Jmol/Depth from surface: Difference between revisions

Revision as of 01:57, 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 Surfacedistance

Here 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 Schemes

The 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").

color property surfacedistance "roygb"

Reporting Surfacedistance

These commands will be much faster, especially for larger molecules, if done in the standalone Jmol Java application. The Jmol command^[2] to report the maximum surfacedistance for any atom in a model is

print {*}.surfacedistance.max # Reports 10.25 for 2ace.

The asterisk "⁎" 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.

NotesNotes

↑ 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.

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

[1] For the list of Jmol's color schemes, look for "set property colorscheme" under set (misc) in the command documentation.

[2] Jmol commands are explained in the interactive scripting documentation at Jmol.org.

[1]

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 ==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.
 The asterisk "<span style="font-size:200%;">&#8270;</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.