Trouble displaying system with NGLview

[gnserafim]

Hi,

I'm current working with a system around 600k atoms and I have trouble visualizing not only the entire sytem but even a small part of it (AtomGroup of 12k atoms).

I followed what was on issue #633 and set NotebookApp.iopub_data_rate_limit as proposed (and even higher) but it didn't work.

Any ideas how to solve this?

As reference, below are the version been used:
jupyterlab 1.2.3
nglview 2.7.5
nglview-js-widgets 2.7.5
jupyterlab-manager 1.1.0

Installation done by pip or jupyter labextensions.

[hainm]

it didn't work.

Please elaborate.

[gnserafim]

Hai,

I set NotebookApp.iopub_data_rate_limit = 10000000 when starting jupyter lab, but nv.show_mdanalysis() doesn't display my system (despite loading the trajectory scroll bar).

If I select a small part o the system, I'm able to get an output (first image), but if I my atom group is larger than 10k atoms nglview will not display it (second image).

My question is if there is a way to visualize larger systems with nglview and how, or if it has a limit that forbid working large system with this tool

Thanks,

[hainm]

Thanks for your detail report. What does the terminal (where you launch the notebook) say?

[gnserafim]

Hey Hai,

When I launch the notebook, the below output appears at my terminal:

I don't know if this is relevantor not, but due to quarentine reasons, I'm accessing my work's computer via ssh from my personal laptop

[hainm]

thanks. I meant after you running your code, what does the terminal say?

Additionally, does it work in traditional notebook?

[gnserafim]

thanks. I meant after you running your code, what does the terminal say?

So, this is the last call of the terminal, even after running the cell of the notebook

Additionally, does it work in traditional notebook?

Yes. The same thing happens

[hainm]

uhm, do you mind sharing your file (pdb) or a toy model so I can play with it?

[gnserafim]

Let me know if you need anything else :)

test.zip

[hainm]

hi @gnserafim

nglview is actually able to show your system but you need to properly center it.
(I guess nglview is not robust in this case).

[gnserafim]

Hey @hainm

First, sorry about not replaying you early. Busy week

Thank you for the solution found! I was able to visualize my system centering it the way you did it :)

One more question: your solution only worked in a notebook created through notebook and not through jupyter lab. Any idea why?

[hainm]

One more question: your solution only worked in a notebook created through notebook and not through jupyter lab. Any idea why?

@gnserafim I am not sure why. Does nglview work in your lab notebook at all (nglview.demo())