Find a tool which can do trajectory visualization in the cloud (e.g. on Colab) and insert it into notebooks

[davidlmobley]

Several notebooks do trajectory visualization with nglview; it would be helpful to migrate those to something which will work on Colab. The most important seem to be:

• MD sandbox on molecules
• Solvation sandbox/lecture

[hainm]

Several notebooks do trajectory visualization with nglview; it would be helpful to migrate those to something which will work on Colab.

FYI: nglview does work in Colab now: nglviewer/nglview#995

[davidlmobley]

@hainm - it now works (yay!) but seems to result in incorrect visualizations when I load TRAJECTORIES, at least here. Here's a notebook which works correctly for me locally, but on Colab my molecule comes out jumbled (attached image) and the trajectory says it has 0 frames; locally it is correct. Here's the notebook and it has a button to load it on Colab (unfortunately it requires an OpenEye license to run; if needed I could probably prepare an alterantive which uses RDKit): https://github.com/MobleyLab/drug-computing/blob/master/uci-pharmsci/lectures/MD/MD_Sandbox_Molecule.ipynb

[hainm]

hi @blois, I encountered the same issue when testing nglview. Do you have any idea why? thanks.

[daveminh]

@hainm - it now works (yay!) but seems to result in incorrect visualizations when I load TRAJECTORIES, at least here. Here's a notebook which works correctly for me locally, but on Colab my molecule comes out jumbled (attached image) and the trajectory says it has 0 frames; locally it is correct. Here's the notebook and it has a button to load it on Colab (unfortunately it requires an OpenEye license to run; if needed I could probably prepare an alterantive which uses RDKit): https://github.com/MobleyLab/drug-computing/blob/master/uci-pharmsci/lectures/MD/MD_Sandbox_Molecule.ipynb

I also have the same problem.