Jmol/Surfaces: Difference between revisions
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==Showing surfaces in Jmol== | ==Showing surfaces in Jmol== | ||
Proteins are often shown as cartoon to illustrate their fold. However, the small molecules that interact with proteins do | Proteins are often shown as cartoon to illustrate their fold. However, the small molecules that interact with proteins do not "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. Showing 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. | But how can we using Jmol? This page shows some examples, and editing this page shows the jmol commands used. | ||
<StructureSection load='' size='340' side='right' caption='' scene='87/871286/Rnase_a/2'> | <StructureSection load='' size='340' side='right' caption='' scene='87/871286/Rnase_a/2'> | ||
== Examples and Jmol commands to modify them == | == Examples and Jmol commands to modify them == | ||
=== | === Plain 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". | 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". | ||
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=== Slabbing surfaces === | === Slabbing surfaces === | ||
The 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> | <jmol> | ||
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<scriptWhenUnChecked>isosurface ID "1" transparent 0 | <scriptWhenUnChecked>isosurface ID "1" transparent 0 | ||
</scriptWhenUnChecked> | </scriptWhenUnChecked> | ||
<scriptWhenchecked>isosurface ID "1" transparent | <scriptWhenchecked>isosurface ID "1" transparent | ||
</scriptWhenchecked> | </scriptWhenchecked> | ||
<checked>true</checked> | <checked>true</checked> | ||
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=== Coloring surfaces === | === Coloring surfaces === | ||
You | You can color the surface by <scene name='87/871286/Rnase_a/8'>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> | ||
Latest revision as of 19:10, 21 December 2023
Showing surfaces in JmolShowing surfaces in Jmol
Proteins are often shown as cartoon to illustrate their fold. However, the small molecules that interact with proteins do not "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. Showing 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.
Examples and Jmol commands to modify themPlain vanilla overall surfaceHere is the surface of . 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 also have a choice of lighting modes (front and fully lit look the same if you choose frontonly):
If the image gets too busy, you can hide the cartoon:
Slabbing surfacesThe 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:
You can try these for a solid or a transparent surface:
Coloring surfacesYou can color the surface by , , , or any other atom property (such as the ). |
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