{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Calculating the root mean square deviation of atomic structures\n", "\n", "We calculate the RMSD of domains in adenylate kinase as it transitions from an open to closed structure, and look at calculating weighted RMSDs.\n", "\n", "**Last executed:** Feb 06, 2020 with MDAnalysis 0.20.2-dev0\n", "\n", "**Last updated:** January 2020\n", "\n", "**Minimum version of MDAnalysis:** 0.17.0\n", "\n", "**Packages required:**\n", " \n", "* MDAnalysis (Michaud-Agrawal *et al.*, 2011, Gowers *et al.*, 2016)\n", "* MDAnalysisTests\n", " \n", "**Optional packages for visualisation:**\n", " \n", "* [pandas](https://pandas.pydata.org)\n", "\n", "
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0 | \n", "0.0 | \n", "0.000000 | \n", "7.379926e-07 | \n", "4.559829e-08 | \n", "1.137940e-07 | \n", "7.653031e-08 | \n", "
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2 | \n", "2.0 | \n", "2.000000 | \n", "6.419340e-01 | \n", "5.754419e-01 | \n", "7.940987e-01 | \n", "7.270194e-01 | \n", "
3 | \n", "3.0 | \n", "3.000000 | \n", "7.743983e-01 | \n", "6.739184e-01 | \n", "1.010261e+00 | \n", "8.795031e-01 | \n", "
4 | \n", "4.0 | \n", "4.000000 | \n", "8.588600e-01 | \n", "7.318859e-01 | \n", "1.168398e+00 | \n", "9.612986e-01 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
93 | \n", "93.0 | \n", "92.999992 | \n", "6.817898e+00 | \n", "3.504430e+00 | \n", "1.143376e+01 | \n", "1.029267e+01 | \n", "
94 | \n", "94.0 | \n", "93.999992 | \n", "6.804211e+00 | \n", "3.480681e+00 | \n", "1.141134e+01 | \n", "1.029879e+01 | \n", "
95 | \n", "95.0 | \n", "94.999992 | \n", "6.807987e+00 | \n", "3.508946e+00 | \n", "1.137593e+01 | \n", "1.031958e+01 | \n", "
96 | \n", "96.0 | \n", "95.999992 | \n", "6.821205e+00 | \n", "3.498082e+00 | \n", "1.139156e+01 | \n", "1.037768e+01 | \n", "
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98 rows × 6 columns
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