I think I've got a working version of the my enhancements to jmol in the notebook...

[Jonathan Gutow]

Dear all,

Testers needed!  I think I finally solved all my asynchronicity problems with Jmol and the notebook.  I have now opened a ticket in trac (ticket #9238) with the new javascript libraries attached (Hope that was the right thing to do:).  Please try it out and let me know of problems.  I'm sure I missed some.

The enhancements are:

1) No more than 8 Jmols will be active at once. This prevents running out of memory. The user is provided with a link to wake up sleeping Jmols that they wish to manipulate. Sleeping Jmols are replaced with a static image.

2) A spin on/off check box is now provided.

3) The user may choose among a number of display sizes.

4) In the function tab, the user may change function color and mesh color.

5) The "State" tab displays the Jmol script to get the Jmol display. Eventually this will probably be hidden. If we can get the notebook to store this user views would also transfer across sessions.

Jonathan 

                         Dr. Jonathan H. Gutow

Chemistry Department                                gu...@uwosh.edu

UW-Oshkosh                                          Office: 920-424-1326

800 Algoma Boulevard                                FAX:920-424-2042

Oshkosh, WI 54901

                http://www.uwosh.edu/facstaff/gutow

[Jason Grout]

On 6/14/10 11:17 AM, Jonathan Gutow wrote:
> Dear all,
>
> Testers needed! I think I finally solved all my asynchronicity problems
> with Jmol and the notebook. I have now opened a ticket in trac (ticket
> #9238) with the new javascript libraries attached (Hope that was the
> right thing to do:). Please try it out and let me know of problems. I'm
> sure I missed some.
>
> The enhancements are:
> 1) No more than 8 Jmols will be active at once. This prevents running
> out of memory. The user is provided with a link to wake up sleeping
> Jmols that they wish to manipulate. Sleeping Jmols are replaced with a
> static image.
>
> 2) A spin on/off check box is now provided.
>
> 3) The user may choose among a number of display sizes.
>
> 4) In the function tab, the user may change function color and mesh color.
>
> 5) The "State" tab displays the Jmol script to get the Jmol display.
> Eventually this will probably be hidden. If we can get the notebook to
> store this user views would also transfer across sessions.

I've posted an spkg which includes Jonathan's changes and the new jmol.
To test all of the things above, you should be able to just do:

sage -f http://sage.math.washington.edu/home/jason/sagenb-0.8.p3.spkg

(be aware that this will overwrite your sagenb spkg, so you might do
this on a test version of Sage, unless you want to live on the edge.)

Jason

[Dan Drake]

On Mon, 14 Jun 2010 at 11:17AM -0500, Jonathan Gutow wrote:
> Testers needed! I think I finally solved all my asynchronicity
> problems with Jmol and the notebook. I have now opened a ticket in
> trac (ticket #9238) with the new javascript libraries attached (Hope
> that was the right thing to do:). Please try it out and let me know of
> problems. I'm sure I missed some.
>
> The enhancements are:
> 1) No more than 8 Jmols will be active at once. This prevents running out of memory. The user is provided with a link to wake up sleeping Jmols that they wish to manipulate. Sleeping Jmols are replaced with a static image.
> 2) A spin on/off check box is now provided.
>
> 3) The user may choose among a number of display sizes.
>
> 4) In the function tab, the user may change function color and mesh color.
>
> 5) The "State" tab displays the Jmol script to get the Jmol display.
> Eventually this will probably be hidden. If we can get the notebook to
> store this user views would also transfer across sessions.

I tried Jason's spkg with 4.4.4.alpha0, and I never actually got my plot
to display. The control panel showed up, and Jmol appeared to load, but
I never saw my plot. Then, when I clicked the "spin on" box, Firefox
crashed!

I'm using 64-bit Ubuntu 10.04 with the Iced Tea plugin. Displaying Jmol
applets works with Sage 4.4.

I'll test some more and see if I can get anything to work.

Dan

--
--- Dan Drake
----- http://mathsci.kaist.ac.kr/~drake
-------

[Jonathan]

Dan,
Thanks for the feedback. I'll take a look at it. I'm going to guess
that the problem relates to the IcedTea package. Jmol only supports
the official Sun Java. The fact that you could get Jmol to run using
IcedTea is a major improvement. It didn't used to run at all. If you
get a chance please test with the official Sun Java and let me know
the results.

Thanks,
Jonathan

On Jun 14, 9:15 pm, Dan Drake <dr...@kaist.edu> wrote:
> I tried Jason's spkg with 4.4.4.alpha0, and I never actually got my plot
> to display. The control panel showed up, and Jmol appeared to load, but
> I never saw my plot. Then, when I clicked the "spin on" box, Firefox
> crashed!
>
> I'm using 64-bit Ubuntu 10.04 with the Iced Tea plugin. Displaying Jmol
> applets works with Sage 4.4.
>
> I'll test some more and see if I can get anything to work.
>
> Dan
>
> --
> ---  Dan Drake
> -----  http://mathsci.kaist.ac.kr/~drake
> -------
>

>  signature.asc
> < 1KViewDownload

[Jonathan]

I've now tested Sage 4.4.3 with sun java and ubuntu 10.04 32 bit
(don't have a 64 bit version installed). The 32 bit works fine.

On Jun 14, 9:15 pm, Dan Drake <dr...@kaist.edu> wrote:

> I tried Jason's spkg with 4.4.4.alpha0, and I never actually got my plot
> to display. The control panel showed up, and Jmol appeared to load, but
> I never saw my plot. Then, when I clicked the "spin on" box, Firefox
> crashed!
>
> I'm using 64-bit Ubuntu 10.04 with the Iced Tea plugin. Displaying Jmol
> applets works with Sage 4.4.
>
> I'll test some more and see if I can get anything to work.
>
> Dan
>
> --
> ---  Dan Drake
> -----  http://mathsci.kaist.ac.kr/~drake
> -------
>

>  signature.asc
> < 1KViewDownload

[Dan Drake]

On Tue, 15 Jun 2010 at 05:49AM -0700, Jonathan wrote:
> Thanks for the feedback. I'll take a look at it. I'm going to guess
> that the problem relates to the IcedTea package. Jmol only supports
> the official Sun Java. The fact that you could get Jmol to run using
> IcedTea is a major improvement. It didn't used to run at all. If you
> get a chance please test with the official Sun Java and let me know
> the results.

Okay, I installed Sun^H^H^H Oracle Java and it seems to work. Although
at first, it didn't recognize that I even have a Java plugin installed,
although perhaps Firefox got confused about switching plugins. I'll
check again later, but it does appear to be working.