jmol in OS X on Chrome
William Stein
I'm curious if anybody has a clue how to get Sage JMOL 3d graphics in
the notebook to work with either the released 9.x or beta 10.x
versions of the Google Chrome browser under OS X. I've tried both
the standard jmol that comes with sage-4.6.1 and the updated one here
[1] with no success at all. I just get "You do not have Java applets
enabled in your web browser, or your browser is blocking this
applet.". I had thought for a while that this was just a problem with
not having java installed properly or something, but the jmol examples
on the jmol site [2] work fine for me in Chrome.
I'm giving a plenary talk on Sage at an MAA meeting [3] tomorrow, and
it would be nice to not have to switch from Chrome to Firefox for the
3d Graphics part of my demo.
[1] http://trac.sagemath.org/sage_trac/ticket/9238
[2] E.g., http://jmol.sourceforge.net/demo/atoms/
[3] http://wolfweb.unr.edu/homepage/keppelma/sectionmeetings.html
--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
Jason Grout
> Hi,
>
> I'm curious if anybody has a clue how to get Sage JMOL 3d graphics in
> the notebook to work with either the released 9.x or beta 10.x
> versions of the Google Chrome browser under OS X. I've tried both
> the standard jmol that comes with sage-4.6.1 and the updated one here
> [1] with no success at all. I just get "You do not have Java applets
> enabled in your web browser, or your browser is blocking this
> applet.". I had thought for a while that this was just a problem with
> not having java installed properly or something, but the jmol examples
> on the jmol site [2] work fine for me in Chrome.
>
> I'm giving a plenary talk on Sage at an MAA meeting [3] tomorrow, and
> it would be nice to not have to switch from Chrome to Firefox for the
> 3d Graphics part of my demo.
I wonder if this might be the problem:
http://groups.google.com/group/sage-devel/browse_thread/thread/5abcc25886d9b8b1#
If it is, it sounds like the fix is to upgrade JMOL (e.g., review and
merge Jonathan's fixes and updates)
Jason
Jason Grout
Oops, I should have read your message more carefully. Maybe what I
pointed out wasn't the problem since you already tried the updated jmol
spkg (which apparently includes the fixes talked about in the post). In
that case, I have no clue.
Jason
William Stein
You use OS X. Does Chrome + "Sage 3d graphics with Jmol" work for
you? Or do you not use Chrome?
I'm curious also whether perhaps I just have something weird in my
Chrome configuration...
-- William
Jason Grout
With Sage 4.6.1, it doesn't work for me in:
Chromium 9.0.575.0 (65315)
Chrome 9.0.597.19 beta
Chrome 9.0.597.102
(I get the yellow box that says: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)
Thanks,
Jason
Benjamin Jones
notebook for me for a while. I don't remember when it started to not
work. There was a post on sage-support about this a while back and no
one had an answer. I searched through the Jmol support list for 10 or
20 mins and didn't find any problems using recent Chrome versions.
--
Benjamin Jones
On Feb 25, 11:34 pm, Jason Grout <jason-s...@creativetrax.com> wrote:
> On 2/25/11 11:21 PM, William Stein wrote:
>
>
>
>
>
>
>
>
>
> > On Fri, Feb 25, 2011 at 9:14 PM, Jason Grout
>
> >>> Hi,
>
> >>> I'm curious if anybody has a clue how to get Sage JMOL 3d graphics in
> >>> the notebook to work with either the released 9.x or beta 10.x
> >>> versions of the Google Chrome browser under OS X. I've tried both
> >>> the standard jmol that comes with sage-4.6.1 and the updated one here
> >>> [1] with no success at all. I just get "You do not have Java applets
> >>> enabled in your web browser, or your browser is blocking this
> >>> applet.". I had thought for a while that this was just a problem with
> >>> not having java installed properly or something, but the jmol examples
> >>> on the jmol site [2] work fine for me in Chrome.
>
> >>> I'm giving a plenary talk on Sage at an MAA meeting [3] tomorrow, and
> >>> it would be nice to not have to switch from Chrome to Firefox for the
> >>> 3d Graphics part of my demo.
>
> >>> [1]http://trac.sagemath.org/sage_trac/ticket/9238
William Stein
In contrast to my previous report, "suddenly" somehow using OS X +
beta Chrome (10.0.648.114 beta) and the new version of the jmol
package all *do* work fine together. I don't know why this suddenly
starting work -- perhaps I had to restart something. In any case,
this will be good for my demo tomorrow.
-- William
> --
> To post to this group, send email to sage-s...@googlegroups.com
> To unsubscribe from this group, send email to sage-support...@googlegroups.com
> For more options, visit this group at http://groups.google.com/group/sage-support
> URL: http://www.sagemath.org
Jason Grout
> Hi,
>
> In contrast to my previous report, "suddenly" somehow using OS X +
> beta Chrome (10.0.648.114 beta) and the new version of the jmol
> package all *do* work fine together. I don't know why this suddenly
> starting work -- perhaps I had to restart something. In any case,
> this will be good for my demo tomorrow.
Hopefully good. On the other hand, using a beta version of Chrome and a
not-yet-fully-reviewed jmol spkg could possibly see hangups. Nothing
like living on the edge, though! It would be useful if you could give
some input into the review of the jmol ticket too (I see you already
updated the instructions).
Jason
William Stein
I have been playing around with the new jmol spkg tonight on my system
and have nothing but praise so far for how it works.
-- William
Benjamin Jones
> > Hopefully good. On the other hand, using a beta version of Chrome and a
> > not-yet-fully-reviewed jmol spkg could possibly see hangups. Nothing like
> > living on the edge, though! It would be useful if you could give some input
> > into the review of the jmol ticket too (I see you already updated the
> > instructions).
>
> I have been playing around with the new jmol spkg tonight on my system
> and have nothing but praise so far for how it works.
>
> -- William
10.6.6. I just updated Chrome to 10.0.648.114 beta, and from Trac
#9238, I ran:
./sage -f http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.4.spkg
Jmol in the notebook showed the new side panel, but still failed to
load in the plot window. I rebooted, started a new worksheet with a 3d
plot and Jmol now loads and works great.
The new interface is *really* nice.
--
Benjamin Jones
Benjamin Jones
http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.4.spkg
seems to be corrupted now. I upgraded my Sage to 4.6.2.rc1 and ran ./
sage -f <above URL> and I get error messages saying the archive is
invalid. I ran the same command but pointed to the .spkg I had
downloaded previously (shortly after William started this thread) and
it unpacks and installs just fine.
Has anyone else tried upgrading their Jmol recently?
--
Benjamin Jones
On Feb 26, 3:06 pm, Benjamin Jones <benjaminfjo...@gmail.com> wrote:
> > > Hopefully good. On the other hand, using a beta version of Chrome and a
> > > not-yet-fully-reviewed jmol spkg could possibly see hangups. Nothing like
> > > living on the edge, though! It would be useful if you could give some input
> > > into the review of the jmol ticket too (I see you already updated the
> > > instructions).
>
> > I have been playing around with the new jmol spkg tonight on my system
> > and have nothing but praise so far for how it works.
>
> > -- William
>
> I'm using Sage Version 4.6.1.alpha2 compiled from source under OS X
> 10.6.6. I just updated Chrome to 10.0.648.114 beta, and from Trac
> #9238, I ran:
>
William Stein
> I'm not sure if it's me, but the spkg at:
>
> http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.4.spkg
>
> seems to be corrupted now. I upgraded my Sage to 4.6.2.rc1 and ran ./
> sage -f <above URL> and I get error messages saying the archive is
> invalid. I ran the same command but pointed to the .spkg I had
> downloaded previously (shortly after William started this thread) and
> it unpacks and installs just fine.
>
> Has anyone else tried upgrading their Jmol recently?
Try again. Maybe your download was corrupted.
I just tried downloading the above spkg again and it isn't corrupted.
-- William
>
> --
> Benjamin Jones
>
> On Feb 26, 3:06 pm, Benjamin Jones <benjaminfjo...@gmail.com> wrote:
>> > > Hopefully good. On the other hand, using a beta version of Chrome and a
>> > > not-yet-fully-reviewed jmol spkg could possibly see hangups. Nothing like
>> > > living on the edge, though! It would be useful if you could give some input
>> > > into the review of the jmol ticket too (I see you already updated the
>> > > instructions).
>>
>> > I have been playing around with the new jmol spkg tonight on my system
>> > and have nothing but praise so far for how it works.
>>
>> > -- William
>>
>> I'm using Sage Version 4.6.1.alpha2 compiled from source under OS X
>> 10.6.6. I just updated Chrome to 10.0.648.114 beta, and from Trac
>> #9238, I ran:
>>
>> ./sage -fhttp://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.4....
>>
>> Jmol in the notebook showed the new side panel, but still failed to
>> load in the plot window. I rebooted, started a new worksheet with a 3d
>> plot and Jmol now loads and works great.
>>
>> The new interface is *really* nice.
>>
>> --
>> Benjamin Jones
>
Benjamin Jones
> On Thu, Mar 3, 2011 at 8:23 AM, Benjamin Jones <benjami...@gmail.com> wrote:
>> I'm not sure if it's me, but the spkg at:
>>
>> http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.4.spkg
>>
>> seems to be corrupted now. I upgraded my Sage to 4.6.2.rc1 and ran ./
>> sage -f <above URL> and I get error messages saying the archive is
>> invalid. I ran the same command but pointed to the .spkg I had
>> downloaded previously (shortly after William started this thread) and
>> it unpacks and installs just fine.
>>
>> Has anyone else tried upgrading their Jmol recently?
>
> Try again. Maybe your download was corrupted.
>
> I just tried downloading the above spkg again and it isn't corrupted.
>
> -- William
>
You're right, it's not corrupted. I had to manually delete the .spkg
file in $SAGE_ROOT/spkg/optional and then run `./sage -f <URL>` again.
Thanks,
--
Benjamin Jones
Volker Braun
You're right, it's not corrupted. I had to manually delete the .spkg
file in $SAGE_ROOT/spkg/optional and then run `./sage -f <URL>` again.
kcrisman
a feeling it's a feature rather than a bug for some reason, though you
are very right about it being a trap.
Benjamin Jones
newcomer -- maybe a partial newcomer. It seems like a checksum or hash
could be check at the very least to compare the file or URL give at
the command line and the cached file before anything is unpacked and
installed.
--
Benjamin Jones