diff --git a/AlphaFold2.ipynb b/AlphaFold2.ipynb index 5ca755bb..dc7ff151 100644 --- a/AlphaFold2.ipynb +++ b/AlphaFold2.ipynb @@ -149,8 +149,6 @@ " os.system(\"pip install -q --no-warn-conflicts 'colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold'\")\n", " os.system(\"ln -s /usr/local/lib/python3.*/dist-packages/colabfold colabfold\")\n", " os.system(\"ln -s /usr/local/lib/python3.*/dist-packages/alphafold alphafold\")\n", - " # patch for jax > 0.3.25\n", - " os.system(\"sed -i 's/weights = jax.nn.softmax(logits)/logits=jnp.clip(logits,-1e8,1e8);weights=jax.nn.softmax(logits)/g' alphafold/model/modules.py\")\n", " os.system(\"touch COLABFOLD_READY\")\n", "\n", "if USE_AMBER or USE_TEMPLATES:\n", diff --git a/batch/AlphaFold2_batch.ipynb b/batch/AlphaFold2_batch.ipynb index e96c0974..64d67395 100644 --- a/batch/AlphaFold2_batch.ipynb +++ b/batch/AlphaFold2_batch.ipynb @@ -130,7 +130,6 @@ " pip install -q --no-warn-conflicts \"colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold\"\n", " ln -s /usr/local/lib/python3.*/dist-packages/colabfold colabfold\n", " ln -s /usr/local/lib/python3.*/dist-packages/alphafold alphafold\n", - " sed -i 's/weights = jax.nn.softmax(logits)/logits=jnp.clip(logits,-1e8,1e8);weights=jax.nn.softmax(logits)/g' alphafold/model/modules.py\n", " touch COLABFOLD_READY\n", "fi\n", "\n",