{ "cells": [ { "attachments": {}, "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 updated:** December 2022 with MDAnalysis 2.4.0-dev0\n", "\n", "**Minimum version of MDAnalysis:** 1.0.0\n", "\n", "**Packages required:**\n", " \n", "* MDAnalysis (Michaud-Agrawal *et al.*, 2011, Gowers *et al.*, 2016)\n", "* MDAnalysisTests\n", "* [pandas](https://pandas.pydata.org)\n", "\n", "**See also**\n", "\n", "* [Pairwise (2D) RMSD](pairwise_rmsd.ipynb)\n", "* [RMSF](rmsf.ipynb)\n", "\n", "
\n", " | Frame | \n", "Time (ns) | \n", "Backbone | \n", "CORE | \n", "LID | \n", "NMP | \n", "
---|---|---|---|---|---|---|
0 | \n", "0.0 | \n", "1.000000 | \n", "5.834344e-07 | \n", "3.921486e-08 | \n", "1.197000e-07 | \n", "6.276497e-08 | \n", "
1 | \n", "1.0 | \n", "2.000000 | \n", "4.636592e-01 | \n", "4.550181e-01 | \n", "4.871915e-01 | \n", "4.745572e-01 | \n", "
2 | \n", "2.0 | \n", "3.000000 | \n", "6.419340e-01 | \n", "5.754418e-01 | \n", "7.940994e-01 | \n", "7.270191e-01 | \n", "
3 | \n", "3.0 | \n", "4.000000 | \n", "7.743983e-01 | \n", "6.739184e-01 | \n", "1.010261e+00 | \n", "8.795031e-01 | \n", "
4 | \n", "4.0 | \n", "5.000000 | \n", "8.588600e-01 | \n", "7.318859e-01 | \n", "1.168397e+00 | \n", "9.612989e-01 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
93 | \n", "93.0 | \n", "93.999992 | \n", "6.817898e+00 | \n", "3.504430e+00 | \n", "1.143376e+01 | \n", "1.029266e+01 | \n", "
94 | \n", "94.0 | \n", "94.999992 | \n", "6.804211e+00 | \n", "3.480681e+00 | \n", "1.141134e+01 | \n", "1.029879e+01 | \n", "
95 | \n", "95.0 | \n", "95.999992 | \n", "6.807987e+00 | \n", "3.508946e+00 | \n", "1.137593e+01 | \n", "1.031958e+01 | \n", "
96 | \n", "96.0 | \n", "96.999991 | \n", "6.821205e+00 | \n", "3.498081e+00 | \n", "1.139156e+01 | \n", "1.037768e+01 | \n", "
97 | \n", "97.0 | \n", "97.999991 | \n", "6.820322e+00 | \n", "3.507119e+00 | \n", "1.138474e+01 | \n", "1.036821e+01 | \n", "
98 rows × 6 columns
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