Jmol/Surfaces
From Proteopedia
(Difference between revisions)
| Line 8: | Line 8: | ||
Here is the surface of <scene name='87/871286/Rnase_a/1'>RNAse</scene>. It is shown with the default parameters "frontlit" and "frontonly". | Here is the surface of <scene name='87/871286/Rnase_a/1'>RNAse</scene>. It is shown with the default parameters "frontlit" and "frontonly". | ||
| + | |||
| + | You can decide whether to show or hide the surface occluded by other parts of the surface: | ||
| + | |||
| + | <jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenUnChecked>isosurface ID "1" notfrontonly | ||
| + | </scriptWhenUnChecked> | ||
| + | <scriptWhenchecked>isosurface ID "1" frontonly | ||
| + | </scriptWhenchecked> | ||
| + | <checked>true</checked> | ||
| + | <text>frontonly</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol> | ||
| + | |||
| + | You also have a choice of lighting modes (front and fully lit look the same if you choose frontonly): | ||
<jmol> | <jmol> | ||
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<script>isosurface ID "1" backlit</script> | <script>isosurface ID "1" backlit</script> | ||
<text>Backlit</text> | <text>Backlit</text> | ||
| + | <checked>false</checked> | ||
</item> | </item> | ||
<item> | <item> | ||
<script>isosurface ID "1" fullylit</script> | <script>isosurface ID "1" fullylit</script> | ||
<text>Fullylit</text> | <text>Fullylit</text> | ||
| + | <checked>false</checked> | ||
</item> | </item> | ||
</jmolRadioGroup> | </jmolRadioGroup> | ||
</jmol> | </jmol> | ||
| - | You can decide whether to show or hide the surface occluded by other parts of the surface: | ||
| - | <jmol> | ||
| - | <jmolCheckbox> | ||
| - | <scriptWhenUnChecked>isosurface ID "1" notfrontonly | ||
| - | </scriptWhenUnChecked> | ||
| - | <scriptWhenchecked>isosurface ID "1" frontonly | ||
| - | </scriptWhenchecked> | ||
| - | <checked>true</checked> | ||
| - | <text>frontonly</text> | ||
| - | </jmolCheckbox> | ||
| - | </jmol> | ||
</StructureSection> | </StructureSection> | ||
Revision as of 21:55, 25 December 2020
Showing surface in Jmol
Proteins are often shown as cartoon to illustrate their fold. However, the small molecules that interact with proteins do no "see" the fold, they interact with the surface of the protein. How they interact depends on the shape of the surface, the distribution of charges, functional groups and hydrophobic patches. The conservation of surface residues among related proteins from different organisms gives clues about functionally important sites on the surface. Show a protein in a surface representation with a color scheme that highlights features is an excellent way to communicate structural information.
But how can we using Jmol?
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