Jmol/Cavities pockets and tunnels - Revision history

Eric Martz at 17:54, 3 January 2021

Eric Martz — Sun, 03 Jan 2021 17:54:49 GMT

←Older revision		Revision as of 17:54, 3 January 2021
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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/~~1wp1_pacupp_ep_24~~/1'>24 Å is sufficient to fill the cavity solidly with pseudoatoms</scene> (pseudoatom separation 3.5 Å).	+	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>

Eric Martz at 00:25, 3 January 2021

Eric Martz — Sun, 03 Jan 2021 00:25:17 GMT

←Older revision		Revision as of 00:25, 3 January 2021
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	===Cavity Volumes: Closed and Small 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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	\|}		\|}

		+	====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).		[[#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).

Eric Martz at 00:23, 3 January 2021

Eric Martz — Sun, 03 Jan 2021 00:23:56 GMT

←Older revision		Revision as of 00:23, 3 January 2021
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	\|}		\|}

-	[[#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).	+	[[#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===

Eric Martz at 00:21, 3 January 2021

Eric Martz — Sun, 03 Jan 2021 00:21:01 GMT

←Older revision		Revision as of 00:21, 3 January 2021
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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===

	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>)
	\|}		\|}
		+
		+	[[#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).

	===Increasing the Cavity Probe Radius===		===Increasing the Cavity Probe Radius===

Eric Martz at 23:50, 2 January 2021

Eric Martz — Sat, 02 Jan 2021 23:50:02 GMT

←Older revision		Revision as of 23:50, 2 January 2021
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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]].

Eric Martz at 23:47, 2 January 2021

Eric Martz — Sat, 02 Jan 2021 23:47:53 GMT

←Older revision		Revision as of 23:47, 2 January 2021
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-	<font color="red">'''CAUTION: This page is under construction and is not ready for use. When this page is adequately completed, this notice will be removed. [[User:Eric Martz\|Eric Martz]] 01:02, 1 January 2021 (UTC)'''</font>
-
	<StructureSection load='' size='350' side='right' caption='' scene=''>		<StructureSection load='' size='350' side='right' caption='' scene=''>
	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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	==Preparing Isosurface Scenes for Proteopedia==		==Preparing Isosurface Scenes for Proteopedia==
-
-	<font color="red">'''This section is under construction and awaits major revisions. It is not ready for use.</font>

	===Speed of Rendering===		===Speed of Rendering===

Eric Martz at 23:45, 2 January 2021

Eric Martz — Sat, 02 Jan 2021 23:45:22 GMT

←Older revision		Revision as of 23:45, 2 January 2021
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	*You want to show both closed interior cavities and open-mouthed surface pockets.		*You want to show both closed interior cavities and open-mouthed surface pockets.
	*You want to show multiple pieces of a single isosurface.		*You want to show multiple pieces of a single isosurface.
-	At present, Jmol can show only one piece of an isosurface. For example, above are shown three pocket entrances to the interior chamber of the spike protein cavity. Each pocket is displayed with an <tt>isosurface set <integer></tt> command. But only one can be shown at a time. To display all 3, the JVXL file (see below) must be loaded 3 times, giving each a different ID, and then one pocket displayed from each. To also display the interior closed chamber, a 4th isosurface must be loaded. Below are scripts illustrating this.	+	At present, Jmol can show only one piece of an isosurface. For example, [[#Increasing the Cavity Probe Radius\|above are shown three pocket entrances]] to the interior chamber of the spike protein cavity. Each pocket is displayed with an <tt>isosurface set <integer></tt> command. But only one can be shown at a time. To display all 3, the JVXL file (see below) must be loaded 3 times, giving each a different ID, and then one pocket displayed from each. To also display the interior closed chamber, a 4th isosurface must be loaded. Below are scripts illustrating this.

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

Eric Martz at 23:00, 2 January 2021

Eric Martz — Sat, 02 Jan 2021 23:00:59 GMT

←Older revision		Revision as of 23:00, 2 January 2021
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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 24 Å is sufficient to fill the cavity solidly with pseudoatoms (pseudoatom separation 3.5 Å).	+	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_24/1'>24 Å is sufficient to fill the cavity solidly with pseudoatoms</scene> (pseudoatom separation 3.5 Å).
-		+

	</StructureSection>		</StructureSection>

Eric Martz at 22:54, 2 January 2021

Eric Martz — Sat, 02 Jan 2021 22:54:59 GMT

←Older revision		Revision as of 22:54, 2 January 2021
Line 110:		Line 110:
	:<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.	+	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 24 Å is sufficient to fill the cavity solidly with pseudoatoms (pseudoatom separation 3.5 Å).

Eric Martz at 22:35, 2 January 2021

Eric Martz — Sat, 02 Jan 2021 22:35:44 GMT

←Older revision		Revision as of 22:35, 2 January 2021
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	==Large Cavity Example==		==Large Cavity Example==
-	Jmol is unable to produce isosurfaces representing cavities whose interior diameters exceed the maximum diameter of Jmol's envelope probe, 20 Å. As an example, consider OprM of ''Pseudomonas aeruginosa''. This bottle-shaped integral membrane protein is believed to function as the drug discharge duct across the outer membrane<ref name="1wp1">PMID: 15507433</ref>. The [[biological assembly]] of [[1wp1]] has pocket with a single mouth, about 110 Å deep. The inside diameter of this pocket varies from a bit less than 20 Å to about 27 Å. Jmol can, of course, make an isosurface over the entire "bottle", inside and out (command: <tt>isosurface minset 1000 solvent 2.0</tt>), shown here in cross section with the protein in sticks (wireframe):	+	Jmol is unable to produce isosurfaces representing cavities whose interior diameters exceed the '''maximum diameter of Jmol's envelope probe, 20 Å'''. As an example, consider OprM of ''Pseudomonas aeruginosa''. This bottle-shaped integral membrane protein is believed to function as the drug discharge duct across the outer membrane<ref name="1wp1">PMID: 15507433</ref>. The [[biological assembly]] of [[1wp1]] has a pocket with a single mouth, about 110 Å deep. The inside diameter of this pocket varies from a bit less than 20 Å to about 27 Å. Jmol can, of course, make an isosurface over the entire "bottle", inside and out (command: <tt>isosurface minset 1000 solvent 2.0</tt>), shown here in cross section with the protein in sticks (wireframe):
-	~~<br>~~[[Image:1wp1-solvent-surface-slab.png\|300px]]	+
		+	[[Image:1wp1-solvent-surface-slab.png\|300px]]
		+
		+	Jmol is able to represent the narrow ends of this cavity, but not the larger middle:
		+	:<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.
		+

	</StructureSection>		</StructureSection>