Jmol/Depth from surface
From Proteopedia
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The asterisk "<span style="font-size:200%;">⁎</span>" means "all atoms". The atom expression must be enclosed in curly brackets "{...}". Anything after "#" is a comment, which is not part of the command to Jmol. | The asterisk "<span style="font-size:200%;">⁎</span>" means "all atoms". The atom expression must be enclosed in curly brackets "{...}". Anything after "#" is a comment, which is not part of the command to Jmol. | ||
| - | Three enzymes that are roughly spherical with 527-575 amino acids each are [[2ace]], [[1crl|1CRL]], and [[1o86]]. Their maximum surfacedepth values are 10.25, 9.58, and 7.94 Å respectively. [https://proteopedia.org/wiki/images/b/b5/Surfacedistance-reports.spt A script that you can download] (right click, save link as) reports the average surfacedepth values for each amino acid, secondary structures, and common chemical elements. In the list below, average values were normalized to a maximum depth of 10.0 Å, and averaged. For this small sample of 3 enzymes: | + | Three enzymes that are roughly spherical with 527-575 amino acids each are [[2ace]], [[1crl|1CRL]], and [[1o86]]. Their maximum surfacedepth values are 10.25, 9.58, and 7.94 Å respectively. [https://proteopedia.org/wiki/images/b/b5/Surfacedistance-reports.spt A script that you can download] (right click, save link as) reports the average surfacedepth values for each amino acid, secondary structures, and common chemical elements. In the list below, average surfacedistance values were normalized to a maximum depth of 10.0 Å, and averaged for these 3 models. For this small sample of 3 enzymes: |
*The sidechain of Trp was deepest (2.5). | *The sidechain of Trp was deepest (2.5). | ||
*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. | ||
Revision as of 19:27, 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.
