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<!DOCTYPE html>
<html >
<head>
<meta charset="UTF-8">
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<title>A Guide to YASARA</title>
<meta name="description" content="A guide for the visualization program YASARA and the uses of the program">
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<meta property="og:description" content="A guide for the visualization program YASARA and the uses of the program" />
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<meta name="twitter:description" content="A guide for the visualization program YASARA and the uses of the program" />
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<meta name="author" content="Chris Berndsen">
<meta name="date" content="2018-08-15">
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<nav role="navigation">
<ul class="summary">
<li><a href="./">A guide to biomolecule visualization and analysis in YASARA</a></li>
<li class="divider"></li>
<li class="chapter" data-level="1" data-path="introduction.html"><a href="introduction.html"><i class="fa fa-check"></i><b>1</b> Introduction</a><ul>
<li class="chapter" data-level="1.1" data-path="introduction.html"><a href="introduction.html#why-read-this-book"><i class="fa fa-check"></i><b>1.1</b> Why read this book</a></li>
<li class="chapter" data-level="1.2" data-path="introduction.html"><a href="introduction.html#what-is-in-this-guide"><i class="fa fa-check"></i><b>1.2</b> What is in this guide?</a></li>
<li class="chapter" data-level="1.3" data-path="introduction.html"><a href="introduction.html#a-note-on-using-the-command-line"><i class="fa fa-check"></i><b>1.3</b> A note on using the command line</a></li>
<li class="chapter" data-level="1.4" data-path="introduction.html"><a href="introduction.html#end-of-section-checks-and-active-reading"><i class="fa fa-check"></i><b>1.4</b> End of section checks and active reading</a></li>
<li class="chapter" data-level="1.5" data-path="introduction.html"><a href="introduction.html#questions-and-corrections"><i class="fa fa-check"></i><b>1.5</b> Questions and corrections</a></li>
<li class="chapter" data-level="1.6" data-path="introduction.html"><a href="introduction.html#acknowledgements"><i class="fa fa-check"></i><b>1.6</b> Acknowledgements</a><ul>
<li class="chapter" data-level="1.6.1" data-path="introduction.html"><a href="introduction.html#who-owns-yasara-and-the-other-programs-in-this-book"><i class="fa fa-check"></i><b>1.6.1</b> Who owns YASARA and the other programs in this book</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="2" data-path="obtaining-yasara.html"><a href="obtaining-yasara.html"><i class="fa fa-check"></i><b>2</b> Obtaining YASARA</a><ul>
<li class="chapter" data-level="2.1" data-path="obtaining-yasara.html"><a href="obtaining-yasara.html#what-is-yasara"><i class="fa fa-check"></i><b>2.1</b> What is YASARA</a></li>
<li class="chapter" data-level="2.2" data-path="obtaining-yasara.html"><a href="obtaining-yasara.html#download-yasaraview"><i class="fa fa-check"></i><b>2.2</b> Download YASARA<sub>view</sub></a></li>
<li class="chapter" data-level="2.3" data-path="obtaining-yasara.html"><a href="obtaining-yasara.html#installing-yasara"><i class="fa fa-check"></i><b>2.3</b> Installing YASARA</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html"><i class="fa fa-check"></i><b>3</b> The YASARA user interface</a><ul>
<li class="chapter" data-level="3.1" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#HUD"><i class="fa fa-check"></i><b>3.1</b> Heads Up Display (HUD)</a><ul>
<li class="chapter" data-level="3.1.1" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#atom-properties"><i class="fa fa-check"></i><b>3.1.1</b> Atom Properties</a></li>
<li class="chapter" data-level="3.1.2" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#content"><i class="fa fa-check"></i><b>3.1.2</b> Scene Content</a></li>
<li class="chapter" data-level="3.1.3" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#hiding-the-hud"><i class="fa fa-check"></i><b>3.1.3</b> Hiding the HUD</a></li>
</ul></li>
<li class="chapter" data-level="3.2" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#console"><i class="fa fa-check"></i><b>3.2</b> The Console</a><ul>
<li class="chapter" data-level="3.2.1" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#up-arrow"><i class="fa fa-check"></i><b>3.2.1</b> Up Arrow!</a></li>
<li class="chapter" data-level="3.2.2" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#tangent-on-using-the-command-line-and-the-interactive-menus"><i class="fa fa-check"></i><b>3.2.2</b> Tangent on using the command line and the interactive menus</a></li>
</ul></li>
<li class="chapter" data-level="3.3" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#seq"><i class="fa fa-check"></i><b>3.3</b> Sequence Bar</a></li>
<li class="chapter" data-level="3.4" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#Menu"><i class="fa fa-check"></i><b>3.4</b> Menu System</a><ul>
<li class="chapter" data-level="3.4.1" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#top-menu"><i class="fa fa-check"></i><b>3.4.1</b> Top Menu</a></li>
<li class="chapter" data-level="3.4.2" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#top-row-buttons"><i class="fa fa-check"></i><b>3.4.2</b> Top row buttons</a></li>
<li class="chapter" data-level="3.4.3" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#pop-up-menu"><i class="fa fa-check"></i><b>3.4.3</b> Pop-up menu</a></li>
</ul></li>
<li class="chapter" data-level="3.5" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#help"><i class="fa fa-check"></i><b>3.5</b> Where to find help</a><ul>
<li class="chapter" data-level="3.5.1" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#searchdoc"><i class="fa fa-check"></i><b>3.5.1</b> SearchDoc</a></li>
<li class="chapter" data-level="3.5.2" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#help-movies"><i class="fa fa-check"></i><b>3.5.2</b> Help Movies</a></li>
</ul></li>
<li class="chapter" data-level="3.6" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#files"><i class="fa fa-check"></i><b>3.6</b> File system</a><ul>
<li class="chapter" data-level="3.6.1" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#naming-files-and-data-management"><i class="fa fa-check"></i><b>3.6.1</b> Naming files and Data Management</a></li>
</ul></li>
<li class="chapter" data-level="3.7" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#knowledge-self-checks"><i class="fa fa-check"></i><b>3.7</b> Knowledge Self-Checks</a></li>
</ul></li>
<li class="chapter" data-level="4" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html"><i class="fa fa-check"></i><b>4</b> File types and how to work with them in YASARA</a><ul>
<li class="chapter" data-level="4.1" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#types"><i class="fa fa-check"></i><b>4.1</b> Common model file types</a><ul>
<li class="chapter" data-level="4.1.1" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#pdb-files"><i class="fa fa-check"></i><b>4.1.1</b> .pdb files</a></li>
<li class="chapter" data-level="4.1.2" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#yob-files-yasara-object"><i class="fa fa-check"></i><b>4.1.2</b> .yob files (YASARA object)</a></li>
<li class="chapter" data-level="4.1.3" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#sce-files-scene-files"><i class="fa fa-check"></i><b>4.1.3</b> .sce files (Scene files)</a></li>
</ul></li>
<li class="chapter" data-level="4.2" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#starting-to-work-with-models-in-yasara"><i class="fa fa-check"></i><b>4.2</b> Starting to work with models in YASARA</a></li>
<li class="chapter" data-level="4.3" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#load"><i class="fa fa-check"></i><b>4.3</b> Loading a model</a><ul>
<li class="chapter" data-level="4.3.1" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#pdb-files-1"><i class="fa fa-check"></i><b>4.3.1</b> .pdb files</a></li>
<li class="chapter" data-level="4.3.2" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#getting-a-.pdb-file-from-the-internet"><i class="fa fa-check"></i><b>4.3.2</b> Getting a .pdb file from the internet</a></li>
<li class="chapter" data-level="4.3.3" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#yob-files"><i class="fa fa-check"></i><b>4.3.3</b> .yob files</a></li>
<li class="chapter" data-level="4.3.4" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#sce-files"><i class="fa fa-check"></i><b>4.3.4</b> .sce files</a></li>
</ul></li>
<li class="chapter" data-level="4.4" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#what-does-obj-vs.mol-vs.res-vs.atom-mean"><i class="fa fa-check"></i><b>4.4</b> What does Obj vs. Mol vs. Res vs. Atom mean?</a><ul>
<li class="chapter" data-level="4.4.1" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#why-is-the-organization-important"><i class="fa fa-check"></i><b>4.4.1</b> Why is the organization important?</a></li>
</ul></li>
<li class="chapter" data-level="4.5" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#build"><i class="fa fa-check"></i><b>4.5</b> Building a molecule</a></li>
<li class="chapter" data-level="4.6" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#save"><i class="fa fa-check"></i><b>4.6</b> Saving Models</a><ul>
<li class="chapter" data-level="4.6.1" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#pdb-files-2"><i class="fa fa-check"></i><b>4.6.1</b> .pdb files</a></li>
<li class="chapter" data-level="4.6.2" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#yob-files-1"><i class="fa fa-check"></i><b>4.6.2</b> .yob files</a></li>
<li class="chapter" data-level="4.6.3" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#sce-files-1"><i class="fa fa-check"></i><b>4.6.3</b> .sce files</a></li>
</ul></li>
<li class="chapter" data-level="4.7" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#remove"><i class="fa fa-check"></i><b>4.7</b> Adding and Removing Objects</a></li>
<li class="chapter" data-level="4.8" data-path="file-types-and-how-to-work-with-them-in-yasara.html"><a href="file-types-and-how-to-work-with-them-in-yasara.html#knowledge-self-checks-1"><i class="fa fa-check"></i><b>4.8</b> Knowledge Self-Checks</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="manipulate.html"><a href="manipulate.html"><i class="fa fa-check"></i><b>5</b> Manipulating the model</a><ul>
<li class="chapter" data-level="5.1" data-path="manipulate.html"><a href="manipulate.html#orient"><i class="fa fa-check"></i><b>5.1</b> Positioning and orienting the model</a><ul>
<li class="chapter" data-level="5.1.1" data-path="manipulate.html"><a href="manipulate.html#making-reproducible-views"><i class="fa fa-check"></i><b>5.1.1</b> Making Reproducible Views</a></li>
</ul></li>
<li class="chapter" data-level="5.2" data-path="manipulate.html"><a href="manipulate.html#style"><i class="fa fa-check"></i><b>5.2</b> Changing how the model looks</a><ul>
<li class="chapter" data-level="5.2.1" data-path="manipulate.html"><a href="manipulate.html#stylizing-individual-amino-acids"><i class="fa fa-check"></i><b>5.2.1</b> Stylizing individual amino acids</a></li>
<li class="chapter" data-level="5.2.2" data-path="manipulate.html"><a href="manipulate.html#hide"><i class="fa fa-check"></i><b>5.2.2</b> Showing and Hiding Atoms and Amino Acids</a></li>
</ul></li>
<li class="chapter" data-level="5.3" data-path="manipulate.html"><a href="manipulate.html#colors"><i class="fa fa-check"></i><b>5.3</b> Setting the Colors of the Model</a><ul>
<li class="chapter" data-level="5.3.1" data-path="manipulate.html"><a href="manipulate.html#color-wheel"><i class="fa fa-check"></i><b>5.3.1</b> Color Wheel</a></li>
<li class="chapter" data-level="5.3.2" data-path="manipulate.html"><a href="manipulate.html#color-by-element-and-other-features"><i class="fa fa-check"></i><b>5.3.2</b> Color by Element and other features</a></li>
<li class="chapter" data-level="5.3.3" data-path="manipulate.html"><a href="manipulate.html#changing-the-color-scheme"><i class="fa fa-check"></i><b>5.3.3</b> Changing the color scheme</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="manipulate.html"><a href="manipulate.html#surfaces"><i class="fa fa-check"></i><b>5.4</b> Adding a surface</a><ul>
<li class="chapter" data-level="5.4.1" data-path="manipulate.html"><a href="manipulate.html#hiding-a-surface"><i class="fa fa-check"></i><b>5.4.1</b> Hiding a surface</a></li>
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<i class="fa fa-circle-o-notch fa-spin"></i><a href="./">A Guide to YASARA</a>
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<h1 class="title">A Guide to YASARA</h1>
<h4 class="author"><em>Chris Berndsen</em></h4>
<h4 class="date"><em>2018-08-15</em></h4>
</div>
<div id="introduction" class="section level1">
<h1><span class="header-section-number">Chapter 1</span> Introduction</h1>
<div id="why-read-this-book" class="section level2">
<h2><span class="header-section-number">1.1</span> Why read this book</h2>
<p>This guide serves to introduce students, educators, and other interested parties to the basics of the program <em>YASARA</em> and its use in illustrating and analyzing biomolecule structure. I wrote this for students in my class, however it developed into a guide for those who wanted to explore structures using freely available resources.</p>
</div>
<div id="what-is-in-this-guide" class="section level2">
<h2><span class="header-section-number">1.2</span> What is in this guide?</h2>
<p>This guide contains 3 main parts:</p>
<ol style="list-style-type: decimal">
<li><p>Guide to YASARA functions for users</p></li>
<li><p>Analysis and Illustration of molecular structure using YASARA</p></li>
<li><p>Incorporating YASARA into an educational setting</p></li>
</ol>
</div>
<div id="a-note-on-using-the-command-line" class="section level2">
<h2><span class="header-section-number">1.3</span> A note on using the command line</h2>
<p>GUIs are great, however it is worth knowing how to use the command line to increase speed and control. Yes, it is not as easy, especially for new users, but restricting your use to activities that are easy is a limited existence.</p>
<p>As often as possible, I will always describe <strong>both</strong> ways of doing things in YASARA by menu list:</p>
<p>Menu1>menu2>menu3>choice</p>
<p>and code chunk with comments:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># This is a comment in code which includes explanation</span>
<span class="op">></span>This is code that can be executed</code></pre></div>
<p>For in-text mentions of commands I will highlight the command such as <code>BuildRes</code> which describes the command to build an amino acid described in section <a href="file-types-and-how-to-work-with-them-in-yasara.html#build">4.5</a>.</p>
<p>For R scripts, it will be via code chunks and for Excel via menus. Other programs will be described as appropriate with images.</p>
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<div id="end-of-section-checks-and-active-reading" class="section level2">
<h2><span class="header-section-number">1.4</span> End of section checks and active reading</h2>
<p>I encourage you to <strong>actively read</strong> this book. Try to follow along descriptions in the program and recreate my results. Most sections in Parts 1 and 2 will end with a few tasks to complete to ensure that the reader understands the material. This is not required or graded, just an aid in learning to use the program. Answers are provided in the answers chapter along with explanations.</p>
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<div id="questions-and-corrections" class="section level2">
<h2><span class="header-section-number">1.5</span> Questions and corrections</h2>
<p>I make mistakes. If you find an error or something does not make sense let me know via the <a href="https://github.com/CEBerndsen/YASARA-guide">GitHub page for this book</a>. You can also maka pull request for corrections or helpful additions.</p>
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<div id="acknowledgements" class="section level2">
<h2><span class="header-section-number">1.6</span> Acknowledgements</h2>
<div id="who-owns-yasara-and-the-other-programs-in-this-book" class="section level3">
<h3><span class="header-section-number">1.6.1</span> Who owns YASARA and the other programs in this book</h3>
<p>I have no claims to YASARA or any of the other programs described in this guide. Citations and links are provided where appropriate to give authors credit where due. I receive no compensation from any of the developers; I just enjoy using their software.</p>
<p>I have written macros and R scripts that are referenced in this guide and I have made those freely available <a href="https://github.com/CEBerndsen/YASARA-guide">here</a> under an MIT License.</p>
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