Jmol/Cavities pockets and tunnels

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Revision as of 22:10, 31 December 2020

CAUTION: This page is under construction and is not ready for use. Also, cavity counts and volumes, and scenes of cavities, are provisional. Some inconsistencies noted below in italics suggest that Jmol may have some "isosurface interior cavity" bugs. These are being investigated. Once they are resolved, and when this page is adequately updated, this notice will be removed. Eric Martz 18:54, 25 December 2020 (UTC)

Jmol can find and display cavities, pockets, and tunnels as isosurfaces. This page explains how to do that, and how to show the results in Proteopedia. An alternative method for finding and displaying cavities is PACUPP. Several other methods are summarized at Cavity programs.

1 Terminology
2 How To Show Cavities In Proteopedia
3 Two Probes
4 Small Cavity Example
5 Large Cavity Example

Terminology

For definitions of the terms cavity, pocket, tunnel, channel and void please see Cavity programs.

How To Show Cavities In Proteopedia

Below are shown Jmol commands to identify and display cavities as isosurfaces, with their results. Using these commands, and displaying the results in Proeopedia, require several extra steps outside of Proteopedia's usual Scene Authoring Tools (SAT). In brief, cavity isosurfaces should be generated in the stand-alone Jmol application and captured in a PNGJ file, which is then uploaded to Proteopedia for use in the SAT. Instructions are at the end of this page under Preparing Isosurface Scenes for Proteopedia. You may also wish to consider an alternative method which represents cavities with pseudoatoms, PACUPP.

Two Probes

Jmol uses two "rolling" spherical probes to identify cavities.

The smaller cavity probe detects the cavities. Its default radius is 1.2 Å. For comparison, the van der Waals radius of a carbon atom is 1.7 Å^[1]. The effective radius of a water molecule is generally taken to be 1.4 Å^[2]; a sphere of that radius has a volume of 11.5 Å³. However, the volume actually occupied per water molecule in macromolecular environments is ~25 Å³^[3], slightly larger than the 22 Å³ volume of a cube of diameter 2.8 Å.
The larger envelope probe defines the outer boundary of the macromolecule. By definition, cavities may not extend beyond this envelope boundary. By default, the envelope probe radius is 10.0 Å. The envelope is a smoothed macromolecular surface. When the cavity probe fits between the envelope and the atoms of the macromolecule, a pocket is defined.

Small Cavity Example

The coronavirus (SARS-CoV-2 and others) spike protein has a small, membrane proximal cavity (). It is a potential drug target.

The simplest Jmol cavity command is

This produces pockets, tunnels, and cavities of all sizes. There are 426 separate surfaces. The largest is a convoluted tunnel with many mouths, volume 60,197 Å³. Many are very tiny.

Hiding Tiny Cavities: minset

Since we are not interested in the tiny ones, we can hide them by specifying a value for minset. Cavities rendered with fewer than the number of triangles specified for minset will not be shown. By trial and error, a good minset number is 1000, making the Jmol command:

isosurface minset 1000 cavity Image:6zgi-m1000-cav.pngj

Legend: Spike protein 6zgi: isosurface minset 1000 cavity.

Now only the largest two cavities are shown. The larger one is a convoluted tunnel with many mouths, volume 60,197 Å³. The smaller one is the membrane-proximal cavity of interest, volume 7,591 Å³.

Isolating One Cavity

The command to display only the smaller cavity is:

isosurface set 2 Image:6zgi-m1000-cav-set2.pngj

Legend: Spike protein 6zgi showing the membrane-proximal cavity with probe radius 1.2 Å.

Coloring By Depth

It is revealing to color this cavity by distance from the surface with this command:

isosurface map property surfacedistance Image:6zgi-m1000-cav-set2-sd.pngj

Legend: Spike protein 6zgi showing the membrane-proximal cavity: At Surface, Deeper.

GREEN LINK Close examination

6zgi-m1000-cav-set2-sd-detail.pngj Ditto legend + mouths closed.

shows that the red parts, which are at or near the protein surface, are mostly closed. The "cavity" command, without modifiers, generates closed isosurfaces.

Interior Cavities vs. Pockets

To show the entrances or mouths of a cavity as open, the modifier pockets is needed. This modifier also hides cavities that lack openings to the macromolecular surface at the cavity probe radius employed.

In contrast, the modifier interior shows only cavities with no openings to the surface at the cavity probe radius employed. In our example, using the default cavity probe radius 1.2 Å, there are no interior cavities.

Here is the command to show our cavity-of-interest's entrances from the surface as open:

isosurface minset 1000 pockets cavity Image:6zgi-m100-pcav-set2-sd-detail.pngj

Legend: Spike protein 6zgi showing the membrane-proximal cavity with entrances open: At Surface, Deeper.

Spike protein is a homotrimer. Close inspection reveals that the membrane-proximal cavity has three narrow connections to the surface. Below is explained how this view was obtained.

Increasing the Cavity Probe Radius

Cavity Probe Radius 1.2 Å

First, we will limit the result to interior cavities (excluding tunnels and pockets):

isosurface interior cavity

This generates 212 cavities, ranging in volume from 353 down to 1.9 Å³. Comparing this with the initial 2-cavity result (green link above), note that neither of the cavities of interest is here. The largest cavity here is much smaller than the smaller cavity in the initial result. By trial and error, this appears to be because the cavity probe size is too small. The default probe radius is 1.2Å. The distinction between interior cavities and pockets/tunnels is whether the space intersects with an envelope of the molecule. Such an intersection represents a mouth. The default probe radius for the envelope is 10 Å. Quoting from the Jmol documentation, "Smaller numbers for the cavity radius lead to more detailed cavities; smaller numbers for the envelope radius lead to cavities that are more internal and extend less toward the outer edge of the molecule." A minimum volume of 1.9 Å³ is puzzling since it is smaller than the volume of the spherical probe: 1.2 Å is the default radius; spherical probe volume is 7.2 Å³. At least no negative volumes are reported.

Cavity Probe Radius 2.0 Å

Increasing the cavity probe radius to 2.0 Å still does not display the cavities of interest (not shown). 44 separate cavities are displayed. Of concern is that most have volumes much less than the spherical volume of the probe (33.5 Å^3), and it is not clear how a cavity smaller than the probe can be detected. Of further concern is that several cavities report negative volumes.

Cavity Probe Radius 2.6 Å

Increasing the cavity probe radius to 2.6 Å finally displays the smaller cavity of interest, but not the larger.

isosurface interior cavity 2.6 10.0

This cavity probe radius gives a volume of 1,855 Å³ for the smaller cavity of interest, 16% larger than with the 3.0 Å probe. 10 cavities are reported. The volume of the smallest is reported to be 0.10 Å³, and the next-to-smallest, 30.3 Å³. The spherical volume of this probe is 73.6 Å³.

Cavity Probe Radius 3.0 Å

Increasing the cavity probe radius to 3.0 Å finally shows both cavities of interest.

isosurface interior cavity 3.0 10.0

However there are two smaller cavities that are not of interest. To avoid these, we can specify a minimum number of triangles for cavity surfaces with the parameter minset. Using "minset 100" (value determined by trial and error), we arrive at the command shown at the beginning, which shows only the two cavities of interest. Using "minset 50" eliminated only the smaller of the two unwanted cavities.

Summary of Volumes

The volumes of the two cavities of interest for 6zgi are reported by Jmol as follows:

Cavity Probe Radius, Å	Larger Cavity Volume, Å³	Smaller Cavity Volume, Å³
2.6	not detected	1,855
3.0	5,564	1,606
4.0	4,675	1,032
5.0	3,194	523

Reducing the Envelope Probe Radius

We have used the default envelope probe radius of 10.0 Å in all the above examples. If it is reduced to 7.0, the two cavities of interest fail to be displayed [not shown]. This is presumably because a more detailed envelope with more indentations created mouths in the two cavities of interest, rendering them pockets or tunnels, rather than interior cavities with no mouths. If it is reduced to 3.0 Å, no cavities are displayed [not shown]. Two are reported with negative volumes of -560.8 and -3.3. The maximum envelope probe radius allowed by Jmol is 10.0.

Large Cavity Example

. An X-ray structure, 3hyc, reveals a large central cavity, approximately 35 Å in diameter. This cavity connects to the protein surface with four "mouth" openings, each about 10-12 Å in diameter. These openings are in a plane, 90° apart. Here, you can .

1 Preparing Isosurface Scenes for Proteopedia
2 See Also
3 References and Notes

Preparing Isosurface Scenes for Proteopedia

This section is under construction and awaits major revisions. It is not ready for use.

Speed of Rendering

If you use the isosurface commands below, do so in the Jmol Java application, not in JSmol in Proteopedia. Depending on the size of the molecule, cavity isosurface commands take about a minute to complete in the Java application, which is many times faster than JSmol. You would have to wait many minutes for completion in JSmol.

Saving Pre-Calculated Isosurfaces

In order to speed up the green links below, the isosurfaces were pre-calculated in the Jmol Java application and then saved into .jvxl (Jmol voxel) files (and uploaded to Proteopedia). These can be quickly loaded without re-computing the isosurfaces. After a cavity isosurface command has completed, the calculated surfaces can be saved with the Jmol command

write filename.jvxl

Later, you can load the saved isosurfaces without re-calculating them using the command

isosurface filename.jvxl

Generating Cavity Isosurfaces

The Jmol commands for generating cavity isosurfaces will be found in the Jmol/JSmol Interacive Scripting Documention under isosurfaces: molecular/solvent surfaces. Near the bottom of that very long section, important commands for after the cavity isosurfaces are calculated:

isosurface area set (integer) reports the surface area of one isosurface in Å².
isosurface delete to clear existing isosurfaces before a new calculation.
isosurface set (integer) displays just one of the isosurfaces.
isosurface set 0 displays all of the isosurfaces.
isosurface volume set (integer) reports the volume of one isosurface in Å³.

References and Notes

↑ Bondi, A., J. Phys. Chem. 68:441, 1964.
↑ Diameter of water molecule at B10NUMB3R5, a collaboration between Harvard Medical School and the Weizmann Institute of Science. See also Distance between water molecules in bulk water.
↑ Volume of water molecule bound to an amino acid at B10NUMB3R5, a collaboration between Harvard Medical School and the Weizmann Institute of Science.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

Retrieved from "http://52.214.119.220/wiki/index.php/Jmol/Cavities_pockets_and_tunnels"

@@ Line 54: / Line 54: @@
 Ditto legend + mouths closed.
-shows that the red parts, which are at or near the protein surface, are mostly closed. The "cavity" command, without modifiers, generates closed isosurfaces. To show the entrances or mouths of a cavity as open, the modifier ''pockets'' is needed. This modifier also hides cavities that lack connections to the macromolecular surface at the cavity probe radius employed.
+shows that the red parts, which are at or near the protein surface, are mostly closed. The "cavity" command, without modifiers, generates closed isosurfaces.
+===Interior Cavities vs. Pockets===
+To show the entrances or mouths of a cavity as open, the modifier ''pockets'' is needed. This modifier also hides cavities that lack openings to the macromolecular surface at the cavity probe radius employed.
+:In contrast, the modifier ''interior'' shows only cavities with no openings to the surface at the cavity probe radius employed. In our example, using the default cavity probe radius 1.2 Å, there are no interior cavities.
+Here is the command to show our cavity-of-interest's entrances from the surface as '''open''':
+:<tt>isosurface minset 1000 '''pockets''' cavity</tt> Image:6zgi-m100-pcav-set2-sd-detail.pngj
+Legend: Spike protein [[6zgi]] showing the membrane-proximal cavity <i>with entrances open</i>: <span class="text-red"><b>At Surface</b></span>, <span class="bg-lightgreen">Deeper</span>.