Cavity programs: Difference between revisions

(43 intermediate revisions by the same user not shown)

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*A '''tunnel''' connects two or more locations, and may or may not have entrances from the surface<ref name="damborsky3">PMID: 27957758</ref><ref name="kingsley">PMID: 25663659</ref><ref name="caverweb" />.

*A '''channel''' connects two entrances<ref name="caverweb" />.

*Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref>.

*A '''pore''' may mean a trans-membrane channel through an integral membrane protein<ref name="moleonline" />

*Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="moleonline" /><ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref><ref name="avp">The term ''void'' is used for the program [http://www.bioinf.org.uk/software/avp/ AVP (Another Void Program)] from the group of Andrew C. R. Martin at University College, London UK.</ref>.

Nearly all proteins have irregular surfaces with shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a pocket can also be termed a tunnel accessing ~~the~~ catalytic site<ref name="damborsky3" /><ref name="kingsley" />.

Nearly all proteins have irregular surfaces with shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a deep pocket can also be termed a tunnel accessing a functional or catalytic site<ref name="damborsky3" /><ref name="kingsley" />.

The '''example illustrated below''' is the membrane-proximal cavity of [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]). The membrane-proximal cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection. ~~Programs are~~ listed alphabetically.

The '''example illustrated below''' is the membrane-proximal cavity of [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]). The membrane-proximal cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection.

__NOTOC__

==Cavities vs. Channels==

The programs listed alphabetically below can be categorized as follows.

===I. Cavities===

These programs identify any cavities between atoms of the macromolecule, or pockets beneath a smoothed macromolecular surface, that are larger than the probe diameter. '''No starting position need be specified'''.

*[[#AVP|AVP]]

*[[#CASTp|CASTp]]

*[[#Jmol|Jmol]] Cavities as isosurfaces.

*[[#PACUPP|PACUPP]] Cavities filled with pseudoatoms.

===II. Channels/Tunnels===

These programs '''require that one or more starting locations be specified'''. Thus, they may not identify cavities unrelated to the specified starting point(s). They look for channels/tunnels connecting a starting point with the surface, or with a specified end point.

*[[#CAVER|CAVER]] ''Personal note: unable to run program in macOS or Windows 10 (December, 2020).''

*[[#CAVER Web|CAVER Web]] ''Appeared to be '''out of order''' in December, 2020.''

*[[#ChExVis|ChExVis]] Limited to channels with 2 entrances.

*[[#MolAxis|MolAxis]] ''Server appeared to be '''out of order''' in December, 2020.''

*[[#MOLEonline|MOLEonline]]

===III. Other===

*[[#MAP_CHANNELS|MAP_CHANNELS]] for solvent channels in crystals of macromolecules.

</td></tr></table>

==AVP==

[http://www.bioinf.org.uk/software/avp/ AVP (Another Void Program)]: "Voids are defined as

holes in the protein that are not accessible to solvent, but into

which a molecule of a given radius (such as a water) can fit. ... Initially a course grid is used (default 1A), but close to the protein a finer grid (default 0.1A) is

used and off-grid locations are explored." In addition to locating voids, the program assesses packing quality.

(<font color="red">To be continued ...</font>)

==CASTp==

Line 20:

Line 51:

[[Image:Castp-6zgi.png|200px]]

</td></tr></table>

[http://sts.bioe.uic.edu/castp/index.html CASTp]: '''C'''omputed '''A'''tlas of '''S'''urface '''T'''opography of '''p'''roteins. "CASTp is based on recent theorectical and algorithmic results of Computational Geometry. It has many advantages: 1) pockets and cavities are identified analytically, 2) the boundary between the bulk solvent and the pocket is defined precisely, 3) all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points." (See Comparison Note<ref name="hitormiss">In contrast with CASTP, PACUPP uses grid points. Therefore, its cavity boundaries are slightly different when the grid points are offset by half of the spacing between points -- an option it offers. See ''Offset: Hit or Miss & Cavity Volume'' in [http://molviz.org/pacupp/1-How-To-Use-PACUPP.pdf How To Use PACUPP].</ref>.) '''Shallow pockets''' (no cross section exceeds the mouth diameter) are not shown.

[http://sts.bioe.uic.edu/castp/index.html CASTp]: '''C'''omputed '''A'''tlas of '''S'''urface '''T'''opography of '''p'''roteins. "CASTp is based on recent theorectical and algorithmic results of Computational Geometry. It has many advantages: 1) pockets and cavities are identified analytically, 2) the boundary between the bulk solvent and the pocket is defined precisely, 3) all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points." (See Comparison Note<ref name="hitormiss">In contrast with CASTP, PACUPP uses grid points. Therefore, its cavity boundaries are slightly different when the grid points are offset by half of the spacing between points -- an option it offers. See ''Offset: Hit or Miss & Cavity Volume'' in [http://molviz.org/pacupp/1-How-To-Use-PACUPP.pdf How To Use PACUPP].</ref>.) '''Shallow pockets''' (no cross section exceeds the mouth diameter) are not shown. '''No starting position is required'''. The probe radius (default 1.4 Å) is adjustable.

Displays protein sequences indicating which residues line the displayed cavities. Clicking on a residue centers the 3D view accordingly.

Line 65:

Line 96:

[[Image:Jmol-cavities-6zgi-1.4-10.png|200px]]

</td></tr></table>

[[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands.

[[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands. Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.2 Å, configurable), or pockets between a smoothed macromolecular surface (default surface probe radius 10 Å, configurable) and atoms of the macromolecule. Starting point(s) are not relevant. '''Pockets''' are depicted with open mouths (illustrated here: pink, orange, yellow, blue); '''Interior Cavities''' (buried cavities; voids) are depicted as closed isosurfaces (illustrated here: green).

Jmol has an extensive command language that provides great flexibility in visualizing cavities. However, displaying more than one isosurface fragment at a time, and coloring the fragments differently (as in the left snapshot) is cumbersome.

Line 71:

Line 102:

The Jmol Java standalone application is downloadable from [http://jmol.org jmol.org]. It is also available as JSmol, a Javascript implementation used in most pages in Proteopedia.

Jmol is updated often, most ~~recently~~ November 19, 2020.

Jmol is updated often. In December, 2020, the most recent update was November 19, 2020.

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==MOLEonline==

~~==PACUPP==~~

<span style="font-size:120%; font-weight:bold;">MOLEonline:</span><br>Membrane-proximal cavity in the [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]) rendered as 3 tunnels from a specified point (center of the deepest part of the cavity).

Line 89:

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[[Image:Moleonline-6zgi.png|240px]]

</td></tr></table>

[https://mole.upol.cz/ MOLEonline]<ref name="moleonline">PMID: 29718451</ref> locates and characterizes channels, tunnels and pores. Visualization in LiteMol, which has many menu options for rendering, but does not offer transparency. The thin "C-α trace" is the least obscuring. One can specify ''starting points'' and ''end points'' by selections (clickable sequence listing), residue lists, or XYZ points. Any subset of detected cavities can be displayed via checkboxes. After a cavity has been selected by clicking in the 3D rendering: Lining residues are listed (not spreadsheet ready); Properties are listed such as bottleneck (radius?) and length (but not area nor volume); a graphic is displayed showing selected properties (hydropathy, hydrophobicity, charge, polarity, etc.) along the length of the channel.

[https://mole.upol.cz/ MOLEonline]<ref name="moleonline">PMID: 29718451</ref> locates and characterizes channels, tunnels and pores. Best results are obtained when starting points are specified, which can be obtained from the ''Catalytic Site Atlas'' (CSA). Channels are represented as chains of overlapping spheres, thus radially symmetric. Visualization is in LiteMol, which has many menu options for rendering, but does not offer transparency. The thin "C-α trace" is the least obscuring. One can specify ''starting points'' and ''end points'' by selections (clickable sequence listing), residue lists, or XYZ points. Any subset of detected cavities can be displayed via checkboxes. After a cavity has been selected by clicking in the 3D rendering: Lining residues are listed (not spreadsheet ready); Properties are listed such as bottleneck (radius?) and length (but not area nor volume); a graphic is displayed showing selected properties (hydropathy, hydrophobicity, charge, polarity, etc.) along the length of the channel.

Results can be downloaded in many formats, including for PyMOL, VMD, and Chimera. When PDB format is downloaded, a channel is represented by atoms of element 'X', group 'TUN', with sequence number = tunnel ID.

Personal experience: When SARS-CoV-2 spike protein [[6zgi]] is submitted, cavities (connecting to the surface) and voids were displayed automatically. None represented the membrane-proximal cavity. When the center of the deepest part of the membrane-proximal cavity was specified via XYZ (215.6, 215.6, 157.6), ''tunnels'' were detected, including the three pictured at right. This was with the default ''Cavity parameter: probe radius'' of 5 Å. No ''tunnels'' were detected with that parameter set to 1.4 or 2.0 Å.

Personal experience: When SARS-CoV-2 spike protein [[6zgi]] was submitted, cavities (connecting to the surface) and voids were displayed automatically. None represented the membrane-proximal cavity. When the center of the deepest part of the membrane-proximal cavity was specified via XYZ (215.6, 215.6, 157.6), ''tunnels'' were detected, including the three pictured at right. This was with the default ''Cavity parameter: probe radius'' of 5 Å. No ''tunnels'' were detected with that parameter set to 1.4 or 2.0 Å.

==PACUPP==

Line 103:

Line 135:

[[Image:Pacupp-6zgi-fine.png|200px]]

</td></tr></table>

PACUPP, '''P'''ockets '''A'''nd '''C'''avities '''U'''sing '''P'''seudoatoms in '''P'''roteins, identifies cavities by filling them with pseudoatoms (holmium, Ho, think "holes"; see comparison note<ref name="hitormiss" />). An example is presented in some detail at [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]. Further examples with demonstrations of how to use PACUPP are in a YouTube video and a slideshow, available from [http://molviz.org/pacupp molviz.org/pacupp], where you can also download the program.

<br>

[[Image:1vot-pacupp-xfine-inside.png|220px]]

</td><td>

[[Image:1vot-pacupp-xfine-measure.png|220px]]

</td></tr><tr><td>

Inhibitor and 3 water oxygens inside cavity.

</td><td>

Cavity measurements.

</td></tr><tr><td colspan="2">

Catalytic pocket of acetylcholinesterase [[1vot]] containing the inhibitor huperzine A. Colored by depth from the <font color="red">surface entrance</font>. Cavity detail: extra fine. See [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins|how to obtain these views in PACUPP]].

</td></tr></table>

[http://molviz.org/pacupp PACUPP]], '''P'''ockets '''A'''nd '''C'''avities '''U'''sing '''P'''seudoatoms in '''P'''roteins, identifies cavities by filling them with pseudoatoms (holmium, Ho, think "holes"; see comparison note<ref name="hitormiss" />). Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.5 Å, configurable), or pockets between a smoothed macromolecular surface (default surface probe radius 10 Å, configurable) and atoms of the macromolecule. Starting point(s) are not relevant. An example is presented in some detail at [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]. Further examples with demonstrations of how to use PACUPP are in a YouTube video and a slideshow, available from [http://molviz.org/pacupp molviz.org/pacupp], where you can also download the program.

PACUPP offers a number of [http://molviz.org/pacupp/commands-alphabetical.pdf simple commands specialized for visualizing cavities], mostly single letter commands. Some call up a dialog where the use enters information. Lists cavity-lining atoms in a spreadsheet-ready text file. Learning the PACUPP commands is much easier than learning Jmol commands.

PACUPP offers a number of [http://molviz.org/pacupp/commands-alphabetical.pdf simple commands specialized for visualizing cavities], mostly single letter commands. Some call up a dialog where the use enters information. Lists cavity-lining atoms in a '''spreadsheet-ready''' text file. Learning the PACUPP commands is much easier than learning Jmol commands.

PACUPP is a Jmol script. It processes 2/3 of the entries in the [[Protein Data Bank]] in ≤15 sec each. For large models such as ribosomes or proteasomes that may take many minutes, PACUPP offers an unattended batch mode.

First released December, 2020.

==See Also==

*[[Jmol/Cavities pockets and tunnels]]

*[[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]

*[[Jmol/Depth from surface]]

*[[SARS-CoV-2 spike protein fusion transformation]] which discusses the spike protein cavity used as an example above.

==References==

Cavity programs: Difference between revisions

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@@ Line 4: / Line 4: @@
 *A '''tunnel''' connects two or more locations, and may or may not have entrances from the surface<ref name="damborsky3">PMID: 27957758</ref><ref name="kingsley">PMID: 25663659</ref><ref name="caverweb" />.
 *A '''channel''' connects two entrances<ref name="caverweb" />.
-*Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref>.
+*A '''pore''' may mean a trans-membrane channel through an integral membrane protein<ref name="moleonline" />
+*Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="moleonline" /><ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref><ref name="avp">The term ''void'' is used for the program [http://www.bioinf.org.uk/software/avp/ AVP (Another Void Program)] from the group of Andrew C. R. Martin at University College, London UK.</ref>.
-Nearly all proteins have irregular surfaces with shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a pocket can also be termed a tunnel accessing the catalytic site<ref name="damborsky3" /><ref name="kingsley" />.
+Nearly all proteins have irregular surfaces with shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a deep pocket can also be termed a tunnel accessing a functional or catalytic site<ref name="damborsky3" /><ref name="kingsley" />.
-The '''example illustrated below''' is the membrane-proximal cavity of [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]). The membrane-proximal cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection. Programs are listed alphabetically.
+The '''example illustrated below''' is the membrane-proximal cavity of [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]). The membrane-proximal cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection.
+__NOTOC__
+==Cavities vs. Channels==
+<table style="background-color:#e0e0e0;" class="wikitable"><tr><td>
+The programs listed alphabetically below can be categorized as follows.
+===I. Cavities===
+These programs identify any cavities between atoms of the macromolecule, or pockets beneath a smoothed macromolecular surface, that are larger than the probe diameter. '''No starting position need be specified'''.
+*[[#AVP|AVP]]
+*[[#CASTp|CASTp]]
+*[[#Jmol|Jmol]] Cavities as isosurfaces.
+*[[#PACUPP|PACUPP]] Cavities filled with pseudoatoms.
+===II. Channels/Tunnels===
+These programs '''require that one or more starting locations be specified'''. Thus, they may not identify cavities unrelated to the specified starting point(s). They look for channels/tunnels connecting a starting point with the surface, or with a specified end point.
+*[[#CAVER|CAVER]] ''Personal note: unable to run program in macOS or Windows 10 (December, 2020).''
+*[[#CAVER Web|CAVER Web]] ''Appeared to be '''out of order''' in December, 2020.''
+*[[#ChExVis|ChExVis]] Limited to channels with 2 entrances.
+*[[#MolAxis|MolAxis]] ''Server appeared to be '''out of order''' in December, 2020.''
+*[[#MOLEonline|MOLEonline]]
+===III. Other===
+*[[#MAP_CHANNELS|MAP_CHANNELS]] for solvent channels in crystals of macromolecules.
+</td></tr></table>
+==AVP==
+[http://www.bioinf.org.uk/software/avp/ AVP (Another Void Program)]: "Voids are defined as
+holes in the protein that are not accessible to solvent, but into
+which a molecule of a given radius (such as a water) can fit. ... Initially a course grid is used (default 1A), but close to the protein a finer grid (default 0.1A) is
+used and off-grid locations are explored." In addition to locating voids, the program assesses packing quality.
+(<font color="red">To be continued ...</font>)
 ==CASTp==
@@ Line 20: / Line 51: @@
 [[Image:Castp-6zgi.png|200px]]
 </td></tr></table>
-[http://sts.bioe.uic.edu/castp/index.html CASTp]: '''C'''omputed '''A'''tlas of '''S'''urface '''T'''opography of '''p'''roteins. "CASTp is based on recent theorectical and algorithmic results of Computational Geometry. It has many advantages: 1) pockets and cavities are identified analytically, 2) the boundary between the bulk solvent and the pocket is defined precisely, 3) all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points." (See Comparison Note<ref name="hitormiss">In contrast with CASTP, PACUPP uses grid points. Therefore, its cavity boundaries are slightly different when the grid points are offset by half of the spacing between points -- an option it offers. See ''Offset: Hit or Miss & Cavity Volume'' in [http://molviz.org/pacupp/1-How-To-Use-PACUPP.pdf How To Use PACUPP].</ref>.) '''Shallow pockets''' (no cross section exceeds the mouth diameter) are not shown.
+[http://sts.bioe.uic.edu/castp/index.html CASTp]: '''C'''omputed '''A'''tlas of '''S'''urface '''T'''opography of '''p'''roteins. "CASTp is based on recent theorectical and algorithmic results of Computational Geometry. It has many advantages: 1) pockets and cavities are identified analytically, 2) the boundary between the bulk solvent and the pocket is defined precisely, 3) all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points." (See Comparison Note<ref name="hitormiss">In contrast with CASTP, PACUPP uses grid points. Therefore, its cavity boundaries are slightly different when the grid points are offset by half of the spacing between points -- an option it offers. See ''Offset: Hit or Miss & Cavity Volume'' in [http://molviz.org/pacupp/1-How-To-Use-PACUPP.pdf How To Use PACUPP].</ref>.) '''Shallow pockets''' (no cross section exceeds the mouth diameter) are not shown. '''No starting position is required'''. The probe radius (default 1.4 Å) is adjustable.
 Displays protein sequences indicating which residues line the displayed cavities. Clicking on a residue centers the 3D view accordingly.
@@ Line 65: / Line 96: @@
 [[Image:Jmol-cavities-6zgi-1.4-10.png|200px]]
 </td></tr></table>
-[[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands.
+[[Jmol]] can identify and display pockets and cavities as isosurfaces. Examples are shown at [[Jmol/Cavities pockets and tunnels]], where you will also find explanations of the interior cavity and pocket commands. Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.2 Å, configurable), or pockets between a smoothed macromolecular surface (default surface probe radius 10 Å, configurable) and atoms of the macromolecule. Starting point(s) are not relevant. '''Pockets''' are depicted with open mouths (illustrated here: pink, orange, yellow, blue); '''Interior Cavities''' (buried cavities; voids) are depicted as closed isosurfaces (illustrated here: green).
 Jmol has an extensive command language that provides great flexibility in visualizing cavities. However, displaying more than one isosurface fragment at a time, and coloring the fragments differently (as in the left snapshot) is cumbersome.
@@ Line 71: / Line 102: @@
 The Jmol Java standalone application is downloadable from [http://jmol.org jmol.org]. It is also available as JSmol, a Javascript implementation used in most pages in Proteopedia.
-Jmol is updated often, most recently November 19, 2020.
+Jmol is updated often. In December, 2020, the most recent update was November 19, 2020.
 <br clear="both">
@@ Line 83: / Line 114: @@
 ==MOLEonline==
-==PACUPP==
 <table align="right" width="440" cellpadding="5" hspace="8" style="border: 1px solid black; border-collapse:collapse;padding-left:8px;"><tr><td>
 <span style="font-size:120%; font-weight:bold;">MOLEonline:</span><br>Membrane-proximal cavity in the [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]) rendered as 3 tunnels from a specified point (center of the deepest part of the cavity).
@@ Line 89: / Line 119: @@
 [[Image:Moleonline-6zgi.png|240px]]
 </td></tr></table>
-[https://mole.upol.cz/ MOLEonline]<ref name="moleonline">PMID: 29718451</ref> locates and characterizes channels, tunnels and pores. Visualization in LiteMol, which has many menu options for rendering, but does not offer transparency. The thin "C-&alpha; trace" is the least obscuring. One can specify ''starting points'' and ''end points'' by selections (clickable sequence listing), residue lists, or XYZ points. Any subset of detected cavities can be displayed via checkboxes. After a cavity has been selected by clicking in the 3D rendering: Lining residues are listed (not spreadsheet ready); Properties are listed such as bottleneck (radius?) and length (but not area nor volume); a graphic is displayed showing selected properties (hydropathy, hydrophobicity, charge, polarity, etc.) along the length of the channel.
+[https://mole.upol.cz/ MOLEonline]<ref name="moleonline">PMID: 29718451</ref> locates and characterizes channels, tunnels and pores. Best results are obtained when starting points are specified, which can be obtained from the ''Catalytic Site Atlas'' (CSA). Channels are represented as chains of overlapping spheres, thus radially symmetric. Visualization is in LiteMol, which has many menu options for rendering, but does not offer transparency. The thin "C-&alpha; trace" is the least obscuring. One can specify ''starting points'' and ''end points'' by selections (clickable sequence listing), residue lists, or XYZ points. Any subset of detected cavities can be displayed via checkboxes. After a cavity has been selected by clicking in the 3D rendering: Lining residues are listed (not spreadsheet ready); Properties are listed such as bottleneck (radius?) and length (but not area nor volume); a graphic is displayed showing selected properties (hydropathy, hydrophobicity, charge, polarity, etc.) along the length of the channel.
+Results can be downloaded in many formats, including for PyMOL, VMD, and Chimera. When PDB format is downloaded, a channel is represented by atoms of element 'X', group 'TUN', with sequence number = tunnel ID.
-Personal experience: When SARS-CoV-2 spike protein [[6zgi]] is submitted, cavities (connecting to the surface) and voids were displayed automatically. None represented the membrane-proximal cavity. When the center of the deepest part of the membrane-proximal cavity was specified via XYZ (215.6, 215.6, 157.6), ''tunnels'' were detected, including the three pictured at right. This was with the default ''Cavity parameter: probe radius'' of 5 Å. No ''tunnels'' were detected with that parameter set to 1.4 or 2.0 Å.
+Personal experience: When SARS-CoV-2 spike protein [[6zgi]] was submitted, cavities (connecting to the surface) and voids were displayed automatically. None represented the membrane-proximal cavity. When the center of the deepest part of the membrane-proximal cavity was specified via XYZ (215.6, 215.6, 157.6), ''tunnels'' were detected, including the three pictured at right. This was with the default ''Cavity parameter: probe radius'' of 5 Å. No ''tunnels'' were detected with that parameter set to 1.4 or 2.0 Å.
 ==PACUPP==
@@ Line 103: / Line 135: @@
 [[Image:Pacupp-6zgi-fine.png|200px]]
 </td></tr></table>
-PACUPP, '''P'''ockets '''A'''nd '''C'''avities '''U'''sing '''P'''seudoatoms in '''P'''roteins, identifies cavities by filling them with pseudoatoms (holmium, Ho, think "holes"; see comparison note<ref name="hitormiss" />). An example is presented in some detail at [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]. Further examples with demonstrations of how to use PACUPP are in a YouTube video and a slideshow, available from [http://molviz.org/pacupp molviz.org/pacupp], where you can also download the program.
+<br>
+<table align="right" width="440" cellpadding="5" hspace="8" style="border: 1px solid black; border-collapse:collapse;padding-left:8px;"><tr><td>
+[[Image:1vot-pacupp-xfine-inside.png|220px]]
+</td><td>
+[[Image:1vot-pacupp-xfine-measure.png|220px]]
+</td></tr><tr><td>
+Inhibitor and 3 water oxygens inside cavity.
+</td><td>
+Cavity measurements.
+</td></tr><tr><td colspan="2">
+Catalytic pocket of acetylcholinesterase [[1vot]] containing the inhibitor huperzine A. Colored by depth from the <font color="red">surface entrance</font>. Cavity detail: extra fine. See [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins|how to obtain these views in PACUPP]].
+</td></tr></table>
+[http://molviz.org/pacupp PACUPP]], '''P'''ockets '''A'''nd '''C'''avities '''U'''sing '''P'''seudoatoms in '''P'''roteins, identifies cavities by filling them with pseudoatoms (holmium, Ho, think "holes"; see comparison note<ref name="hitormiss" />). Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.5 Å, configurable), or pockets between a smoothed macromolecular surface (default surface probe radius 10 Å, configurable) and atoms of the macromolecule. Starting point(s) are not relevant. An example is presented in some detail at [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]. Further examples with demonstrations of how to use PACUPP are in a YouTube video and a slideshow, available from [http://molviz.org/pacupp molviz.org/pacupp], where you can also download the program.
-PACUPP offers a number of [http://molviz.org/pacupp/commands-alphabetical.pdf simple commands specialized for visualizing cavities], mostly single letter commands. Some call up a dialog where the use enters information. Lists cavity-lining atoms in a spreadsheet-ready text file. Learning the PACUPP commands is much easier than learning Jmol commands.
+PACUPP offers a number of [http://molviz.org/pacupp/commands-alphabetical.pdf simple commands specialized for visualizing cavities], mostly single letter commands. Some call up a dialog where the use enters information. Lists cavity-lining atoms in a '''spreadsheet-ready''' text file. Learning the PACUPP commands is much easier than learning Jmol commands.
 PACUPP is a Jmol script. It processes 2/3 of the entries in the [[Protein Data Bank]] in &le;15 sec each. For large models such as ribosomes or proteasomes that may take many minutes, PACUPP offers an unattended batch mode.
 First released December, 2020.
+==See Also==
+*[[Jmol/Cavities pockets and tunnels]]
+*[[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]
+*[[Jmol/Depth from surface]]
+*[[SARS-CoV-2 spike protein fusion transformation]] which discusses the spike protein cavity used as an example above.
 ==References==
 <references />