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User:Karsten Theis/Favorite 3D scenes
From Proteopedia
< User:Karsten Theis(Difference between revisions)
(→Consideration for a BioMolViz category tag) |
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===Conservation of residues on the surface of the helicase UvrB=== | ===Conservation of residues on the surface of the helicase UvrB=== | ||
| - | <scene name='78/780454/Conservation/1'>3D scene</scene> and [http://proteopedia.org/w/User:Karsten_Theis/overall_views#oriented%20as%202D%20figure] | + | <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] |
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: | 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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<scriptWhenUnchecked>set picking identify</scriptWhenUnchecked> | <scriptWhenUnchecked>set picking identify</scriptWhenUnchecked> | ||
<checked>false</checked> | <checked>false</checked> | ||
| - | <text>click | + | <text>mouse click centers molecule</text> |
</jmolCheckbox> | </jmolCheckbox> | ||
</jmol> | </jmol> | ||
| + | |||
| + | ===Active site of alpha-galactosidase mutant=== | ||
| + | <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] | ||
| + | |||
| + | Alpha-galactosidase usually bind to galactose, but this mutant also binds to N-acetyl galactosamine. Show the model of the <jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>hide none</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>hide a2g:A</scriptWhenUnchecked> | ||
| + | <checked>false</checked> | ||
| + | <text>sugar</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol> in the active site. | ||
</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.
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Place holder
and page context
