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, cavity 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
Generating Cavity Isosurfaces
The Jmol commands for generating cavity isosurfaces will be found in the Jmol/JSmol Interacive Scripting Documention under isosurfaces: molecular/solvent surfaces. Near the bottom of that very long section, important commands for after the cavity isosurfaces are calculated:
- isosurface area set (integer) reports the surface area of one isosurface in Å2.
- isosurface delete to clear existing isosurfaces before a new calculation.
- isosurface set (integer) displays just one of the isosurfaces.
- isosurface set 0 displays all of the isosurfaces.
- isosurface volume set (integer) reports the volume of one isosurface in Å3.
Small Cavities Example
The coronavirus (SARS-CoV-2 and others) spike protein, in its closed conformation, has
. The smaller one is a potential drug target: here is an explanation. These cavities were rendered with the Jmol command
- isosurface minset 100 interior cavity 3.0 10.0
Below we will show the importance of each part of this command.
The simplest command is
- isosurface cavity
This produces pockets, tunnels, and cavities of all sizes. There are 426 separate surfaces. The largest is a convoluted tunnel with many mouths, volume 60,197 Å3. The volume of the smallest is 3.2 Å3; depending on its shape, this one may be just large enough to accomodate a single water molecule.
First, we will limit the result to cavities (excluding tunnels and pockets):
- isosurface interior cavity
