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Jmol in published worksheets

asked 2011-04-08 18:01:27 +0200

niles gravatar image

One of my main interests in publishing worksheets was the thought that it would be an easy way to let people interact with 3D diagrams I produced, using Jmol.

But now Jmol is finally working on the flask notebook server, and I've finally published a worksheet there constructing some 3D diagrams, and it seems that the diagrams aren't shown unless one logs in to "Edit" the worksheet. I thought maybe adding "#auto" tags to each cell would help, but alas it did not.

Is there another way to make sure people can use the Jmol 3D diagrams? Or does someone know how to use the Jmol "export" feature to export to a standalone format?

If you want to take a look, the published worksheet is here. For now there's not much explanation, but there are two places where 3D diagrams (moduli spaces of quadrilaterals) are supposed to be drawn: and

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Kelvin Li gravatar imageKelvin Li ( 2011-04-09 22:07:46 +0200 )edit

Thanks -- so you're suggesting that I could somehow use jmol_repr to display the object?

niles gravatar imageniles ( 2011-04-10 09:40:33 +0200 )edit

You mentioned the option of "exporting" to a stand-alone viewer, which I conjecture jmol_repr would accomplish. According to (, Jmol can be run as a stand-alone application. I don't know anything beyond that.

Kelvin Li gravatar imageKelvin Li ( 2011-04-11 03:28:49 +0200 )edit

I think this is a change in how Jonathan dealt with some memory issues. You should email him directly, or at the very least look at #9238.

kcrisman gravatar imagekcrisman ( 2011-04-12 00:03:46 +0200 )edit

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answered 2011-04-15 22:32:44 +0200

niles gravatar image

Thanks for the tips everyone. I've made some progress -- seems like I'm still missing some things though. Here's what I've done:

  • Download the necessary Jmol files.
  • Use the "export to html" option from the Jmol viewer to produce a basic webpage with links to what Jmol thinks are all the necessary files.
  • Add in the header links to the java and javascript files referenced in the header of the sage notebook.

With this, I have embedded Jmol viewers which show only the axes, but not the tetrahedron I'm testing with. Any ideas of what I'm missing? Here's a link to my jmol test page.

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Asked: 2011-04-08 18:01:27 +0200

Seen: 502 times

Last updated: Apr 15 '11