Jmol/Surfaces
From Proteopedia
(Difference between revisions)
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== Examples and Jmol commands to modify them == | == Examples and Jmol commands to modify them == | ||
| - | Here is the surface of <scene name='87/871286/Rnase_a/2'>RNAse</scene>. It is shown with the default parameters "frontlit" and "frontonly". | + | === Plan vanilla overall surface === |
| + | |||
| + | Here is the surface of <scene name='87/871286/Rnase_a/2'>RNAse</scene>. It was created with the [[Scene Authoring Tools]], and 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: | You can decide whether to show or hide the surface occluded by other parts of the surface: | ||
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</jmolCheckbox> | </jmolCheckbox> | ||
</jmol> | </jmol> | ||
| + | |||
| + | === Slabbing surfaces === | ||
| + | |||
| + | Surface can get busy easily. One way to make the scene easier to understand is to cut away the parts of the surface that are less important for the point you are trying to get across. Here are two examples of slabbing: | ||
| + | |||
| + | <jmol> | ||
| + | <jmolRadioGroup> | ||
| + | <item> | ||
| + | <script>isosurface ID "1" slab none</script> | ||
| + | <text>intact</text> | ||
| + | <checked>true</checked> | ||
| + | </item> | ||
| + | <item> | ||
| + | <script>isosurface ID "1" slab none; isosurface ID "1" slab within 12.0 {@44} | ||
| + | </script> | ||
| + | <text>clipped by 12 A sphere</text> | ||
| + | <checked>false</checked> | ||
| + | </item> | ||
| + | <item> | ||
| + | <script>isosurface ID "1" slab none; isosurface ID "1" slab -(atomno=343) (atomno=858) (atomno=587) | ||
| + | </script> | ||
| + | <text>on one side of plane</text> | ||
| + | <checked>false</checked> | ||
| + | </item> | ||
| + | </jmolRadioGroup> | ||
| + | </jmol> | ||
| + | |||
| + | You can try these for a solid or a transparent surface: | ||
| + | |||
| + | <jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenUnChecked>isosurface ID "1" transparent 0 | ||
| + | </scriptWhenUnChecked> | ||
| + | <scriptWhenchecked>isosurface ID "1" transparent 60 | ||
| + | </scriptWhenchecked> | ||
| + | <checked>true</checked> | ||
| + | <text>transparent</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol> | ||
| + | |||
</StructureSection> | </StructureSection> | ||
Revision as of 14:20, 26 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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