Jmol/Depth from surface: Difference between revisions
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The [https://chemapps.stolaf.edu/jmol/docs/#atomproperties atom property] ''surfacedistance'' in [[Jmol/Index|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, [[Jmol/Cavities pockets and tunnels|cavity/pocket/tunnel isosurfaces]], and other objects can be colored by distance from the surface. | The [https://chemapps.stolaf.edu/jmol/docs/#atomproperties atom property] ''surfacedistance'' in [[Jmol/Index|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, [[Jmol/Cavities pockets and tunnels|cavity/pocket/tunnel isosurfaces]], and other objects can be colored by distance from the surface. | ||
<StructureSection load='' size='350' side='right' caption='' scene=''> | <StructureSection load='' size='350' side='right' caption='' scene='87/872319/2ixb_tunnel/1'> | ||
==Atoms Colored By Surfacedistance== | ==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 | ||
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===Color Schemes=== | ===Color Schemes=== | ||
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 | 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 blue-white-red, "bwr" in Jmol command language. You can apply other color schemes, such as the <scene name='87/872319/2ace_surfacedistance/2'>spectral color scheme red-orange-yellow-green-blue</scene> ("roygb"). | ||
<pre> | <pre> | ||
color property surfacedistance "roygb"</pre> | color property surfacedistance "roygb"</pre> | ||
==Tunnel Isosurface Colored By Surfacedistance== | |||
*<scene name='87/872319/2ixb_tunnel/1'>Example to be explained, scene version 1</scene> | |||
*<scene name='87/872319/2ixb_tunnel/2'>Example to be explained, scene version 2</scene> | |||
==Reporting Surfacedistance== | ==Reporting Surfacedistance== | ||
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*Lys and Glu (0.3, 0.5) are shallower than Asp and Arg (~1). | *Lys and Glu (0.3, 0.5) are shallower than Asp and Arg (~1). | ||
*In order of increasing depth: atoms in coil 1.3 < helices 1.6 < β strands 2.4 Å. | *In order of increasing depth: atoms in coil 1.3 < helices 1.6 < β strands 2.4 Å. | ||
==Selecting By Surfacedistance== | ==Selecting By Surfacedistance== | ||
