\n",
"
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n",
" jupyter labextension install jupyterlab_3dmol
\n",
"
\n",
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"view = py3Dmol.view(js='https://3dmol.org/build/3Dmol.js',height=400,width=600)\n",
"\n",
"view.addModel(open('RMSf_factor.pdb','r').read(),'pdb')\n",
"\n",
"view.setStyle({'cartoon': {'colorscheme': {'prop':'b','gradient': 'roygb','min':min(RMSF_table['RMSF']),'max':max(RMSF_table['RMSF'])}}})\n",
"\n",
"view.show()"
]
},
{
"cell_type": "markdown",
"id": "0a145d08-fdba-4d79-b393-72a6f376b17e",
"metadata": {},
"source": [
"A colorbar to interpret the results"
]
},
{
"cell_type": "code",
"execution_count": 22,
"id": "7aba367f-6428-4d3c-920c-268ba9413421",
"metadata": {},
"outputs": [
{
"data": {
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAV0AAABYCAYAAABWMiSwAAAABHNCSVQICAgIfAhkiAAAAAlwSFlzAAALEgAACxIB0t1+/AAAADh0RVh0U29mdHdhcmUAbWF0cGxvdGxpYiB2ZXJzaW9uMy4xLjMsIGh0dHA6Ly9tYXRwbG90bGliLm9yZy+AADFEAAAM4UlEQVR4nO3de5AlZXnH8e9vZpZbNLAkFCKiFApaCBEKxBvrroiKdy0Qi6RCrYRULiSWAcsLxrBqCGUkkUTUEu+leEEUzQ0TLdxljSKuSokr4qXYxd0SpdhFEAjZM/P4x9tnzju9p/ucnZ3pPjPn96nqOv2+/b5vP6dn5jk93X26FRGYmVkzJtoOwMxsnDjpmpk1yEnXzKxBTrpmZg2aqlog6QrghAZjMTNbLm6JiNf1W1CZdIET9oXVh9HbHVY2lcvduomaNt3yxIAxZtsUFVJvGjoQato0OUa/1xbGCBXT7PsSIc2WAxFZh1TO69PA3fpBfZh91Zwx9mbMhYmjrs8ixRFFufghRIjZi4ZmfzDdH1Q2DSrP0JO3mcnqqGnbr26Y9ZbL8+lT9176zddeZNVv4JkhVjwzYPmwbcrr3FoXbG3S5VHA+cCKrPGKrNOKirqqNoPGmNNmCqaKRism0/yKbqfJotFU1qFcN6ic9xl2jLo+ZG0HtanqsydjVPXJy1MQRd30VJo6kxNFeYrpyUmmi04dJplmarY8TVrWrS/XpfLUbF13eVX7xRijLvaq9lXrXawxpmcm6XSKcmeK6c4k051e3UxnCjqTaQLoCDqkCXrz/cq7irrpUptdWR1Z2+nSGP3qhllvuTyfPnXvJY9rV1ZXaVdpkE5W111eLg9q38n6DWpTXv5R6hKvj+mamTXISdfMrEFOumZmDXLSNTNrkJOumVmDnHTNzBrkpGtm1iAnXTOzBjnpmpk1yEnXzKxBTrpmZg1y0jUza5CTrplZg5x0zcwa5KRrZtYgJ10zswY56ZqZNchJ18ysQU66ZmYNctI1M2uQk66ZWYOcdM3MGuSka2bWICddM7MGOemamTVoqm7hXcCH6GVmZVO53K2bqGnTLU8MGEPARAc0XZTVm4YOhJo2TY7R77WFMULFxEzRZhehDlF0CURkHVI5r08Dd+sH9WH2VXPG2JsxFyaOuj6LFEcU5eKHECFitpN6U28DkQ1aXS5+lHPqyerzPv3a9qsbZr3l8nz61L2XqvlK/QaeGWLFMwOWD9umvM6ttdHWJd1bHga21HZfZL33cxjwizZDGRELuB3yX5glx78PibdDMorb4ZaqBYoY/T88SZsi4uS242ibt0Pi7ZB4OyRLbTv4mK6ZWYOcdM3MGrRUku5VbQcwIrwdEm+HxNshWVLbYUkc0zUzWy6Wyp6umdmy4KRrZtagkU26kh4j6T2SvinpQUkh6ci242qSpLMkfV7SVkkPSbpd0mWSHtl2bE2S9AJJN0i6S9LDkrZJukbSsW3H1jZJXy7+Nv6+7ViaJGlN8b7L071txzZI7TfSWvYE4GzgO8BG4PnthtOK1wN3AhcD24ATgXXAcyQ9MyKG+r7OMnAw6ffgfcDdwGOBNwE3STo+Iuq/ArRMSToHeErbcbTstcC3s3KnrUCGNcpJ98aIOBRA0vmMZ9J9aUTcnZU3SNoBfBxYA9zQSlQNi4hPA5/O6yTdDPwIOAv4pzbiapOkg4B3A38DfKrlcNp0W0Tc1HYQe2JkDy+M0V5cpVLC7ep+qh/eZCwj6J7idVerUbTnH4HNxQeSLSEjm3St0uri9bZWo2iBpElJ+0g6GvgA6Z5Mn2k5rMZJOhU4F/jLtmMZAVdLmpZ0j6RPSXps2wENMsqHF6xE0uHA24GvRsSmtuNpwbeAk4r5nwKnRcSvWoyncZJWkD5wLo+I29uOp0W/Jh1W2gDcRzrfcTHwTUknjvLvhZPuEiHpEcCXSCcKXtNyOG35Y+B3gaNIJxm/IunUiNjSalTNeiOwP3Bp24G0KSK+B3wvq9og6UbgZtLJtb9tJbAhOOkuAZL2A/6NlGxWR8S2lkNqRUR0D6l8S9L1pDuPvgn489aCalDxr/NbgPOBfSXtmy3etzi5dn9ETLcSYMsi4ruSfgw8te1Y6viY7ogr/p38PHAK8KKIuLXlkEZCRNxLOsTwhLZjadBRwH7AJ4Gd2QRpz38ncHw7oY0MMeI3ivae7giTNAFcDTwXePFSuzRmMUk6FHgSafuMi1uA5/Sp/xopEX+Y9EE0liSdDBwDXNN2LHVGOulKOquY7Z48eaGku4G7I2JDS2E16b3Aq0jH7x6Q9PRs2bZxOcwg6Trgu8D3SSdNjiFdn9phjK7RLfbu15frlZ5jtTUidlu2XEm6GriD9HtxL+lE2puB7cB7WgxtoJG+y5ikquA2RMSaJmNpg6QtwOMqFr8tItY1F017JL2R9O3ExwP7AD8nJZ/LxuwkWl/F38mlETGyJ48WmqQ3A+eQ/j4OIF0+eD1wSUSM2qN75hjppGtmttz4RJqZWYOcdM3MGuSka2bWICddM7MGOemamTXISddsniQ9Q9LNknZI+oKkR7Udk40+J12zeZB0CPCfwI+Bl5O+jjzS34Sy0eCkazY/q4CVwD9ExEbS7RZXSVrZblg26px0zTKSTpQ0UzzkcGNN0+3F66uLu3u9ArgfeKBi3JWS7ivG3SbpgAUO3ZYIJ90xIunIiieozkh6QNJPJH2yeDJBv/7r+/R9RUXbC/u0Xden3dGS3ifptiKGh4un/m6WdK2kt0o6otRnbcX7KE/r57GZLifdqQrgspp2dwAzwN+R7u51OnBnRPx/v8YRsZO0NwzpUUsXzSM2WwacdA1SkjmAdFzyj4AbJQ17o/QLdxtMmiTdSLp+pdLzSDex+QvSHcMOIN1b4VDgWOBM0pMyTqoaYyEV8ZxWFG+PiP+qaX4uu//9PFlSXaxXkBI1wBuKPWQbMyN9lzFbdJuAz5Lu0foM4EVFvYB3Svr4EA8IXSXppIj4TlZ3FtU36kkrSLet/EixboAdwOdIj5zfh/QBsIbhHsD52eK9lP18iL65C7L5QQ98rPpQOo/0uPjdRMT24pDFauARpCdhjPQdsWzhOemOt80RcXm3IOkm4GlF8ZBi+mVF32lgspi/kLSHTFYutyk7DnhMVj6zfGtCpXsWPhXo91Tk3Jcj4mMD2tSS9GjgJVlV5ZUIxS02j82qbqV38/BzJF0UEf9X0f0aeg8X/VOcdMeODy9Ybns2P0PvqQT9bKO3R/eq4qGZ3SfVnlLUf7GmfzkZn1Ak2VmR3BwRdwyMfO+dnsW0I3s0UD/nZfM7mfu4oJXAK2v6/m82f3x3u9n4cNI1JO0n6TTgeVn1tVUnhTL/XLyuAP66mL+oz/J+fgQ8lJXfDfxC0nWS1kk6Q9L+Q4QPcIak1/eZnjxkf4BnZ/PfrmpUXHXw6qzqCxHxDeBnWd15VPsB8GBWXl3V0JapiPA0JhNwJOn5UYOm64AD+/Rfn7XZQjo8dWdR3gE8hXRIIYCbij75uOtK4/3VgDh+A7wL2L/Ub+2Q72PtHmyb/L1dVdPu3NI6Ti/qL83qpoHH1Yzx06ztJW3/XnhqdvKerpV9H3hrRPx6UMOI6NA7JrkS+A96/z3V7eV2+18JvAz4Ov0fJvg7pAcufmJw2HvtkGx+R027fC/2l6TnkwF8JqufIH0wVLmnYr02Bpx0x9sm4A3AVUD3xM8fABslPX7IMa4ifSkAeifGtpKeYDxQRPx7RKwCfo909cQ6dv/3/kxJdVdDvCYi1Gf62JDvAXrX5lY3kI5i7mGIa6N43HmkpzRvzpatLR+jrljXwPXa8uKkO942R8S7IuLPSM+b6jqIIc+qF3vEHylV/2s3GQ0rInZGxPUR8baIOAW4stSk9hK0BZBfIXFwRZvzmJskL8i/jAHkx5CPpHfNb1k+/q/2NFBb2px0DYCI+CLw31nVCyWtGrL7FaTjmJCe1vuhQR0kPVrSlTUnu+4vle/p22rh5I8uP6K8sLiu+Nw9HHO3E2rFF0cOq1ivjQFfp2u5twMvyMqXkC6lqhURW4pvcx0I3BUR9w2xrn1IX0a4QNLtpEuptpKO7R5P+jZa1xbgh8O8gb1wI70keXKf5c9nbjLexNwrFrqeTm+v/JWSDiwdHz+O9M27rg3zC9eWKiddmxUR3yjuV7CmqHqupFMj4utD9P3aoDY1nlhM/TwE/ElELPZjq79K78scvy/p6Ij4SbY832sN4JyI2G0vVdJa4KNFcX/gD4H3Z02elc3/ICK2LUDstoT48IKVvaNUXrdI67kTeCZwMXA9cBvpEMI06dDCrcC/AMdFxA2LFMOsiNhOuj9u19ndGUkHk66y6FrfL+EWPsfcQyPlQwxnZ/MfnEeotsRp8XcgzJaG4hDJ/xTFH0bEnny5YpjxDyd92EyQrkE+IiLuXch12Ojznq5ZISK+AnT3qo+VdMYCr+J19P7m3umEO568p2uWkXQi6STZBLAxIp49oMuw4x5E2st9JOkeF8dExIP1vWw5ctI1M2uQDy+YmTXISdfMrEFOumZmDXLSNTNrkJOumVmDnHTNzBr0W7TeP/8001pTAAAAAElFTkSuQmCC\n",
"text/plain": [
"