Jmol: Difference between revisions
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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?== | ||
