Jmol/Depth from surface
From Proteopedia
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*In order of increasing depth: the sidechains nitrogens and oxygens of charged amino acids (Asp, Glu, Lys, Arg) 0.8 < the sidechain O,N of Asn, Gln 1.1 < the entire sidechains of Val, Leu, Ile 1.4 < the entire sidechains of Phe, Tyr, Trp 2.3 Å. | *In order of increasing depth: the sidechains nitrogens and oxygens of charged amino acids (Asp, Glu, Lys, Arg) 0.8 < the sidechain O,N of Asn, Gln 1.1 < the entire sidechains of Val, Leu, Ile 1.4 < the entire sidechains of Phe, Tyr, Trp 2.3 Å. | ||
*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. |
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| + | ==Selecting By Surfacedistance== | ||
| + | |||
| + | ==Tunnel Isosurface Colored By Surfacedistance== | ||
</StructureSection> | </StructureSection> | ||
Revision as of 00:14, 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.
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Notes
- ↑ For the list of Jmol's color schemes, look for "set property colorscheme" under set (misc) in the command documentation.
- ↑ Jmol commands are explained in the interactive scripting documentation at Jmol.org.
