nglview does not work in Colab

[sef43]

The nglview package does not work when running the notebooks in Colab. It would be great to have it working so people can quickly visualize the molecules/trajectories directly in the jupyter notebook.

[jmichel80]

could py3Dmol be a viable alternative?

[sef43]

Using a fix suggested by Toni from here: https://github.com/CCPBioSim/CCP5_Simulation_of_BioMolecules/blob/main/5_Analysis_DR_clustering/3_clustering.ipynb

mamba install ipywidgets=7.6.0 and

# enable third party jupyter widgets
from google.colab import output
output.enable_custom_widget_manager()

allows nglview to display molecules correctly.
However, the trajectory player does not work. It just shows the first frame and will not play the trajectory. This seems to be a know issue with colab and nglview. See here: nglviewer/nglview#995 and here: googlecolab/colabtools#2853

[sef43]

py3Dmol looks like it is based around showing a single frame not a playable trajectory. It can be used to show a trajectory animation but it will not be interactive and the boilerplate code it somewhat substantial.