Jmol: Difference between revisions
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Jmol<ref>Jmol was initiated before 2000 by [http://openscience.org 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, [http://www.stolaf.edu/people/hansonr/ Robert M. Hanson] became lead developer, and has vastly enhanced Jmol's capabilities. For more, see [http://jmol.sourceforge.net/history/ History of Jmol Development].</ref><ref>Biomolecules in the computer: Jmol to the rescue. Angel Herráez,[http://www3.interscience.wiley.com/journal/113449000/abstract ''Biochem. Mol. Biol. Ed.'' '''34''':255-61, 2006].</ref><ref name="jmolparadigmshift" /><ref>[http://wiki.jmol.org:81/index.php/Literature Jmol Literature] at the Jmol.Org wiki.</ref> is a free, open-source [[Molecular modeling and visualization software|molecular visualization]] software package. It is the primary visualization software used in Proteopedia. Jmol is a [http://en.wikipedia.org/wiki/Cross-platform cross-platform] program written in [[Java]], but able to run in an HTML5/Javascript-mode called "'''JSmol'''"<ref>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 [http://onlinelibrary.wiley.com/doi/10.1002/ijch.201300024 ''Israel Journal of Chemistry'' '''33''':207-16, 2013]</ref> that does not require [[Java]]. Jmol is also available as a stand-alone [[Jmol/Application|application]]. See [[#Jmol Has Four Forms| | Jmol<ref>Jmol was initiated before 2000 by [http://openscience.org 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, [http://www.stolaf.edu/people/hansonr/ Robert M. Hanson] became lead developer, and has vastly enhanced Jmol's capabilities. For more, see [http://jmol.sourceforge.net/history/ History of Jmol Development].</ref><ref>Biomolecules in the computer: Jmol to the rescue. Angel Herráez,[http://www3.interscience.wiley.com/journal/113449000/abstract ''Biochem. Mol. Biol. Ed.'' '''34''':255-61, 2006].</ref><ref name="jmolparadigmshift" /><ref>[http://wiki.jmol.org:81/index.php/Literature Jmol Literature] at the Jmol.Org wiki.</ref> is a free, open-source [[Molecular modeling and visualization software|molecular visualization]] software package. It is the primary visualization software used in Proteopedia. Jmol is a [http://en.wikipedia.org/wiki/Cross-platform cross-platform] program written in [[Java]], but able to run in an HTML5/Javascript-mode called "'''JSmol'''"<ref>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 [http://onlinelibrary.wiley.com/doi/10.1002/ijch.201300024 ''Israel Journal of Chemistry'' '''33''':207-16, 2013]</ref> that does not require [[Java]]. Jmol is also available as a stand-alone [[Jmol/Application|application]]. See [[#Jmol Has Four Forms|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. | '''JSmol''' has proven quite satisfactory for interactive displays of most macromolecules in Proteopedia, and is the default. | ||
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==Jmol Has Two Forms== | ==Jmol Has Two Forms== | ||
Originally, Jmol had 4 forms. Two (Java applets, signed and unsigned) are now obsolete. | |||
<center><table border="1" cellpadding="5"> | <center><table border="1" cellpadding="5"> | ||
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No (HTML5)<br>Runs on | No (HTML5).<br>Runs on tablets and smart phones as well as laptop computers. | ||
</td> | </td> | ||
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Slower | Slower, especially if >30,000 atoms or | ||
multiple models, but with patience, can handle up to a million atoms. | |||
multiple models | |||
</td> | </td> | ||
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Jmol.jar application (stand alone; not in web browser) | |||
</td> | </td> | ||
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Yes | Yes, Java is required. | ||
</td> | </td> | ||
<td> | <td> | ||
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Advanced use (usually with [http://chemapps.stolaf.edu/jmol/docs/ Jmol command language]). | Advanced use (usually with [http://chemapps.stolaf.edu/jmol/docs/ Jmol command language]). | ||
[http://firstglance.jmol.org/animation_kit_instructions.pdf Animation Kit of FirstGlance]. | |||
[http://molviz.org/pacupp PACUPP]: Pockets And Cavities Using Pseudoatoms in Proteins. | |||
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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 [[Demonstration of a complex animation playing from a green link|here]]. | 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 [[Demonstration of a complex animation playing from a green link|here]]. | ||
<!--- OBSOLETE, COMMENTED OUT BY ERIC MARTZ DECEMBER 2025. NO WEB BROWSERS STILL ENABLE JAVA APPLETS. | |||
==Distinguishing if Jmol is running in HTML5/Javascript-mode or Java-mode== | ==Distinguishing if Jmol is running in HTML5/Javascript-mode or Java-mode== | ||
Jmol is the primary visualization software used in Proteopedia. Jmol is a [http://en.wikipedia.org/wiki/Cross-platform 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. | Jmol is the primary visualization software used in Proteopedia. Jmol is a [http://en.wikipedia.org/wiki/Cross-platform 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 [[Using Java for Rendering Structures|here]] for how to opt in to Java mode. | '''At this time, Jmol still performs best in Java mode and users are encouraged to use that on Proteoepdia.''' See [[Using Java for Rendering Structures|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 <font color="maroon">Jmol_S</font> in the bottom right corner of the Proteopedia structure scene windows when Jmol is running with the signed Java applet. You'll see <font color="gold">JSmol</font> in the bottom right corner of structure windows when Jmol is operating in HTML/Javascript mode. A visual representation of that can be seen [[Distinguishing the modes of Jmol on Proteopedia|here]]. | You can easily distinguish which mode Jmol is presently running in by looking in the bottom right corner. You'll see <font color="maroon">Jmol_S</font> in the bottom right corner of the Proteopedia structure scene windows when Jmol is running with the signed Java applet. You'll see <font color="gold">JSmol</font> in the bottom right corner of structure windows when Jmol is operating in HTML/Javascript mode. A visual representation of that can be seen [[Distinguishing the modes of Jmol on Proteopedia|here]]. | ||
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==What version of Jmol is running?== | ==What version of Jmol is running?== | ||
