Jmol/Cavities pockets and tunnels: Difference between revisions
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<StructureSection load='' size='350' side='right' caption='' scene='85/858407/6zgi-m1000-cav-sd-set2/1'> | |||
<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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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: | 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: | ||
:<tt>isosurface minset 1000 cavity</tt> | :<tt><scene name='85/858407/6zgi-m1000-c/2'>isosurface minset 1000 cavity</scene></tt><!--6zgi-m1000-cav.pngj--> | ||
Now only the largest two cavities are shown. The larger one is a convoluted tunnel with many mouths, volume 60,197 Å<sup>3</sup>. The smaller one is the membrane-proximal cavity of interest, volume 7,591 Å<sup>3</sup>. | Now only the largest two cavities are shown. The larger one is a convoluted tunnel with many mouths, volume 60,197 Å<sup>3</sup>. The smaller one is the membrane-proximal cavity of interest, volume 7,591 Å<sup>3</sup>. | ||
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The command to display only the smaller cavity is: | The command to display only the smaller cavity is: | ||
:<tt>isosurface set 2</tt> | :<tt><scene name='85/858407/6zgi-m1000-c-set2/2'>isosurface set 2</scene></tt><!--6zgi-m1000-cav-set2.pngj--> | ||
===Coloring By Depth=== | ===Coloring By Depth=== | ||
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It is revealing to color this cavity by distance from the surface with this command: | It is revealing to color this cavity by distance from the surface with this command: | ||
:<tt> | :<tt><scene name='85/858407/6zgi-m1000-cav-sd-set2/1'>isosurface map property surfacedistance</scene></tt><ref>This command works only if a previous <tt>isosurface ... cavity</tt> command has been run in the same session. It will not work if the surface is loaded from a JVXL file alone, because then the surface has not been defined.</ref> <!--6zgi-m1000-cav-sd-set2.pngj--> | ||
6zgi-m1000-cav | |||
shows that the red parts, which are at or near the protein surface, are mostly closed. The "cavity" command, without modifiers, generates closed isosurfaces. | <scene name='85/858407/6zgi-m1000-cav-sd-set2-detail/2'>Close examination</scene><ref>The command for ''close examination'' is based on finding that Asn1107 is close to the deep chamber of the membrane-proximal cavity. The command is <tt>zoomto {1107} 266</tt>. This centers the deep part of the cavity and zooms to 266%.</ref> shows that the red parts, which are at or near the protein surface, are mostly '''closed'''. The "cavity" command, without modifiers, generates closed isosurfaces. <!--Image:6zgi-m1000-cav-sd-set2-detail.pngj--> | ||
===Pockets vs. Interior Cavities=== | ===Pockets vs. Interior Cavities=== | ||
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Here is the command to show our cavity-of-interest's entrances from the protein surface as '''open''': | Here is the command to show our cavity-of-interest's entrances from the protein surface as '''open''': | ||
:<tt> | :<tt><scene name='85/858407/6zgi-m100-pcav-sd-set2-detail/1'>isosurface minset 100 pocket cavity</scene></tt><!--6zgi-m100-pcav-sd-set2-detail--> | ||
[[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>) | ||
|} | |} | ||
====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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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: | 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: | ||
:<tt>isosurface minset 30 cavity | :<tt><scene name='85/858407/6zgi-pocbur_2point5/1'>isosurface minset 30 cavity 2.5</scene></tt><!--6zgi-pocbur2.5 (minset 30)--> | ||
Because the deeper chamber has no entrances from the surface, it will not be shown when the entrance pockets are rendered open with the ''pockets'' modifier. Those open pockets must be combined with a separate isosurface calculation for the ''interior'' chamber. [[#Working Example Scripts|The scripts for doing this are below]]. | |||
==Ligands Inside Cavity== | |||
Bacterial glycosidase (alpha-N-acetylgalactosaminidase) [[2ixb]] has a tunnel containing NAD that includes, at one entrance, a pocket where substrate can access the catalytic site. The tunnel contains both NAD and a substrate molecule. The following commands show the translucent tunnel with its contents rendered as sticks. | |||
:<tt><scene name='85/858407/2ixb/1'>isosurface minset 100 select {protein} only pocket cavity property surfacedistance; isosurface set 2</scene></tt><!--2ixb-m100-poccav-sd-set1-xlu2.pngj--> | |||
*<tt>select {protein} only</tt> means that ligands and solvent are ignored during isosurface creation. | |||
*<tt>property surfacedistance</tt> colors the surface by depth as part of the isosurface creation. | |||
<!--==Large Cavity Example== | |||
<scene name='85/858407/3hyc/2'>''E. coli'' phosphatase KdsC is an 8-chain homo-octamer</scene>. 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 <scene name='85/858407/3hyc/3'>see through one pair of opposite openings</scene>.--> | |||
==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 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): | |||
[[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. [[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). | |||
<scene name='85/858407/ | |||
</StructureSection> | </StructureSection> | ||
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==Preparing Isosurface Scenes for Proteopedia== | ==Preparing Isosurface Scenes for Proteopedia== | ||
===Speed of Rendering=== | |||
If you use the isosurface commands below, do so in the [[Jmol/Application|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. | |||
=== | ===Working Directory=== | ||
Put a copy of Jmol.jar, and perhaps a downloaded copy of the PDB file(s) of interest in a new working directory (folder). By default, JVXL and PNGJ files you write will be written into the directory from which you start Jmol.jar. Any Jmol command script files should also be placed in this working directory. This keeps everything simple. | |||
===Use PNGJ Files=== | ===Use PNGJ Files=== | ||
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*Links to pages outside Proteopedia using single brackets, such as [http://jmol.org jmol.org] (wikitext <nowiki>[http://jmol.org jmol.org]</nowiki>). | *Links to pages outside Proteopedia using single brackets, such as [http://jmol.org jmol.org] (wikitext <nowiki>[http://jmol.org jmol.org]</nowiki>). | ||
*Color keys using <span class="text-red"><b>colored</b></span> <span class="bg-yellow">text</span>. Coloring of text in captions must be done using span classes: see instructions at [[Coloring text]]. (In this example: <span class="text-red"><b>colored</b></span> <span class="bg-yellow">text</span>.) | *Color keys using <span class="text-red"><b>colored</b></span> <span class="bg-yellow">text</span>. Coloring of text in captions must be done using span classes: see instructions at [[Coloring text]]. (In this example: <span class="text-red"><b>colored</b></span> <span class="bg-yellow">text</span>.) | ||
===Multiple Isosurfaces=== | |||
There are two reasons why you may need multiple isosurfaces. | |||
*You want to show both closed interior cavities and open-mouthed surface pockets. | |||
*You want to show multiple pieces of a single isosurface. | |||
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=== | ||
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Here are the steps: | Here are the steps: | ||
<br> | <br> | ||
'''I. In the Jmol Java application:''' | '''I. In the [[Jmol/Application|Jmol Java application]]:''' | ||
:1. Calculate the isosurface(s). Commands are explained above in earlier sections of this article. If you will need more than one isosurface, for example one for pockets and one for interior cavities, assign each a distinct ID when you create them. Prefixing the ID with tilde (~) ensures the ID name does not conflict with an existing term in Jmol. In a Jmol command line, anything after # is a comment, ignored by Jmol. For example: | :1. Calculate the isosurface(s). Commands are explained above in earlier sections of this article. If you will need more than one isosurface, for example one for pockets and one for interior cavities, assign each a distinct ID when you create them. Prefixing the ID with tilde (~) ensures the ID name does not conflict with an existing term in Jmol. In a Jmol command line, anything after # is a comment, ignored by Jmol. For example: | ||
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::isosurface '''~bur''' minset 100 interior cavity # "buried"</tt> | ::isosurface '''~bur''' minset 100 interior cavity # "buried"</tt> | ||
:2. Color the isosurface(s). Coloring by depth from the surface was [[#Coloring By Depth|described above]]. For a plain color, first you must know the ID of the isosurface if there are more than one | :2. Color the isosurface(s). Coloring by depth from the surface was [[#Coloring By Depth|described above]]. For a plain color, first you must know the ID of the isosurface if there are more than one. | ||
::<tt>isosurface ~poc # Select the isosurface to color. Unnecessary if there is only one. | ::<tt>isosurface ~poc # Select the isosurface to color. Unnecessary if there is only one. | ||
::color isosurface pink # color name | ::color isosurface pink # color name | ||
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::color isosurface [x4060FF] # [https://www.rapidtables.com/web/color/RGB_Color.html RGB color]</tt> | ::color isosurface [x4060FF] # [https://www.rapidtables.com/web/color/RGB_Color.html RGB color]</tt> | ||
:3. Write each isosurface as a jvxl (Jmol Voxel) file. | :3. Write each isosurface as a jvxl (Jmol Voxel) file. Coloring is saved in the JVXL file. | ||
::<tt>isosurface ~poc # Select the isosurface to write. Unnecessary if there is only one. | ::<tt>isosurface ~poc # Select the isosurface to write. Unnecessary if there is only one. | ||
::write poc.jvxl | ::write poc.jvxl | ||
::isosurface ~bur # Select a different isosurface to color. | ::isosurface ~bur # Select a different isosurface to color. | ||
::write bur.jvxl</tt> | ::write bur.jvxl</tt> | ||
II. In Proteopedia: | :4. Quit Jmol and start a new session. Load the molecule and then the JVXL file(s). If you are loading more than one JVXL file (or the same JVXL file more than once so you can display multiple pieces of it), assign each load a distinct ID. (ID's are not saved in the jvxl files.) | ||
::<tt>load =6zgi | |||
::isosurface ~poc1 poc.jvxl | |||
::isosurface ~poc2 poc.jvxl | |||
::isosurface ~poc3 poc.jvxl | |||
::isosurface ~bur bur.jvxl</tt> | |||
:5. '''Cache''' the isosurface(s). This is critical. If this step is omitted, the PNGJ file will try to read the isosurfaces from the JVXL files, which will fail in Proteopedia. | |||
::<tt>isosurface cache # A single command caches ALL isosurfaces.</tt> | |||
:6. Write the PNGJ file. It is best if you have rendered and colored the macromolecule exactly as you want the scene to appear in Proteopedia before writing the PNGJ file. | |||
::<tt>write filename.pngj</tt> | |||
'''II. In Proteopedia:''' | |||
:7. Upload your PNGJ file. You do NOT need to compress the PNGJ file because it is already in a compressed format. See [[Help:Uploading molecules]]. Keep a copy of the name of the page for your uploaded PNGJ file. For example, ''Image:6zgi-m1000-cav.pngj''. | |||
:8. Now you are ready to use the [[SAT]] in your Proteopedia page. See [[Proteopedia:How to Make a Page]]. Use the '''load molecule''' tab in the SAT and paste in the name of the page containing your uploaded PNGJ file, such as ''Image:6zgi-m1000-cav.pngj''. Use the '''save scene''' tab. Add a caption, and save the scene, creating a green link. | |||
===Working Example Scripts=== | |||
[[Image:6zgi-pocbur2.5.png|250px|right]] | |||
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. | |||
====Write JVXL Files==== | |||
<pre> | |||
# In the Jmol Java application, | |||
# This script took 2 min 25 sec on a mid-2014 MacBook Pro. | |||
# It would likely take ~20 min in JSmol. | |||
zap # Deletes any molecule and all isosurfaces present in Jmol. | |||
print # Clears the Jmol Script Console. | |||
load =6zgi # Fetches PDB file from the RCSB Protein Data Bank. | |||
# RENDER MOLECULE. Unnecessary but takes no time and looks nice while executing. | |||
background white | |||
rotate x -90 | |||
restrict protein # Selects protein and hides non-protein, e.g. glycosylation. | |||
backbone only | |||
backbone 0.7 | |||
color chain | |||
set translucent false # Shows only the front-most surface of translucent objects. | |||
color translucent 5 # Chain-colored backbones are now translucent. | |||
refresh # Unnecessary, but shows the molecule. | |||
# MAKE POCKETS | |||
isosurface minset 50 pocket cavity 2.5 # Cavity probe radius 2.5 Å. | |||
refresh | |||
isosurface map property surfacedistance # Color pockets by depth. | |||
refresh | |||
write "poc.jvxl" | |||
isosurface delete | |||
# MAKE INTERIOR CAVITY NOT DISPLAYED IN THE POCKETS ISOSURFACE. | |||
isosurface minset 100 interior cavity 2.5 | |||
refresh | |||
isosurface map property surfacedistance | |||
refresh | |||
write "bur.jvxl" # Buried. | |||
</pre> | |||
====Write Cached PNGJ File==== | |||
<pre> | |||
# Execution of this script took 4 seconds on a mid-2014 MacBook Pro. | |||
zap # Deletes any molecule and all isosurfaces present in Jmol. | |||
print # Clears the Jmol Script Console. | |||
load =6zgi # Fetches PDB file from the RCSB Protein Data Bank. | |||
# RENDER MOLECULE | |||
background white | |||
rotate x -90 | |||
restrict protein # Selects protein and hides non-protein, e.g. glycosylation. | |||
backbone only | |||
backbone 0.7 | |||
color chain | |||
set translucent false # Shows only the front-most surface of translucent objects. | |||
color translucent 5 # Chain-colored backbones are now translucent. | |||
refresh # Unnecessary, but shows the molecule. | |||
# DISPLAY OPEN POCKETS. Can display only one piece (set) per isosurface. | |||
# To display three pieces (sets), create 3 (identical) isosurfaces. | |||
# Set numbers determined by trial and error. | |||
isosurface poc1 poc.jvxl | |||
isosurface poc1 set 8 | |||
isosurface poc2 poc.jvxl | |||
isosurface poc2 set 9 | |||
isosurface poc3 poc.jvxl | |||
isosurface poc3 set 11 | |||
# CLOSED DEEPER CHAMBER. | |||
isosurface bur bur.jvxl | |||
isosurface bur set 1 # Unnecessary because set 1 is the only one passing minset 100. | |||
delay 1.0 # shows the molecule with isosurfaces for 1 second. | |||
# Arg1107 surrounds the deeper chamber. | |||
# This centers that region, and zooms to 266%. | |||
zoomto {arg1107} 266 | |||
isosurface cache # Without this, JSmol will fail trying to read the jvxl files absent in Proteopedia. | |||
write "6zgi-pocbur2.5.pngj" # Ready to upload to Proteopedia. | |||
</pre> | |||
=== | ===Managing Cavity Isosurfaces=== | ||
Jmol commands for generating cavity isosurfaces were explained above. Full details will be found in the [https://chemapps.stolaf.edu/jmol/docs/#isosurfacesurfaceobject--molecular/solventsurfaces 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: | |||
* | *<tt>isosurface area set (integer) # Reports the surface area of one piece (set) of an isosurface in Å<sup>2</sup>. | ||
* | *isosurface * delete # Deletes all isosurfaces. | ||
* | *isosurface set (integer) # Displays just one piece (set) of an isosurface. | ||
* | *isosurface set 0 # Displays all pieces of an isosurface = the entire isosurface. | ||
* | *isosurface volume set (integer) # Reports the volume of one '''closed'''<ref name="volume">The volume that Jmol reports for a pocket (open mouth/entrance) is meaningless. Jmol reports meaningful volumes only for closed isosurfaces.</ref> isosurface in Å<sup>3</sup>.</tt> | ||
==See Also== | ==See Also== | ||
* [[Cavity programs]] | * [[Cavity programs]] | ||
* [[PACUPP]]: Pockets And Cavities Using Pseudoatoms in Proteins | |||
==References and Notes== | ==References and Notes== | ||
<references /> | <references /> | ||