Jmol/Surfaces
From Proteopedia
(Difference between revisions)
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=== Coloring surfaces === | === Coloring surfaces === | ||
| - | You cam color surface by <scene name='87/871286/Rnase_a/ | + | You cam color surface by <scene name='87/871286/Rnase_a/9'>hydrophobic/hydrophilic</scene>, <scene name='87/871286/Rnase_a/5'>conservation</scene>, <scene name='87/871286/Rnase_a/7'>temperature factor</scene>, or any other atom property (such as the <scene name='87/871286/Rnase_a/3'>x-coordinate</scene>). |
</StructureSection> | </StructureSection> | ||
Revision as of 01:46, 27 December 2020
Showing surfaces 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? This page shows some examples, and editing this page shows the jmol commands used.
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