jmol troubles with Sage 8.0

[videlec]

On the 8.0 version there is some troubles with jmol. See

• https://ask.sagemath.org/question/39798/
• https://ask.sagemath.org/question/39269/

[embray]

These seem like two separate issues really, and the first one sounds like a problem with the user's computer.

[embray]

Some of the issues with JMol should be fixed by
https://trac.sagemath.org/ticket/25025 and https://trac.sagemath.org/ticket/25088

That said, I have still yet to be able to get JMol graphics to work correctly on Windows.

[wuuzx]

I encounter the second problem on windows 10 too. it looks like jmol is using a virtual path instead of a windows real path, so i just set the sage working directory same as the virtual path, and it works!

[embray]

@wuuzx Would you mind adding a bit more detail? I haven't looked at JMol since...last Spring. But last time I did I couldn't even get it to work on Windows at all so I got frustrated and gave up on the issue.

[wuuzx]

When I first install sage, I set sage working directory as c:\users\myusername. With this configure, JMol doesn't working. When I use plot3d, JMol popup with a blank window. Than I found in JMol java console that JMol searching files in c:\home\sage, that is the problem I think. So I change the sage working directory to c:\home\sage (I create it first of course), then everything is OK.

[HustLion]

I can't get jmol to work even with the info @wuuzx provided. But threejs viewer works. Here's an example:

x, y = var('x,y')
G = plot3d(x^2 + y^2, (x,-2,2), (y,-2,2))
show(G,figsize=(5,5),title="Sample Figure",aspect_ratio=1, viewer='threejs')

ref: https://ask.sagemath.org/question/39269/launched-jmol-viewer-for-graphics3d-object-fails/

[embray]

To my knowledge the JMol viewer has never worked in the Windows version. There are some plans to remove JMol support completely from Sage. In the meantime using ThreeJS will generally work, although it was some problems, I think, with working in the Jupyter Notebook. For a future release on Windows I want to go ahead and change the default 3D graphics viewer, at least on Windows, to use ThreeJS, and to fix any issues with using it in the Notebook.

[williamstein]

On Wed, Mar 27, 2019 at 6:23 AM E. M. Bray ***@***.***> wrote: To my knowledge the JMol viewer has never worked in the Windows version. There are some plans to remove JMol support completely from Sage. In the meantime using ThreeJS will generally work, although it was some problems, I think, with working in the Jupyter Notebook.

You might be thinking of security + configuration issues, like we are trying to do deal with here: sagemathinc/cocalc#1963 (comment) +1 from me to Three.js by default and getting rid of JMol support. (Robert Bradshaw and I spent months integrating jmol into Sage, but that was 12 years ago, and options are better now!)

[Arnache]

I plus the idea to make viewer="threejs" the default for better newbie experience.

[videlec]

Making threejs the default was done in ticket #22408 which was merged in 9.0.beta0 (see this sage-release thread).

I guess we could close the issue.