Jmol/Surfaces

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 them

Plain vanilla overall surface

Here 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 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:

You can try these for a solid or a transparent surface:

Coloring surfaces

You can color the surface by , , , or any other atom property (such as the ).

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis, Eric Martz