User:Eric Martz/Sandbox 4: Difference between revisions
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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. | 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. | 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> | |||
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==Saved | ==Scenes Saved from the SAT== | ||
FAILS BECAUSE CAPTION CONTAINS SEMICOLON: | 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 | <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 | ||
Latest revision as of 00:34, 27 July 2022
Running State ScriptThis 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:
JSmol VersionThe 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 SATFAILS 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.
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