RoseTTAFold.ipynb crashes at "Install and import libraries" step in the google colab

[shafayetrahat]

Expected Behavior

RoseTTAFold.ipynb should install the dependencies and predict the protein structure

Current Behavior

RoseTTAFold.ipynb crashes at "Install and import libraries" step in google colab

Steps to Reproduce (for bugs)

After running the RoseTTAFold.ipynb in google colab you will see this error directly

ColabFold Output (for bugs)

Context

Possible reason is upgrade of google colab cuda driver from cuda 11 to cuda 12. " %shell pip install -q dgl-cu113 -f https://data.dgl.ai/wheels/repo.html" This line can be the origin of the problem. Probably, need to change the dgl library and pytorch library to cuda12. Also, may need to change the rosettafold function accordingly.

[sokrypton]

We've updated the notebook, can you try again at: https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/RoseTTAFold2.ipynb

[shafayetrahat]

I am not using rosettafold2. Using rosettafold in google colab. https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/RoseTTAFold.ipynb