Jmol/Depth from surface
From Proteopedia
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==Reporting Surfacedistance== | ==Reporting Surfacedistance== | ||
| - | These commands will be much faster, especially for larger molecules, if done in the standalone [[Jmol/Application|Jmol Java application]]. The Jmol command to report the maximum surfacedistance for any atom in a model is | + | These commands will be much faster, especially for larger molecules, if done in the standalone [[Jmol/Application|Jmol Java application]]. The Jmol command<ref>Jmol commands are explained in the [https://chemapps.stolaf.edu/jmol/docs/ interactive scripting documentation] at [http://jmol.org Jmol.org].</ref> to report the maximum surfacedistance for any atom in a model is |
print {*}.surfacedistance.max # Reports <b>10.25</b> for 2ace. | print {*}.surfacedistance.max # Reports <b>10.25</b> for 2ace. | ||
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. | ||
Revision as of 22:57, 18 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.
