{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Aligning a trajectory to a reference\n", "\n", "We use `align.AlignTraj` to align a trajectory to a frame in a reference trajectory and write it to a file.\n", "\n", "**Last updated:** December 2022\n", "\n", "**Minimum version of MDAnalysis:** 2.0.0\n", "\n", "**Packages required:**\n", " \n", "* MDAnalysis (Michaud-Agrawal *et al.*, 2011, Gowers *et al.*, 2016)\n", "* MDAnalysisTests\n", " \n", "**Optional packages for molecular visualisation:**\n", " \n", "* [nglview](http://nglviewer.org/nglview/latest) (Nguyen *et al.*, 2018)\n", "\n", "**See also**\n", "\n", "* [Aligning a trajectory to a frame from itself](aligning_trajectory_to_frame.ipynb)\n", "* [Aligning a structure to another](aligning_structure_to_another.ipynb)\n", "* [RMSD](rmsd.ipynb)\n", "\n", "