Sergey O
Sergey O
Should be fixed now! I tracked the bug down to predict() function, turns out when I was making a copy of the dictionary before/after prediction, the copy wasn't being made....
The issue is that google colab upgraded to jax 0.4.4. I've now updated the notebook to downgrade to old version of jax recommended by deepmind in local installations.
Can you try again, but with latest version of the notebook?
@pdeepakb Make sure you are using the latest notebook.
Hi Tom, We are still debugging a few other recently reported issues due to 3.10 python updated. Hopefully these will be resolved this week (I just pushed a patch in...
you can do either locally:
The notebook should work. Can you try again. It looks like maybe the first cell was not executed?
The prediction function can be found here: https://colab.research.google.com/github/sokrypton/ColabDesign/blob/gamma/af/examples/predict.ipynb See end of the notebook on information how to specify cyclic constraints.
We've updated the notebook, can you try again at: https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/RoseTTAFold2.ipynb
The problem is that mmseqs2 doesn't support RNA search. @martin-steinegger @milot-mirdita (at least not yet?)