Jmol/Depth from surface: Difference between revisions
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<StructureSection load='' size='350' side='right' caption='' scene=''> | <StructureSection load='' size='350' side='right' caption='' scene=''> | ||
==Atoms Colored By Surfacedistance== | |||
Here is a cross-section (slab) of acetylcholinesterase ([[2ace]]) with <scene name='87/872319/2ace_surfacedistance/1'>atoms colored by surfacedistance</scene>. The commands are simply | Here is a cross-section (slab) of acetylcholinesterase ([[2ace]]) with <scene name='87/872319/2ace_surfacedistance/1'>atoms colored by surfacedistance</scene>. The commands are simply | ||
<pre> | <pre> | ||
select all | select all | ||
color surfacedistance</pre> | color surfacedistance</pre> | ||
In Proteopedia's [[SAT|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 surfacedisance 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. | |||
The default color scheme<ref>For the list of Jmol's color schemes, look for "set property colorscheme" under [https://chemapps.stolaf.edu/jmol/docs/#setmisc set (misc) in the command documentation].</ref> 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"). | The default color scheme<ref>For the list of Jmol's color schemes, look for "set property colorscheme" under [https://chemapps.stolaf.edu/jmol/docs/#setmisc set (misc) in the command documentation].</ref> 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"). | ||
