diff --git a/examples/ipd_design_pipeline_collab.ipynb b/examples/ipd_design_pipeline_collab.ipynb
index f5ff9d0..30232c9 100644
--- a/examples/ipd_design_pipeline_collab.ipynb
+++ b/examples/ipd_design_pipeline_collab.ipynb
@@ -20,40 +20,73 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# Install dependencies (skip if already done)\n",
-    "import os\n",
+    "import os, sys, subprocess\n",
+    "from pathlib import Path\n",
     "\n",
-    "# Set environment variables\n",
-    "os.environ['CCD_MIRROR_PATH'] = ''\n",
-    "os.environ['PDB_MIRROR_PATH'] = ''\n",
+    "os.environ[\"CCD_MIRROR_PATH\"] = \"\"\n",
+    "os.environ[\"PDB_MIRROR_PATH\"] = \"\"\n",
     "\n",
-    "if not os.path.isfile(\"FOUNDRY_READY\"):\n",
-    "    print(\"Installing rc-foundry...\")\n",
-    "    \n",
-    "    # Uninstall torchvision first to avoid operator conflicts\n",
-    "    os.system(\"pip uninstall -y torchvision\")\n",
-    "    \n",
-    "    # Install rc-foundry\n",
-    "    os.system(\"pip install -q 'rc-foundry[all]'\")\n",
-    "    \n",
-    "    # Mark as ready\n",
-    "    os.system(\"touch FOUNDRY_READY\")\n",
-    "    \n",
-    "    print(\"Done!\")\n",
+    "CKPT_DIR = Path(\"/root/.foundry/checkpoints/\")\n",
+    "CKPT_DIR.mkdir(parents=True, exist_ok=True)\n",
+    "READY_FLAG = Path(\"FOUNDRY_READY\")\n",
+    "LOG = Path(\"foundry_setup.log\")\n",
+    "\n",
+    "CHECKPOINTS = {\n",
+    "    \"rfd3\": {\n",
+    "        \"url\": \"https://files.ipd.uw.edu/pub/rfd3/rfd3_foundry_2025_12_01_remapped.ckpt\",\n",
+    "        \"filename\": \"rfd3_latest.ckpt\",\n",
+    "    },\n",
+    "    \"ligandmpnn\": {\n",
+    "        \"url\": \"https://files.ipd.uw.edu/pub/ligandmpnn/ligandmpnn_v_32_010_25.pt\",\n",
+    "        \"filename\": \"ligandmpnn_v_32_010_25.pt\",\n",
+    "    },\n",
+    "    \"rf3\": {\n",
+    "        \"url\": \"https://files.ipd.uw.edu/pub/rf3/rf3_foundry_01_24_latest_remapped.ckpt\",\n",
+    "        \"filename\": \"rf3_foundry_01_24_latest_remapped.ckpt\",\n",
+    "    },\n",
+    "}\n",
+    "\n",
+    "# Always remove torchvision first\n",
+    "subprocess.check_call([sys.executable, \"-m\", \"pip\", \"uninstall\", \"-y\", \"torchvision\"])\n",
+    "\n",
+    "# Start rc-foundry install in the background (if not done)\n",
+    "pip_proc = None\n",
+    "if not READY_FLAG.exists():\n",
+    "    print(\"Installing rc-foundry (background)...\")\n",
+    "    pip_proc = subprocess.Popen(\n",
+    "        [sys.executable, \"-m\", \"pip\", \"install\", \"-q\", \"rc-foundry[all]\"],\n",
+    "        stdout=LOG.open(\"ab\"),\n",
+    "        stderr=subprocess.STDOUT,\n",
+    "    )\n",
     "else:\n",
-    "    print(\"rc-foundry already installed.\")"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "colab-download-weights",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# Download model weights (skips already-downloaded models automatically)\n",
-    "# In total, ~6GB (3GB for RFD3, 3GB for RF3, <100MB for MPNN); may take a few minutes depending on your connection speed\n",
-    "os.system(\"foundry install rfd3 ligandmpnn rf3\")"
+    "    print(\"rc-foundry already installed.\")\n",
+    "\n",
+    "# Start checkpoint downloads in parallel with correct filenames\n",
+    "dl_procs = []\n",
+    "for name, info in CHECKPOINTS.items():\n",
+    "    dest = CKPT_DIR / info[\"filename\"]\n",
+    "    if dest.exists():\n",
+    "        continue\n",
+    "    print(f\"Downloading {name} -> {dest} (background)...\")\n",
+    "    dl_procs.append(\n",
+    "        subprocess.Popen(\n",
+    "            [\"curl\", \"-L\", \"-o\", str(dest), info[\"url\"]],\n",
+    "            stdout=LOG.open(\"ab\"),\n",
+    "            stderr=subprocess.STDOUT,\n",
+    "        )\n",
+    "    )\n",
+    "\n",
+    "# Wait when you actually need everything ready\n",
+    "if pip_proc:\n",
+    "    rc = pip_proc.wait()\n",
+    "    if rc == 0:\n",
+    "        READY_FLAG.touch()\n",
+    "    else:\n",
+    "        print(f\"pip install failed with code {rc}\")\n",
+    "for p in dl_procs:\n",
+    "    p.wait()\n",
+    "\n",
+    "print(\"Setup steps finished (see foundry_setup.log).\")"
    ]
   },
   {
@@ -298,7 +331,7 @@
     "# Create input from the MPNN-designed structure (first design)\n",
     "# This re-folds the sequence to validate it adopts the intended structure\n",
     "input_structure = InferenceInput.from_atom_array(atom_array, example_id=\"example_protein\")\n",
-    "rf3_outputs = inference_engine.run(inputs=input_structure)\n",
+    "rf3_outputs = inference_engine.run(inputs=input_structure, annotate_b_factor_with_plddt=True)\n",
     "\n",
     "# Outputs: dict mapping example_id -> list[RF3Output] (multiple models per input)\n",
     "print(f\"Output keys: {rf3_outputs.keys()}\")\n",