capsid-distance3.spt].
 
==JSmol Version==
 
The state script was generated by JSmol 14.32.64.
 
The load command in the script includes '''FILTER "*.CA;biomolecule 1;bmchains;/=5"'''.
 
Filters "*.CA;biomolecule 1;" and "/=5" work in JSmol 14.31.8. Filter "bmchains" is ignored, so all copies of chain "1" are also named "1". This does not matter.
 
As long as the atomindex values generated in 14.31.8 match those generated in 14.32.64, the script works. The script does not work if ligand HETATM are present in the AU because new JSmol includes them in BU1 while old JSmol does not. Therefore the scene must be generated in FirstGlance from an AU PDB file from which ligand HETATM have been deleted, and that PDB file must be uploaded for use by Proteopedia, e.g. 6mx4-nohet.pdb.gz.
 
TEST OF NOHET SOLUTION
 
<jmol>
<jmolLink>
<script>
script /wiki/images/e/ee/Echo-loading.spt;
script /wiki/images/5/56/6mx4-capsid-nohet-distance.spt;
spin on;
</script>
<text>6MX4 capsid colored by distance</text>
</jmolLink>
</jmol>
 
 
<!--
Here is an extremely simplified script:
<small><pre>
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;
</pre></small>
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.
-->
 
==Scenes Saved from the SAT==
FAILS BECAUSE CAPTION CONTAINS SEMICOLON:
<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).
 
 
<scene name='85/859610/1ijw/1'>Scene of 1ijw with test caption</scene>.
 
Scene 85/859610/1ijw/1 is wiki/scripts/85/859610/1ijw/1.spt
 
Within function _setState():
ppdiaCaptionCmd = "changeCaption('This is test caption XXX.','white','black');";
  javascript @ppdiaCaptionCmd;
 
<scene name='85/859610/1ijw/2'>Scene of 1ijwd with red words in caption</scene>.
 
<scene name='85/859610/1sva_half_capsid/1'>Half Capsid as Scene</scene> Echos 1SVA but no atoms appear. Loads only 15K atoms instead of 24K.
 
 
</StructureSection>

Latest revision as of 00:34, 27 July 2022


Running 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.

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

Changes to the state script:

  1. load command should load frozen uploaded .pdb.gz file, for example Image:1sva-revdat2009.pdb.gz.
  2. Optional: delete the DATA block in _setDataState()
  3. Caption in _setState(), see 1sva-half-capsid-distance3.spt.

JSmol Version

The state script was generated by JSmol 14.32.64.

The load command in the script includes FILTER "*.CA;biomolecule 1;bmchains;/=5".

Filters "*.CA;biomolecule 1;" and "/=5" work in JSmol 14.31.8. Filter "bmchains" is ignored, so all copies of chain "1" are also named "1". This does not matter.

As long as the atomindex values generated in 14.31.8 match those generated in 14.32.64, the script works. The script does not work if ligand HETATM are present in the AU because new JSmol includes them in BU1 while old JSmol does not. Therefore the scene must be generated in FirstGlance from an AU PDB file from which ligand HETATM have been deleted, and that PDB file must be uploaded for use by Proteopedia, e.g. 6mx4-nohet.pdb.gz.

TEST OF NOHET SOLUTION


Scenes Saved from the SAT

FAILS BECAUSE CAPTION CONTAINS SEMICOLON:

: 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).


.

Scene 85/859610/1ijw/1 is wiki/scripts/85/859610/1ijw/1.spt

Within function _setState(): 

ppdiaCaptionCmd = "changeCaption('This is test caption XXX.','white','black');";
 javascript @ppdiaCaptionCmd;

.

Echos 1SVA but no atoms appear. Loads only 15K atoms instead of 24K.


Drag the structure with the mouse to rotate
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