Jmol/Cavities pockets and tunnels: Difference between revisions

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]].

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:

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

The command to display only the smaller cavity is:

===Coloring By Depth===

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

===Pockets vs. Interior Cavities===

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

[[SARS-CoV-2 spike protein priming by furin|Spike protein is a homotrimer]]. <span class="bg-lightgreen">The membrane-proximal cavity</span> has <span class="bg-yellow">three narrow tunnels</span>, between protein chains, to wider pockets <span class="text-red">'''opening to the protein surface'''</span>.

Jmol is not able to calculate a meaningful volume for a pocket rendered with open entrances. Volumes reported by Jmol for its closed rendering of the membrane-proximal cavity of the spike protein [[6zgi]] are in rough agreement with those independently determined by [[PACUPP]] -- best at cavity probe radii of 1.5 or 2.0 Å.

|3,250<ref>Sum of volumes of 2 clusters of pseudoatoms. One quarter of the cavity failed to be detected with a cavity probe radius of 2.5 Å.</ref><br>(1,000<ref>[[PACUPP]] in offset mode fails to find 3/4 of the cavity with a cavity probe radius of 2.5 Å.</ref>)

|}

===Increasing the Cavity Probe Radius===

As the cavity probe radius increases, cavities are displayed with less detail. Also, cavities or tunnel connections between cavities that are smaller than the probe may fail to be detected. Recall that the deeper chamber of our membrane-proximal cavity of interest is connected to three entrance pockets by narrow tunnels. As the cavity probe radius increases, those narrow tunnels are no longer detected. At 2.0 Å, two of the entrances are no longer connected to the deeper chamber. At 2.5 Å, none are connected. The cavity probe radius in Å can be added to the end of Jmol's isosurface command like this:

</StructureSection>

==Preparing Isosurface Scenes for Proteopedia==

===Speed of Rendering===

*You want to show both closed interior cavities and open-mouthed surface pockets.

*You want to show multiple pieces of a single isosurface.

===Preparing PNGJ Files With Cached Isosurfaces===

===Working Example Scripts===

The following script generates a pocket isosurface (open mouths) and an interior isosurface (closed pieces) for the spike protein, and saves each isosurface as a jvxl file. You can run this script: copy it and save it as a [[Help:Plain text editors|plain text file]] with a filename ending '''.spt'''. Drop the script file into the molecular display window of Jmol. Execution may take several minutes.

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