Jmol commands for molecular surfaces

For full details, see the Jmol Scripting Documentation.

Note: the isoSurface command is complex; we will only scratch the surface.

Concept and types of molecular surfaces:

The isoSurface command

Commands and examples:

Molecular surface around some part of the molecule:

isosurface protSurf select (protein) ignore (not protein) molecular;

isosurface ligSurf select (ligand) ignore (not ligand) molecular;


color $protSurf translucent blueTint;

color $ligSurf yellowTint;

Looking for pockets:

isosurface prot2 select (protein) ignore (not protein) interior cavity 1.2 10;


color $prot2 blue;

color $prot2 translucent;

isosurface prot3 select (protein) ignore (not protein) pocket cavity 1.2 10;


color $prot3 yellow;

hide protein;

hide add water;

hide add carbohydrate;


Saving isosurfaces to a file

Easiest: the most recently generated isosurface can be saved from the pop-up menu > File > Save > Save JVXL isosurface and you will get a "Save As..." dialog

or use the command write isosurface "myFileName"; which will NOT ask for the folder to save into.

Loading isosurfaces from disk

isosurface "myFileName";

isosurface prot4 "myFileName";