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Find a tool which can do trajectory visualization in the cloud (e.g. on Colab) and insert it into notebooks #101

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davidlmobley opened this issue Dec 30, 2021 · 4 comments

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@davidlmobley
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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
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hainm commented Jan 13, 2022

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
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@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

Cursor_and_Copy_of_MD_Sandbox_Molecule_ipynb_-_Colaboratory

@hainm
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hainm commented Jan 17, 2022

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

@daveminh
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@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

Cursor_and_Copy_of_MD_Sandbox_Molecule_ipynb_-_Colaboratory

I also have the same problem.

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