Jmol/Cavities pockets and tunnels

Jmol can find and display cavities, pockets, and tunnels as isosurfaces.

Definitions

• Cavities are open spaces within a macromolecule, large enough to contain a water molecule, or much larger. The term "cavity" is sometimes used to include pockets and tunnels, but in a stricter usage, it means a space with no openings ("mouths") to the outside surface of the molecule.
• Pockets are depressions (concavities) in the surface, or open spaces within the molecule having a single connection ("mouth") to the outside surface of the molecule.
• Tunnels are open spaces within the molecule that have two or more connections ("mouths") to the outside surface of the molecule.

Speed of Rendering

If you use the isosurface commands below, do so in the Jmol Java application, not in JSmol in Proteopedia. Depending on the size of the molecule, isosurface commands take about a minute to complete in the Java application, which is many times faster than JSmol. You would have to wait many minutes for completion in JSmol.

Saving Pre-Calculated Isosurfaces

In order to speed up the green links below, the isosurfaces were pre-calculated in the Jmol Java application and then saved into .jvxl (Jmol voxel) files (and uploaded to Proteopedia). These can be quickly loaded without re-computing the isosurfaces. After a cavity isosurface command has completed, the calculated surfaces can be saved with the Jmol command write filename.jvxl. Later, you can load the saved isosurfaces without re-calculating them using the command isosurface filename.jvxl.