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. | ||
Revision as of 01:36, 19 January 2021
This page is under construction. Eric Martz 00:56, 18 January 2021 (UTC)
The atom property surfacedistance in Jmol is each atom's distance from the surface of the macromolecule. The units of surfacedistance are Ångstroms. You can select atoms by distance from the surface, and report the average, minimum, or maximum surfacedistance of a group of atoms. Atoms, cavity/pocket/tunnel isosurfaces, and other objects can be colored by distance from the surface.
Atoms Colored By SurfacedistanceHere 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 SchemesThe 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").
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NotesNotes
- ↑ For the list of Jmol's color schemes, look for "set property colorscheme" under set (misc) in the command documentation.