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User:Karsten Theis/BioMolViz

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< User:Karsten Theis(Difference between revisions)
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==Visualization framework==
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==Visualization framework ([https://biomolviz.org/ BIOMOLVIZ])==
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<StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''>
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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'>
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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='85/857774/2/1'>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/5'>AR</scene> (<jmol>
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<jmolCheckbox>
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<scriptWhenUnChecked>animation off;
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</scriptWhenUnChecked>
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<scriptWhenchecked>animation mode loop 0.0 0.0; animation FPS 1; animation on
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</scriptWhenchecked>
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<checked>true</checked>
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<text>animation</text>
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</jmolCheckbox>
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</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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<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>
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AR: <scene name='85/857774/Overall/2'>Lysozyme</scene> (and <scene name='85/857774/Overall/1'>alternate view</scene>)
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<scene name='85/857774/Lm/1'>LM</scene>: <scene name='85/857774/Heme/2'>Myoglobin</scene>
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CA: Lac repressor???
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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
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</scene>
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HG: <scene name='85/857774/Heme/2'>Myoglobin</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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MA: <scene name='85/857774/Aquaporin/1'>membrane protein</scene>
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<scene name='85/857774/Md/1'>MD</scene> (<jmol>
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<jmolCheckbox>
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<scriptWhenUnChecked>animation off; delay 1; model 1
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</scriptWhenUnChecked>
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<scriptWhenchecked>animation mode loop; animation on
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</scriptWhenchecked>
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<checked>false</checked>
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<text>animation</text>
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</jmolCheckbox>
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</jmol>): <scene name='User:Wayne_Decatur/1cts_to_2cts_(citrate_synthase)_morph_methods/Camorph/5'>citrate synthase</scene>
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MD: <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> [[User:Karsten Theis/Molecular Interactions|Theme page]]
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MI: <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/Sa/1'>SA</scene> (<jmol>
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<jmolButton>
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<script>rotate Y 180 50</script>
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<text>rotate by 180</text>
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</jmolButton>
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</jmol>): <jmol>
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<jmolLink>
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<script> script /scripts/85/857774/Spider_toxin/1.spt; spin z; spin on;
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</script>
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<text>Spider toxin</text>
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</jmolLink>
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</jmol>, <scene name='85/857774/Ankyrin/1'>ankyrin repeats</scene>
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MR: <scene name='85/857774/Succinylcoa/1'>SuccinylCoA</scene>, <scene name='85/857774/Nad/1'>NAD
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SF: <scene name='85/857774/Chymotrypsin/3'>active site of chymotrypsin
</scene>
</scene>
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SA: dsDNA, <scene name='85/857774/Ankyrin/1'>ankyrin repeats</scene>
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<scene name='85/857774/Sk/1'>SK</scene>: <scene name='85/857774/Calmodulin/4'>Calmodulin</scene> https://pubmed.ncbi.nlm.nih.gov/25554228/
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SF: active site
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<scene name='85/857774/Tc/1'>TC</scene>: <scene name='85/857774/Zinc_finger/1'>triple zinc finger</scene>
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SK: B-factor, NMR worm, multiple conformation, wrong structures
 
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TC: <scene name='85/857774/Zinc_finger/1'>triple zinc finger</scene>
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</StructureSection>
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==Resources for teaching==
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</StructureSection>
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by Eric Martz:
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* Hemoglobin tutorial, http://hemoglobin.molviz.org
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* Atlas of Macromolecules, http://atlas.molviz.org
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* DNA tutorial, http://dna.molviz.org

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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