Atoms Colored By Surfacedistance
Here is a cross-section (slab) of acetylcholinesterase (2ace) with . 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 ("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 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.
