Small fixes for the GFP notebook.

evolutionaryscale · Aug 5, 2024 · 6ca193d · 6ca193d
1 parent 973f13c
commit 6ca193d
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/examples/gfp_design.ipynb b/examples/gfp_design.ipynb
@@ -312,7 +312,7 @@
       "cell_type": "code",
       "source": [
         "view = py3Dmol.view(width=1000, height=500)\n",
-        "view.addModel(structure_generation_protein.to_pdb_string(), \"pdb\")\n",
+        "view.addModel(structure_generation_protein.to_protein_chain().infer_oxygen().to_pdb_string(), \"pdb\")\n",
         "view.setStyle({\"cartoon\": {\"color\": \"lightgreen\"}})\n",
         "view.zoomTo()\n",
         "view.show()"
@@ -340,7 +340,7 @@
         "constrained_site_positions = [59, 62, 63, 64, 93, 219]\n",
         "\n",
         "template_chain = template_gfp.to_protein_chain()\n",
-        "generation_chain = structure_generation_protein.to_pdb_string()\n",
+        "generation_chain = structure_generation_protein.to_protein_chain()\n",
         "\n",
         "constrained_site_rmsd = template_chain[constrained_site_positions].rmsd(\n",
         "    generation_chain[constrained_site_positions]\n",