User:Eric Martz/Sandbox 4: Difference between revisions
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</jmolLink> | </jmolLink> | ||
</jmol> | </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== | ==JSmol Version== | ||
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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 | ||
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<scene name='85/859610/1ijw/2'>Scene of 1ijwd with red words in caption</scene>. | <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> | <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> | </StructureSection> | ||