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Thomas Patko
Unregistered guest
Posted on Thursday, February 12, 2009 - 10:41 pm:   

Is there any possibility to export a structure, MO, geometry optimization, IRC, ....etc to a JMol format/webpage for sharing on the web? I recall that WebMO is based at least in part on some JMol components so I was wondering how easy or difficult such an export feature might be to add?

As an example, there is extensive use of the JMol export on the following website:

http://www.chemtube3d.com/index.html

In particular, when the larger view button is clicked very many options appear that I think are a rather good way of sharing computational results quickly (without passing 100MB files around).

Any ideas or thoughts? If there is already another good path to automate the creation of such JMol webpages that I would appreciate a link.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 77
Registered: 11-2006
Posted on Thursday, February 12, 2009 - 10:52 pm:   

We are looking into this possibility.

In the mean time, check out the 'HTML Export' feature (under 'Download' in the Job Manager). This can be used to create an interactive HTML page that can be posted on a web site, independent of the rest of WebMO.
Thomas Patko
Unregistered guest
Posted on Wednesday, February 18, 2009 - 9:17 am:   

Hello JR:

Thanks for the tip. I see that the export to HTML option does offer a basic HTML sharing feature. Unfortunately, I get the following error when I try to open the result of such an export. Also, I will look forward to hearing if implementation of the JMol type export with the various user options can be supported. It would be terrific.

Jmol applet jmolApplet0__029904983142163__ destroyed
load: class net.webmo.applet.ViewerApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.ViewerApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.SpectrumApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.SpectrumApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.TranslatorApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.TranslatorApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.ViewerApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.ViewerApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.SpectrumApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.SpectrumApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.TranslatorApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.TranslatorApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Exception in thread "AWT-EventQueue-6" java.lang.IllegalThreadStateException: forbid thread creation in disposed TG
at sun.plugin.security.ActivatorSecurityManager.checkAccess(Unknown Source)
at java.lang.ThreadGroup.checkAccess(Unknown Source)
at java.lang.Thread.init(Unknown Source)
at java.lang.Thread.<init>(Unknown Source)
at java.awt.EventDispatchThread.<init>(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.EventQueue.initDispatchThread(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Jmol applet jmolApplet0__672915895808716__ destroyed
load: class net.webmo.applet.ViewerApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.ViewerApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.SpectrumApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.SpectrumApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.TranslatorApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.TranslatorApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.ViewerApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.ViewerApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.SpectrumApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.SpectrumApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.TranslatorApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.TranslatorApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.ViewerApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.ViewerApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.SpectrumApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.SpectrumApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
load: class net.webmo.applet.TranslatorApplet.class not found.
java.lang.ClassNotFoundException: net.webmo.applet.TranslatorApplet.class
at sun.applet.AppletClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.applet.AppletClassLoader.loadCode(Unknown Source)
at sun.applet.AppletPanel.createApplet(Unknown Source)
at sun.plugin.AppletViewer.createApplet(Unknown Source)
at sun.applet.AppletPanel.runLoader(Unknown Source)
at sun.applet.AppletPanel.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
JR Schmidt
Moderator
Username: Schmidt

Post Number: 79
Registered: 11-2006
Posted on Wednesday, February 18, 2009 - 9:45 am:   

I just tried this on both Firefox and IE on Windows, without any issues? What browser/OS are you using?

You need more than just the HTML file, as the Java files (which are included in the downloaded tar/zip file) are required too!
Thomas Patko
Unregistered guest
Posted on Saturday, February 21, 2009 - 9:22 am:   

Hello JR:

Just as an FYI, I was able to export a geometry optimization to JMol with the following steps:

1) Open all geometry optimizations of interest in MacMolPlt and then went to File -> Export -> chose to export each optimization as a XMOL .xyz (all structures to be included chose yes).

2) I opened each optimization .xyz file in JMol and then selected File -> Export -> Export to Web Page and selected the options as appropriate (for my system I chose 600X600 pixel size and 80% of the window for the applet).

3) Copied all Jmol files to the directory selected when the Export to Web Page operation was done in JMol (default is .. so I just dumped everything into the root directory of my JMOL-EXPORT folder).

This would seem a perfect sort of thing for WebMO to handle as the procedure is reasonably straight forward but an automation of the process would be rather nice (particularly for large steps of jobs). In addition, it is clear that export very many geometry optimization, SPE, IRC, Vibration, .... job to a single integrated web page would also make sense for a number of situations (JMol Export to Web Page does support this option). It would also be nice for some typical "buttons" or view of interest that can be supported by JMol to be available as checkbox options (animation, play, animation stop, animation rewind, larger view, show charges, rotate, .....). These are all also available if the user right clicks, but this is not quite as web intuitive I think.

Cheers,

Thomas

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