Skip to content

Instantly share code, notes, and snippets.

@asford

asford/180212_polybb_test_system.ipynb

Last active February 13, 2018 08:22
Show Gist options
  • Save asford/a814a15b829f46abd8377de4c83593b7 to your computer and use it in GitHub Desktop.
Save asford/a814a15b829f46abd8377de4c83593b7 to your computer and use it in GitHub Desktop.
Download ZIP
workspace/tmol/dev/180212_polybb_test_system.ipynb
Display the source blob
Display the rendered blob
Raw
180212_polybb_test_system.ipynb
{
"cells": [
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "import torch\nfrom torch.autograd import Variable",
"execution_count": 1,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "import numpy\nimport scipy.optimize",
"execution_count": 2,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "import requests\nimport traitlets",
"execution_count": 3,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "import py3dmol",
"execution_count": 4,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "import pdb_parsing\n\ndef fetch_pdb(pdbid):\n return requests.get(\"https://files.rcsb.org/download/%s.pdb\" % str.upper(pdbid)).text",
"execution_count": 5,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "class FixedNamedAtomSystem(traitlets.TraitType):\n def __init__(self, atoms):\n self.atoms = atoms\n \n @property\n def dtype(self):\n return numpy.dtype([(n, \"f4\", 3) for n in self.atoms])\n \n def from_pdb(self, pdb):\n atoms = pdb_parsing.parse_pdb(pdb)\n atoms = atoms[atoms.apply(lambda r: r[\"atomn\"] in self.atoms, axis=1)]\n for t in (\"model\", \"chain\"):\n assert atoms[t].nunique() == 1\n resi = atoms[\"resi\"].unique()\n assert numpy.all(resi == numpy.arange(resi[0], resi[-1] + 1))\n \n atoms = atoms.set_index([\"resi\", \"atomn\"])\n \n result = numpy.empty_like(resi, dtype=self.dtype)\n \n for i, ri in enumerate(resi):\n for a in result.dtype.names:\n result[i][a] = atoms.loc[ri, a][[\"x\", \"y\", \"z\"]].values\n \n return result\n \n def to_pdb(self, value, b = None):\n atom_records = numpy.zeros((len(value), 4), dtype=pdb_parsing.atom_record_dtype)\n\n atom_records[\"resn\"] = \"CEN\"\n atom_records[\"chain\"] = \"X\"\n atom_records[\"resi\"] = numpy.arange(len(value)).reshape((-1, 1))\n\n for i, n in enumerate(value.dtype.names):\n atom_records[:,i][\"atomn\"] = n\n atom_records[:,i][\"x\"] = value[n][:,0]\n atom_records[:,i][\"y\"] = value[n][:,1]\n atom_records[:,i][\"z\"] = value[n][:,2]\n \n atom_records = atom_records.ravel()\n atom_records[\"atomi\"] = numpy.arange(len(atom_records))\n if b is not None:\n atom_records[\"b\"] = b\n \n return pdb_parsing.to_pdb(atom_records.ravel())\n \n def validate(self, obj, value):\n if isinstance(value, str):\n value = self.from_pdb(value)\n \n value = numpy.array(value, dtype=self.dtype, copy=False)\n assert value.ndim == 1\n \n return value",
"execution_count": 6,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "class BBModel(traitlets.HasTraits):\n state = FixedNamedAtomSystem((\"N\", \"C\", \"CA\", \"O\"))\n \n @property\n def coords(self):\n return self.state.view(dtype=\"f4\").reshape((-1, 3))\n \n \nclass PDBModelViewer(object):\n def __init__(self, target, score=None):\n self.target = target\n self.view = py3dmol.view(1200, 600)\n \n self.target.observe(lambda c: self.update(), \"state\")\n self.score = score\n \n self.pdb = None\n \n self.update()\n self.view.zoomTo()\n self.update()\n \n def update(self):\n self.view.clear()\n self.pdb = self.target.traits()[\"state\"].to_pdb(\n self.target.state,\n b= self.score(self.target.coords).atom_scores.numpy() if self.score else None)\n self.view.addModel(self.pdb, \"pdb\")\n if self.score:\n self.view.setStyle({\"sphere\" : {\"colorscheme\" : {\"prop\":'b',\"gradient\": 'rwb',\"min\":1,\"max\":-1}}})\n else:\n self.view.setStyle({\"sphere\" : {}})\n \n display(self.view.update())\n\nclass StupidLJScore:\n def __init__(self, r_m = 1.0, epsilon = 1.0):\n self.r_m = r_m\n self.epsilon = epsilon\n \n def __call__(self, coords):\n self.coords = Variable(torch.Tensor(coords), requires_grad=True)\n ind = Variable(torch.Tensor(numpy.arange(self.coords.shape[0])), requires_grad=False)\n\n ind_a = ind.view((-1, 1))\n ind_b = ind.view((1, -1))\n deltas = self.coords.view((-1, 1, 3)) - self.coords.view((1, -1, 3))\n\n dist = torch.norm(deltas, 2, -1)\n\n fd = (self.r_m / dist)\n fd2 = fd * fd\n fd6 = fd2 * fd2 * fd2\n fd12 = fd6 * fd6\n lj = self.epsilon * (fd12 - 3 * fd6)\n\n self.lj = torch.where(\n ind_a != ind_b,\n lj,\n Variable(torch.Tensor([0.0]), requires_grad=False)\n )\n\n\n self.atom_scores = torch.sum(self.lj.detach(), dim=-1)\n self.total_score = torch.sum(self.lj)\n (self.grads,) = torch.autograd.grad(self.total_score, self.coords)\n \n return self\n\nclass StupidMinimizer:\n def __init__(self, system, scorefn):\n self.system = system\n self.scorefn = scorefn\n \n def fun(self, x):\n coords = x.reshape((-1, 3))\n \n score = self.scorefn(coords)\n return (\n score.total_score.detach().numpy(),\n score.grads.numpy().reshape(-1)\n )\n \n def update_system(self, x):\n self.system.coords[:] = x.reshape(self.system.coords.shape)\n self.system.state = self.system.state\n \n def minimize(self):\n self.result = scipy.optimize.minimize(\n self.fun,\n self.system.coords.reshape(-1),\n jac=True,\n tol=1,\n options = dict(disp=False, maxiter=100),\n callback=self.update_system\n )\n \n return self",
"execution_count": 17,
"outputs": []
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "start_model = BBModel(state=fetch_pdb(\"1ubq\"))\nstart_view = PDBModelViewer(start_model)",
"execution_count": 18,
"outputs": [
{
"output_type": "stream",
"text": "/home/fordas/.conda/envs/tmol/lib/python3.5/site-packages/traitlets/traitlets.py:567: FutureWarning: elementwise == comparison failed and returning scalar instead; this will raise an error or perform elementwise comparison in the future.\n silent = bool(old_value == new_value)\n",
"name": "stderr"
},
{
"output_type": "display_data",
"data": {
"text/html": "<div id=\"3dmolviewer_1518510157964233\" style=\"position: relative; width: 1200px; height: 600px\">\n<script>\nif(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('https://3dmol.csb.pitt.edu/build/3Dmol.js'))\nvar viewer_1518510157964233 = null;\n$3Dmolpromise.done(function() {\nviewer_1518510157964233 = $3Dmol.createViewer($(\"#3dmolviewer_1518510157964233\"),{backgroundColor:\"white\"});\n\tviewer_1518510157964233.clear();\n\tviewer_1518510157964233.addModel(\"MODEL \\nATOM 0 N CEN X 0 27.340 24.430 2.614 0.00 0.00\\nATOM 1 C CEN X 0 26.913 26.639 3.531 0.00 0.00\\nATOM 2 CA CEN X 0 26.266 25.413 2.842 0.00 0.00\\nATOM 3 O CEN X 0 27.886 26.463 4.263 0.00 0.00\\nATOM 4 N CEN X 1 26.335 27.770 3.258 0.00 0.00\\nATOM 5 C CEN X 1 26.100 29.253 5.202 0.00 0.00\\nATOM 6 CA CEN X 1 26.850 29.021 3.898 0.00 0.00\\nATOM 7 O CEN X 1 24.865 29.024 5.330 0.00 0.00\\nATOM 8 N CEN X 2 26.849 29.656 6.217 0.00 0.00\\nATOM 9 C CEN X 2 26.882 31.428 7.862 0.00 0.00\\nATOM 10 CA CEN X 2 26.235 30.058 7.497 0.00 0.00\\nATOM 11 O CEN X 2 27.906 31.711 7.264 0.00 0.00\\nATOM 12 N CEN X 3 26.214 32.097 8.771 0.00 0.00\\nATOM 13 C CEN X 3 27.151 33.362 10.650 0.00 0.00\\nATOM 14 CA CEN X 3 26.772 33.436 9.197 0.00 0.00\\nATOM 15 O CEN X 3 26.350 32.778 11.395 0.00 0.00\\nATOM 16 N CEN X 4 28.260 33.943 11.096 0.00 0.00\\nATOM 17 C CEN X 4 28.638 35.461 12.900 0.00 0.00\\nATOM 18 CA CEN X 4 28.605 33.965 12.503 0.00 0.00\\nATOM 19 O CEN X 4 29.522 36.103 12.320 0.00 0.00\\nATOM 20 N CEN X 5 27.751 35.867 13.740 0.00 0.00\\nATOM 21 C CEN X 5 28.469 37.475 15.420 0.00 0.00\\nATOM 22 CA CEN X 5 27.691 37.315 14.143 0.00 0.00\\nATOM 23 O CEN X 5 28.213 36.753 16.411 0.00 0.00\\nATOM 24 N CEN X 6 29.426 38.430 15.446 0.00 0.00\\nATOM 25 C CEN X 6 29.664 39.839 17.434 0.00 0.00\\nATOM 26 CA CEN X 6 30.225 38.643 16.662 0.00 0.00\\nATOM 27 O CEN X 6 28.850 40.565 16.859 0.00 0.00\\nATOM 28 N CEN X 7 30.132 40.069 18.642 0.00 0.00\\nATOM 29 C CEN X 7 30.075 42.538 18.984 0.00 0.00\\nATOM 30 CA CEN X 7 29.607 41.180 19.467 0.00 0.00\\nATOM 31 O CEN X 7 29.586 43.570 19.483 0.00 0.00\\nATOM 32 N CEN X 8 30.991 42.571 17.998 0.00 0.00\\nATOM 33 C CEN X 8 30.755 44.351 16.277 0.00 0.00\\nATOM 34 CA CEN X 8 31.422 43.940 17.553 0.00 0.00\\nATOM 35 O CEN X 8 31.207 45.268 15.566 0.00 0.00\\nATOM 36 N CEN X 9 29.721 43.673 15.885 0.00 0.00\\nATOM 37 C CEN X 9 29.604 43.507 13.393 0.00 0.00\\nATOM 38 CA CEN X 9 28.978 43.960 14.678 0.00 0.00\\nATOM 39 O CEN X 9 29.219 43.981 12.301 0.00 0.00\\nATOM 40 N CEN X 10 30.563 42.623 13.495 0.00 0.00\\nATOM 41 C CEN X 10 30.459 40.666 12.130 0.00 0.00\\nATOM 42 CA CEN X 10 31.191 42.012 12.331 0.00 0.00\\nATOM 43 O CEN X 10 30.253 39.991 13.133 0.00 0.00\\nATOM 44 N CEN X 11 30.163 40.338 10.886 0.00 0.00\\nATOM 45 C CEN X 11 30.494 38.261 9.729 0.00 0.00\\nATOM 46 CA CEN X 11 29.542 39.020 10.653 0.00 0.00\\nATOM 47 O CEN X 11 30.849 38.850 8.706 0.00 0.00\\nATOM 48 N CEN X 12 30.795 37.015 10.095 0.00 0.00\\nATOM 49 C CEN X 12 30.955 35.211 8.459 0.00 0.00\\nATOM 50 CA CEN X 12 31.720 36.289 9.176 0.00 0.00\\nATOM 51 O CEN X 12 30.025 34.618 9.040 0.00 0.00\\nATOM 52 N CEN X 13 31.244 34.986 7.197 0.00 0.00\\nATOM 53 C CEN X 13 31.409 32.680 6.446 0.00 0.00\\nATOM 54 CA CEN X 13 30.505 33.884 6.512 0.00 0.00\\nATOM 55 O CEN X 13 32.619 32.812 6.125 0.00 0.00\\nATOM 56 N CEN X 14 30.884 31.485 6.666 0.00 0.00\\nATOM 57 C CEN X 14 31.022 29.288 5.665 0.00 0.00\\nATOM 58 CA CEN X 14 31.677 30.275 6.639 0.00 0.00\\nATOM 59 O CEN X 14 29.809 29.395 5.545 0.00 0.00\\nATOM 60 N CEN X 15 31.834 28.412 5.125 0.00 0.00\\nATOM 61 C CEN X 15 31.440 26.079 5.080 0.00 0.00\\nATOM 62 CA CEN X 15 31.220 27.341 4.275 0.00 0.00\\nATOM 63 O CEN X 15 32.576 25.802 5.461 0.00 0.00\\nATOM 64 N CEN X 16 30.310 25.458 5.384 0.00 0.00\\nATOM 65 C CEN X 16 29.279 23.227 5.641 0.00 0.00\\nATOM 66 CA CEN X 16 30.288 24.245 6.193 0.00 0.00\\nATOM 67 O CEN X 16 28.478 23.522 4.725 0.00 0.00\\nATOM 68 N CEN X 17 29.380 22.057 6.232 0.00 0.00\\nATOM 69 C CEN X 17 27.819 20.609 7.316 0.00 0.00\\nATOM 70 CA CEN X 17 28.468 20.940 5.980 0.00 0.00\\nATOM 71 O CEN X 17 28.449 20.674 8.360 0.00 0.00\\nATOM 72 N CEN X 18 26.559 20.220 7.288 0.00 0.00\\nATOM 73 C CEN X 18 26.541 18.732 9.251 0.00 0.00\\nATOM 74 CA CEN X 18 25.829 19.825 8.494 0.00 0.00\\nATOM 75 O CEN X 18 26.333 18.536 10.457 0.00 0.00\\nATOM 76 N CEN X 19 27.361 17.959 8.559 0.00 0.00\\nATOM 77 C CEN X 19 29.258 17.318 9.984 0.00 0.00\\nATOM 78 CA CEN X 19 28.054 16.835 9.210 0.00 0.00\\nATOM 79 O CEN X 19 29.930 16.477 10.606 0.00 0.00\\nATOM 80 N CEN X 20 29.599 18.599 9.828 0.00 0.00\\nATOM 81 C CEN X 20 30.491 19.162 12.040 0.00 0.00\\nATOM 82 CA CEN X 20 30.796 19.083 10.566 0.00 0.00\\nATOM 83 O CEN X 20 29.367 19.523 12.441 0.00 0.00\\nATOM 84 N CEN X 21 31.510 18.936 12.852 0.00 0.00\\nATOM 85 C CEN X 21 31.593 20.553 14.655 0.00 0.00\\nATOM 86 CA CEN X 21 31.398 19.064 14.286 0.00 0.00\\nATOM 87 O CEN X 21 32.159 21.311 13.861 0.00 0.00\\nATOM 88 N CEN X 22 31.113 20.863 15.860 0.00 0.00\\nATOM 89 C CEN X 22 32.776 22.519 16.577 0.00 0.00\\nATOM 90 CA CEN X 22 31.288 22.201 16.417 0.00 0.00\\nATOM 91 O CEN X 22 33.233 23.659 16.384 0.00 0.00\\nATOM 92 N CEN X 23 33.548 21.526 16.950 0.00 0.00\\nATOM 93 C CEN X 23 35.615 22.190 15.759 0.00 0.00\\nATOM 94 CA CEN X 23 35.031 21.722 17.069 0.00 0.00\\nATOM 95 O CEN X 23 36.532 23.046 15.724 0.00 0.00\\nATOM 96 N CEN X 24 35.139 21.624 14.662 0.00 0.00\\nATOM 97 C CEN X 24 35.238 23.382 12.920 0.00 0.00\\nATOM 98 CA CEN X 24 35.590 21.945 13.302 0.00 0.00\\nATOM 99 O CEN X 24 36.066 24.109 12.333 0.00 0.00\\nATOM 100 N CEN X 25 34.007 23.745 13.250 0.00 0.00\\nATOM 101 C CEN X 25 34.441 26.099 13.684 0.00 0.00\\nATOM 102 CA CEN X 25 33.533 25.097 12.978 0.00 0.00\\nATOM 103 O CEN X 25 34.883 27.090 13.093 0.00 0.00\\nATOM 104 N CEN X 26 34.734 25.822 14.949 0.00 0.00\\nATOM 105 C CEN X 26 36.975 26.826 15.107 0.00 0.00\\nATOM 106 CA CEN X 26 35.596 26.715 15.736 0.00 0.00\\nATOM 107 O CEN X 26 37.579 27.926 15.159 0.00 0.00\\nATOM 108 N CEN X 27 37.499 25.743 14.571 0.00 0.00\\nATOM 109 C CEN X 27 38.728 26.591 12.611 0.00 0.00\\nATOM 110 CA CEN X 27 38.794 25.761 13.880 0.00 0.00\\nATOM 111 O CEN X 27 39.704 27.346 12.277 0.00 0.00\\nATOM 112 N CEN X 28 37.633 26.543 11.867 0.00 0.00\\nATOM 113 C CEN X 28 37.441 28.882 11.052 0.00 0.00\\nATOM 114 CA CEN X 28 37.471 27.391 10.668 0.00 0.00\\nATOM 115 O CEN X 28 38.020 29.772 10.382 0.00 0.00\\nATOM 116 N CEN X 29 36.811 29.170 12.192 0.00 0.00\\nATOM 117 C CEN X 29 38.148 30.981 13.069 0.00 0.00\\nATOM 118 CA CEN X 29 36.731 30.570 12.645 0.00 0.00\\nATOM 119 O CEN X 29 38.544 32.150 12.856 0.00 0.00\\nATOM 120 N CEN X 30 38.883 30.110 13.713 0.00 0.00\\nATOM 121 C CEN X 30 41.092 30.808 12.851 0.00 0.00\\nATOM 122 CA CEN X 30 40.269 30.508 14.115 0.00 0.00\\nATOM 123 O CEN X 30 41.828 31.808 12.681 0.00 0.00\\nATOM 124 N CEN X 31 41.001 29.878 11.931 0.00 0.00\\nATOM 125 C CEN X 31 41.399 31.338 9.967 0.00 0.00\\nATOM 126 CA CEN X 31 41.718 30.022 10.643 0.00 0.00\\nATOM 127 O CEN X 31 42.260 32.036 9.381 0.00 0.00\\nATOM 128 N CEN X 32 40.117 31.750 9.988 0.00 0.00\\nATOM 129 C CEN X 32 39.837 34.271 9.995 0.00 0.00\\nATOM 130 CA CEN X 32 39.808 32.994 9.233 0.00 0.00\\nATOM 131 O CEN X 32 40.164 35.323 9.345 0.00 0.00\\nATOM 132 N CEN X 33 39.655 34.335 11.285 0.00 0.00\\nATOM 133 C CEN X 33 40.675 35.527 13.200 0.00 0.00\\nATOM 134 CA CEN X 33 39.676 35.547 12.072 0.00 0.00\\nATOM 135 O CEN X 33 40.814 36.528 13.911 0.00 0.00\\nATOM 136 N CEN X 34 41.317 34.393 13.432 0.00 0.00\\nATOM 137 C CEN X 34 41.949 34.076 15.842 0.00 0.00\\nATOM 138 CA CEN X 34 42.345 34.269 14.431 0.00 0.00\\nATOM 139 O CEN X 34 42.829 34.000 16.739 0.00 0.00\\nATOM 140 N CEN X 35 40.642 33.916 16.112 0.00 0.00\\nATOM 141 C CEN X 35 40.449 32.278 17.945 0.00 0.00\\nATOM 142 CA CEN X 35 40.226 33.716 17.509 0.00 0.00\\nATOM 143 O CEN X 35 39.936 31.336 17.315 0.00 0.00\\nATOM 144 N CEN X 36 41.189 32.085 19.031 0.00 0.00\\nATOM 145 C CEN X 36 40.168 30.026 19.918 0.00 0.00\\nATOM 146 CA CEN X 36 41.461 30.751 19.594 0.00 0.00\\nATOM 147 O CEN X 36 39.264 30.662 20.521 0.00 0.00\\nATOM 148 N CEN X 37 40.059 28.758 19.607 0.00 0.00\\nATOM 149 C CEN X 37 38.421 28.048 21.341 0.00 0.00\\nATOM 150 CA CEN X 37 38.817 28.020 19.889 0.00 0.00\\nATOM 151 O CEN X 37 37.213 28.036 21.704 0.00 0.00\\nATOM 152 N CEN X 38 39.374 28.090 22.240 0.00 0.00\\nATOM 153 C CEN X 38 38.365 29.335 24.159 0.00 0.00\\nATOM 154 CA CEN X 38 39.063 28.063 23.695 0.00 0.00\\nATOM 155 O CEN X 38 37.684 29.390 25.221 0.00 0.00\\nATOM 156 N CEN X 39 38.419 30.373 23.341 0.00 0.00\\nATOM 157 C CEN X 39 36.334 31.742 23.087 0.00 0.00\\nATOM 158 CA CEN X 39 37.738 31.637 23.712 0.00 0.00\\nATOM 159 O CEN X 39 35.574 32.618 23.483 0.00 0.00\\nATOM 160 N CEN X 40 36.000 30.860 22.172 0.00 0.00\\nATOM 161 C CEN X 40 33.589 30.189 22.181 0.00 0.00\\nATOM 162 CA CEN X 40 34.738 30.875 21.473 0.00 0.00\\nATOM 163 O CEN X 40 33.580 29.009 22.499 0.00 0.00\\nATOM 164 N CEN X 41 32.478 30.917 22.269 0.00 0.00\\nATOM 165 C CEN X 41 30.210 30.509 21.650 0.00 0.00\\nATOM 166 CA CEN X 41 31.200 30.329 22.780 0.00 0.00\\nATOM 167 O CEN X 41 29.978 31.726 21.269 0.00 0.00\\nATOM 168 N CEN X 42 29.694 29.436 21.054 0.00 0.00\\nATOM 169 C CEN X 42 27.331 29.317 20.364 0.00 0.00\\nATOM 170 CA CEN X 42 28.762 29.573 19.906 0.00 0.00\\nATOM 171 O CEN X 42 27.101 28.346 21.097 0.00 0.00\\nATOM 172 N CEN X 43 26.436 30.232 20.004 0.00 0.00\\nATOM 173 C CEN X 43 24.101 30.149 19.196 0.00 0.00\\nATOM 174 CA CEN X 43 25.034 30.170 20.401 0.00 0.00\\nATOM 175 O CEN X 43 24.196 30.948 18.287 0.00 0.00\\nATOM 176 N CEN X 44 23.141 29.187 19.241 0.00 0.00\\nATOM 177 C CEN X 44 20.835 28.629 18.904 0.00 0.00\\nATOM 178 CA CEN X 44 22.126 29.062 18.183 0.00 0.00\\nATOM 179 O CEN X 44 20.821 27.734 19.749 0.00 0.00\\nATOM 180 N CEN X 45 19.810 29.378 18.578 0.00 0.00\\nATOM 181 C CEN X 45 18.453 28.941 20.591 0.00 0.00\\nATOM 182 CA CEN X 45 18.443 29.143 19.083 0.00 0.00\\nATOM 183 O CEN X 45 17.860 27.994 21.128 0.00 0.00\\nATOM 184 N CEN X 46 19.172 29.808 21.243 0.00 0.00\\nATOM 185 C CEN X 46 20.083 28.729 23.321 0.00 0.00\\nATOM 186 CA CEN X 46 19.399 29.894 22.655 0.00 0.00\\nATOM 187 O CEN X 46 19.991 28.584 24.561 0.00 0.00\\nATOM 188 N CEN X 47 20.801 27.931 22.578 0.00 0.00\\nATOM 189 C CEN X 47 23.046 27.087 22.913 0.00 0.00\\nATOM 190 CA CEN X 47 21.550 26.796 23.133 0.00 0.00\\nATOM 191 O CEN X 47 23.383 27.627 21.870 0.00 0.00\\nATOM 192 N CEN X 48 23.880 26.727 23.851 0.00 0.00\\nATOM 193 C CEN X 48 25.743 25.586 22.922 0.00 0.00\\nATOM 194 CA CEN X 48 25.349 26.872 23.643 0.00 0.00\\nATOM 195 O CEN X 48 25.325 24.489 23.378 0.00 0.00\\nATOM 196 N CEN X 49 26.465 25.689 21.833 0.00 0.00\\nATOM 197 C CEN X 49 27.994 23.781 21.643 0.00 0.00\\nATOM 198 CA CEN X 49 26.826 24.521 21.012 0.00 0.00\\nATOM 199 O CEN X 49 28.904 24.444 22.098 0.00 0.00\\nATOM 200 N CEN X 50 27.942 22.448 21.648 0.00 0.00\\nATOM 201 C CEN X 50 29.942 21.106 21.240 0.00 0.00\\nATOM 202 CA CEN X 50 29.015 21.657 22.288 0.00 0.00\\nATOM 203 O CEN X 50 29.470 20.677 20.190 0.00 0.00\\nATOM 204 N CEN X 51 31.233 21.090 21.459 0.00 0.00\\nATOM 205 C CEN X 51 32.128 19.364 19.750 0.00 0.00\\nATOM 206 CA CEN X 51 32.262 20.670 20.514 0.00 0.00\\nATOM 207 O CEN X 51 32.546 19.317 18.558 0.00 0.00\\nATOM 208 N CEN X 52 31.697 18.311 20.406 0.00 0.00\\nATOM 209 C CEN X 52 30.320 16.698 19.051 0.00 0.00\\nATOM 210 CA CEN X 52 31.568 16.962 19.825 0.00 0.00\\nATOM 211 O CEN X 52 30.198 15.657 18.366 0.00 0.00\\nATOM 212 N CEN X 53 29.340 17.594 19.076 0.00 0.00\\nATOM 213 C CEN X 53 28.375 17.999 16.887 0.00 0.00\\nATOM 214 CA CEN X 53 28.108 17.439 18.276 0.00 0.00\\nATOM 215 O CEN X 53 29.326 18.786 16.690 0.00 0.00\\nATOM 216 N CEN X 54 27.510 17.689 15.954 0.00 0.00\\nATOM 217 C CEN X 54 26.482 19.280 14.432 0.00 0.00\\nATOM 218 CA CEN X 54 27.574 18.192 14.563 0.00 0.00\\nATOM 219 O CEN X 54 25.609 19.388 15.287 0.00 0.00\\nATOM 220 N CEN X 55 26.585 20.063 13.378 0.00 0.00\\nATOM 221 C CEN X 55 24.241 20.436 12.857 0.00 0.00\\nATOM 222 CA CEN X 55 25.594 21.109 13.072 0.00 0.00\\nATOM 223 O CEN X 55 23.264 20.951 13.329 0.00 0.00\\nATOM 224 N CEN X 56 24.240 19.233 12.246 0.00 0.00\\nATOM 225 C CEN X 56 22.229 18.244 13.325 0.00 0.00\\nATOM 226 CA CEN X 56 22.924 18.583 12.025 0.00 0.00\\nATOM 227 O CEN X 56 20.963 18.253 13.395 0.00 0.00\\nATOM 228 N CEN X 57 22.997 17.978 14.366 0.00 0.00\\nATOM 229 C CEN X 57 21.460 18.737 16.163 0.00 0.00\\nATOM 230 CA CEN X 57 22.418 17.638 15.693 0.00 0.00\\nATOM 231 O CEN X 57 20.497 18.506 16.900 0.00 0.00\\nATOM 232 N CEN X 58 21.846 19.954 15.905 0.00 0.00\\nATOM 233 C CEN X 58 20.142 21.590 15.149 0.00 0.00\\nATOM 234 CA CEN X 58 21.079 21.149 16.251 0.00 0.00\\nATOM 235 O CEN X 58 19.499 22.645 15.321 0.00 0.00\\nATOM 236 N CEN X 59 19.993 20.884 14.049 0.00 0.00\\nATOM 237 C CEN X 59 19.442 22.745 12.510 0.00 0.00\\nATOM 238 CA CEN X 59 19.065 21.352 12.999 0.00 0.00\\nATOM 239 O CEN X 59 18.571 23.610 12.289 0.00 0.00\\nATOM 240 N CEN X 60 20.717 22.964 12.260 0.00 0.00\\nATOM 241 C CEN X 60 21.110 24.111 10.173 0.00 0.00\\nATOM 242 CA CEN X 60 21.184 24.263 11.690 0.00 0.00\\nATOM 243 O CEN X 60 21.841 23.198 9.686 0.00 0.00\\nATOM 244 N CEN X 61 20.291 24.875 9.507 0.00 0.00\\nATOM 245 C CEN X 61 20.822 25.914 7.332 0.00 0.00\\nATOM 246 CA CEN X 61 20.081 24.773 8.033 0.00 0.00\\nATOM 247 O CEN X 61 21.323 26.830 8.008 0.00 0.00\\nATOM 248 N CEN X 62 20.924 25.862 6.006 0.00 0.00\\nATOM 249 C CEN X 62 21.127 28.240 5.574 0.00 0.00\\nATOM 250 CA CEN X 62 21.656 26.847 5.240 0.00 0.00\\nATOM 251 O CEN X 62 19.958 28.465 5.842 0.00 0.00\\nATOM 252 N CEN X 63 22.099 29.163 5.605 0.00 0.00\\nATOM 253 C CEN X 63 21.466 30.953 7.261 0.00 0.00\\nATOM 254 CA CEN X 63 21.907 30.563 5.881 0.00 0.00\\nATOM 255 O CEN X 63 21.066 32.112 7.533 0.00 0.00\\nATOM 256 N CEN X 64 21.674 30.034 8.191 0.00 0.00\\nATOM 257 C CEN X 64 22.504 31.228 10.136 0.00 0.00\\nATOM 258 CA CEN X 64 21.419 30.253 9.620 0.00 0.00\\nATOM 259 O CEN X 64 23.579 31.321 9.554 0.00 0.00\\nATOM 260 N CEN X 65 22.241 31.873 11.241 0.00 0.00\\nATOM 261 C CEN X 65 23.509 32.224 13.290 0.00 0.00\\nATOM 262 CA CEN X 65 23.212 32.762 11.891 0.00 0.00\\nATOM 263 O CEN X 65 22.544 31.942 14.034 0.00 0.00\\nATOM 264 N CEN X 66 24.790 32.021 13.618 0.00 0.00\\nATOM 265 C CEN X 66 25.698 32.876 15.669 0.00 0.00\\nATOM 266 CA CEN X 66 25.149 31.609 14.980 0.00 0.00\\nATOM 267 O CEN X 66 26.158 33.730 14.894 0.00 0.00\\nATOM 268 N CEN X 67 25.621 32.945 16.950 0.00 0.00\\nATOM 269 C CEN X 67 27.475 33.651 18.304 0.00 0.00\\nATOM 270 CA CEN X 67 26.179 34.127 17.650 0.00 0.00\\nATOM 271 O CEN X 67 27.507 32.587 18.958 0.00 0.00\\nATOM 272 N CEN X 68 28.525 34.447 18.189 0.00 0.00\\nATOM 273 C CEN X 68 30.052 35.042 20.004 0.00 0.00\\nATOM 274 CA CEN X 68 29.801 34.145 18.829 0.00 0.00\\nATOM 275 O CEN X 68 30.105 36.305 19.788 0.00 0.00\\nATOM 276 N CEN X 69 30.124 34.533 21.191 0.00 0.00\\nATOM 277 C CEN X 69 31.901 34.910 22.728 0.00 0.00\\nATOM 278 CA CEN X 69 30.479 35.369 22.374 0.00 0.00\\nATOM 279 O CEN X 69 32.190 33.696 22.635 0.00 0.00\\nATOM 280 N CEN X 70 32.763 35.831 23.090 0.00 0.00\\nATOM 281 C CEN X 70 34.239 35.353 24.979 0.00 0.00\\nATOM 282 CA CEN X 70 34.145 35.472 23.481 0.00 0.00\\nATOM 283 O CEN X 70 33.707 36.197 25.728 0.00 0.00\\nATOM 284 N CEN X 71 34.930 34.384 25.451 0.00 0.00\\nATOM 285 C CEN X 71 36.671 34.296 27.089 0.00 0.00\\nATOM 286 CA CEN X 71 35.161 34.174 26.896 0.00 0.00\\nATOM 287 O CEN X 71 37.305 33.233 26.795 0.00 0.00\\nATOM 288 N CEN X 72 37.197 35.397 27.513 0.00 0.00\\nATOM 289 C CEN X 72 39.076 34.931 29.031 0.00 0.00\\nATOM 290 CA CEN X 72 38.668 35.502 27.680 0.00 0.00\\nATOM 291 O CEN X 72 38.297 34.946 29.996 0.00 0.00\\nATOM 292 N CEN X 73 40.294 34.412 29.045 0.00 0.00\\nATOM 293 C CEN X 73 41.765 34.829 30.944 0.00 0.00\\nATOM 294 CA CEN X 73 40.873 33.802 30.253 0.00 0.00\\nATOM 295 O CEN X 73 42.945 34.994 30.583 0.00 0.00\\nATOM 296 N CEN X 74 41.165 35.531 31.898 0.00 0.00\\nATOM 297 C CEN X 74 41.251 37.941 32.588 0.00 0.00\\nATOM 298 CA CEN X 74 41.845 36.550 32.686 0.00 0.00\\nATOM 299 O CEN X 74 41.102 38.523 31.500 0.00 0.00\\nATOM 300 N CEN X 75 40.946 38.472 33.757 0.00 0.00\\nATOM 301 C CEN X 75 40.031 39.992 35.432 0.00 0.00\\nATOM 302 CA CEN X 75 40.373 39.813 33.944 0.00 0.00\\nATOM 303 O CEN X 75 38.933 40.525 35.687 0.00 0.00\\nTER\\nENDMDL\\n\",\"pdb\");\n\tviewer_1518510157964233.setStyle({\"sphere\": {}});\nviewer_1518510157964233.render();\n});\n</script><script>\n $3Dmolpromise.done(function() { //wrap in promise for non-interactive functionality\n \n viewer_1518510157964233.render();\n });\n </script>",
"text/plain": "<IPython.core.display.HTML object>"
},
"metadata": {}
},
{
"output_type": "display_data",
"data": {
"text/html": "<script>\n $3Dmolpromise.done(function() { //wrap in promise for non-interactive functionality\n \tviewer_1518510157964233.zoomTo();\n\tviewer_1518510157964233.clear();\n\tviewer_1518510157964233.addModel(\"MODEL \\nATOM 0 N CEN X 0 27.340 24.430 2.614 0.00 0.00\\nATOM 1 C CEN X 0 26.913 26.639 3.531 0.00 0.00\\nATOM 2 CA CEN X 0 26.266 25.413 2.842 0.00 0.00\\nATOM 3 O CEN X 0 27.886 26.463 4.263 0.00 0.00\\nATOM 4 N CEN X 1 26.335 27.770 3.258 0.00 0.00\\nATOM 5 C CEN X 1 26.100 29.253 5.202 0.00 0.00\\nATOM 6 CA CEN X 1 26.850 29.021 3.898 0.00 0.00\\nATOM 7 O CEN X 1 24.865 29.024 5.330 0.00 0.00\\nATOM 8 N CEN X 2 26.849 29.656 6.217 0.00 0.00\\nATOM 9 C CEN X 2 26.882 31.428 7.862 0.00 0.00\\nATOM 10 CA CEN X 2 26.235 30.058 7.497 0.00 0.00\\nATOM 11 O CEN X 2 27.906 31.711 7.264 0.00 0.00\\nATOM 12 N CEN X 3 26.214 32.097 8.771 0.00 0.00\\nATOM 13 C CEN X 3 27.151 33.362 10.650 0.00 0.00\\nATOM 14 CA CEN X 3 26.772 33.436 9.197 0.00 0.00\\nATOM 15 O CEN X 3 26.350 32.778 11.395 0.00 0.00\\nATOM 16 N CEN X 4 28.260 33.943 11.096 0.00 0.00\\nATOM 17 C CEN X 4 28.638 35.461 12.900 0.00 0.00\\nATOM 18 CA CEN X 4 28.605 33.965 12.503 0.00 0.00\\nATOM 19 O CEN X 4 29.522 36.103 12.320 0.00 0.00\\nATOM 20 N CEN X 5 27.751 35.867 13.740 0.00 0.00\\nATOM 21 C CEN X 5 28.469 37.475 15.420 0.00 0.00\\nATOM 22 CA CEN X 5 27.691 37.315 14.143 0.00 0.00\\nATOM 23 O CEN X 5 28.213 36.753 16.411 0.00 0.00\\nATOM 24 N CEN X 6 29.426 38.430 15.446 0.00 0.00\\nATOM 25 C CEN X 6 29.664 39.839 17.434 0.00 0.00\\nATOM 26 CA CEN X 6 30.225 38.643 16.662 0.00 0.00\\nATOM 27 O CEN X 6 28.850 40.565 16.859 0.00 0.00\\nATOM 28 N CEN X 7 30.132 40.069 18.642 0.00 0.00\\nATOM 29 C CEN X 7 30.075 42.538 18.984 0.00 0.00\\nATOM 30 CA CEN X 7 29.607 41.180 19.467 0.00 0.00\\nATOM 31 O CEN X 7 29.586 43.570 19.483 0.00 0.00\\nATOM 32 N CEN X 8 30.991 42.571 17.998 0.00 0.00\\nATOM 33 C CEN X 8 30.755 44.351 16.277 0.00 0.00\\nATOM 34 CA CEN X 8 31.422 43.940 17.553 0.00 0.00\\nATOM 35 O CEN X 8 31.207 45.268 15.566 0.00 0.00\\nATOM 36 N CEN X 9 29.721 43.673 15.885 0.00 0.00\\nATOM 37 C CEN X 9 29.604 43.507 13.393 0.00 0.00\\nATOM 38 CA CEN X 9 28.978 43.960 14.678 0.00 0.00\\nATOM 39 O CEN X 9 29.219 43.981 12.301 0.00 0.00\\nATOM 40 N CEN X 10 30.563 42.623 13.495 0.00 0.00\\nATOM 41 C CEN X 10 30.459 40.666 12.130 0.00 0.00\\nATOM 42 CA CEN X 10 31.191 42.012 12.331 0.00 0.00\\nATOM 43 O CEN X 10 30.253 39.991 13.133 0.00 0.00\\nATOM 44 N CEN X 11 30.163 40.338 10.886 0.00 0.00\\nATOM 45 C CEN X 11 30.494 38.261 9.729 0.00 0.00\\nATOM 46 CA CEN X 11 29.542 39.020 10.653 0.00 0.00\\nATOM 47 O CEN X 11 30.849 38.850 8.706 0.00 0.00\\nATOM 48 N CEN X 12 30.795 37.015 10.095 0.00 0.00\\nATOM 49 C CEN X 12 30.955 35.211 8.459 0.00 0.00\\nATOM 50 CA CEN X 12 31.720 36.289 9.176 0.00 0.00\\nATOM 51 O CEN X 12 30.025 34.618 9.040 0.00 0.00\\nATOM 52 N CEN X 13 31.244 34.986 7.197 0.00 0.00\\nATOM 53 C CEN X 13 31.409 32.680 6.446 0.00 0.00\\nATOM 54 CA CEN X 13 30.505 33.884 6.512 0.00 0.00\\nATOM 55 O CEN X 13 32.619 32.812 6.125 0.00 0.00\\nATOM 56 N CEN X 14 30.884 31.485 6.666 0.00 0.00\\nATOM 57 C CEN X 14 31.022 29.288 5.665 0.00 0.00\\nATOM 58 CA CEN X 14 31.677 30.275 6.639 0.00 0.00\\nATOM 59 O CEN X 14 29.809 29.395 5.545 0.00 0.00\\nATOM 60 N CEN X 15 31.834 28.412 5.125 0.00 0.00\\nATOM 61 C CEN X 15 31.440 26.079 5.080 0.00 0.00\\nATOM 62 CA CEN X 15 31.220 27.341 4.275 0.00 0.00\\nATOM 63 O CEN X 15 32.576 25.802 5.461 0.00 0.00\\nATOM 64 N CEN X 16 30.310 25.458 5.384 0.00 0.00\\nATOM 65 C CEN X 16 29.279 23.227 5.641 0.00 0.00\\nATOM 66 CA CEN X 16 30.288 24.245 6.193 0.00 0.00\\nATOM 67 O CEN X 16 28.478 23.522 4.725 0.00 0.00\\nATOM 68 N CEN X 17 29.380 22.057 6.232 0.00 0.00\\nATOM 69 C CEN X 17 27.819 20.609 7.316 0.00 0.00\\nATOM 70 CA CEN X 17 28.468 20.940 5.980 0.00 0.00\\nATOM 71 O CEN X 17 28.449 20.674 8.360 0.00 0.00\\nATOM 72 N CEN X 18 26.559 20.220 7.288 0.00 0.00\\nATOM 73 C CEN X 18 26.541 18.732 9.251 0.00 0.00\\nATOM 74 CA CEN X 18 25.829 19.825 8.494 0.00 0.00\\nATOM 75 O CEN X 18 26.333 18.536 10.457 0.00 0.00\\nATOM 76 N CEN X 19 27.361 17.959 8.559 0.00 0.00\\nATOM 77 C CEN X 19 29.258 17.318 9.984 0.00 0.00\\nATOM 78 CA CEN X 19 28.054 16.835 9.210 0.00 0.00\\nATOM 79 O CEN X 19 29.930 16.477 10.606 0.00 0.00\\nATOM 80 N CEN X 20 29.599 18.599 9.828 0.00 0.00\\nATOM 81 C CEN X 20 30.491 19.162 12.040 0.00 0.00\\nATOM 82 CA CEN X 20 30.796 19.083 10.566 0.00 0.00\\nATOM 83 O CEN X 20 29.367 19.523 12.441 0.00 0.00\\nATOM 84 N CEN X 21 31.510 18.936 12.852 0.00 0.00\\nATOM 85 C CEN X 21 31.593 20.553 14.655 0.00 0.00\\nATOM 86 CA CEN X 21 31.398 19.064 14.286 0.00 0.00\\nATOM 87 O CEN X 21 32.159 21.311 13.861 0.00 0.00\\nATOM 88 N CEN X 22 31.113 20.863 15.860 0.00 0.00\\nATOM 89 C CEN X 22 32.776 22.519 16.577 0.00 0.00\\nATOM 90 CA CEN X 22 31.288 22.201 16.417 0.00 0.00\\nATOM 91 O CEN X 22 33.233 23.659 16.384 0.00 0.00\\nATOM 92 N CEN X 23 33.548 21.526 16.950 0.00 0.00\\nATOM 93 C CEN X 23 35.615 22.190 15.759 0.00 0.00\\nATOM 94 CA CEN X 23 35.031 21.722 17.069 0.00 0.00\\nATOM 95 O CEN X 23 36.532 23.046 15.724 0.00 0.00\\nATOM 96 N CEN X 24 35.139 21.624 14.662 0.00 0.00\\nATOM 97 C CEN X 24 35.238 23.382 12.920 0.00 0.00\\nATOM 98 CA CEN X 24 35.590 21.945 13.302 0.00 0.00\\nATOM 99 O CEN X 24 36.066 24.109 12.333 0.00 0.00\\nATOM 100 N CEN X 25 34.007 23.745 13.250 0.00 0.00\\nATOM 101 C CEN X 25 34.441 26.099 13.684 0.00 0.00\\nATOM 102 CA CEN X 25 33.533 25.097 12.978 0.00 0.00\\nATOM 103 O CEN X 25 34.883 27.090 13.093 0.00 0.00\\nATOM 104 N CEN X 26 34.734 25.822 14.949 0.00 0.00\\nATOM 105 C CEN X 26 36.975 26.826 15.107 0.00 0.00\\nATOM 106 CA CEN X 26 35.596 26.715 15.736 0.00 0.00\\nATOM 107 O CEN X 26 37.579 27.926 15.159 0.00 0.00\\nATOM 108 N CEN X 27 37.499 25.743 14.571 0.00 0.00\\nATOM 109 C CEN X 27 38.728 26.591 12.611 0.00 0.00\\nATOM 110 CA CEN X 27 38.794 25.761 13.880 0.00 0.00\\nATOM 111 O CEN X 27 39.704 27.346 12.277 0.00 0.00\\nATOM 112 N CEN X 28 37.633 26.543 11.867 0.00 0.00\\nATOM 113 C CEN X 28 37.441 28.882 11.052 0.00 0.00\\nATOM 114 CA CEN X 28 37.471 27.391 10.668 0.00 0.00\\nATOM 115 O CEN X 28 38.020 29.772 10.382 0.00 0.00\\nATOM 116 N CEN X 29 36.811 29.170 12.192 0.00 0.00\\nATOM 117 C CEN X 29 38.148 30.981 13.069 0.00 0.00\\nATOM 118 CA CEN X 29 36.731 30.570 12.645 0.00 0.00\\nATOM 119 O CEN X 29 38.544 32.150 12.856 0.00 0.00\\nATOM 120 N CEN X 30 38.883 30.110 13.713 0.00 0.00\\nATOM 121 C CEN X 30 41.092 30.808 12.851 0.00 0.00\\nATOM 122 CA CEN X 30 40.269 30.508 14.115 0.00 0.00\\nATOM 123 O CEN X 30 41.828 31.808 12.681 0.00 0.00\\nATOM 124 N CEN X 31 41.001 29.878 11.931 0.00 0.00\\nATOM 125 C CEN X 31 41.399 31.338 9.967 0.00 0.00\\nATOM 126 CA CEN X 31 41.718 30.022 10.643 0.00 0.00\\nATOM 127 O CEN X 31 42.260 32.036 9.381 0.00 0.00\\nATOM 128 N CEN X 32 40.117 31.750 9.988 0.00 0.00\\nATOM 129 C CEN X 32 39.837 34.271 9.995 0.00 0.00\\nATOM 130 CA CEN X 32 39.808 32.994 9.233 0.00 0.00\\nATOM 131 O CEN X 32 40.164 35.323 9.345 0.00 0.00\\nATOM 132 N CEN X 33 39.655 34.335 11.285 0.00 0.00\\nATOM 133 C CEN X 33 40.675 35.527 13.200 0.00 0.00\\nATOM 134 CA CEN X 33 39.676 35.547 12.072 0.00 0.00\\nATOM 135 O CEN X 33 40.814 36.528 13.911 0.00 0.00\\nATOM 136 N CEN X 34 41.317 34.393 13.432 0.00 0.00\\nATOM 137 C CEN X 34 41.949 34.076 15.842 0.00 0.00\\nATOM 138 CA CEN X 34 42.345 34.269 14.431 0.00 0.00\\nATOM 139 O CEN X 34 42.829 34.000 16.739 0.00 0.00\\nATOM 140 N CEN X 35 40.642 33.916 16.112 0.00 0.00\\nATOM 141 C CEN X 35 40.449 32.278 17.945 0.00 0.00\\nATOM 142 CA CEN X 35 40.226 33.716 17.509 0.00 0.00\\nATOM 143 O CEN X 35 39.936 31.336 17.315 0.00 0.00\\nATOM 144 N CEN X 36 41.189 32.085 19.031 0.00 0.00\\nATOM 145 C CEN X 36 40.168 30.026 19.918 0.00 0.00\\nATOM 146 CA CEN X 36 41.461 30.751 19.594 0.00 0.00\\nATOM 147 O CEN X 36 39.264 30.662 20.521 0.00 0.00\\nATOM 148 N CEN X 37 40.059 28.758 19.607 0.00 0.00\\nATOM 149 C CEN X 37 38.421 28.048 21.341 0.00 0.00\\nATOM 150 CA CEN X 37 38.817 28.020 19.889 0.00 0.00\\nATOM 151 O CEN X 37 37.213 28.036 21.704 0.00 0.00\\nATOM 152 N CEN X 38 39.374 28.090 22.240 0.00 0.00\\nATOM 153 C CEN X 38 38.365 29.335 24.159 0.00 0.00\\nATOM 154 CA CEN X 38 39.063 28.063 23.695 0.00 0.00\\nATOM 155 O CEN X 38 37.684 29.390 25.221 0.00 0.00\\nATOM 156 N CEN X 39 38.419 30.373 23.341 0.00 0.00\\nATOM 157 C CEN X 39 36.334 31.742 23.087 0.00 0.00\\nATOM 158 CA CEN X 39 37.738 31.637 23.712 0.00 0.00\\nATOM 159 O CEN X 39 35.574 32.618 23.483 0.00 0.00\\nATOM 160 N CEN X 40 36.000 30.860 22.172 0.00 0.00\\nATOM 161 C CEN X 40 33.589 30.189 22.181 0.00 0.00\\nATOM 162 CA CEN X 40 34.738 30.875 21.473 0.00 0.00\\nATOM 163 O CEN X 40 33.580 29.009 22.499 0.00 0.00\\nATOM 164 N CEN X 41 32.478 30.917 22.269 0.00 0.00\\nATOM 165 C CEN X 41 30.210 30.509 21.650 0.00 0.00\\nATOM 166 CA CEN X 41 31.200 30.329 22.780 0.00 0.00\\nATOM 167 O CEN X 41 29.978 31.726 21.269 0.00 0.00\\nATOM 168 N CEN X 42 29.694 29.436 21.054 0.00 0.00\\nATOM 169 C CEN X 42 27.331 29.317 20.364 0.00 0.00\\nATOM 170 CA CEN X 42 28.762 29.573 19.906 0.00 0.00\\nATOM 171 O CEN X 42 27.101 28.346 21.097 0.00 0.00\\nATOM 172 N CEN X 43 26.436 30.232 20.004 0.00 0.00\\nATOM 173 C CEN X 43 24.101 30.149 19.196 0.00 0.00\\nATOM 174 CA CEN X 43 25.034 30.170 20.401 0.00 0.00\\nATOM 175 O CEN X 43 24.196 30.948 18.287 0.00 0.00\\nATOM 176 N CEN X 44 23.141 29.187 19.241 0.00 0.00\\nATOM 177 C CEN X 44 20.835 28.629 18.904 0.00 0.00\\nATOM 178 CA CEN X 44 22.126 29.062 18.183 0.00 0.00\\nATOM 179 O CEN X 44 20.821 27.734 19.749 0.00 0.00\\nATOM 180 N CEN X 45 19.810 29.378 18.578 0.00 0.00\\nATOM 181 C CEN X 45 18.453 28.941 20.591 0.00 0.00\\nATOM 182 CA CEN X 45 18.443 29.143 19.083 0.00 0.00\\nATOM 183 O CEN X 45 17.860 27.994 21.128 0.00 0.00\\nATOM 184 N CEN X 46 19.172 29.808 21.243 0.00 0.00\\nATOM 185 C CEN X 46 20.083 28.729 23.321 0.00 0.00\\nATOM 186 CA CEN X 46 19.399 29.894 22.655 0.00 0.00\\nATOM 187 O CEN X 46 19.991 28.584 24.561 0.00 0.00\\nATOM 188 N CEN X 47 20.801 27.931 22.578 0.00 0.00\\nATOM 189 C CEN X 47 23.046 27.087 22.913 0.00 0.00\\nATOM 190 CA CEN X 47 21.550 26.796 23.133 0.00 0.00\\nATOM 191 O CEN X 47 23.383 27.627 21.870 0.00 0.00\\nATOM 192 N CEN X 48 23.880 26.727 23.851 0.00 0.00\\nATOM 193 C CEN X 48 25.743 25.586 22.922 0.00 0.00\\nATOM 194 CA CEN X 48 25.349 26.872 23.643 0.00 0.00\\nATOM 195 O CEN X 48 25.325 24.489 23.378 0.00 0.00\\nATOM 196 N CEN X 49 26.465 25.689 21.833 0.00 0.00\\nATOM 197 C CEN X 49 27.994 23.781 21.643 0.00 0.00\\nATOM 198 CA CEN X 49 26.826 24.521 21.012 0.00 0.00\\nATOM 199 O CEN X 49 28.904 24.444 22.098 0.00 0.00\\nATOM 200 N CEN X 50 27.942 22.448 21.648 0.00 0.00\\nATOM 201 C CEN X 50 29.942 21.106 21.240 0.00 0.00\\nATOM 202 CA CEN X 50 29.015 21.657 22.288 0.00 0.00\\nATOM 203 O CEN X 50 29.470 20.677 20.190 0.00 0.00\\nATOM 204 N CEN X 51 31.233 21.090 21.459 0.00 0.00\\nATOM 205 C CEN X 51 32.128 19.364 19.750 0.00 0.00\\nATOM 206 CA CEN X 51 32.262 20.670 20.514 0.00 0.00\\nATOM 207 O CEN X 51 32.546 19.317 18.558 0.00 0.00\\nATOM 208 N CEN X 52 31.697 18.311 20.406 0.00 0.00\\nATOM 209 C CEN X 52 30.320 16.698 19.051 0.00 0.00\\nATOM 210 CA CEN X 52 31.568 16.962 19.825 0.00 0.00\\nATOM 211 O CEN X 52 30.198 15.657 18.366 0.00 0.00\\nATOM 212 N CEN X 53 29.340 17.594 19.076 0.00 0.00\\nATOM 213 C CEN X 53 28.375 17.999 16.887 0.00 0.00\\nATOM 214 CA CEN X 53 28.108 17.439 18.276 0.00 0.00\\nATOM 215 O CEN X 53 29.326 18.786 16.690 0.00 0.00\\nATOM 216 N CEN X 54 27.510 17.689 15.954 0.00 0.00\\nATOM 217 C CEN X 54 26.482 19.280 14.432 0.00 0.00\\nATOM 218 CA CEN X 54 27.574 18.192 14.563 0.00 0.00\\nATOM 219 O CEN X 54 25.609 19.388 15.287 0.00 0.00\\nATOM 220 N CEN X 55 26.585 20.063 13.378 0.00 0.00\\nATOM 221 C CEN X 55 24.241 20.436 12.857 0.00 0.00\\nATOM 222 CA CEN X 55 25.594 21.109 13.072 0.00 0.00\\nATOM 223 O CEN X 55 23.264 20.951 13.329 0.00 0.00\\nATOM 224 N CEN X 56 24.240 19.233 12.246 0.00 0.00\\nATOM 225 C CEN X 56 22.229 18.244 13.325 0.00 0.00\\nATOM 226 CA CEN X 56 22.924 18.583 12.025 0.00 0.00\\nATOM 227 O CEN X 56 20.963 18.253 13.395 0.00 0.00\\nATOM 228 N CEN X 57 22.997 17.978 14.366 0.00 0.00\\nATOM 229 C CEN X 57 21.460 18.737 16.163 0.00 0.00\\nATOM 230 CA CEN X 57 22.418 17.638 15.693 0.00 0.00\\nATOM 231 O CEN X 57 20.497 18.506 16.900 0.00 0.00\\nATOM 232 N CEN X 58 21.846 19.954 15.905 0.00 0.00\\nATOM 233 C CEN X 58 20.142 21.590 15.149 0.00 0.00\\nATOM 234 CA CEN X 58 21.079 21.149 16.251 0.00 0.00\\nATOM 235 O CEN X 58 19.499 22.645 15.321 0.00 0.00\\nATOM 236 N CEN X 59 19.993 20.884 14.049 0.00 0.00\\nATOM 237 C CEN X 59 19.442 22.745 12.510 0.00 0.00\\nATOM 238 CA CEN X 59 19.065 21.352 12.999 0.00 0.00\\nATOM 239 O CEN X 59 18.571 23.610 12.289 0.00 0.00\\nATOM 240 N CEN X 60 20.717 22.964 12.260 0.00 0.00\\nATOM 241 C CEN X 60 21.110 24.111 10.173 0.00 0.00\\nATOM 242 CA CEN X 60 21.184 24.263 11.690 0.00 0.00\\nATOM 243 O CEN X 60 21.841 23.198 9.686 0.00 0.00\\nATOM 244 N CEN X 61 20.291 24.875 9.507 0.00 0.00\\nATOM 245 C CEN X 61 20.822 25.914 7.332 0.00 0.00\\nATOM 246 CA CEN X 61 20.081 24.773 8.033 0.00 0.00\\nATOM 247 O CEN X 61 21.323 26.830 8.008 0.00 0.00\\nATOM 248 N CEN X 62 20.924 25.862 6.006 0.00 0.00\\nATOM 249 C CEN X 62 21.127 28.240 5.574 0.00 0.00\\nATOM 250 CA CEN X 62 21.656 26.847 5.240 0.00 0.00\\nATOM 251 O CEN X 62 19.958 28.465 5.842 0.00 0.00\\nATOM 252 N CEN X 63 22.099 29.163 5.605 0.00 0.00\\nATOM 253 C CEN X 63 21.466 30.953 7.261 0.00 0.00\\nATOM 254 CA CEN X 63 21.907 30.563 5.881 0.00 0.00\\nATOM 255 O CEN X 63 21.066 32.112 7.533 0.00 0.00\\nATOM 256 N CEN X 64 21.674 30.034 8.191 0.00 0.00\\nATOM 257 C CEN X 64 22.504 31.228 10.136 0.00 0.00\\nATOM 258 CA CEN X 64 21.419 30.253 9.620 0.00 0.00\\nATOM 259 O CEN X 64 23.579 31.321 9.554 0.00 0.00\\nATOM 260 N CEN X 65 22.241 31.873 11.241 0.00 0.00\\nATOM 261 C CEN X 65 23.509 32.224 13.290 0.00 0.00\\nATOM 262 CA CEN X 65 23.212 32.762 11.891 0.00 0.00\\nATOM 263 O CEN X 65 22.544 31.942 14.034 0.00 0.00\\nATOM 264 N CEN X 66 24.790 32.021 13.618 0.00 0.00\\nATOM 265 C CEN X 66 25.698 32.876 15.669 0.00 0.00\\nATOM 266 CA CEN X 66 25.149 31.609 14.980 0.00 0.00\\nATOM 267 O CEN X 66 26.158 33.730 14.894 0.00 0.00\\nATOM 268 N CEN X 67 25.621 32.945 16.950 0.00 0.00\\nATOM 269 C CEN X 67 27.475 33.651 18.304 0.00 0.00\\nATOM 270 CA CEN X 67 26.179 34.127 17.650 0.00 0.00\\nATOM 271 O CEN X 67 27.507 32.587 18.958 0.00 0.00\\nATOM 272 N CEN X 68 28.525 34.447 18.189 0.00 0.00\\nATOM 273 C CEN X 68 30.052 35.042 20.004 0.00 0.00\\nATOM 274 CA CEN X 68 29.801 34.145 18.829 0.00 0.00\\nATOM 275 O CEN X 68 30.105 36.305 19.788 0.00 0.00\\nATOM 276 N CEN X 69 30.124 34.533 21.191 0.00 0.00\\nATOM 277 C CEN X 69 31.901 34.910 22.728 0.00 0.00\\nATOM 278 CA CEN X 69 30.479 35.369 22.374 0.00 0.00\\nATOM 279 O CEN X 69 32.190 33.696 22.635 0.00 0.00\\nATOM 280 N CEN X 70 32.763 35.831 23.090 0.00 0.00\\nATOM 281 C CEN X 70 34.239 35.353 24.979 0.00 0.00\\nATOM 282 CA CEN X 70 34.145 35.472 23.481 0.00 0.00\\nATOM 283 O CEN X 70 33.707 36.197 25.728 0.00 0.00\\nATOM 284 N CEN X 71 34.930 34.384 25.451 0.00 0.00\\nATOM 285 C CEN X 71 36.671 34.296 27.089 0.00 0.00\\nATOM 286 CA CEN X 71 35.161 34.174 26.896 0.00 0.00\\nATOM 287 O CEN X 71 37.305 33.233 26.795 0.00 0.00\\nATOM 288 N CEN X 72 37.197 35.397 27.513 0.00 0.00\\nATOM 289 C CEN X 72 39.076 34.931 29.031 0.00 0.00\\nATOM 290 CA CEN X 72 38.668 35.502 27.680 0.00 0.00\\nATOM 291 O CEN X 72 38.297 34.946 29.996 0.00 0.00\\nATOM 292 N CEN X 73 40.294 34.412 29.045 0.00 0.00\\nATOM 293 C CEN X 73 41.765 34.829 30.944 0.00 0.00\\nATOM 294 CA CEN X 73 40.873 33.802 30.253 0.00 0.00\\nATOM 295 O CEN X 73 42.945 34.994 30.583 0.00 0.00\\nATOM 296 N CEN X 74 41.165 35.531 31.898 0.00 0.00\\nATOM 297 C CEN X 74 41.251 37.941 32.588 0.00 0.00\\nATOM 298 CA CEN X 74 41.845 36.550 32.686 0.00 0.00\\nATOM 299 O CEN X 74 41.102 38.523 31.500 0.00 0.00\\nATOM 300 N CEN X 75 40.946 38.472 33.757 0.00 0.00\\nATOM 301 C CEN X 75 40.031 39.992 35.432 0.00 0.00\\nATOM 302 CA CEN X 75 40.373 39.813 33.944 0.00 0.00\\nATOM 303 O CEN X 75 38.933 40.525 35.687 0.00 0.00\\nTER\\nENDMDL\\n\",\"pdb\");\n\tviewer_1518510157964233.setStyle({\"sphere\": {}});\n\n viewer_1518510157964233.render();\n });\n </script>",
"text/plain": "<IPython.core.display.HTML object>"
},
"metadata": {}
}
]
},
{
"metadata": {
"trusted": true
},
"cell_type": "code",
"source": "test_model = BBModel(state=fetch_pdb(\"1ubq\"))\ntest_score = StupidLJScore(r_m=1.5)\nStupidMinimizer(test_model, test_score).minimize()\nview = PDBModelViewer(test_model, test_score)",
"execution_count": 19,
"outputs": [
{
"output_type": "stream",
"text": "/home/fordas/.conda/envs/tmol/lib/python3.5/site-packages/traitlets/traitlets.py:567: FutureWarning: elementwise == comparison failed and returning scalar instead; this will raise an error or perform elementwise comparison in the future.\n silent = bool(old_value == new_value)\n",
"name": "stderr"
},
{
"output_type": "display_data",
"data": {
"text/html": "<div id=\"3dmolviewer_1518510165543592\" style=\"position: relative; width: 1200px; height: 600px\">\n<script>\nif(typeof $3Dmolpromise === 'undefined') $3Dmolpromise = $.when($.getScript('https://3dmol.csb.pitt.edu/build/3Dmol.js'))\nvar viewer_1518510165543592 = null;\n$3Dmolpromise.done(function() {\nviewer_1518510165543592 = $3Dmol.createViewer($(\"#3dmolviewer_1518510165543592\"),{backgroundColor:\"white\"});\n\tviewer_1518510165543592.clear();\n\tviewer_1518510165543592.addModel(\"MODEL \\nATOM 0 N CEN X 0 28.392 28.154 6.778 0.00 -9.64\\nATOM 1 C CEN X 0 27.006 28.044 5.315 0.00-12.87\\nATOM 2 CA CEN X 0 25.658 27.551 5.024 0.00 -3.78\\nATOM 3 O CEN X 0 30.262 25.722 7.215 0.00 -4.18\\nATOM 4 N CEN X 1 28.180 27.338 5.656 0.00-13.23\\nATOM 5 C CEN X 1 27.129 27.564 6.627 0.00-14.88\\nATOM 6 CA CEN X 1 27.295 26.348 5.997 0.00-11.76\\nATOM 7 O CEN X 1 26.210 29.174 6.049 0.00-13.12\\nATOM 8 N CEN X 2 29.965 31.171 4.839 0.00 -5.32\\nATOM 9 C CEN X 2 26.941 30.021 6.748 0.00-14.48\\nATOM 10 CA CEN X 2 26.722 28.744 7.265 0.00-13.26\\nATOM 11 O CEN X 2 28.261 29.992 6.672 0.00-13.07\\nATOM 12 N CEN X 3 24.944 31.746 13.672 0.00 -5.03\\nATOM 13 C CEN X 3 29.386 34.344 10.988 0.00-15.36\\nATOM 14 CA CEN X 3 29.114 33.456 9.955 0.00 -9.29\\nATOM 15 O CEN X 3 28.678 35.543 10.993 0.00-20.42\\nATOM 16 N CEN X 4 27.178 35.165 10.329 0.00 -8.35\\nATOM 17 C CEN X 4 27.823 34.470 11.703 0.00 -9.82\\nATOM 18 CA CEN X 4 27.160 35.666 11.492 0.00 -8.30\\nATOM 19 O CEN X 4 28.124 35.927 9.775 0.00-10.92\\nATOM 20 N CEN X 5 30.782 36.871 15.861 0.00 -3.35\\nATOM 21 C CEN X 5 29.481 36.084 14.108 0.00 -9.33\\nATOM 22 CA CEN X 5 29.525 37.675 13.732 0.00-16.64\\nATOM 23 O CEN X 5 28.481 36.526 15.186 0.00 -7.78\\nATOM 24 N CEN X 6 27.539 40.020 14.533 0.00 -5.60\\nATOM 25 C CEN X 6 29.811 39.036 15.904 0.00 -9.56\\nATOM 26 CA CEN X 6 29.768 37.074 14.967 0.00-12.86\\nATOM 27 O CEN X 6 28.804 39.534 14.668 0.00-15.23\\nATOM 28 N CEN X 7 29.280 38.312 14.901 0.00-13.06\\nATOM 29 C CEN X 7 29.390 40.317 15.615 0.00-14.78\\nATOM 30 CA CEN X 7 28.315 39.455 15.985 0.00 -9.12\\nATOM 31 O CEN X 7 28.523 41.287 15.167 0.00 -9.26\\nATOM 32 N CEN X 8 29.980 39.948 14.203 0.00-17.52\\nATOM 33 C CEN X 8 30.107 41.613 15.017 0.00-14.47\\nATOM 34 CA CEN X 8 30.949 49.574 20.261 0.00 -0.00\\nATOM 35 O CEN X 8 31.511 41.527 14.221 0.00 -9.59\\nATOM 36 N CEN X 9 30.965 40.542 14.942 0.00-11.52\\nATOM 37 C CEN X 9 30.342 41.133 13.664 0.00-18.02\\nATOM 38 CA CEN X 9 30.527 42.465 14.001 0.00 -9.05\\nATOM 39 O CEN X 9 31.279 40.218 13.014 0.00 -9.74\\nATOM 40 N CEN X 10 28.367 36.892 13.874 0.00-11.62\\nATOM 41 C CEN X 10 29.905 40.213 12.775 0.00-11.30\\nATOM 42 CA CEN X 10 29.080 41.728 13.908 0.00 -9.92\\nATOM 43 O CEN X 10 29.672 38.929 13.260 0.00-13.91\\nATOM 44 N CEN X 11 30.549 37.350 12.904 0.00-10.06\\nATOM 45 C CEN X 11 29.199 37.342 12.406 0.00-11.25\\nATOM 46 CA CEN X 11 30.984 38.767 12.785 0.00 -8.98\\nATOM 47 O CEN X 11 31.009 36.687 11.313 0.00 -5.97\\nATOM 48 N CEN X 12 28.160 34.273 10.421 0.00-14.34\\nATOM 49 C CEN X 12 29.382 36.288 9.747 0.00-10.86\\nATOM 50 CA CEN X 12 29.579 36.646 11.197 0.00-12.43\\nATOM 51 O CEN X 12 29.041 34.895 9.656 0.00-16.91\\nATOM 52 N CEN X 13 28.060 30.611 7.844 0.00 -8.80\\nATOM 53 C CEN X 13 30.292 34.432 9.916 0.00 -9.93\\nATOM 54 CA CEN X 13 30.095 35.504 10.791 0.00-14.60\\nATOM 55 O CEN X 13 28.932 31.415 7.067 0.00-10.96\\nATOM 56 N CEN X 14 28.645 30.550 4.839 0.00 -6.35\\nATOM 57 C CEN X 14 29.889 32.202 6.438 0.00 -5.45\\nATOM 58 CA CEN X 14 28.099 32.106 7.869 0.00 -5.03\\nATOM 59 O CEN X 14 29.722 30.720 6.210 0.00 -9.13\\nATOM 60 N CEN X 15 31.690 24.104 8.513 0.00 -0.31\\nATOM 61 C CEN X 15 27.276 30.032 5.395 0.00-11.04\\nATOM 62 CA CEN X 15 27.584 28.926 6.098 0.00-18.22\\nATOM 63 O CEN X 15 30.349 23.462 6.174 0.00 -1.51\\nATOM 64 N CEN X 16 28.873 26.000 6.563 0.00 -9.50\\nATOM 65 C CEN X 16 29.151 25.195 5.541 0.00-10.10\\nATOM 66 CA CEN X 16 30.562 25.212 5.704 0.00 -5.28\\nATOM 67 O CEN X 16 28.061 25.865 4.855 0.00-10.93\\nATOM 68 N CEN X 17 28.578 20.046 9.640 0.00 -9.10\\nATOM 69 C CEN X 17 27.684 25.092 6.122 0.00 -9.92\\nATOM 70 CA CEN X 17 27.620 24.532 4.800 0.00 -5.88\\nATOM 71 O CEN X 17 27.973 21.284 10.649 0.00 -9.97\\nATOM 72 N CEN X 18 30.291 21.207 11.167 0.00-13.00\\nATOM 73 C CEN X 18 29.208 20.427 10.761 0.00-16.93\\nATOM 74 CA CEN X 18 28.399 19.879 8.256 0.00 -2.68\\nATOM 75 O CEN X 18 27.691 20.809 12.015 0.00 -9.90\\nATOM 76 N CEN X 19 30.118 20.868 12.814 0.00-17.94\\nATOM 77 C CEN X 19 28.971 21.278 11.808 0.00-17.00\\nATOM 78 CA CEN X 19 27.890 19.962 10.866 0.00-10.41\\nATOM 79 O CEN X 19 30.069 20.045 11.797 0.00-14.74\\nATOM 80 N CEN X 20 30.380 19.975 10.004 0.00 -5.71\\nATOM 81 C CEN X 20 28.762 20.113 12.774 0.00-11.50\\nATOM 82 CA CEN X 20 29.558 18.144 12.582 0.00 -3.23\\nATOM 83 O CEN X 20 29.959 19.559 13.035 0.00-12.94\\nATOM 84 N CEN X 21 33.391 21.473 13.798 0.00-10.99\\nATOM 85 C CEN X 21 30.603 21.494 13.898 0.00-10.63\\nATOM 86 CA CEN X 21 31.483 20.256 13.012 0.00-11.37\\nATOM 87 O CEN X 21 29.978 22.180 11.919 0.00 -8.05\\nATOM 88 N CEN X 22 33.471 23.536 14.990 0.00-10.59\\nATOM 89 C CEN X 22 32.722 21.265 14.976 0.00-15.36\\nATOM 90 CA CEN X 22 31.725 20.748 14.225 0.00-12.40\\nATOM 91 O CEN X 22 32.737 22.609 15.652 0.00-13.43\\nATOM 92 N CEN X 23 31.265 21.349 12.193 0.00-13.66\\nATOM 93 C CEN X 23 32.710 22.770 14.100 0.00-14.32\\nATOM 94 CA CEN X 23 33.982 20.958 15.574 0.00 -7.29\\nATOM 95 O CEN X 23 34.822 23.646 15.038 0.00 -6.08\\nATOM 96 N CEN X 24 32.149 22.062 13.118 0.00-10.55\\nATOM 97 C CEN X 24 31.711 22.129 14.900 0.00-12.30\\nATOM 98 CA CEN X 24 33.775 22.143 14.930 0.00-16.13\\nATOM 99 O CEN X 24 37.677 26.671 10.776 0.00 -1.17\\nATOM 100 N CEN X 25 33.697 22.305 16.536 0.00 -6.35\\nATOM 101 C CEN X 25 40.844 23.119 15.953 0.00 -0.08\\nATOM 102 CA CEN X 25 34.929 24.851 14.363 0.00 -3.34\\nATOM 103 O CEN X 25 37.671 27.541 12.459 0.00 -9.72\\nATOM 104 N CEN X 26 38.130 23.388 15.017 0.00 -0.24\\nATOM 105 C CEN X 26 39.122 27.814 12.949 0.00-11.66\\nATOM 106 CA CEN X 26 35.353 27.136 13.419 0.00 -0.64\\nATOM 107 O CEN X 26 39.304 28.283 14.331 0.00-10.28\\nATOM 108 N CEN X 27 37.039 28.707 12.145 0.00 -8.30\\nATOM 109 C CEN X 27 37.950 28.329 13.499 0.00-14.71\\nATOM 110 CA CEN X 27 39.332 28.184 15.741 0.00 -3.19\\nATOM 111 O CEN X 27 38.977 29.169 13.314 0.00-19.78\\nATOM 112 N CEN X 28 32.206 27.910 11.798 0.00 -0.06\\nATOM 113 C CEN X 28 37.735 29.619 12.733 0.00-17.13\\nATOM 114 CA CEN X 28 38.530 28.655 11.895 0.00-14.02\\nATOM 115 O CEN X 28 38.354 31.171 12.062 0.00-17.10\\nATOM 116 N CEN X 29 36.642 25.547 15.482 0.00 -0.68\\nATOM 117 C CEN X 29 39.441 30.148 14.170 0.00-15.84\\nATOM 118 CA CEN X 29 36.822 31.040 12.433 0.00 -5.80\\nATOM 119 O CEN X 29 38.194 30.731 13.332 0.00-20.50\\nATOM 120 N CEN X 30 41.867 24.454 11.052 0.00 -0.02\\nATOM 121 C CEN X 30 38.894 29.938 12.196 0.00-16.20\\nATOM 122 CA CEN X 30 40.005 31.201 14.660 0.00-14.36\\nATOM 123 O CEN X 30 39.892 31.364 11.454 0.00-10.68\\nATOM 124 N CEN X 31 39.580 32.204 12.452 0.00-19.62\\nATOM 125 C CEN X 31 38.311 30.874 10.713 0.00 -5.11\\nATOM 126 CA CEN X 31 39.469 30.972 13.053 0.00-21.89\\nATOM 127 O CEN X 31 41.804 32.343 10.904 0.00 -4.30\\nATOM 128 N CEN X 32 38.504 32.072 13.252 0.00-18.45\\nATOM 129 C CEN X 32 39.341 33.390 13.193 0.00-14.13\\nATOM 130 CA CEN X 32 41.143 33.423 10.745 0.00 -3.92\\nATOM 131 O CEN X 32 40.710 32.437 11.719 0.00-14.81\\nATOM 132 N CEN X 33 40.020 32.178 13.707 0.00-24.86\\nATOM 133 C CEN X 33 41.113 31.679 12.780 0.00-12.85\\nATOM 134 CA CEN X 33 40.781 33.042 12.950 0.00-14.09\\nATOM 135 O CEN X 33 40.293 33.447 14.186 0.00-14.48\\nATOM 136 N CEN X 34 38.621 31.400 14.500 0.00-19.14\\nATOM 137 C CEN X 34 38.913 32.706 14.360 0.00-15.39\\nATOM 138 CA CEN X 34 41.432 32.426 13.807 0.00 -8.80\\nATOM 139 O CEN X 34 41.098 32.748 15.038 0.00 -9.46\\nATOM 140 N CEN X 35 38.824 30.349 15.327 0.00 -9.86\\nATOM 141 C CEN X 35 39.436 32.107 15.496 0.00-12.04\\nATOM 142 CA CEN X 35 40.361 33.162 16.088 0.00 -5.48\\nATOM 143 O CEN X 35 38.449 29.164 20.059 0.00 -7.43\\nATOM 144 N CEN X 36 38.675 30.727 20.166 0.00-11.02\\nATOM 145 C CEN X 36 38.098 29.991 21.133 0.00-11.32\\nATOM 146 CA CEN X 36 39.679 28.757 19.586 0.00 -2.73\\nATOM 147 O CEN X 36 37.812 31.721 20.174 0.00-13.83\\nATOM 148 N CEN X 37 37.992 31.332 21.548 0.00-17.07\\nATOM 149 C CEN X 37 36.752 31.602 21.033 0.00-15.15\\nATOM 150 CA CEN X 37 37.207 30.439 20.231 0.00-11.34\\nATOM 151 O CEN X 37 36.132 30.864 21.984 0.00-16.53\\nATOM 152 N CEN X 38 38.999 32.178 20.902 0.00 -8.60\\nATOM 153 C CEN X 38 37.691 32.647 21.230 0.00-11.53\\nATOM 154 CA CEN X 38 37.422 25.896 25.293 0.00 -0.01\\nATOM 155 O CEN X 38 36.512 32.494 22.332 0.00-14.02\\nATOM 156 N CEN X 39 37.862 29.782 14.215 0.00-13.37\\nATOM 157 C CEN X 39 36.346 29.956 23.132 0.00 -8.26\\nATOM 158 CA CEN X 39 36.032 31.592 23.196 0.00-17.48\\nATOM 159 O CEN X 39 35.056 30.722 22.831 0.00-14.36\\nATOM 160 N CEN X 40 37.388 30.633 22.630 0.00-10.51\\nATOM 161 C CEN X 40 33.794 31.513 22.561 0.00-17.33\\nATOM 162 CA CEN X 40 34.715 31.857 23.555 0.00-19.51\\nATOM 163 O CEN X 40 35.217 31.931 22.140 0.00-18.96\\nATOM 164 N CEN X 41 33.570 32.478 21.570 0.00-14.29\\nATOM 165 C CEN X 41 33.038 31.327 21.042 0.00 -8.52\\nATOM 166 CA CEN X 41 32.388 30.876 22.230 0.00 -6.76\\nATOM 167 O CEN X 41 32.165 32.406 21.570 0.00 -9.72\\nATOM 168 N CEN X 42 26.541 31.214 20.674 0.00-10.21\\nATOM 169 C CEN X 42 24.788 30.702 19.837 0.00-13.86\\nATOM 170 CA CEN X 42 25.772 31.871 19.267 0.00 -5.78\\nATOM 171 O CEN X 42 25.915 29.925 20.762 0.00-11.97\\nATOM 172 N CEN X 43 26.207 30.618 19.496 0.00 -9.85\\nATOM 173 C CEN X 43 24.702 29.252 21.017 0.00-19.97\\nATOM 174 CA CEN X 43 24.125 29.648 19.279 0.00-10.75\\nATOM 175 O CEN X 43 23.770 30.078 20.551 0.00-18.64\\nATOM 176 N CEN X 44 24.021 30.086 21.895 0.00-13.56\\nATOM 177 C CEN X 44 22.535 29.640 19.927 0.00-12.53\\nATOM 178 CA CEN X 44 24.920 30.866 21.202 0.00-12.45\\nATOM 179 O CEN X 44 23.303 27.531 20.816 0.00-17.84\\nATOM 180 N CEN X 45 22.749 29.972 21.352 0.00-12.66\\nATOM 181 C CEN X 45 23.765 27.652 19.415 0.00 -9.58\\nATOM 182 CA CEN X 45 22.382 28.206 20.095 0.00-14.56\\nATOM 183 O CEN X 45 21.108 28.087 20.255 0.00 -5.62\\nATOM 184 N CEN X 46 23.608 28.745 21.776 0.00-21.49\\nATOM 185 C CEN X 46 22.309 28.709 21.388 0.00-17.27\\nATOM 186 CA CEN X 46 21.689 27.539 21.361 0.00-10.08\\nATOM 187 O CEN X 46 22.834 27.605 22.085 0.00-14.31\\nATOM 188 N CEN X 47 23.534 28.797 20.325 0.00-22.97\\nATOM 189 C CEN X 47 24.790 28.099 21.832 0.00-12.48\\nATOM 190 CA CEN X 47 22.932 28.382 23.186 0.00 -5.83\\nATOM 191 O CEN X 47 24.602 28.018 20.444 0.00-14.98\\nATOM 192 N CEN X 48 24.794 25.542 20.551 0.00 -6.98\\nATOM 193 C CEN X 48 24.018 26.595 22.708 0.00 -7.19\\nATOM 194 CA CEN X 48 25.098 26.817 21.614 0.00-11.04\\nATOM 195 O CEN X 48 24.423 25.409 21.842 0.00 -9.97\\nATOM 196 N CEN X 49 28.405 24.805 22.843 0.00 -4.48\\nATOM 197 C CEN X 49 25.676 24.392 21.834 0.00 -6.38\\nATOM 198 CA CEN X 49 25.802 25.695 21.530 0.00-10.23\\nATOM 199 O CEN X 49 27.994 23.776 22.038 0.00 -4.12\\nATOM 200 N CEN X 50 28.751 21.954 19.922 0.00 -4.54\\nATOM 201 C CEN X 50 28.747 19.707 20.293 0.00 -2.92\\nATOM 202 CA CEN X 50 26.994 24.943 22.486 0.00 -6.87\\nATOM 203 O CEN X 50 29.075 20.113 18.110 0.00-15.07\\nATOM 204 N CEN X 51 29.307 20.761 19.387 0.00-11.42\\nATOM 205 C CEN X 51 29.632 21.010 17.102 0.00-14.31\\nATOM 206 CA CEN X 51 28.993 21.690 18.263 0.00-11.48\\nATOM 207 O CEN X 51 30.113 20.921 18.382 0.00-12.42\\nATOM 208 N CEN X 52 27.929 20.918 18.245 0.00 -6.72\\nATOM 209 C CEN X 52 30.496 19.879 17.218 0.00-16.07\\nATOM 210 CA CEN X 52 30.387 18.512 17.545 0.00 -6.58\\nATOM 211 O CEN X 52 29.947 19.983 15.851 0.00-12.88\\nATOM 212 N CEN X 53 31.210 21.045 17.660 0.00 -6.62\\nATOM 213 C CEN X 53 28.775 19.756 16.753 0.00-10.66\\nATOM 214 CA CEN X 53 29.616 18.706 16.410 0.00-10.53\\nATOM 215 O CEN X 53 31.055 19.210 15.948 0.00 -8.16\\nATOM 216 N CEN X 54 24.609 20.418 15.169 0.00 -7.11\\nATOM 217 C CEN X 54 24.643 19.304 14.331 0.00-10.36\\nATOM 218 CA CEN X 54 30.182 19.504 14.381 0.00 -7.88\\nATOM 219 O CEN X 54 23.537 20.129 14.416 0.00-17.25\\nATOM 220 N CEN X 55 27.833 15.512 19.209 0.00 -0.03\\nATOM 221 C CEN X 55 23.660 19.268 13.256 0.00-13.41\\nATOM 222 CA CEN X 55 24.840 20.642 13.903 0.00-11.38\\nATOM 223 O CEN X 55 22.886 21.071 13.450 0.00-21.59\\nATOM 224 N CEN X 56 26.227 17.597 14.876 0.00 -0.37\\nATOM 225 C CEN X 56 22.832 20.145 12.508 0.00-20.34\\nATOM 226 CA CEN X 56 23.360 22.584 12.762 0.00-10.36\\nATOM 227 O CEN X 56 21.464 20.195 13.194 0.00-14.06\\nATOM 228 N CEN X 57 24.128 21.649 13.465 0.00-12.76\\nATOM 229 C CEN X 57 22.410 19.359 13.708 0.00-13.74\\nATOM 230 CA CEN X 57 21.795 19.253 12.195 0.00 -7.88\\nATOM 231 O CEN X 57 22.211 20.494 14.445 0.00-12.28\\nATOM 232 N CEN X 58 24.216 20.401 12.751 0.00-14.99\\nATOM 233 C CEN X 58 21.846 21.928 13.530 0.00-14.86\\nATOM 234 CA CEN X 58 21.225 21.980 14.884 0.00 -4.10\\nATOM 235 O CEN X 58 21.944 21.183 12.395 0.00-20.76\\nATOM 236 N CEN X 59 22.536 21.065 11.115 0.00-12.11\\nATOM 237 C CEN X 59 23.466 21.364 12.099 0.00-18.71\\nATOM 238 CA CEN X 59 15.424 19.511 15.012 0.00 -0.01\\nATOM 239 O CEN X 59 21.622 23.131 11.177 0.00 -9.75\\nATOM 240 N CEN X 60 22.967 22.399 11.072 0.00-11.01\\nATOM 241 C CEN X 60 22.131 22.594 12.402 0.00-16.21\\nATOM 242 CA CEN X 60 20.781 22.497 12.964 0.00 -9.08\\nATOM 243 O CEN X 60 21.431 21.808 11.328 0.00-13.24\\nATOM 244 N CEN X 61 22.248 27.874 9.551 0.00-15.12\\nATOM 245 C CEN X 61 20.972 27.860 9.116 0.00 -7.53\\nATOM 246 CA CEN X 61 20.292 22.830 11.565 0.00 -6.94\\nATOM 247 O CEN X 61 21.998 28.211 7.971 0.00-10.96\\nATOM 248 N CEN X 62 20.722 27.662 7.842 0.00 -4.69\\nATOM 249 C CEN X 62 23.236 28.367 8.686 0.00-15.47\\nATOM 250 CA CEN X 62 23.308 27.046 9.087 0.00 -6.67\\nATOM 251 O CEN X 62 22.294 29.265 10.308 0.00-14.43\\nATOM 252 N CEN X 63 23.234 28.271 10.370 0.00 -9.96\\nATOM 253 C CEN X 63 23.488 29.360 9.582 0.00-14.94\\nATOM 254 CA CEN X 63 22.158 29.102 8.959 0.00-17.02\\nATOM 255 O CEN X 63 23.549 31.075 8.184 0.00 -6.02\\nATOM 256 N CEN X 64 25.840 29.964 7.460 0.00 -6.19\\nATOM 257 C CEN X 64 22.411 30.325 9.470 0.00-15.60\\nATOM 258 CA CEN X 64 21.352 30.963 10.063 0.00 -6.56\\nATOM 259 O CEN X 64 23.432 29.685 8.269 0.00-11.10\\nATOM 260 N CEN X 65 22.339 31.538 8.824 0.00 -6.59\\nATOM 261 C CEN X 65 26.041 32.510 13.717 0.00 -6.76\\nATOM 262 CA CEN X 65 22.475 30.496 10.945 0.00 -7.50\\nATOM 263 O CEN X 65 27.192 31.229 14.088 0.00 -3.28\\nATOM 264 N CEN X 66 27.705 36.397 12.513 0.00 -6.85\\nATOM 265 C CEN X 66 26.551 32.052 15.475 0.00-14.64\\nATOM 266 CA CEN X 66 25.453 32.773 14.964 0.00 -9.33\\nATOM 267 O CEN X 66 25.524 31.218 15.117 0.00 -9.22\\nATOM 268 N CEN X 67 27.691 32.472 16.412 0.00 -6.97\\nATOM 269 C CEN X 67 26.805 31.566 16.911 0.00 -9.03\\nATOM 270 CA CEN X 67 25.567 31.755 16.446 0.00-10.21\\nATOM 271 O CEN X 67 26.387 32.880 16.584 0.00-10.15\\nATOM 272 N CEN X 68 28.340 33.255 20.598 0.00-10.34\\nATOM 273 C CEN X 68 29.446 32.411 20.986 0.00 -6.19\\nATOM 274 CA CEN X 68 27.610 32.036 21.205 0.00 -7.27\\nATOM 275 O CEN X 68 29.485 33.410 19.638 0.00 -6.23\\nATOM 276 N CEN X 69 32.908 33.505 22.220 0.00 -9.56\\nATOM 277 C CEN X 69 28.232 32.030 20.028 0.00 -9.43\\nATOM 278 CA CEN X 69 28.269 33.154 19.104 0.00 -6.98\\nATOM 279 O CEN X 69 32.862 32.458 23.108 0.00-12.14\\nATOM 280 N CEN X 70 35.327 32.463 24.689 0.00-11.18\\nATOM 281 C CEN X 70 33.888 32.723 24.460 0.00 -9.13\\nATOM 282 CA CEN X 70 34.145 32.864 22.862 0.00-19.21\\nATOM 283 O CEN X 70 35.637 32.849 23.367 0.00-18.70\\nATOM 284 N CEN X 71 36.320 34.961 27.247 0.00 -1.39\\nATOM 285 C CEN X 71 35.128 33.973 22.892 0.00 -9.83\\nATOM 286 CA CEN X 71 35.268 33.805 24.306 0.00-11.08\\nATOM 287 O CEN X 71 36.478 33.757 23.715 0.00 -7.00\\nATOM 288 N CEN X 72 38.407 35.210 29.815 0.00 -8.44\\nATOM 289 C CEN X 72 39.690 35.736 29.565 0.00-10.48\\nATOM 290 CA CEN X 72 37.802 35.074 26.462 0.00 -1.39\\nATOM 291 O CEN X 72 39.277 35.407 30.883 0.00-16.37\\nATOM 292 N CEN X 73 38.737 36.499 30.228 0.00-15.73\\nATOM 293 C CEN X 73 38.240 37.488 31.165 0.00-11.95\\nATOM 294 CA CEN X 73 37.995 36.073 31.270 0.00-10.68\\nATOM 295 O CEN X 73 40.060 36.725 30.795 0.00-14.14\\nATOM 296 N CEN X 74 38.571 37.679 32.470 0.00 -7.53\\nATOM 297 C CEN X 74 39.127 36.572 31.773 0.00-17.02\\nATOM 298 CA CEN X 74 39.614 37.798 31.491 0.00 -9.88\\nATOM 299 O CEN X 74 40.047 35.679 32.174 0.00 -6.98\\nATOM 300 N CEN X 75 40.881 35.654 30.602 0.00 -6.89\\nATOM 301 C CEN X 75 49.169 32.027 38.957 0.00 -0.00\\nATOM 302 CA CEN X 75 38.038 40.527 27.698 0.00 -2.24\\nATOM 303 O CEN X 75 37.082 40.607 28.758 0.00 -2.25\\nTER\\nENDMDL\\n\",\"pdb\");\n\tviewer_1518510165543592.setStyle({\"sphere\": {\"colorscheme\": {\"min\": 1, \"gradient\": \"rwb\", \"prop\": \"b\", \"max\": -1}}});\nviewer_1518510165543592.render();\n});\n</script><script>\n $3Dmolpromise.done(function() { //wrap in promise for non-interactive functionality\n \n viewer_1518510165543592.render();\n });\n </script>",
"text/plain": "<IPython.core.display.HTML object>"
},
"metadata": {}
},
{
"output_type": "display_data",
"data": {
"text/html": "<script>\n $3Dmolpromise.done(function() { //wrap in promise for non-interactive functionality\n \tviewer_1518510165543592.zoomTo();\n\tviewer_1518510165543592.clear();\n\tviewer_1518510165543592.addModel(\"MODEL \\nATOM 0 N CEN X 0 28.392 28.154 6.778 0.00 -9.64\\nATOM 1 C CEN X 0 27.006 28.044 5.315 0.00-12.87\\nATOM 2 CA CEN X 0 25.658 27.551 5.024 0.00 -3.78\\nATOM 3 O CEN X 0 30.262 25.722 7.215 0.00 -4.18\\nATOM 4 N CEN X 1 28.180 27.338 5.656 0.00-13.23\\nATOM 5 C CEN X 1 27.129 27.564 6.627 0.00-14.88\\nATOM 6 CA CEN X 1 27.295 26.348 5.997 0.00-11.76\\nATOM 7 O CEN X 1 26.210 29.174 6.049 0.00-13.12\\nATOM 8 N CEN X 2 29.965 31.171 4.839 0.00 -5.32\\nATOM 9 C CEN X 2 26.941 30.021 6.748 0.00-14.48\\nATOM 10 CA CEN X 2 26.722 28.744 7.265 0.00-13.26\\nATOM 11 O CEN X 2 28.261 29.992 6.672 0.00-13.07\\nATOM 12 N CEN X 3 24.944 31.746 13.672 0.00 -5.03\\nATOM 13 C CEN X 3 29.386 34.344 10.988 0.00-15.36\\nATOM 14 CA CEN X 3 29.114 33.456 9.955 0.00 -9.29\\nATOM 15 O CEN X 3 28.678 35.543 10.993 0.00-20.42\\nATOM 16 N CEN X 4 27.178 35.165 10.329 0.00 -8.35\\nATOM 17 C CEN X 4 27.823 34.470 11.703 0.00 -9.82\\nATOM 18 CA CEN X 4 27.160 35.666 11.492 0.00 -8.30\\nATOM 19 O CEN X 4 28.124 35.927 9.775 0.00-10.92\\nATOM 20 N CEN X 5 30.782 36.871 15.861 0.00 -3.35\\nATOM 21 C CEN X 5 29.481 36.084 14.108 0.00 -9.33\\nATOM 22 CA CEN X 5 29.525 37.675 13.732 0.00-16.64\\nATOM 23 O CEN X 5 28.481 36.526 15.186 0.00 -7.78\\nATOM 24 N CEN X 6 27.539 40.020 14.533 0.00 -5.60\\nATOM 25 C CEN X 6 29.811 39.036 15.904 0.00 -9.56\\nATOM 26 CA CEN X 6 29.768 37.074 14.967 0.00-12.86\\nATOM 27 O CEN X 6 28.804 39.534 14.668 0.00-15.23\\nATOM 28 N CEN X 7 29.280 38.312 14.901 0.00-13.06\\nATOM 29 C CEN X 7 29.390 40.317 15.615 0.00-14.78\\nATOM 30 CA CEN X 7 28.315 39.455 15.985 0.00 -9.12\\nATOM 31 O CEN X 7 28.523 41.287 15.167 0.00 -9.26\\nATOM 32 N CEN X 8 29.980 39.948 14.203 0.00-17.52\\nATOM 33 C CEN X 8 30.107 41.613 15.017 0.00-14.47\\nATOM 34 CA CEN X 8 30.949 49.574 20.261 0.00 -0.00\\nATOM 35 O CEN X 8 31.511 41.527 14.221 0.00 -9.59\\nATOM 36 N CEN X 9 30.965 40.542 14.942 0.00-11.52\\nATOM 37 C CEN X 9 30.342 41.133 13.664 0.00-18.02\\nATOM 38 CA CEN X 9 30.527 42.465 14.001 0.00 -9.05\\nATOM 39 O CEN X 9 31.279 40.218 13.014 0.00 -9.74\\nATOM 40 N CEN X 10 28.367 36.892 13.874 0.00-11.62\\nATOM 41 C CEN X 10 29.905 40.213 12.775 0.00-11.30\\nATOM 42 CA CEN X 10 29.080 41.728 13.908 0.00 -9.92\\nATOM 43 O CEN X 10 29.672 38.929 13.260 0.00-13.91\\nATOM 44 N CEN X 11 30.549 37.350 12.904 0.00-10.06\\nATOM 45 C CEN X 11 29.199 37.342 12.406 0.00-11.25\\nATOM 46 CA CEN X 11 30.984 38.767 12.785 0.00 -8.98\\nATOM 47 O CEN X 11 31.009 36.687 11.313 0.00 -5.97\\nATOM 48 N CEN X 12 28.160 34.273 10.421 0.00-14.34\\nATOM 49 C CEN X 12 29.382 36.288 9.747 0.00-10.86\\nATOM 50 CA CEN X 12 29.579 36.646 11.197 0.00-12.43\\nATOM 51 O CEN X 12 29.041 34.895 9.656 0.00-16.91\\nATOM 52 N CEN X 13 28.060 30.611 7.844 0.00 -8.80\\nATOM 53 C CEN X 13 30.292 34.432 9.916 0.00 -9.93\\nATOM 54 CA CEN X 13 30.095 35.504 10.791 0.00-14.60\\nATOM 55 O CEN X 13 28.932 31.415 7.067 0.00-10.96\\nATOM 56 N CEN X 14 28.645 30.550 4.839 0.00 -6.35\\nATOM 57 C CEN X 14 29.889 32.202 6.438 0.00 -5.45\\nATOM 58 CA CEN X 14 28.099 32.106 7.869 0.00 -5.03\\nATOM 59 O CEN X 14 29.722 30.720 6.210 0.00 -9.13\\nATOM 60 N CEN X 15 31.690 24.104 8.513 0.00 -0.31\\nATOM 61 C CEN X 15 27.276 30.032 5.395 0.00-11.04\\nATOM 62 CA CEN X 15 27.584 28.926 6.098 0.00-18.22\\nATOM 63 O CEN X 15 30.349 23.462 6.174 0.00 -1.51\\nATOM 64 N CEN X 16 28.873 26.000 6.563 0.00 -9.50\\nATOM 65 C CEN X 16 29.151 25.195 5.541 0.00-10.10\\nATOM 66 CA CEN X 16 30.562 25.212 5.704 0.00 -5.28\\nATOM 67 O CEN X 16 28.061 25.865 4.855 0.00-10.93\\nATOM 68 N CEN X 17 28.578 20.046 9.640 0.00 -9.10\\nATOM 69 C CEN X 17 27.684 25.092 6.122 0.00 -9.92\\nATOM 70 CA CEN X 17 27.620 24.532 4.800 0.00 -5.88\\nATOM 71 O CEN X 17 27.973 21.284 10.649 0.00 -9.97\\nATOM 72 N CEN X 18 30.291 21.207 11.167 0.00-13.00\\nATOM 73 C CEN X 18 29.208 20.427 10.761 0.00-16.93\\nATOM 74 CA CEN X 18 28.399 19.879 8.256 0.00 -2.68\\nATOM 75 O CEN X 18 27.691 20.809 12.015 0.00 -9.90\\nATOM 76 N CEN X 19 30.118 20.868 12.814 0.00-17.94\\nATOM 77 C CEN X 19 28.971 21.278 11.808 0.00-17.00\\nATOM 78 CA CEN X 19 27.890 19.962 10.866 0.00-10.41\\nATOM 79 O CEN X 19 30.069 20.045 11.797 0.00-14.74\\nATOM 80 N CEN X 20 30.380 19.975 10.004 0.00 -5.71\\nATOM 81 C CEN X 20 28.762 20.113 12.774 0.00-11.50\\nATOM 82 CA CEN X 20 29.558 18.144 12.582 0.00 -3.23\\nATOM 83 O CEN X 20 29.959 19.559 13.035 0.00-12.94\\nATOM 84 N CEN X 21 33.391 21.473 13.798 0.00-10.99\\nATOM 85 C CEN X 21 30.603 21.494 13.898 0.00-10.63\\nATOM 86 CA CEN X 21 31.483 20.256 13.012 0.00-11.37\\nATOM 87 O CEN X 21 29.978 22.180 11.919 0.00 -8.05\\nATOM 88 N CEN X 22 33.471 23.536 14.990 0.00-10.59\\nATOM 89 C CEN X 22 32.722 21.265 14.976 0.00-15.36\\nATOM 90 CA CEN X 22 31.725 20.748 14.225 0.00-12.40\\nATOM 91 O CEN X 22 32.737 22.609 15.652 0.00-13.43\\nATOM 92 N CEN X 23 31.265 21.349 12.193 0.00-13.66\\nATOM 93 C CEN X 23 32.710 22.770 14.100 0.00-14.32\\nATOM 94 CA CEN X 23 33.982 20.958 15.574 0.00 -7.29\\nATOM 95 O CEN X 23 34.822 23.646 15.038 0.00 -6.08\\nATOM 96 N CEN X 24 32.149 22.062 13.118 0.00-10.55\\nATOM 97 C CEN X 24 31.711 22.129 14.900 0.00-12.30\\nATOM 98 CA CEN X 24 33.775 22.143 14.930 0.00-16.13\\nATOM 99 O CEN X 24 37.677 26.671 10.776 0.00 -1.17\\nATOM 100 N CEN X 25 33.697 22.305 16.536 0.00 -6.35\\nATOM 101 C CEN X 25 40.844 23.119 15.953 0.00 -0.08\\nATOM 102 CA CEN X 25 34.929 24.851 14.363 0.00 -3.34\\nATOM 103 O CEN X 25 37.671 27.541 12.459 0.00 -9.72\\nATOM 104 N CEN X 26 38.130 23.388 15.017 0.00 -0.24\\nATOM 105 C CEN X 26 39.122 27.814 12.949 0.00-11.66\\nATOM 106 CA CEN X 26 35.353 27.136 13.419 0.00 -0.64\\nATOM 107 O CEN X 26 39.304 28.283 14.331 0.00-10.28\\nATOM 108 N CEN X 27 37.039 28.707 12.145 0.00 -8.30\\nATOM 109 C CEN X 27 37.950 28.329 13.499 0.00-14.71\\nATOM 110 CA CEN X 27 39.332 28.184 15.741 0.00 -3.19\\nATOM 111 O CEN X 27 38.977 29.169 13.314 0.00-19.78\\nATOM 112 N CEN X 28 32.206 27.910 11.798 0.00 -0.06\\nATOM 113 C CEN X 28 37.735 29.619 12.733 0.00-17.13\\nATOM 114 CA CEN X 28 38.530 28.655 11.895 0.00-14.02\\nATOM 115 O CEN X 28 38.354 31.171 12.062 0.00-17.10\\nATOM 116 N CEN X 29 36.642 25.547 15.482 0.00 -0.68\\nATOM 117 C CEN X 29 39.441 30.148 14.170 0.00-15.84\\nATOM 118 CA CEN X 29 36.822 31.040 12.433 0.00 -5.80\\nATOM 119 O CEN X 29 38.194 30.731 13.332 0.00-20.50\\nATOM 120 N CEN X 30 41.867 24.454 11.052 0.00 -0.02\\nATOM 121 C CEN X 30 38.894 29.938 12.196 0.00-16.20\\nATOM 122 CA CEN X 30 40.005 31.201 14.660 0.00-14.36\\nATOM 123 O CEN X 30 39.892 31.364 11.454 0.00-10.68\\nATOM 124 N CEN X 31 39.580 32.204 12.452 0.00-19.62\\nATOM 125 C CEN X 31 38.311 30.874 10.713 0.00 -5.11\\nATOM 126 CA CEN X 31 39.469 30.972 13.053 0.00-21.89\\nATOM 127 O CEN X 31 41.804 32.343 10.904 0.00 -4.30\\nATOM 128 N CEN X 32 38.504 32.072 13.252 0.00-18.45\\nATOM 129 C CEN X 32 39.341 33.390 13.193 0.00-14.13\\nATOM 130 CA CEN X 32 41.143 33.423 10.745 0.00 -3.92\\nATOM 131 O CEN X 32 40.710 32.437 11.719 0.00-14.81\\nATOM 132 N CEN X 33 40.020 32.178 13.707 0.00-24.86\\nATOM 133 C CEN X 33 41.113 31.679 12.780 0.00-12.85\\nATOM 134 CA CEN X 33 40.781 33.042 12.950 0.00-14.09\\nATOM 135 O CEN X 33 40.293 33.447 14.186 0.00-14.48\\nATOM 136 N CEN X 34 38.621 31.400 14.500 0.00-19.14\\nATOM 137 C CEN X 34 38.913 32.706 14.360 0.00-15.39\\nATOM 138 CA CEN X 34 41.432 32.426 13.807 0.00 -8.80\\nATOM 139 O CEN X 34 41.098 32.748 15.038 0.00 -9.46\\nATOM 140 N CEN X 35 38.824 30.349 15.327 0.00 -9.86\\nATOM 141 C CEN X 35 39.436 32.107 15.496 0.00-12.04\\nATOM 142 CA CEN X 35 40.361 33.162 16.088 0.00 -5.48\\nATOM 143 O CEN X 35 38.449 29.164 20.059 0.00 -7.43\\nATOM 144 N CEN X 36 38.675 30.727 20.166 0.00-11.02\\nATOM 145 C CEN X 36 38.098 29.991 21.133 0.00-11.32\\nATOM 146 CA CEN X 36 39.679 28.757 19.586 0.00 -2.73\\nATOM 147 O CEN X 36 37.812 31.721 20.174 0.00-13.83\\nATOM 148 N CEN X 37 37.992 31.332 21.548 0.00-17.07\\nATOM 149 C CEN X 37 36.752 31.602 21.033 0.00-15.15\\nATOM 150 CA CEN X 37 37.207 30.439 20.231 0.00-11.34\\nATOM 151 O CEN X 37 36.132 30.864 21.984 0.00-16.53\\nATOM 152 N CEN X 38 38.999 32.178 20.902 0.00 -8.60\\nATOM 153 C CEN X 38 37.691 32.647 21.230 0.00-11.53\\nATOM 154 CA CEN X 38 37.422 25.896 25.293 0.00 -0.01\\nATOM 155 O CEN X 38 36.512 32.494 22.332 0.00-14.02\\nATOM 156 N CEN X 39 37.862 29.782 14.215 0.00-13.37\\nATOM 157 C CEN X 39 36.346 29.956 23.132 0.00 -8.26\\nATOM 158 CA CEN X 39 36.032 31.592 23.196 0.00-17.48\\nATOM 159 O CEN X 39 35.056 30.722 22.831 0.00-14.36\\nATOM 160 N CEN X 40 37.388 30.633 22.630 0.00-10.51\\nATOM 161 C CEN X 40 33.794 31.513 22.561 0.00-17.33\\nATOM 162 CA CEN X 40 34.715 31.857 23.555 0.00-19.51\\nATOM 163 O CEN X 40 35.217 31.931 22.140 0.00-18.96\\nATOM 164 N CEN X 41 33.570 32.478 21.570 0.00-14.29\\nATOM 165 C CEN X 41 33.038 31.327 21.042 0.00 -8.52\\nATOM 166 CA CEN X 41 32.388 30.876 22.230 0.00 -6.76\\nATOM 167 O CEN X 41 32.165 32.406 21.570 0.00 -9.72\\nATOM 168 N CEN X 42 26.541 31.214 20.674 0.00-10.21\\nATOM 169 C CEN X 42 24.788 30.702 19.837 0.00-13.86\\nATOM 170 CA CEN X 42 25.772 31.871 19.267 0.00 -5.78\\nATOM 171 O CEN X 42 25.915 29.925 20.762 0.00-11.97\\nATOM 172 N CEN X 43 26.207 30.618 19.496 0.00 -9.85\\nATOM 173 C CEN X 43 24.702 29.252 21.017 0.00-19.97\\nATOM 174 CA CEN X 43 24.125 29.648 19.279 0.00-10.75\\nATOM 175 O CEN X 43 23.770 30.078 20.551 0.00-18.64\\nATOM 176 N CEN X 44 24.021 30.086 21.895 0.00-13.56\\nATOM 177 C CEN X 44 22.535 29.640 19.927 0.00-12.53\\nATOM 178 CA CEN X 44 24.920 30.866 21.202 0.00-12.45\\nATOM 179 O CEN X 44 23.303 27.531 20.816 0.00-17.84\\nATOM 180 N CEN X 45 22.749 29.972 21.352 0.00-12.66\\nATOM 181 C CEN X 45 23.765 27.652 19.415 0.00 -9.58\\nATOM 182 CA CEN X 45 22.382 28.206 20.095 0.00-14.56\\nATOM 183 O CEN X 45 21.108 28.087 20.255 0.00 -5.62\\nATOM 184 N CEN X 46 23.608 28.745 21.776 0.00-21.49\\nATOM 185 C CEN X 46 22.309 28.709 21.388 0.00-17.27\\nATOM 186 CA CEN X 46 21.689 27.539 21.361 0.00-10.08\\nATOM 187 O CEN X 46 22.834 27.605 22.085 0.00-14.31\\nATOM 188 N CEN X 47 23.534 28.797 20.325 0.00-22.97\\nATOM 189 C CEN X 47 24.790 28.099 21.832 0.00-12.48\\nATOM 190 CA CEN X 47 22.932 28.382 23.186 0.00 -5.83\\nATOM 191 O CEN X 47 24.602 28.018 20.444 0.00-14.98\\nATOM 192 N CEN X 48 24.794 25.542 20.551 0.00 -6.98\\nATOM 193 C CEN X 48 24.018 26.595 22.708 0.00 -7.19\\nATOM 194 CA CEN X 48 25.098 26.817 21.614 0.00-11.04\\nATOM 195 O CEN X 48 24.423 25.409 21.842 0.00 -9.97\\nATOM 196 N CEN X 49 28.405 24.805 22.843 0.00 -4.48\\nATOM 197 C CEN X 49 25.676 24.392 21.834 0.00 -6.38\\nATOM 198 CA CEN X 49 25.802 25.695 21.530 0.00-10.23\\nATOM 199 O CEN X 49 27.994 23.776 22.038 0.00 -4.12\\nATOM 200 N CEN X 50 28.751 21.954 19.922 0.00 -4.54\\nATOM 201 C CEN X 50 28.747 19.707 20.293 0.00 -2.92\\nATOM 202 CA CEN X 50 26.994 24.943 22.486 0.00 -6.87\\nATOM 203 O CEN X 50 29.075 20.113 18.110 0.00-15.07\\nATOM 204 N CEN X 51 29.307 20.761 19.387 0.00-11.42\\nATOM 205 C CEN X 51 29.632 21.010 17.102 0.00-14.31\\nATOM 206 CA CEN X 51 28.993 21.690 18.263 0.00-11.48\\nATOM 207 O CEN X 51 30.113 20.921 18.382 0.00-12.42\\nATOM 208 N CEN X 52 27.929 20.918 18.245 0.00 -6.72\\nATOM 209 C CEN X 52 30.496 19.879 17.218 0.00-16.07\\nATOM 210 CA CEN X 52 30.387 18.512 17.545 0.00 -6.58\\nATOM 211 O CEN X 52 29.947 19.983 15.851 0.00-12.88\\nATOM 212 N CEN X 53 31.210 21.045 17.660 0.00 -6.62\\nATOM 213 C CEN X 53 28.775 19.756 16.753 0.00-10.66\\nATOM 214 CA CEN X 53 29.616 18.706 16.410 0.00-10.53\\nATOM 215 O CEN X 53 31.055 19.210 15.948 0.00 -8.16\\nATOM 216 N CEN X 54 24.609 20.418 15.169 0.00 -7.11\\nATOM 217 C CEN X 54 24.643 19.304 14.331 0.00-10.36\\nATOM 218 CA CEN X 54 30.182 19.504 14.381 0.00 -7.88\\nATOM 219 O CEN X 54 23.537 20.129 14.416 0.00-17.25\\nATOM 220 N CEN X 55 27.833 15.512 19.209 0.00 -0.03\\nATOM 221 C CEN X 55 23.660 19.268 13.256 0.00-13.41\\nATOM 222 CA CEN X 55 24.840 20.642 13.903 0.00-11.38\\nATOM 223 O CEN X 55 22.886 21.071 13.450 0.00-21.59\\nATOM 224 N CEN X 56 26.227 17.597 14.876 0.00 -0.37\\nATOM 225 C CEN X 56 22.832 20.145 12.508 0.00-20.34\\nATOM 226 CA CEN X 56 23.360 22.584 12.762 0.00-10.36\\nATOM 227 O CEN X 56 21.464 20.195 13.194 0.00-14.06\\nATOM 228 N CEN X 57 24.128 21.649 13.465 0.00-12.76\\nATOM 229 C CEN X 57 22.410 19.359 13.708 0.00-13.74\\nATOM 230 CA CEN X 57 21.795 19.253 12.195 0.00 -7.88\\nATOM 231 O CEN X 57 22.211 20.494 14.445 0.00-12.28\\nATOM 232 N CEN X 58 24.216 20.401 12.751 0.00-14.99\\nATOM 233 C CEN X 58 21.846 21.928 13.530 0.00-14.86\\nATOM 234 CA CEN X 58 21.225 21.980 14.884 0.00 -4.10\\nATOM 235 O CEN X 58 21.944 21.183 12.395 0.00-20.76\\nATOM 236 N CEN X 59 22.536 21.065 11.115 0.00-12.11\\nATOM 237 C CEN X 59 23.466 21.364 12.099 0.00-18.71\\nATOM 238 CA CEN X 59 15.424 19.511 15.012 0.00 -0.01\\nATOM 239 O CEN X 59 21.622 23.131 11.177 0.00 -9.75\\nATOM 240 N CEN X 60 22.967 22.399 11.072 0.00-11.01\\nATOM 241 C CEN X 60 22.131 22.594 12.402 0.00-16.21\\nATOM 242 CA CEN X 60 20.781 22.497 12.964 0.00 -9.08\\nATOM 243 O CEN X 60 21.431 21.808 11.328 0.00-13.24\\nATOM 244 N CEN X 61 22.248 27.874 9.551 0.00-15.12\\nATOM 245 C CEN X 61 20.972 27.860 9.116 0.00 -7.53\\nATOM 246 CA CEN X 61 20.292 22.830 11.565 0.00 -6.94\\nATOM 247 O CEN X 61 21.998 28.211 7.971 0.00-10.96\\nATOM 248 N CEN X 62 20.722 27.662 7.842 0.00 -4.69\\nATOM 249 C CEN X 62 23.236 28.367 8.686 0.00-15.47\\nATOM 250 CA CEN X 62 23.308 27.046 9.087 0.00 -6.67\\nATOM 251 O CEN X 62 22.294 29.265 10.308 0.00-14.43\\nATOM 252 N CEN X 63 23.234 28.271 10.370 0.00 -9.96\\nATOM 253 C CEN X 63 23.488 29.360 9.582 0.00-14.94\\nATOM 254 CA CEN X 63 22.158 29.102 8.959 0.00-17.02\\nATOM 255 O CEN X 63 23.549 31.075 8.184 0.00 -6.02\\nATOM 256 N CEN X 64 25.840 29.964 7.460 0.00 -6.19\\nATOM 257 C CEN X 64 22.411 30.325 9.470 0.00-15.60\\nATOM 258 CA CEN X 64 21.352 30.963 10.063 0.00 -6.56\\nATOM 259 O CEN X 64 23.432 29.685 8.269 0.00-11.10\\nATOM 260 N CEN X 65 22.339 31.538 8.824 0.00 -6.59\\nATOM 261 C CEN X 65 26.041 32.510 13.717 0.00 -6.76\\nATOM 262 CA CEN X 65 22.475 30.496 10.945 0.00 -7.50\\nATOM 263 O CEN X 65 27.192 31.229 14.088 0.00 -3.28\\nATOM 264 N CEN X 66 27.705 36.397 12.513 0.00 -6.85\\nATOM 265 C CEN X 66 26.551 32.052 15.475 0.00-14.64\\nATOM 266 CA CEN X 66 25.453 32.773 14.964 0.00 -9.33\\nATOM 267 O CEN X 66 25.524 31.218 15.117 0.00 -9.22\\nATOM 268 N CEN X 67 27.691 32.472 16.412 0.00 -6.97\\nATOM 269 C CEN X 67 26.805 31.566 16.911 0.00 -9.03\\nATOM 270 CA CEN X 67 25.567 31.755 16.446 0.00-10.21\\nATOM 271 O CEN X 67 26.387 32.880 16.584 0.00-10.15\\nATOM 272 N CEN X 68 28.340 33.255 20.598 0.00-10.34\\nATOM 273 C CEN X 68 29.446 32.411 20.986 0.00 -6.19\\nATOM 274 CA CEN X 68 27.610 32.036 21.205 0.00 -7.27\\nATOM 275 O CEN X 68 29.485 33.410 19.638 0.00 -6.23\\nATOM 276 N CEN X 69 32.908 33.505 22.220 0.00 -9.56\\nATOM 277 C CEN X 69 28.232 32.030 20.028 0.00 -9.43\\nATOM 278 CA CEN X 69 28.269 33.154 19.104 0.00 -6.98\\nATOM 279 O CEN X 69 32.862 32.458 23.108 0.00-12.14\\nATOM 280 N CEN X 70 35.327 32.463 24.689 0.00-11.18\\nATOM 281 C CEN X 70 33.888 32.723 24.460 0.00 -9.13\\nATOM 282 CA CEN X 70 34.145 32.864 22.862 0.00-19.21\\nATOM 283 O CEN X 70 35.637 32.849 23.367 0.00-18.70\\nATOM 284 N CEN X 71 36.320 34.961 27.247 0.00 -1.39\\nATOM 285 C CEN X 71 35.128 33.973 22.892 0.00 -9.83\\nATOM 286 CA CEN X 71 35.268 33.805 24.306 0.00-11.08\\nATOM 287 O CEN X 71 36.478 33.757 23.715 0.00 -7.00\\nATOM 288 N CEN X 72 38.407 35.210 29.815 0.00 -8.44\\nATOM 289 C CEN X 72 39.690 35.736 29.565 0.00-10.48\\nATOM 290 CA CEN X 72 37.802 35.074 26.462 0.00 -1.39\\nATOM 291 O CEN X 72 39.277 35.407 30.883 0.00-16.37\\nATOM 292 N CEN X 73 38.737 36.499 30.228 0.00-15.73\\nATOM 293 C CEN X 73 38.240 37.488 31.165 0.00-11.95\\nATOM 294 CA CEN X 73 37.995 36.073 31.270 0.00-10.68\\nATOM 295 O CEN X 73 40.060 36.725 30.795 0.00-14.14\\nATOM 296 N CEN X 74 38.571 37.679 32.470 0.00 -7.53\\nATOM 297 C CEN X 74 39.127 36.572 31.773 0.00-17.02\\nATOM 298 CA CEN X 74 39.614 37.798 31.491 0.00 -9.88\\nATOM 299 O CEN X 74 40.047 35.679 32.174 0.00 -6.98\\nATOM 300 N CEN X 75 40.881 35.654 30.602 0.00 -6.89\\nATOM 301 C CEN X 75 49.169 32.027 38.957 0.00 -0.00\\nATOM 302 CA CEN X 75 38.038 40.527 27.698 0.00 -2.24\\nATOM 303 O CEN X 75 37.082 40.607 28.758 0.00 -2.25\\nTER\\nENDMDL\\n\",\"pdb\");\n\tviewer_1518510165543592.setStyle({\"sphere\": {\"colorscheme\": {\"min\": 1, \"gradient\": \"rwb\", \"prop\": \"b\", \"max\": -1}}});\n\n viewer_1518510165543592.render();\n });\n </script>",
"text/plain": "<IPython.core.display.HTML object>"
},
"metadata": {}
}
]
}
],
"metadata": {
"gist": {
"id": "a814a15b829f46abd8377de4c83593b7",
"data": {
"description": "workspace/tmol/dev/180212_polybb_test_system.ipynb",
"public": true
}
},
"_draft": {
"nbviewer_url": "https://gist.github.com/a814a15b829f46abd8377de4c83593b7"
},
"language_info": {
"pygments_lexer": "ipython3",
"nbconvert_exporter": "python",
"name": "python",
"codemirror_mode": {
"version": 3,
"name": "ipython"
},
"file_extension": ".py",
"version": "3.5.4",
"mimetype": "text/x-python"
},
"kernelspec": {
"name": "conda-env-tmol-py",
"display_name": "Python [conda env:tmol]",
"language": "python"
},
"toc": {
"nav_menu": {},
"number_sections": true,
"sideBar": true,
"skip_h1_title": false,
"toc_cell": false,
"toc_position": {},
"toc_section_display": "block",
"toc_window_display": false
}
},
"nbformat": 4,
"nbformat_minor": 2
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment