<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Root Mean Squared Fluctuation (RMSF) · MIToS</title><meta name="title" content="Root Mean Squared Fluctuation (RMSF) · MIToS"/><meta property="og:title" content="Root Mean Squared Fluctuation (RMSF) · MIToS"/><meta property="twitter:title" content="Root Mean Squared Fluctuation (RMSF) · MIToS"/><meta name="description" content="Documentation for MIToS."/><meta property="og:description" content="Documentation for MIToS."/><meta property="twitter:description" content="Documentation for MIToS."/><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link 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href="https://github.com/diegozea/MIToS.jl/blob/master/docs/src/cookbook/03_RMSF.jl" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Root-Mean-Squared-Fluctuation-(RMSF)"><a class="docs-heading-anchor" href="#Root-Mean-Squared-Fluctuation-(RMSF)">Root Mean Squared Fluctuation (RMSF)</a><a id="Root-Mean-Squared-Fluctuation-(RMSF)-1"></a><a class="docs-heading-anchor-permalink" href="#Root-Mean-Squared-Fluctuation-(RMSF)" title="Permalink"></a></h1><p>md # <a href="https://mybinder.org/v2/gh/diegozea/MIToS.jl/gh-pages?filepath=dev/cookbook/notebooks/03_RMSF.ipynb"><img src="https://mybinder.org/badge_logo.svg" alt/></a> md # <a href="https://nbviewer.jupyter.org/github/diegozea/MIToS.jl/blob/gh-pages/dev/cookbook/notebooks/03_RMSF.ipynb"><img src="https://img.shields.io/badge/show-nbviewer-579ACA.svg" alt/></a></p><h2 id="Problem-description"><a class="docs-heading-anchor" href="#Problem-description">Problem description</a><a id="Problem-description-1"></a><a class="docs-heading-anchor-permalink" href="#Problem-description" title="Permalink"></a></h2><p>The <a href="https://en.wikipedia.org/wiki/Mean_squared_displacement">Root Mean Squared Fluctuation (RMSF)</a> is a common way to measure residue flexibility in a structural ensemble. It is a measure of how far is the residue moving from its average position in the group of structures. Usually, we represent a residue position with the spatial coordinates of its alpha carbon.</p><p>The protein structures should be previously superimposed to calculate the RMSF, for example, by using the <code>superimpose</code> function of the <a href="../PDB/#Module-PDB"><code>PDB</code> module of <code>MIToS</code></a>. In this example, we are going to measure the RMSF of each residue from an NMR ensemble using the <code>rmsf</code> function.</p><p>The structure superimposition could be the most complicated step of the process, depending on the input data. In particular, it structures come from different PDB structures or homologous proteins can require the use of external programs, as <a href="https://ub.cbm.uam.es/software/online/mamothmult.php">MAMMOTH-mult</a> or <a href="https://lcb.infotech.monash.edu/mustang/">MUSTANG</a> among others, tailored for this task.</p><p>In this case, we are going to use an NMR ensemble. Therefore, we are not going to need to superimpose the structures as NMR models have the same protein sequence and are, usually, well-aligned.</p><h2 id="MIToS-solution"><a class="docs-heading-anchor" href="#MIToS-solution">MIToS solution</a><a id="MIToS-solution-1"></a><a class="docs-heading-anchor-permalink" href="#MIToS-solution" title="Permalink"></a></h2><pre><code class="language-julia hljs">import MIToS
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