Jmol works from command line, but not notebook
Dan Drake
Jmol is not working for me from the notebook, but works fine from the
command line. I'm using 3.4.1 in Ubuntu Jaunty, with Firefox and the
"icedtea" Java plugin.
When I do this in a terminal, a Jmol window pops up and works great:
sage: u, v = var('u, v')
sage: parametric_plot3d([u*v, u, v^2], (u, -1,1), (v,-1,1))
The same commands in the notebook result in a black Jmol window and the
error message "Jmol script terminated" in the bottom bar of Firefox.
Here's the error messages printed to the terminal by Firefox:
Jmol applet jmolApplet1__440664173941044__ destroyed
Jmol applet jmolApplet2__440664173941044__ initializing
AppletRegistry.checkIn(jmolApplet2__440664173941044__)
urlImage=jar:file:/home/drake/.icedteaplugin/cache/https/sagenb.kaist.ac.kr/java/jmol/JmolApplet0.jar!/jmol75x29x8.gif
applet context: -applet
appletDocumentBase=https://sagenb.kaist.ac.kr:8022/home/admin/0/
appletCodeBase=https://sagenb.kaist.ac.kr:8022/java/jmol/
(C) 2008 Jmol Development
Jmol Version 11.6.16 2008-11-24 13:39
java.vendor:Sun Microsystems Inc.
java.version:1.6.0_0
os.name:Linux
memory:44.7/71.8
useCommandThread: false
appletId:jmolApplet2__440664173941044__
FileManager opening https://sagenb.kaist.ac.kr:8022/java/jmol/appletweb/SageMenu.mnu
defaults = "Jmol"
backgroundColor = "black"
language=en_US
FileManager opening https://sagenb.kaist.ac.kr:8022/home/admin/0/cells/3/sage0-size500.jmol?1241679757
script compiler ERROR: command expected
----line 1 command 1 of /home/admin/0/cells/3/sage0-size500.jmol?1241679757:
>>>> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"> <<<<
script ERROR: script compiler ERROR: command expected
----line 1 command 1 of /home/admin/0/cells/3/sage0-size500.jmol?1241679757:
>>>> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"> <<<<
eval ERROR:
----line 1 command 1:
script >> "/home/admin/0/cells/3/sage0-size500.jmol?1241679757" <<
The applet on the Jmol main page works fine, as well as their "browser
check" page. Other Java applets work fine.
A colleague here told me that Jmol wouldn't work for him at all, and
he was using IE and Chrome. (I'm not sure if he's having the same
problem, although he is using the same server.) Any ideas on what's wrong?
Dan
--
--- Dan Drake <dr...@kaist.edu>
----- KAIST Department of Mathematical Sciences
------- http://mathsci.kaist.ac.kr/~drake
Dan Drake
Java plugin fixed the problem for me in Linux. However, now I'm home on
my Macbook, and Jmol isn't working here!
In Firefox, I get the same problem, where it's just a black box. Every
other Java thing works here, including the Jmol stuff on their website,
so this does seem like some kind of Sage or Firefox problem.
Everything works fine in Safari, so it's not a system Java issue.
Any ideas?