Jmol/Depth from surface

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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.

Contents

Atoms Colored By Surfacedistance

Here is a cross-section (slab) of acetylcholinesterase (2ace) with atoms colored by surfacedistance. The commands are simply 

hide 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 blue-white-red, "bwr" in Jmol command language. You can apply other color schemes, such as the spectral color scheme red-orange-yellow-green-blue ("roygb"). 

color property surfacedistance "roygb"

Tunnel Isosurface Colored By Surfacedistance

  • Example to be explained, scene version 1
  • Example to be explained, scene version 2

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.

Three enzymes that are roughly spherical with 527-575 amino acids each are 2ace, 1CRL, and 1o86. Their maximum surfacedepth values are 10.25, 9.58, and 7.94 Å respectively. 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).
  • 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).
  • In order of increasing depth: atoms in coil 1.3 < helices 1.6 < β strands 2.4 Å.

Selecting By Surfacedistance

Bacterial glycosidase 2ixb showing its channel containing NAD and substrate.
Drag the structure with the mouse to rotate

Notes

  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.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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