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    "# Displaying Surfaces\n",
    "py3Dmol supports the following surface types:\n",
    "\n",
    "* VDW - van der Waals surface\n",
    "* MS - molecular surface\n",
    "* SES - solvent excluded surface\n",
    "* SAS - solvent accessible surface"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import py3Dmol"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Add surface\n",
    "In the structure below (HLA complex with antigen peptide pVR), we add a solvent excluded surface (SES) to the heavy chain to highlight the binding pocket for the antigen peptide (rendered as spheres)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
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       "        <p id=\"3dmolwarning_159190262115632\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the 3dmol extension: <br>\n",
       "        <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n",
       "        </div>\n",
       "<script>\n",
       "\n",
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       "$3Dmolpromise = null;\n",
       "  $3Dmolpromise = loadScriptAsync('https://3dmol.csb.pitt.edu/build/3Dmol.js');\n",
       "}\n",
       "\n",
       "var viewer_159190262115632 = null;\n",
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       "if(warn) {\n",
       "    warn.parentNode.removeChild(warn);\n",
       "}\n",
       "$3Dmolpromise.then(function() {\n",
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       "$3Dmol.download(\"pdb:5XS3\", viewer_159190262115632, {}, function() {\n",
       "\tviewer_159190262115632.setStyle({\"chain\": \"A\"},{\"cartoon\": {\"color\": \"blue\"}});\n",
       "\tviewer_159190262115632.setStyle({\"chain\": \"B\"},{\"cartoon\": {\"color\": \"yellow\"}});\n",
       "\tviewer_159190262115632.setStyle({\"chain\": \"C\"},{\"sphere\": {\"colorscheme\": \"orangeCarbon\"}});\n",
       "\tviewer_159190262115632.addSurface(4,{\"opacity\": 0.9, \"color\": \"lightblue\"},{\"chain\": \"A\"});\n",
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       "});\n",
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     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "viewer = py3Dmol.view(query='pdb:5XS3')\n",
    "\n",
    "heavychain = {'chain':'A'}\n",
    "lightchain = {'chain':'B'}\n",
    "antigen = {'chain':'C'}\n",
    "\n",
    "viewer.setStyle(heavychain,{'cartoon':{'color':'blue'}})\n",
    "viewer.setStyle(lightchain,{'cartoon':{'color':'yellow'}})\n",
    "viewer.setStyle(antigen,{'sphere':{'colorscheme':'orangeCarbon'}})\n",
    "\n",
    "viewer.addSurface(py3Dmol.SES,{'opacity':0.9,'color':'lightblue'}, heavychain)\n",
    "viewer.show()"
   ]
  },
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   "cell_type": "code",
   "execution_count": null,
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   "source": []
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