Mod:Hunt Research Group/jmolsurfaces

Visualizing Surfaces using Jmol

1. Open coordinate file using jmol - i.e. jmol test.xyz

2. Click File --> "Console"

3. Solvent Accessible Surfaces:

  To generate the surface enter "isosurface sasurface 1.2"  
  If you want the area enter  "isosurface sasurface 1.2 area"
  If you want the volume enter  "isosurface sasurface 1.2 volume"

1.2 can be changed to a number corresponding to the radius of the probe you want

4. Connolly Surfaces:

  To generate the surface enter "isosurface solvent 1.2"  
  If you want the area enter  "isosurface solvent 1.2 area"
  If you want the volume enter  "isosurface solvent 1.2 volume"