Help:Jmol in EcoliWiki

Jmol is a Java-based molecular visualization tool. Extensive documentation can be found on the Jmol website. This page describes how you can embed images and set scenes inside EcoliWiki using Jmol's MediaWiki extension.

Working with Jmol in EcoliWiki is a bit of an advanced topic, so it may be useful to familiarize yourself with Mediawiki markup conventions. See Category:Help

Embedding Jmol by transclusion

See Help:Jmol in EcoliWiki Lex A C-terminal domain, residues 68-202 PDB:1JHE <jmol> <jmolApplet> <color>white</color> <uploadedFileContents >1JHE.pdb</uploadedFileContents> <script> wireframe off; spacefill off; trace off; rotate ON; select *:A; spacefill on; color cyan; select *:B; cartoon on; color monomer; select *:3; color cyan; </script> </jmolApplet> </jmol> <jmol> <jmolCheckbox > <scriptWhenChecked > rotate on; </scriptWhenChecked > <scriptWhenUnchecked > rotate off; </scriptWhenUnchecked > <checked>true</checked> <text>rotate</text> </jmolCheckbox > <jmolButton><script>reset; select all; wireframe off; spacefill off; trace off; rotate ON; select *:A; spacefill on; color cyan; select *:B; cartoon on; color monomer; select *:3; color cyan; </script><text>reset</text></jmolButton> </jmol>

The markup for Jmol can be verbose, and putting Jmol scripts directly in pages can make them hard to edit. So we suggest making a page for your Jmol viewer and including it in the desired page by transclusion. A convenient way to do this is to use the Image page created by uploading a .pdb coordinate file. For example, the page at Image:1JHE.pdb was created when the JHE.pdb file was uploaded to the wiki. The page was then edited to add the Jmol viewer. To put it in this page, we used {{Image:1JHE.pdb}}, where the curly brackets tell Mediawiki to copy the content of the Image page. Similar approaches can be used to transclude an image from any other page in the wiki, in case you want different default behavior.

Making the viewer

You can build a viewer from scratch, or you can start by using {{subst:Jmol_template}} and saving to incorporate a template viewer. You'll still have to edit it, but this will put the viewer in a box that allows text to wrap around it on the right, add the Help link, set the background to white, and so on.

The viewer block

The viewer settings reside inside flanking jmol and jmolApplet tags. For example:

 <jmol>
  <jmolApplet>
   <color>white</color>
   <uploadedFileContents >1JHE.pdb</uploadedFileContents>
   <script>
        wireframe off; trace off;
       rotate on;
       spacefill on;
       color chain;
  </script>
  </jmolApplet>
 </jmol>

The script tags are used in several contexts in the Jmol extension. Here, they tell the applet the default script to run when the applet loads.

Setting the pdb file

Put the name of the pdb file between

<uploadedFileContents >pdb file name</uploadedFileContents>

Note that this is just the filename, without Image: or Media; prefixes. Alternatively, you can create a wiki page with the the coordinates and use

<wikiPageContents>page of the wiki containing the molecular data</wikiPageContents>

or use

<inlineContents>contents of the molecular file</inlineContents>

to put the coordinates right in the viewer.

Making external links to control the viewer

As with the viewers, we suggest making link scripts on a separate wiki page and including them by transclusion. A convenient way to arrange these is to put some documentation for Jmol links in the talk page for an uploaded pdb file, and make the scripts as subpages. For example,

• The structure above is at [:Image:1JHE.pdb]]
• Discussion of the structure file is at Image_talk:1JHE.pdb
• Subpages of the talk page can be used for scripts that save specific views.

Example: Image_talk:1JHE.pdb/catalytic_site contains a Jmol link script, which is incorporated to make this link <jmol> <jmolLink> <script> rotate off; select *:B; color grey; select *:A; ribbon on; spacefill off; select 84, 85; spacefill; color yellow; select all; select 119, 156; spacefill; color cpk; select hoh; spacefill off; zoomto (84:A) 500; </script> <text>(highlight cleavage site and S119, K156A)</text> </jmolLink> </jmol>using {{Image_talk:1JHE.pdb/catalytic_site}}

Known bugs

• the transclusion does not work if the markup is included in the wiki markup for a list or indented text
• start the next word after the transclusion immediately after - don't leave a space.

More examples

• Image:1LMB.pdb, Image_talk:1LMB.pdb, and lambda_repressor/N-domain

Jmol scripting

Here, we'll just cover a few commonly used commands. See below for links to more extensive documentation and tutorials.

Command	Notes	Examples
select [atom-expression]	You need to select things to work on them selectively. Atom expressions include: numbers for residues :chain_id for chains (subunits) backbone sidechains	select 1-10; selects residues 1-10 in all chains select *:A; selects all atoms in chain A select 84:A, 156:B; selects two residues, one in chain A and one in chain B.
spacefill (on/off/only) (synonym: cpk)	Shows atoms as VdW sized spheres
wireframe (on/off/only)	shows the bonds between atoms.
cartoon (on/off/only)	shows helices and sheets in cartoon form.
zoom (atom-expression) %zoom zoomto (atom-expression) %zoom	centers on atom-expression and zooms there to the specified percentage of the 100% default. The zoom factor can range from 5 to 20,000, where larger numbers are zoomed in.	zoomto (84:A) 500;
color [drawn-object] [RGB-color]	if drawn-object is ommitted, color uses whatever is selected. Colors can be: color names: white, blue, red, cyan, etc. special names monomer - gives a rainbow from N to C cpk amino - by aa type for proteins shapely - by base type for nucleic acids structure - helices and sheets chain - subunits hex values: [xRRGGBB] (brackets needed) RGB triples: [255,0,255]
edit table

See also

• Scripting on the Jmol wiki.
• Colors
• scripting commands

References

See Help:References for how to manage references in EcoliWiki.