Atoms Colored By Surfacedistance
Here is a cross-section (slab) of acetylcholinesterase (2ace) with atoms colored by surfacedistance. The commands are simply
restrict not solvent # hides water
spacefill only
select ach # acetylcholine substrate model
color black
select protein
color surfacedistance
In Proteopedia's Molecular Scene Authoring Tools (SAT), you can enter these commands in the slot below the molecule. There will be a delay (about 20 sec on my computer) while JSmol calculates the surfacedistance for each atom. However, once the scene is saved as a green link, the colors are saved and displayed without re-calculation when the green link is clicked.
Color Schemes
The default color scheme[1] for surfacedistance is red-white-blue, "rwb" in Jmol command language. You can apply other color schemes, such as the spectral color scheme red-orange-yellow-green-blue ("roygb").
color property surfacedistance "roygb"
Reporting Surfacedistance
These commands will be much faster, especially for larger molecules, if done in the standalone Jmol Java application. The Jmol command[2] to report the maximum surfacedistance for any atom in a model is
print {*}.surfacedistance.max # Reports 10.25 for 2ace.
The asterisk "⁎" means "all atoms". The atom expression must be enclosed in curly brackets "{...}". Anything after "#" is a comment, which is not part of the command to Jmol.
