Trp-Cage_AnalysisAndVisualization.ipynb

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   "source": [
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "import mdtraj as md\n",
    "import nglview as nv\n",
    "%matplotlib inline"
   ]
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    "First load the trajectory:"
   ]
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   "source": [
    "traj = md.load_dcd('trajectory.dcd', top='trpcage.pdb')"
   ]
  },
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   "cell_type": "markdown",
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   "source": [
    "And here are a couple of different ways of visualizing the trajectory:"
   ]
  },
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   "cell_type": "code",
   "execution_count": 22,
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   "source": [
    "view = nv.show_mdtraj(traj)\n",
    "view.clear_representations()\n",
    "view.add_representation(repr_type='cartoon', selection='protein', color='forestgreen')\n",
    "view.add_representation('licorice', selection='protein')\n",
    "## the next two commented lines may be useful for those who are doing ##\n",
    "## the first option in the activity (adding an extra force)           ## \n",
    "#view.add_representation('surface', selection='1.CA or 20.CA', surfaceType='vws')\n",
    "#view.add_distance(atom_pair=[['1.CA', '20.CA']],label_color='black')\n",
    "view"
   ]
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    "view.clear_representations()\n",
    "view.add_representation(repr_type='cartoon', selection='protein', color='forestgreen')\n",
    "view.add_representation('licorice', selection='water')\n",
    "view"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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