Merge pull request #35 from RosettaCommons/fix/notebook

fix: notebook

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"
   },