diff --git a/examples/all.ipynb b/examples/all.ipynb index d191938..748b1eb 100644 --- a/examples/all.ipynb +++ b/examples/all.ipynb @@ -25,13 +25,28 @@ "```\n", "RFD3 (backbone) → MPNN (sequence) → RF3 (validation) → RMSD comparison\n", "```\n", + "---\n", + "\n", + "## Section 0: Installation\n", + "\n", + "Install the Foundry package (includes RFD3, MPNN, and RF3):\n", + "\n", + "```bash\n", + "pip install 'rc-foundry[all]'\n", + "```\n", + "\n", + "Download the model weights (~6GB total, takes a couple minutes):\n", + "\n", + "```bash\n", + "foundry install rfd3 ligandmpnn rf3\n", + "```\n", "\n", "---" ] }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "id": "819e8193", "metadata": {}, "outputs": [], @@ -75,7 +90,7 @@ "# Configure RFD3 inference\n", "config = RFD3InferenceConfig(\n", " specification={\n", - " 'length': 15, # Generate 80-residue proteins\n", + " 'length': 80, # Generate 80-residue proteins\n", " },\n", " diffusion_batch_size=2, # Generate 2 structures per batch\n", ")\n", @@ -145,7 +160,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "id": "d07ae413", "metadata": {}, "outputs": [], @@ -236,7 +251,7 @@ "\n", "\n", "# Initialize RF3 inference engine\n", - "inference_engine = RF3InferenceEngine(ckpt_path='rf3_preprint_921', verbose=False)\n", + "inference_engine = RF3InferenceEngine(ckpt_path='rf3', verbose=False)\n", "\n", "# Create input from the MPNN-designed structure (first design)\n", "# This re-folds the sequence to validate it adopts the intended structure\n", @@ -388,7 +403,7 @@ ], "metadata": { "kernelspec": { - "display_name": "modelworks", + "display_name": "Python 3", "language": "python", "name": "python3" },