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Right click options not showing up for jsmol

asked 2017-12-01 16:28:29 -0500

Nonlocal gravatar image

I'm using implicit_plot3d to create an image. Everything works great setting up the image and jsmol produces a nice looking plot. I right click to be able to interact with the plot such as zoom; however, when I highlight the zoom option (as well as many of the other options), the set of sub-options does not appear. I've tried in multiple browsers (firefox, chrome, and internet explorer), but I'm not having success with any of them. It appears the sub-menu options are trying to appear but they do not have space to display them. Any help would be greatly appreciated. I took a picture of it to make it a little easier to see, but I don't seem to have the karma to upload or link. It can be found at this address though:

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answered 2017-12-02 07:43:01 -0500

eric_g gravatar image

Unfortunately, this is a known bug with the default 3D viewer (Jmol) in Jupyter notebook. Use instead the new threejs viewer, like in this example:

var('x y z')
T = RDF(golden_ratio)
F = 2 - (cos(x+T*y) + cos(x-T*y) + cos(y+T*z) + cos(y-T*z) + cos(z-T*x) + cos(z+T*x))
r = 4.77
G = implicit_plot3d(F, (x,-r,r), (y,-r,r), (z,-r,r), plot_points=40, color='darkkhaki')
show(G, viewer='threejs')

Then, you can perform the following actions with the mouse buttons:

  • left to rotate the object
  • middle to zoom in/out
  • right to translate the object
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Okay thanks for the info. I actually was trying threejs today, but I was having trouble using a colormap. Does threejs have this capability or is it only for single color schemes?

Nonlocal gravatar imageNonlocal ( 2017-12-02 08:56:59 -0500 )edit

Not at the moment...The list of currently supported options of theejs is here.

eric_g gravatar imageeric_g ( 2017-12-02 10:23:45 -0500 )edit

I see. Well thanks for the help. I appreciate it.

Nonlocal gravatar imageNonlocal ( 2017-12-02 22:20:33 -0500 )edit

for completeness, the issue is here

j.c. gravatar imagej.c. ( 2018-03-03 07:05:53 -0500 )edit

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Asked: 2017-12-01 16:28:06 -0500

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Last updated: Dec 02 '17