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Jmol in Notebook

asked 13 years ago

Anne Schilling gravatar image

updated 13 years ago

kcrisman gravatar image

Hi!

I am trying to use the following commands in the notebook:

sage: x, y, z = var('x, y, z')
sage: plot3d(x^2 + y^2, (x,-2,2), (y,-2,2))

but Jmol terminates and just returns a black picture. These commands work fine in the command line. I tried this both on my laptop and on the notebook server at sage.lacim.uqam.ca. Is there some configuration necessary to display jmol pictures in the notebook?

Thanks,

Anne

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This is almost certainly to do with your specific configuration. We have had these kinds of issues on a recurring basis. I would suggest searching sage-support (though it's hard to do sometimes) for this. Sometimes it's a Linux thing, sometimes you need to update your Java, and sometimes it's a bug. What version do you have? We did fix some of these things in patches that should be in 4.7.

kcrisman gravatar imagekcrisman ( 13 years ago )

If you are using Mac OS X + Chrome there is a good thread on sage-support, although that problem was fixed (at least in 4.7.1). You may need to enable your browser to load java applets. Try going to http://jmol.sourceforge.net/demo/alphahelix/ and see if the jmol applet loads.

benjaminfjones gravatar imagebenjaminfjones ( 13 years ago )

Thank you for your answers. I am running sage-4.7.1 under Mac OS. The jmol applet loads fine for me when I go to http://jmol.sourceforge.net/demo/alphahelix/ . I am not sure which operating system http://sage.lacim.uqam.ca uses, but the sage version there is sage-4.7. You can get a free account and see whether the problem also occurs for you there.

Anne Schilling gravatar imageAnne Schilling ( 13 years ago )

Thank you for your answers. I am running sage-4.7.1 under Mac OS. The jmol applet loads fine for me when I go to http://jmol.sourceforge.net/demo/alphahelix/ . I am not sure which operating system http://sage.lacim.uqam.ca uses, but the sage version there is sage-4.7. You can get a free account and see whether the problem also occurs for you there.

Anne Schilling gravatar imageAnne Schilling ( 13 years ago )

PS: I am using Firefox.

Anne Schilling gravatar imageAnne Schilling ( 13 years ago )

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answered 13 years ago

benjaminfjones gravatar image

updated 13 years ago

I just tried pasting your code into the server http://sage.lacim.uqam.ca where I created a new account. Everything worked like it should for me, jMol starts (slowly, but that's ok), and I get a 3d interactive plot.

I've had problems with jMol before that were miraculously solved by clearing my browser cache and history data. I'd recommend:

  1. update firefox to the most recent version
  2. clear all browsing data (cache, cookies, etc..)
  3. try again

See if that solves the problem. This reminds me about a joke involving an engineer, a physicist, and a computer scientist in a broken down car...

-- Update --

If it seems to work in Safari, try putting this in your .bashrc (or .bash_profile) file:

export SAGE_BROWSER='open -a Safari'
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Well, I updated to Firefox 6.0, cleared all browsing data, but it still does not work for me. I still get a black picture and a little note saying "jmol script terminated". It does work with Safari, however. But then I am having trouble getting sage to use a non-default browser. I put export SAGE_BROWSER="/Applications/Safari.app/Contents/MacOS/Safari" in my .bashrc file, but then Safari complains that it cannot find certain files. Did you use firefox when you tried the lacim server?

Anne Schilling gravatar imageAnne Schilling ( 13 years ago )

My problem seems to be the same as in http://groups.google.com/group/sage-support/browse_frm/thread/f726900d8281508e/0fb1328060b9b83c?tvc=1&q=Jmol#0fb1328060b9b83c . There is no answer there. Was this issue ever resolved?

Anne Schilling gravatar imageAnne Schilling ( 13 years ago )

Thank you, your export statement for Safari works! It would still be good to understand the Firefox problem at some point since from the threads in sage-support it seems that others have had the same problem.

Anne Schilling gravatar imageAnne Schilling ( 13 years ago )

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Asked: 13 years ago

Seen: 1,687 times

Last updated: Aug 20 '11