#16004: Update notebook to utilize pure javascript JSmol for default live 3-D
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Reporter: gutow | Owner: gutow
Type: enhancement | Status: needs_review
Priority: major | Milestone: sage-6.2
Component: notebook | Resolution:
Keywords: Jmol 3D 3-D | Merged in:
Authors: gutow | Reviewers:
Report Upstream: N/A | Work issues:
Branch: | Commit:
Dependencies: #16003 | Stopgaps:
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Comment (by gutow):
Replying to [comment:31 kcrisman]:
> Okay, I got it working. Preliminary thoughts:
> * Snappier than advertised. But SO SLOW with lots of points; a sparse
vector field or basic plot is not so horrible. Of course, so was the Java
version...
> * The load 3d live button is precisely what the doctor ordered.
Thought this is what people were asking for.
> * Is it possible that inside interacts the load 3d live button doesn't
work (that is, interacts are always live?) Or is it possible that you can
only turn that button on, but not off (counter the expectation when
clicking it)? I observed some unusual behavior, but maybe it was just
something dumb I did.
I believe I wrote the code so that if that box is checked all Jmol/JSmols
will load live. If it is not checked they should not load live. I am not
aware of anything interacts do that should force a live load.
> * How do you turn a plot "off" if there are too many open? (Or is that
not a problem like it was with the sleeping Java applets?)
Turning them off is presently not possible. For the javascript version
(JSmol) I do not think it will matter as long as you do not have the ones
you are not interacting with doing things that require continuous
computations like spinning or running an animation (something Jmol/JSmol
can do, but Sage presently does not generate the input for).
> * I see no way to get the things I used to with right-click (like
stereo glasses, color, axes, whatever). Does jsmol just not have that?
Right-click still brings up a menu. For the time being I've left the
default Jmol menu as it provides access to some file writing features.
You were not able to get it? I'll look into that.
> * The icon for activating the plot is ... not obvious. I still really
find the auto-disable piece annoying, and I know that some people have
just hacked that away, though I also know I won't convince you otherwise
;-)
It is just the default image (a standard stock "play" icon) stored in the
JSmol tree. If we can come up with something better it can be replaced.
> * Please remove the icons for new cells. They are cute, and probably
an improvement in some ways, but it should really be orthogonal to this
issue. There's enough moving parts to think about as it is.
**Especially** since the blue bars have been the way to make new cells for
many years! That's a pretty big change.
I agree that it would be nice to separate this "big" change in the
interface out. Unfortunately, I really could not get the old key+click
actions to work with the new jquery that is required to support JSmol.
Unless somebody else can make it work without breaking JSmol these icons
are going to be part of this change. I'm open to suggestions on exactly
how things should look, but built it using the standard jquery-ui tools
that are part of sagenb.
> * I figure out what strogdon is talking about. Try activating a jsmol,
and then move it around a bit, and then try clicking in a cell *without*
clicking alllll the way on the right to "lose focus" from the jsmol.
(This is a problem anyway, of having to go all the way to the right to
scroll - not limited to jsmol, though, threejs in the cell server has this
problem as well.) You won't be able to, at least often not; you have to
somehow get off focus and there is some timing delay.
I'll play with this. Haven't noticed it, at least not anymore than most
GUI based software.
> * I also haven't tried all the zillions of options out there for 3d
plots to see if it still obeys them all, but presumably if it's pretty
similar to jmol it will do fine.
If it worked in Jmol it works in JSmol as JSmol is just just cross
compiled to javascript. There have been some minor oddities, but the
demands of the X-ray crystallography users are much more severe than what
is usually being done here. I think Bob Hanson and the others working on
the conversion between Java and Javascript have found most of problems by
now. The chemistry community has been replacing java applet only versions
with this for 9-12 months now.
> * Does it require WebGL turned on? I think not, but I'm not sure.
I have set it up to use HTML5 only. WebGL support exists, but has
problems with transparency and other such things.
>
> Hope this helps! Actually, it's fairly comparable to the current setup,
so probably we could get it in sooner rather than later. Especially if
you have any thoughts on the "viewer" thing - to me, this would be by far
the easiest way to switch back and forth between functionality.
I'll keep working on this. I think if I can get it working cleanly in the
GUI, it will be easy to couple it to the viewer option.
>
> Once this has been tested enough and the "right" commits used, I think
that you can just do a pull request to sagenb on github with your branch
for this. Yay! Thanks for what is clearly very good hard work.
--
Ticket URL: <http://trac.sagemath.org/ticket/16004#comment:32>
Sage <http://www.sagemath.org>
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