Changes between Initial Version and Version 1 of Ticket #10115

Timestamp:

Nov 8, 2023, 11:04:58 AM (2 years ago)

Author:

Tom Goddard

Comment:

Fixed.

I updated ColabFold to the November 1, 2023 github source code. This error had been reported before to the ColabFold github

​https://github.com/sokrypton/ColabFold/issues/508

The problem arose because Google Colab updated CUDA version from 11 to 12 that required a jax update (jax is the library Colabfold uses to run calculations on the GPU with CUDA) and the jax update broke the Colabfold call to singular value decomposition (SVD) that was being used to orient the molecules when plotting them in the output. The fix had been hacked into the ColabFold repository in its web server script by changing a line in AlphaFold, and the ChimeraX code to install Colabfold needed to do the same hack. Here were the added lines

# patch for jax > 0.3.25
sed -i 's/weights = jax.nn.softmax(logits)/logits=jnp.clip(logits,-1e8,1e8);weights=jax.nn.softmax(logits)/g' /usr/local/lib/python{python_version}/dist-packages/alphafold/model/modules.py

I tested predicting chains A and B in PDB 1a0m which exhibited the error and now runs correctly.