Jmol/Cavities pockets and tunnels: Difference between revisions
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<StructureSection load='' size='350' side='right' caption='' scene=''> | <StructureSection load='' size='350' side='right' caption='' scene='85/858407/6zgi-m1000-cav-sd-set2/1'> | ||
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]]. | 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]]. | ||
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[[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>. | [[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>. | ||
===Cavity Volumes: Closed Only=== | ===Cavity Volumes: Closed and Small Only=== | ||
====Volumes for Closed Cavities Only==== | |||
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. | 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. | ||
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|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>) | |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>) | ||
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====Volumes for Small Cavities Only==== | |||
[[#Large Cavity Example|Below is explained]] why Jmol cannot render isosurfaces representing large cavities. Therefore it cannot estimate volumes of such cavities. The example below, [[1wp1]], is described as having a cavity volume of 25,000 Å<sup>3</sup> by its authors<ref name="1wp1" />. [[PACUPP]] estimates the volume as 30,000 Å<sup>3</sup> (pseudoatom spacing 4.0 Å, "moderate" cavity detail), or 25,000 Å<sup>3</sup> (pseudoatom spacing 5.0 Å, "coarse" cavity detail). | |||
===Increasing the Cavity Probe Radius=== | ===Increasing the Cavity Probe Radius=== | ||
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:<tt><scene name='85/858407/1wp1_m400_cav_3point0/1'>isosurface minset 400 select {protein} only cavity 3.0 property surfacedistance</scene></tt><!--1wp1-m400-proteinonly-cav3.0.pngj--> | :<tt><scene name='85/858407/1wp1_m400_cav_3point0/1'>isosurface minset 400 select {protein} only cavity 3.0 property surfacedistance</scene></tt><!--1wp1-m400-proteinonly-cav3.0.pngj--> | ||
Since Jmol does not allow an envelope probe diameter exceeding 20 Å, this is the best it can do for this large cavity. [[PACUPP]] renders the cavity similarly <scene name='85/858407/1wp1_pacupp_ep_20/1'>using the same envelope probe diameter of 20 Å</scene> (pseudoatom separation 3.5 Å). Unlike Jmol, however, PACUPP allows envelope probe diameters up to 60 Å. An increase of PACUPP's envelope probe diameter to <scene name='85/858407/ | Since Jmol does not allow an envelope probe diameter exceeding 20 Å, this is the best it can do for this large cavity. [[PACUPP]] renders the cavity similarly <scene name='85/858407/1wp1_pacupp_ep_20/1'>using the same envelope probe diameter of 20 Å</scene> (pseudoatom separation 3.5 Å). Unlike Jmol, however, PACUPP allows envelope probe diameters up to 60 Å. | ||
An increase of PACUPP's envelope probe diameter to <scene name='85/858407/1wp1_pacupp_ep_24_v2/1'>24 Å is sufficient to fill the cavity solidly with pseudoatoms</scene> (pseudoatom separation 3.5 Å). | |||
</StructureSection> | </StructureSection> | ||