Unit cell not displaying in Pluto

[eahenle]

Great tool! I am building a UI in Pluto for a project with @CorySimon and have found that the unit cell box does not display when using viewfile. The same code and input files produce the correct result in Jupyter, oddly enough.

[jgreener64]

I can reproduce this with:

viewfile("IRMOF-1.xyz", "xyz", isosurface=IsoSurface("IRMOF-1.cube", -5.0), vtkcell="IRMOF-1.vtk")

It works in Jupyter but not in Pluto. I don't know why, sadly, and won't have time to look in detail.

[diegozea]

Hi!

I could not understand the problem, but it looks related to how Pluto is executing the JavaScript. For these lines (files are in the example folder of this repo):

using Bio3DView

isosurface = IsoSurface("SBMOF-1.cube", 100.0, wireframe=true,
                color="green") # contours at -5 kJ/mol

viewfile("SBMOF-1.xyz", "xyz"; isosurface=isosurface, vtkcell="SBMOF-1.vtk",
            axes=Axes(5, 0.3), cameraangle=CameraAngle(0, 0, 0, 0, 0, 0, 0, 1))

The error in the JavaScript console is:

That's related to this part on Plutos' js code:

My JavaScript knowledge isn't good enough to understand what is going on here. But, maybe @fonsp can give us a hint :)

Cheers

[jgreener64]

Thanks for having a look Diego. Possibly a scoping issue.

[fonsp]

What is the question exactly?

[eahenle]

@fonsp we are trying to determine why the code:

using Bio3DView

box = Box([0.0, 0.0, 0.0], [6.0, 6.0, 6.0])

viewfile("benzene.sdf", "sdf", box=box)

Produces a different result in Pluto vs. Jupyter. Side-by-side:

The box is missing in Pluto :(

@diegozea noticed Uncaught ReferenceErrors in the JS console. I guess the question really is: does the fix for this exist on Bio3DView's end, or Pluto's?

[fonsp]

Can you take this screenshot again but without cropping?

[eahenle]

Not much else to see:

Complete output text: localhost-1606835271833.log

[diegozea]

Hi! I was looking into this problem, and I found that the Uncaught ReferenceError: $3Dmol is not defined error only appears when we do:

js_3dmol = read(path_3dmol, String)
"<script type='text/javascript'>$js_3dmol</script>"

If we change that to using an online source, the problem disappears, i.e.:

"<script type='text/javascript' src='https://3Dmol.org/build/3Dmol-min.js'></script>"

So, I tried using src and a relative URL to the local file, e.g.:

"<script type='text/javascript' src='$path_3dmol'></script>"

But this doesn't work as Pluto is looking for the file at http://localhost:1234 (that looks related to this Pluto issue: https://github.com/fonsp/Pluto.jl/issues/171)

@fonsp Do you have an idea about what could be the difference between including the js code inside the script tag or using it with a source URL? However, we also include the JQuery code inside a script tag without problems, so maybe there is something strange with the 3Dmol code. Also, do you know how we can reference a local javascript located at this Julia repo? I guess that could solve this problem. Thanks in advance,

Cheers,