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User:Karsten Theis/Favorite 3D scenes

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< User:Karsten Theis(Difference between revisions)
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(New page: ==Consideration for a BioMolViz category tag== This is a collection of scenes I like. They show what is possible in Jmol, and they illustrate the power of biomolecular visualization partic...)
Current revision (01:18, 11 October 2020) (edit) (undo)
(→Consideration for a BioMolViz category tag)
 
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<scene name='82/824000/Contacts/4'>3D scene</scene> and [http://proteopedia.org/w/Cellulose#multiple%20layers%20stack page context]
<scene name='82/824000/Contacts/4'>3D scene</scene> and [http://proteopedia.org/w/Cellulose#multiple%20layers%20stack page context]
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This shows a model of cellulose (based on structural data, but not a crystal structure). The scene shows interactions of one glucose unit (hydrogen bonding within the layer, hydrophobic interactions between layers) explaining why cellulose is water insoluble and hard to hydrolyze. The scene makes use of slabbing so we can see the context while not obscuring the focal point. It uses the Jmol "contact" command to show both hydrogen bonds and hydrophobic contacts.
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This shows a model of cellulose (based on structural data, but not a crystal structure). The scene shows interactions of one glucose unit (hydrogen bonding within the layer, hydrophobic interactions between layers) explaining why cellulose is water insoluble and hard to hydrolyze. The scene makes use of slabbing so we can see the context while not obscuring the focal point. It uses the Jmol "contact" command to show both hydrogen bonds and hydrophobic contacts. You can turn off the <jmol>
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<jmolCheckbox>
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<scriptWhenChecked>contact on</scriptWhenChecked>
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<scriptWhenUnchecked>contact off</scriptWhenUnchecked>
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<checked>true</checked>
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<text>contacts</text>
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</jmolCheckbox>
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</jmol> to see the hydrogen bond lengths.
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===Conservation of residues on the surface of the helicase UvrB===
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<scene name='78/780454/Conservation/1'>3D scene</scene> and [http://proteopedia.org/w/User:Karsten_Theis/overall_views#oriented%20as%202D%20figure page context]
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The original figures of the primary citation used a trick to see better into the active site between domains 1a and 3: domain 3 was rotated outwards to open up the view. You can use the control below to achieve a similar effect:
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<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select 415-600;rotateselected {558.CA}{580.CA} 120 </scriptWhenChecked>
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<scriptWhenUnchecked>select 415-600;rotateselected {558.CA}{580.CA} -120</scriptWhenUnchecked>
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<checked>false</checked>
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<text>butterflied molecule</text>
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</jmolCheckbox>
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</jmol>
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<jmol>
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<jmolRadioGroup>
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<item>
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<script>hide (hidden and not protein) or (protein and not (1-90, 117-156, 245-414))</script>
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<text>domain 1(a+b)</text>
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</item>
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<item>
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<script>hide (hidden and not protein) or (protein and not (157-244))</script>
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<text>domain 2</text>
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</item>
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<item>
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<script>hide (hidden and not protein) or (protein and not (415-600))</script>
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<text>domain 3</text>
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</item>
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<item>
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<script>hide (hidden and not protein) or (protein and not 91-116)</script>
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<text>hairpin</text>
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</item>
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<item>
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<script>display displayed or protein</script>
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<text>all domains</text>
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<checked>true</checked>
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</item>
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</jmolRadioGroup>
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</jmol>
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===Hydrogen bonds in lysozyme===
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<scene name='37/376372/Hbonds/1'>3D scene</scene> and [http://proteopedia.org/w/Lysozyme#Hydrogen%20Bonding page context] (click on green links to see scene).
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This scene shows the hydrogen bonding in a helix, with the entire lysozyme molecule in the background. Slabbing and fading are used to be able to see the detail. You can recenter on any atom to explore other parts of the molecule after checking the box below.
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<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>set picking center</scriptWhenChecked>
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<scriptWhenUnchecked>set picking identify</scriptWhenUnchecked>
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<checked>false</checked>
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<text>mouse click centers molecule</text>
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</jmolCheckbox>
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</jmol>
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===Active site of alpha-galactosidase mutant===
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<jmol><jmolLink><script>script "/scripts/78/786673/Fig2a_galnac_complex/2.spt"; ppdiaCaptionCmd = "changeCaption('Crystal structure of GAL(SA) bound to N-acetyl galactosamine. GAL(SA) active site residues are shown in yellow and the product, N-acetyl galactosamine, is in gray when shown. The blue mesh around the sugar represents its (2Fo-Fc) electron density.','white','black');";javascript @ppdiaCaptionCmd;model 2; model 2; hide a2g:A</script><text>3D scene</text></jmolLink></jmol> and [https://proteopedia.org/w/Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities#galactose page context]
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Alpha-galactosidase usually bind to galactose, but this mutant also binds to N-acetyl galactosamine. Show the model of the <jmol>
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<jmolCheckbox>
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<scriptWhenChecked>hide none</scriptWhenChecked>
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<scriptWhenUnchecked>hide a2g:A</scriptWhenUnchecked>
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<checked>false</checked>
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<text>sugar</text>
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</jmolCheckbox>
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</jmol> in the active site.
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http://proteopedia.org/wiki/index.php/Cellulose#multiple%20layers%20stack
 
</StructureSection>
</StructureSection>

Current revision

Consideration for a BioMolViz category tag

This is a collection of scenes I like. They show what is possible in Jmol, and they illustrate the power of biomolecular visualization particularly well. Each scene comes with one green link to show the scene on this page, and a regular link to see it in the context of the page where I found it.

Drag the structure with the mouse to rotate

Place holder

and page context

References

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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