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User:Karsten Theis/BioMolViz

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< User:Karsten Theis(Difference between revisions)
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Current revision (19:51, 22 October 2020) (edit) (undo)
 
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<StructureSection load='' size='450' side='right' caption='One of the 12 overarching themes is MI, molecular interactions, illustrated here by the lambda repressor bound to the major grooves of double-stranded DNA' scene='85/857774/Molecularinteraction/1'>
<StructureSection load='' size='450' side='right' caption='One of the 12 overarching themes is MI, molecular interactions, illustrated here by the lambda repressor bound to the major grooves of double-stranded DNA' scene='85/857774/Molecularinteraction/1'>
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The 3D scenes are mostly from Proteopedia articles or sandboxes, sometimes imported as is and sometimes adapted.
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For each category, the first scene is a Jmol equivalent of the BioMolViz example, and the following scenes are mostly from Proteopedia articles or sandboxes, sometimes imported as is and sometimes adapted, that illustrate the same theme.
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AG: <scene name='85/857774/Glucose/1'>Glucose</scene>
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<scene name='85/857774/Ag/1'>AG</scene>: <scene name='85/857774/Glucose/1'>Glucose</scene>
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asd
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<scene name='85/857774/Ar/4'>AR</scene> (<jmol>
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<scene name='85/857774/Ar/5'>AR</scene> (<jmol>
<jmolCheckbox>
<jmolCheckbox>
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<scriptWhenUnChecked>animation off; delay 1; model 0
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<scriptWhenUnChecked>animation off;
</scriptWhenUnChecked>
</scriptWhenUnChecked>
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<scriptWhenchecked>animation mode loop; animation on
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<scriptWhenchecked>animation mode loop 0.0 0.0; animation FPS 1; animation on
</scriptWhenchecked>
</scriptWhenchecked>
<checked>true</checked>
<checked>true</checked>
Line 17: Line 17:
</jmolCheckbox>
</jmolCheckbox>
</jmol>): <scene name='85/857774/Overall/2'>Lysozyme</scene> (and <scene name='85/857774/Overall/3'>alternate view</scene>)
</jmol>): <scene name='85/857774/Overall/2'>Lysozyme</scene> (and <scene name='85/857774/Overall/3'>alternate view</scene>)
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asdf
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<scene name='85/857774/Ca/1'>CA</scene> (<jmol>
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<jmolLink>
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<scene name='85/857774/Ca/1'>CA</scene>: <scene name='85/857774/Aquaporin/1'>membrane protein</scene>
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<script>select protein and *:A; isosurface ignore (not selected) SASURFACE 1.2 MAP property color translucent 0.6
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</script>
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<text>with surface</text>
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</jmolLink>
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</jmol>): <scene name='85/857774/Aquaporin/1'>membrane protein</scene>
<scene name='85/857774/Lm/1'>LM</scene>: <scene name='85/857774/Heme/2'>Myoglobin</scene>
<scene name='85/857774/Lm/1'>LM</scene>: <scene name='85/857774/Heme/2'>Myoglobin</scene>
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<scene name='85/857774/Ma/1'>MA</scene>: <scene name='85/857774/Lipid_bilayer/2'>lipid bilayer</scene>, <scene name='85/857774/Virus_capsid/1'>virus capsid
<scene name='85/857774/Ma/1'>MA</scene>: <scene name='85/857774/Lipid_bilayer/2'>lipid bilayer</scene>, <scene name='85/857774/Virus_capsid/1'>virus capsid
</scene>
</scene>
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<scene name='85/857774/Mb/1'>MB</scene>: <scene name='85/857774/Succinylcoa/1'>SuccinylCoA</scene>, <scene name='85/857774/Nad/1'>NAD
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</scene>
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<scene name='85/857774/Md/1'>MD</scene> (<jmol>
<scene name='85/857774/Md/1'>MD</scene> (<jmol>
<jmolCheckbox>
<jmolCheckbox>
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<scriptWhenUnChecked>animation off; delay 1; model 0
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<scriptWhenUnChecked>animation off; delay 1; model 1
</scriptWhenUnChecked>
</scriptWhenUnChecked>
<scriptWhenchecked>animation mode loop; animation on
<scriptWhenchecked>animation mode loop; animation on
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</jmol>): <scene name='User:Wayne_Decatur/1cts_to_2cts_(citrate_synthase)_morph_methods/Camorph/5'>citrate synthase</scene>
</jmol>): <scene name='User:Wayne_Decatur/1cts_to_2cts_(citrate_synthase)_morph_methods/Camorph/5'>citrate synthase</scene>
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<scene name='85/857774/Molecularinteraction/1'>MI</scene>: <scene name='85/857774/Molecularinteraction/1'>major groove interaction</scene>, <scene name='85/857774/Dna/1'>base stacking</scene>, <scene name='85/857774/Dna/2'>G-protein</scene>
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<scene name='85/857774/Molecularinteraction/1'>MI</scene>: <scene name='85/857774/Molecularinteraction/1'>major groove interaction</scene>, <scene name='85/857774/Dna/1'>base stacking</scene>, <scene name='85/857774/Dna/2'>G-protein</scene> [[User:Karsten Theis/Molecular Interactions|Theme page]]
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<scene name='85/857774/Mb/1'>MB</scene>: <scene name='85/857774/Succinylcoa/1'>SuccinylCoA</scene>, <scene name='85/857774/Nad/1'>NAD
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</scene>
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<scene name='85/857774/Sa/1'>SA</scene> (<jmol>
<scene name='85/857774/Sa/1'>SA</scene> (<jmol>

Current revision

Visualization framework (BIOMOLVIZ)

One of the 12 overarching themes is MI, molecular interactions, illustrated here by the lambda repressor bound to the major grooves of double-stranded DNA

Drag the structure with the mouse to rotate

Resources for teaching

by Eric Martz:

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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