ASKSAGE: Sage Q&A Forum - Individual question feedhttp://ask.sagemath.org/questions/Q&A Forum for SageenCopyright Sage, 2010. Some rights reserved under creative commons license.Wed, 30 Jan 2013 06:20:58 -0600Jmol in Notebookhttp://ask.sagemath.org/question/8282/jmol-in-notebook/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
Fri, 19 Aug 2011 05:47:02 -0500http://ask.sagemath.org/question/8282/jmol-in-notebook/Comment by benjaminfjones for <p>Hi!</p>
<p>I am trying to use the following commands in the notebook:</p>
<pre><code>sage: x, y, z = var('x, y, z')
sage: plot3d(x^2 + y^2, (x,-2,2), (y,-2,2))
</code></pre>
<p>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?</p>
<p>Thanks,</p>
<p>Anne</p>
http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21338#post-id-21338If 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.Fri, 19 Aug 2011 07:31:34 -0500http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21338#post-id-21338Comment by Anne Schilling for <p>Hi!</p>
<p>I am trying to use the following commands in the notebook:</p>
<pre><code>sage: x, y, z = var('x, y, z')
sage: plot3d(x^2 + y^2, (x,-2,2), (y,-2,2))
</code></pre>
<p>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?</p>
<p>Thanks,</p>
<p>Anne</p>
http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21336#post-id-21336Thank 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.Fri, 19 Aug 2011 12:15:42 -0500http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21336#post-id-21336Comment by kcrisman for <p>Hi!</p>
<p>I am trying to use the following commands in the notebook:</p>
<pre><code>sage: x, y, z = var('x, y, z')
sage: plot3d(x^2 + y^2, (x,-2,2), (y,-2,2))
</code></pre>
<p>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?</p>
<p>Thanks,</p>
<p>Anne</p>
http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21339#post-id-21339This 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.Fri, 19 Aug 2011 06:06:05 -0500http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21339#post-id-21339Comment by Anne Schilling for <p>Hi!</p>
<p>I am trying to use the following commands in the notebook:</p>
<pre><code>sage: x, y, z = var('x, y, z')
sage: plot3d(x^2 + y^2, (x,-2,2), (y,-2,2))
</code></pre>
<p>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?</p>
<p>Thanks,</p>
<p>Anne</p>
http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21337#post-id-21337Thank 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.Fri, 19 Aug 2011 12:15:41 -0500http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21337#post-id-21337Comment by Luiz Roberto Meier for <p>Hi!</p>
<p>I am trying to use the following commands in the notebook:</p>
<pre><code>sage: x, y, z = var('x, y, z')
sage: plot3d(x^2 + y^2, (x,-2,2), (y,-2,2))
</code></pre>
<p>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?</p>
<p>Thanks,</p>
<p>Anne</p>
http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=18322#post-id-18322Try to the examples of the tutorial (the first example of plot3d) if you are using version 5.5 or 5.6 and please tell me if it works fine (without the black image). I'm having trouble to run the spinning of a plot3d inside the tutorial/help but it works fine if I create a new notebook. No matter if I use linux, windows , virtual machine or even the livecd. Thanks.Wed, 30 Jan 2013 06:20:58 -0600http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=18322#post-id-18322Comment by Anne Schilling for <p>Hi!</p>
<p>I am trying to use the following commands in the notebook:</p>
<pre><code>sage: x, y, z = var('x, y, z')
sage: plot3d(x^2 + y^2, (x,-2,2), (y,-2,2))
</code></pre>
<p>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?</p>
<p>Thanks,</p>
<p>Anne</p>
http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21335#post-id-21335PS: I am using Firefox.Fri, 19 Aug 2011 12:23:53 -0500http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21335#post-id-21335Answer by benjaminfjones for <p>Hi!</p>
<p>I am trying to use the following commands in the notebook:</p>
<pre><code>sage: x, y, z = var('x, y, z')
sage: plot3d(x^2 + y^2, (x,-2,2), (y,-2,2))
</code></pre>
<p>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?</p>
<p>Thanks,</p>
<p>Anne</p>
http://ask.sagemath.org/question/8282/jmol-in-notebook/?answer=12593#post-id-12593I 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'
Fri, 19 Aug 2011 18:14:27 -0500http://ask.sagemath.org/question/8282/jmol-in-notebook/?answer=12593#post-id-12593Comment by Anne Schilling for <p>I just tried pasting your code into the server <a href="http://sage.lacim.uqam.ca">http://sage.lacim.uqam.ca</a> 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.</p>
<p>I've had problems with jMol before that were miraculously solved by clearing my browser cache and history data. I'd recommend:</p>
<ol>
<li>update firefox to the most recent version</li>
<li>clear all browsing data (cache, cookies, etc..)</li>
<li>try again</li>
</ol>
<p>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...</p>
<p>-- Update --</p>
<p>If it seems to work in Safari, try putting this in your .bashrc (or .bash_profile) file:</p>
<pre><code>export SAGE_BROWSER='open -a Safari'
</code></pre>
http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21332#post-id-21332Thank 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.Sat, 20 Aug 2011 19:32:08 -0500http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21332#post-id-21332Comment by Anne Schilling for <p>I just tried pasting your code into the server <a href="http://sage.lacim.uqam.ca">http://sage.lacim.uqam.ca</a> 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.</p>
<p>I've had problems with jMol before that were miraculously solved by clearing my browser cache and history data. I'd recommend:</p>
<ol>
<li>update firefox to the most recent version</li>
<li>clear all browsing data (cache, cookies, etc..)</li>
<li>try again</li>
</ol>
<p>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...</p>
<p>-- Update --</p>
<p>If it seems to work in Safari, try putting this in your .bashrc (or .bash_profile) file:</p>
<pre><code>export SAGE_BROWSER='open -a Safari'
</code></pre>
http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21333#post-id-21333My 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?Sat, 20 Aug 2011 14:40:10 -0500http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21333#post-id-21333Comment by Anne Schilling for <p>I just tried pasting your code into the server <a href="http://sage.lacim.uqam.ca">http://sage.lacim.uqam.ca</a> 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.</p>
<p>I've had problems with jMol before that were miraculously solved by clearing my browser cache and history data. I'd recommend:</p>
<ol>
<li>update firefox to the most recent version</li>
<li>clear all browsing data (cache, cookies, etc..)</li>
<li>try again</li>
</ol>
<p>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...</p>
<p>-- Update --</p>
<p>If it seems to work in Safari, try putting this in your .bashrc (or .bash_profile) file:</p>
<pre><code>export SAGE_BROWSER='open -a Safari'
</code></pre>
http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21334#post-id-21334Well, 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?Sat, 20 Aug 2011 08:31:26 -0500http://ask.sagemath.org/question/8282/jmol-in-notebook/?comment=21334#post-id-21334