Graphics window seems to be "broken"

[sneshyba]

I'm using jupyter on ubuntu (via jupyterhub), a notebook with %matplotlib notebook selected. And while nglview.show_structure_file is trying to do something, all get is this broken graphics window. Sorry, I'm new to this, not sure if the image below will paste properly.

[hainm]

hi @sneshyba, you need to display the 3D viewer before rendering it.

# cell 1
view = ...
view # live

# cell 2
view.render_image()

# cell 3
view._display_image() # just for displaying in static notebook. 

Please check this example: https://github.com/arose/nglview/raw/master/examples/images/membrane.gif

[sneshyba]

Yes, I had done that before. The results are similar, but still not rendered:

[hainm]

@sneshyba did you follow the install guide here? https://github.com/arose/nglview#released-version

If you did, please read further here: https://github.com/arose/nglview/blob/master/docs/FAQ.md#widget-not-shown

[sneshyba]

I did -- but then I re-checked and realized that enabling nglview had given a permission error. So I used sudo and that solved it!

jupyter-nbextension enable nglview --py --sys-prefix (gave a permission error)
sudo jupyter-nbextension enable nglview --py --sys-prefix (worked)

Thank you so much! I'm really liking MDAnalysis, especially since my students are not able to get in front of a workstation easily -- now they can do a lot more remotely.

I still have to figure out how to display my .gro files properly -- but I think that's a different ticket.