Jmol problem

[Kwankyu]

Hi,

In my Sage 3.3 notebook on Mac OS 10.5/Firefox 3.07, Jmol 3d graphics
are shown as just black rectangles. I know this was a problem that
other people experienced. But is it now fixed? If this occurs only to
me, how can I fix it?

[Jason Grout]

Can you view some demos on the jmol website?

http://jmol.sourceforge.net/demo/atoms/

http://jmol.sourceforge.net/demo/animation/

Jason

[John Cremona]

When I try to view the frst demo I get this (and similarly from within
Sage) in a yellow fram in the window.

You do not have Java applets enabled in your web browser, or your
browser is blocking this applet.
Check the warning message from your browser and/or enable Java applets in
your web browser preferences, or install the Java Runtime Environment
from www.java.com

In the past I tried several ways to solve this but to no avail: I *do*
have Java applets enabled in Firefox, there is no warning message from
Firefox, and I have all sorts of version of JRE installed (this is in
ubuntu). I just gave up, since I can do without graphics, but it
would be nice to know what the problem is.

John Cremona

2009/3/7 Jason Grout <jason...@creativetrax.com>:

[Rob Beezer]

John et al,

I've been doing without JMOL on 64-bit Ubuntu, since Sun had not made
a 64-bit plugin until just recently. VERY inconvenient. ;-) I've
had similar frustrations as John with all sorts of JRE's around/
installed.

However, I got this new plugin installed last night in about 5
minutes. The instructions might help others on different platforms -
the Sun download area has RPM's, etc.

Here is the Ubuntu thread, just follow the first poster's instructions
modified/adjusted to fit your situation.

http://ubuntuforums.org/showthread.php?t=1011899

Rob

On Mar 7, 6:57 am, John Cremona <john.crem...@gmail.com> wrote:
> When I try to view the frst demo I get this (and similarly from within
> Sage) in a yellow fram in the window.
>
> You do not have Java applets enabled in your web browser, or your
> browser is blocking this applet.
> Check the warning message from your browser and/or enable Java applets in
> your web browser preferences, or install the Java Runtime Environment
> fromwww.java.com
>
> In the past I tried several ways to solve this but to no avail: I *do*
> have Java applets enabled in Firefox, there is no warning message from
> Firefox, and I have all sorts of version of JRE installed (this is in
> ubuntu).  I just gave up, since I can do without graphics, but it
> would be nice to know what the problem is.
>
> John Cremona
>

> 2009/3/7 Jason Grout <jason-s...@creativetrax.com>:

[gerhard]

> with all sorts of JRE's

one possible reason for this problem is
the plugin firefox may be using.

check by typing
about:plugins
in the title bar,
and make sure it is the plugin you expect
(sun's jre)

[John Cremona]

That's interesting -- there is no java at all listed in the list of
plugins. This is with 32-bit ubuntu.

John

2009/3/7 gerhard <ge0...@yahoo.de>:

[Rob Beezer]

I'd forgotten that about:plugins is so useful.

Do you know the Debian/Ubuntu alternatives scheme? Its a way to
specify a system-wide default editor, etc. See "man update-
alternatives"

On Ubuntu Hardy 8.04 I had to use (as root)

update-alternatives --config xulrunner-1.9-javaplugin.so

You can see the possible "alternatives" via
ls -al /etc/alternatives. The update-alternatives command manages
asll these symbolic links.

You want to have the xul-runner thing point to a Sun plug in, not an
Open JDK or IcedTea or some such thing. You'll probably get some
choices. (Presuming you have the right packages installed.)

THEN check about:plugins after a restart of Firefox. Good luck. ;-)

On Mar 7, 12:43 pm, John Cremona <john.crem...@gmail.com> wrote:
> That's interesting -- there is no java at all listed in the list of
> plugins.  This is with 32-bit ubuntu.
>
> John
>

> 2009/3/7 gerhard <ge01...@yahoo.de>:

[John Cremona]

Thanks for the detailed instructions. I have never heard of
xulrunner. Something of that name was installed but I installed a
newer (?) version using synaptic. I also used update-alternatives to
get java to point to the sun version. Now I have this:

john@ubuntu%sudo update-alternatives --display java
java - status is manual.
link currently points to /usr/lib/jvm/java-6-sun/jre/bin/java
/usr/lib/jvm/java-6-openjdk/jre/bin/java - priority 1061
slave java.1.gz: /usr/lib/jvm/java-6-openjdk/jre/man/man1/java.1.gz
/usr/bin/gij-4.2 - priority 42
slave java.1.gz: /usr/share/man/man1/gij-4.2.1.gz
/usr/lib/jvm/java-6-sun/jre/bin/java - priority 63
slave java.1.gz: /usr/lib/jvm/java-6-sun/jre/man/man1/java.1.gz
Current `best' version is /usr/lib/jvm/java-6-openjdk/jre/bin/java.

john@ubuntu%sudo update-alternatives --display xulrunner
xulrunner - status is auto.
link currently points to /usr/bin/xulrunner-1.9
/usr/bin/xulrunner-1.9 - priority 50
/usr/lib/xulrunner/xulrunner - priority 50
Current `best' version is /usr/bin/xulrunner-1.9.

I don't know what 'best' means, it still seems to like the look of the
open jdk for java.

After all this and restarting firefox there is still no mention of
java in about:plugins. I find it hard to believe that it is not there
since the Preferences setting for jave is enabled" and surely there
are many other web things which would not work without java (gmail for
a start).

The jmol demo page shows exactly the same message as before.

Never mind,

John

2009/3/7 Rob Beezer <goo...@beezer.cotse.net>:

[Jason Grout]

Gmail almost surely uses javascript, not java, which is different.

Jason

[Rob Beezer]

John,

java will point to something to run java programs locally on your
machine.

I think xulrunner is some Firefox/Mozilla thing.

You want a java *plugin* for Firefox.

Try the combo deal:

update-alternatives --config xulrunner-1.9-javaplugin.so

and pick the one that looks like it comes from Sun.

Rob

[John Cremona]

Problem solved. When I did

update-alternatives --config xulrunner-1.9-javaplugin.so

it complained that there was no such alternative. Googling that file
name led me to ubuntu forums and hence to the package name
sun-java6-plugin, which I did not have installed. So I installed it,
restarted firefox, and now it works!

I'm sure it is worth putting this information into the FAQ list, even
if it only applies to ubuntu machines: for jmol to work you need to
have the package sun-java6-plugin installed.

thanks for your help, now I can demo Sage's animated 3D graphics to people!

[Rob Beezer]

John,

Super! Thanks for the information. Yes, maybe I should add something
to the FAQ. Spring break is in a week. ;-)

The JMOL applet for the 3D plots is really powerful. Jason Grout and
I have been passing worksheets back and forth for the multivariate
calculus courses we are teaching and they are *really* enhancing my
course. They should all migrate to the Interact/Calculus section of
the wiki when we get a chance.

But Java is a pain to get working. Right up there with the Flash
plugin. Its always the proprietary bits. ;-)

Rob

[Kwankyu]

I solved my problem just by reinstalling Firefox. ^^ Thank you anyway!

Kwankyu