Jmol

From Proteopedia

Jmol^[1][2][3][4] is a free, open-source molecular visualization software package. It is the primary visualization software used in Proteopedia. Jmol is a cross-platform program written in Java, but able to run in an HTML5/Javascript-mode called "JSmol"^[5] that does not require Java. Jmol is also available as a stand-alone application. See 2 forms of Jmol and How JSmol Works. An overview of other Jmol resources is at Jmol/Index.

JSmol has proven quite satisfactory for interactive displays of most macromolecules in Proteopedia, and is the default.

For very large assemblies, the Mol* (Molstar) viewer is used instead of JSmol (example: 6mx4).

For more information and downloads: See Also.

Jmol Has Two Forms

Use in Scientific Journals

Jmol is used in traditional scientific journals in three main ways.

1. Interactive 3D Complement pages in Proteopedia. Authors of scientific journal publications, working in collaboration with a dedicated team in Proteopedia, develop rich interactive pages that complement their journal paper, making its structural aspects more comprehensible to a wider audience. See examples at Interactive 3D Complements.
2. Interactive 3D figures. Following the lead set by Protein Science with Kinemages in the early 1990's, figures in scientific journal articles have been implemented in Jmol so they can be rotated, etc. This involves manual implementation of each figure, a laborious task requiring a person knowledgeable in Jmol programming. Probably the first instance was in November, 2006, in ACS Chemical Biology, and subsequently in June, 2007, in Biochemical Journal with interactive 3D figures in Jmol implemented by Frieda Reichsman. Authoring of these interactive 3D figures remains time consuming, and only about a dozen articles have been so illustrated as of early 2010 (listed at Reichsman's site MoleculesInMotion.Com). In 2008, the International Union of Crystallography developed a toolkit to facilitate the authoring of interactive figures in Jmol in their journals^[6]. Outstanding examples are in the 2010 article by Robert M. Hanson (principal author of Jmol after 2005) Jmol – a paradigm shift in crystallographic visualization^[3], as well as in a talk given by him in early 2011 at the ICSTI Workshop ^[7]. In 2009, Protein Science began using this technology^[8].

3. FirstGlance in Jmol is used by several journals for interactive 3D display and exploration of newly published macromolecular structures. Typically, a link labeled 3D View appears in the online journal articles and contents. The first journal to do this was Nature Structural and Molecular Biology in February, 2006, and others, including Nature, soon followed -- see Adoptions of FirstGlance in Jmol.

See also:

• Proteopedia:Supplementary materials
• Journals using Jmol.

Command Scripting Language

Jmol has an extensive and powerful command language^[9] that specifies molecular scenes. A molecular scene consists of the rendering or display for each part of the molecular model (e.g. ribbon cartoon, ball and stick, etc.), optionally hiding some parts of the model, the color or color scheme for each moiety, optional labels (attached to an atom) or signs (text in fixed locations), and the orientation and zoom (magnification) of the molecule. Jmol's command language is a superset of the RasMol and Chime command languages.

A command script or simply script is a series of commands recorded in a file. Script files are plain text, and their filenames end with .spt.

Proteopedia's Scene Authoring Tools free Proteopedia users from the burden of learning Jmol's command language, by enabling them to author complex molecular scenes from menus, buttons, checkboxes and forms. Further, Proteopedia saves customized molecular scenes in the form of state scripts.

For advanced users who wish to use Jmol commands, instructions are provided:

• Using Jmol commands in the applet
• Using Jmol commands in the application

State Scripts

Jmol has the capability to generate a command script that will recreate whatever molecular scene it is currently displaying, including all details and the orientation of the molecule. Proteopedia uses this capability to save scenes created with its Scene Authoring Tools so they can be displayed in its web pages and thereby easily shared.

A state script recreates a single molecular scene, possibly including an animation among multiple models (when the PDB file contains more than one model -- see Morphs). Each green link in Proteopedia runs a state script in Jmol, recreating a single scene.

Complex Animations

In addition to the straightforward animations and/or Morphs which were mentioned in the previous paragraph and that can be specified in the Scene authoring tools, more complex animations, typically involving timed transitions between multiple scenes, can also be played in Proteopedia. Examples are may be seen at Molecular Playground/Tamiflu and Molecular Playground/HIV Protease Inhibitor. Command scripts for complex animations must be authored by hand by someone familiar with Jmol's command language. The resulting script file(s) are then uploaded to Proteopedia. Uploaded scripts are not played by typical green scene links, but can be played from buttons (see the above-linked examples) or text linked to the script that looks like the typical Proteopedia green scene links, as described here.

Distinguishing if Jmol is running in HTML5/Javascript-mode or Java-mode

Jmol is the primary visualization software used in Proteopedia. Jmol is a cross-platform program written in Java, but able to run in an HTML/Javascript-mode that does not require Java. The HTML/Javascript mode is presently the default on Proteopedia as it runs on more platforms.

At this time, Jmol still performs best in Java mode and users are encouraged to use that on Proteoepdia. See here for how to opt in to Java mode.

You can easily distinguish which mode Jmol is presently running in by looking in the bottom right corner. You'll see Jmol_S in the bottom right corner of the Proteopedia structure scene windows when Jmol is running with the signed Java applet. You'll see JSmol in the bottom right corner of structure windows when Jmol is operating in HTML/Javascript mode. A visual representation of that can be seen here.

What version of Jmol is running?

The version of Jmol currently running in Proteopedia is reported in the line JmolExtension at Special:Version in the column (now loaded Jmol version .....).

Loading Pages with Custom Versions of the Jmol applet

Advanced users may wish to load a Proteopedia page with a version of the Jmol applet other than the currently used version. This works best when Jmol comes from the Proteopedia.Org server, in which case both the unsigned and signed applets work. Testing new versions of the Jmol applet in Proteopedia, or running the signed applet in order to save an image file in the local drive, would involve running such custom versions.

To load a page with a custom version of the Jmol applet, in your browser's address bar, immediately after the normal Proteopedia page URL, paste code that is similar to below pointing at the files for the chosen version of the Jmol applet. The normal Proteopedia page URL in this example is 'http://proteopedia.org/wiki/index.php/1stp'.

EXAMPLE CODE TO PASTE AFTER A TYPICAL PROTEOPEDIA PAGE URL IN THE ADDRESS BAR:

?JMOLJAR=http://proteopedia.org/jmol12.2.16/JmolAppletSigned0.jar

Resulting example of the URL in your browser's address bar of:

http://proteopedia.org/wiki/index.php/1stp?JMOLJAR=http://proteopedia.org/jmol12.2.16/JmolAppletSigned0.jar

Please note that although URLs, such as 'http://www.proteopedia.org/wiki/index.php/1stp', will work to load a normal Proteopedia page, you cannot have 'www.' in front of 'proteopedia.org' for URLs where you want to load custom Jmol versions.

Available previous Jmol versions

Proteopedia used Jmol 11.8.24 until March 25, 2012, when it was upgraded to 12.2.19.

?JMOLJAR=http://proteopedia.org/old/11.8.24/JmolAppletSigned0.jar
?JMOLJAR=http://proteopedia.org/old/11.8.24/JmolApplet0.jar

?JMOLJAR=http://proteopedia.org/old/12.2.19/JmolAppletSigned0.jar
?JMOLJAR=http://proteopedia.org/old/12.3.20/JmolAppletSigned0.jar
?JMOLJAR=http://proteopedia.org/old/12.3.22/JmolAppletSigned0.jar
?JMOLJAR=http://proteopedia.org/old/13.0.1/JmolAppletSigned0.jar

Versions of Jmol in use by Proteopedia at various dates (incomplete list):

• April 23, 2008: Using 11.5.24
• May 7, 2008: Upgraded to 11.5.35
• October, 2009: Using 11.6.14
• October 21, 2009: Upgrade to 11.8.7 then reverted to 11.6.14
• Nov 12, 2009: Upgraded to 11.8.9
• March 21, 2012: Upgraded to 12.2.19_dev
• April 17, 2012: Upgraded to 12.3.22
• June 27, 2012: Upgraded to 12.3.32
• August 23, 2012: Upgraded to 13.0.1
• January 26, 2014: Upgraded to 14.0.7 - Proteopedia upgraded to using a version of Jmol that allows two modes. Proteopedia defaults to run Jmol in an HTML5/Javascript-mode not requiring Java, but users can optionally use Jmol running as a signed Java applet. See here for how to opt in to Java mode.
• June 23, 2016: Upgraded to 14.6.0
• February 20, 2017: Upgraded to 14.9.1
• January 25, 2018: Upgraded to 14.28.4
•  ??: Upgraded to 14.29.16

The version of Jmol currently running in Proteopedia is reported in the line JmolExtension at Special:Version in the column (now loaded Jmol version .....)

See Also

• Jmol/Index, a list of Jmol resources.
• How JSmol Works (Minimally technical.)
• Jmol.Org: Download all forms of Jmol here. Wiki has lots of documentation.
• Jmol at Wikipedia
• FirstGlance in Jmol
• Using JSmol: User:Eric_Martz/JSmol_Notes
• Jmol/Visualizing large molecules
• Jmol/Application: How to use the Jmol application.
• Jmol/Synchronization of two or more molecules so they rotate and zoom together.
• Scene authoring tools
• Journals Using Jmol
• Proteopedia:Supplementary materials
• Molecular modeling and visualization software
• Jmol Script Command Reference Manual for advanced users. Proteopedia's Scene authoring tools make learning this language unnecessary for most Proteopedia users.

• Molstar (Mol*), an alternative to JSmol in Proteopedia. Molstar is especially suited to very large molecules.

References

1. ↑ Jmol was initiated before 2000 by Dan Gezelter, and many programmers contributed to it including Bradley A. Smith, Egon Willighagen, and Cristoph Steinbeck. In 2002, Miguel Howard volunteered as the primary developer. He made many major enhancements including drastically improved performance, support for macromolecules, and implementation of the RasMol / Chime script command language. Howard's work culminated in the release of an open-source replacement for Chime in 2006. Subsequently, Robert M. Hanson became lead developer, and has vastly enhanced Jmol's capabilities. For more, see History of Jmol Development.
2. ↑ Biomolecules in the computer: Jmol to the rescue. Angel Herráez,Biochem. Mol. Biol. Ed. 34:255-61, 2006.
3. ↑ ^{3.0 3.1} Hanson, R. M. Jmol – a paradigm shift in crystallographic visualization. J. Appl. Crystallography 43 (2010). Open Access doi:10.1107/S0021889810030256
4. ↑ Jmol Literature at the Jmol.Org wiki.
5. ↑ Hanson, RH, Prilusky, J, Renjian, Z, Nakane, T & Sussman, JL. JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia Israel Journal of Chemistry 33:207-16, 2013
6. ↑ McMahon B, Hanson RM. A toolkit for publishing enhanced figures. J Appl Crystallogr. 2008 Aug 1;41(Pt 4):811-814. Epub 2008 Jul 1. PMID:19461848 doi:10.1107/S0021889808015616
7. ↑ Robert Hanson's talk is about 37 minutes in at the International Council for Scientific and Technical Information 2011 Workshop "Multimedia & Visualization for Science", @ Microsoft Research, Redmond, WA Feb. 8 2011
8. ↑ A. G. Palmer and B. W. Matthews, Interactive graphics return to protein science, Protein Science 18:677 (2009).
9. ↑ Documentation for Jmol's command language is available from Jmol.Org. An overview is at jmol.org/docs, and additional coverage of specific topics is at the Jmol Wiki. The command reference manual is at chemapps.stolaf.edu/jmol/docs/.