nglview on google colab

[andresilvapimentel]

It would be great if nglview could be run on google colab.

Is there a installation procedure for nglview on google colab?

[hainm]

hi @andresilvapimentel, it's up to google to implement the feature.

googlecolab/colabtools#1049

[hainm]

hi @andresilvapimentel it seems nglview will work in codelab soon: googlecolab/colab-cdn-widget-manager#13

[blois]

This should now be working:
https://colab.research.google.com/gist/blois/5ac0123ff66583f2578858fce7fdaf0b/nglview.ipynb

[hainm]

@blois thanks. But the trajectory player does not seem to work.

[blois]

Ah, good to know. Will dig into that.

[blois]

I believe that the trajectory player should now be working.

[hainm]

I believe that the trajectory player should now be working.

Thanks @blois. The molecule structure looks weird (duplicated) in codelab.

Saying I move the slider to value of 40.

In codelab: Try to slide the slider to see what I mean.

In Jupyter notebook:

[hainm]

It would be great if nglview could be run on google colab.

Thanks to @blois, we can run nglview on google colab now. Cheers.

[davidlmobley]

I'm having problems with the trajectory viewer in Colab. I can confirm nglview now works, but the trajectory viewer is giving me jumbled molecules. Example to reproduce MobleyLab/drug-computing#101

[elizabeththrall]

Hello all, I'm also having an issue with the ngl trajectory viewer in Colab. The trajectory plays, but the first frame remains superimposed on all the subsequent frames. The trajectory plays properly without the duplicated first frame in a Jupyter notebook outside of Colab.

I am using the MDAnalysis package to create a Universe object from an .xyz file and then show_mdanalysis to visualize it. The notebook is attached in case it helps. Thanks for supporting this great tool!

notebookfile.zip

[hainm]

Hi, It’s something colab should fix. I filed a case in colab repo and hopefully google will fix it.

…

On Wed, Jul 6, 2022 at 1:37 PM elizabeththrall ***@***.***> wrote: Hello all, I'm also having an issue with the ngl trajectory viewer in Colab. The trajectory plays, but the first frame remains superimposed on all the subsequent frames. The trajectory plays properly without the duplicated first frame in a Jupyter notebook outside of Colab. I am using the MDAnalysis package to create a Universe object from an .xyz file and then show_mdanalysis to visualize it. The notebook is attached in case it helps. Thanks for supporting this great tool! notebookfile.zip <https://github.com/nglviewer/nglview/files/9056954/notebookfile.zip> — Reply to this email directly, view it on GitHub <#995 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABB645P5M7ZY55AI7QK6TALVSW75BANCNFSM5D2B7TCQ> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

[hainm]

Here is the tracked case: googlecolab/colabtools#2853 (comment)