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   "source": [
    "# 5-Bioassembly\n",
    "By default, py3Dmol loads the content of a PDB entry, which represents the asymmetric unit for structures determined by crystographic methods and some structures determined by 3D electron microscopy. The asymmetric unit contains the unique part of a structure, but may not represent the biologically active form of a structures. See [PDB-101 tutorial](https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies#Anchor-BioUnit).\n",
    "\n",
    "An asymmetric unit may contain:\n",
    "* one biological assembly\n",
    "* a portion of a biological assembly\n",
    "* multiple biological assemblies\n",
    "\n",
    "This example has been copied from [py3Dmol tutorial](http://nbviewer.jupyter.org/github/3dmol/3Dmol.js/blob/9050b97144e81f065df7eecc87ba9a16723ab14b/py3Dmol/examples.ipynb)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import py3Dmol"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Display the asymmetric unit \n",
    "In this example below (3DEM structure of Zika virus) we load the content of the asymmetric unit. In this case, the asymmetric unit represents a portion of the biological assembly."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "view = py3Dmol.view(query='pdb:5ire')\n",
    "view.setStyle({'cartoon':{'color':'spectrum'}})\n",
    "view.show()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Display the biological assembly\n",
    "Using the 'doAssembly' option, the biological assembly will be created using symmetry operations in the PDB entry."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "view = py3Dmol.view(query='pdb:5ire',options={'doAssembly':True})\n",
    "view.setStyle({'cartoon':{'color':'spectrum'}})\n",
    "view.show()"
   ]
  }
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