Jmol/Depth from surface: Difference between revisions
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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 | restrict not solvent # hides water | ||
spacefill only | |||
select ach # acetylcholine substrate model | |||
color black | |||
select protein | |||
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 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. | 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 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. | ||
