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<!DOCTYPE html>
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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 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">
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<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="" data-path="preface.html"><a href="preface.html"><i class="fa fa-check"></i>Preface</a><ul>
<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#why-read-this-book"><i class="fa fa-check"></i>Why read this book</a></li>
<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#what-is-in-this-guide"><i class="fa fa-check"></i>What is in this guide?</a></li>
<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#a-note-on-using-the-command-line"><i class="fa fa-check"></i>A note on using the command line</a></li>
<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#end-of-section-checks-and-active-reading"><i class="fa fa-check"></i>End of section checks and active reading</a></li>
<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#questions-and-corrections"><i class="fa fa-check"></i>Questions and corrections</a></li>
<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#copyright"><i class="fa fa-check"></i>Copyright</a></li>
<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#acknowledgements"><i class="fa fa-check"></i>Acknowledgements</a><ul>
<li class="chapter" data-level="" data-path="preface.html"><a href="preface.html#who-owns-yasara-and-the-other-programs-in-this-book"><i class="fa fa-check"></i>Who owns YASARA and the other programs in this book</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="1" data-path="obtaining-yasara.html"><a href="obtaining-yasara.html"><i class="fa fa-check"></i><b>1</b> Obtaining YASARA</a><ul>
<li class="chapter" data-level="1.1" data-path="obtaining-yasara.html"><a href="obtaining-yasara.html#what-is-yasara"><i class="fa fa-check"></i><b>1.1</b> What is YASARA</a></li>
<li class="chapter" data-level="1.2" data-path="obtaining-yasara.html"><a href="obtaining-yasara.html#download-yasaraview"><i class="fa fa-check"></i><b>1.2</b> Download YASARA<sub>view</sub></a></li>
<li class="chapter" data-level="1.3" data-path="obtaining-yasara.html"><a href="obtaining-yasara.html#installing-yasara"><i class="fa fa-check"></i><b>1.3</b> Installing YASARA</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html"><i class="fa fa-check"></i><b>2</b> The YASARA user interface</a><ul>
<li class="chapter" data-level="2.1" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#HUD"><i class="fa fa-check"></i><b>2.1</b> Heads Up Display (HUD)</a><ul>
<li class="chapter" data-level="2.1.1" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#atom-properties"><i class="fa fa-check"></i><b>2.1.1</b> Atom Properties</a></li>
<li class="chapter" data-level="2.1.2" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#content"><i class="fa fa-check"></i><b>2.1.2</b> Scene Content</a></li>
<li class="chapter" data-level="2.1.3" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#hiding-the-hud"><i class="fa fa-check"></i><b>2.1.3</b> Hiding the HUD</a></li>
</ul></li>
<li class="chapter" data-level="2.2" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#console"><i class="fa fa-check"></i><b>2.2</b> The Console</a><ul>
<li class="chapter" data-level="2.2.1" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#up-arrow"><i class="fa fa-check"></i><b>2.2.1</b> Up Arrow!</a></li>
<li class="chapter" data-level="2.2.2" 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>2.2.2</b> Tangent on using the command line and the interactive menus</a></li>
</ul></li>
<li class="chapter" data-level="2.3" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#seq"><i class="fa fa-check"></i><b>2.3</b> Sequence Bar</a></li>
<li class="chapter" data-level="2.4" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#Menu"><i class="fa fa-check"></i><b>2.4</b> Menu System</a><ul>
<li class="chapter" data-level="2.4.1" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#top-menu"><i class="fa fa-check"></i><b>2.4.1</b> Top Menu</a></li>
<li class="chapter" data-level="2.4.2" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#toprow"><i class="fa fa-check"></i><b>2.4.2</b> Top row buttons</a></li>
<li class="chapter" data-level="2.4.3" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#pop-up-menu"><i class="fa fa-check"></i><b>2.4.3</b> Pop-up menu</a></li>
</ul></li>
<li class="chapter" data-level="2.5" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#help"><i class="fa fa-check"></i><b>2.5</b> Where to find help</a><ul>
<li class="chapter" data-level="2.5.1" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#searchdoc"><i class="fa fa-check"></i><b>2.5.1</b> SearchDoc</a></li>
<li class="chapter" data-level="2.5.2" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#help-movies"><i class="fa fa-check"></i><b>2.5.2</b> Help Movies</a></li>
</ul></li>
<li class="chapter" data-level="2.6" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#files"><i class="fa fa-check"></i><b>2.6</b> File system</a><ul>
<li class="chapter" data-level="2.6.1" 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>2.6.1</b> Naming files and Data Management</a></li>
</ul></li>
<li class="chapter" data-level="2.7" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#knowledge-self-checks"><i class="fa fa-check"></i><b>2.7</b> Knowledge Self-Checks</a></li>
</ul></li>
<li class="chapter" data-level="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"><i class="fa fa-check"></i><b>3</b> File types and how to work with them in YASARA</a><ul>
<li class="chapter" data-level="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#types"><i class="fa fa-check"></i><b>3.1</b> Common model file types</a><ul>
<li class="chapter" data-level="3.1.1" 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>3.1.1</b> .pdb files</a></li>
<li class="chapter" data-level="3.1.2" 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>3.1.2</b> .yob files (YASARA object)</a></li>
<li class="chapter" data-level="3.1.3" 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>3.1.3</b> .sce files (Scene files)</a></li>
</ul></li>
<li class="chapter" data-level="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#starting-to-work-with-models-in-yasara"><i class="fa fa-check"></i><b>3.2</b> Starting to work with models in YASARA</a></li>
<li class="chapter" data-level="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#load"><i class="fa fa-check"></i><b>3.3</b> Loading a model</a><ul>
<li class="chapter" data-level="3.3.1" 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>3.3.1</b> .pdb files</a></li>
<li class="chapter" data-level="3.3.2" 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>3.3.2</b> Getting a .pdb file from the internet</a></li>
<li class="chapter" data-level="3.3.3" 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>3.3.3</b> .yob files</a></li>
<li class="chapter" data-level="3.3.4" 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>3.3.4</b> .sce files</a></li>
</ul></li>
<li class="chapter" data-level="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#what-does-obj-vs.mol-vs.res-vs.atom-mean"><i class="fa fa-check"></i><b>3.4</b> What does Obj vs. Mol vs. Res vs. Atom mean?</a><ul>
<li class="chapter" data-level="3.4.1" 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>3.4.1</b> Why is the organization important?</a></li>
</ul></li>
<li class="chapter" data-level="3.5" 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>3.5</b> Building a molecule</a></li>
<li class="chapter" data-level="3.6" 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>3.6</b> Saving Models</a><ul>
<li class="chapter" data-level="3.6.1" 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>3.6.1</b> .pdb files</a></li>
<li class="chapter" data-level="3.6.2" 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>3.6.2</b> .yob files</a></li>
<li class="chapter" data-level="3.6.3" 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>3.6.3</b> .sce files</a></li>
</ul></li>
<li class="chapter" data-level="3.7" 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>3.7</b> Adding and Removing Objects</a></li>
<li class="chapter" data-level="3.8" 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#clearing-the-scene"><i class="fa fa-check"></i><b>3.8</b> Clearing the scene</a></li>
<li class="chapter" data-level="3.9" 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>3.9</b> Knowledge Self-Checks</a></li>
</ul></li>
<li class="chapter" data-level="4" data-path="manipulate.html"><a href="manipulate.html"><i class="fa fa-check"></i><b>4</b> Manipulating the model</a><ul>
<li class="chapter" data-level="4.1" data-path="manipulate.html"><a href="manipulate.html#orient"><i class="fa fa-check"></i><b>4.1</b> Positioning and orienting the model</a><ul>
<li class="chapter" data-level="4.1.1" data-path="manipulate.html"><a href="manipulate.html#making-reproducible-views"><i class="fa fa-check"></i><b>4.1.1</b> Making Reproducible Views</a></li>
</ul></li>
<li class="chapter" data-level="4.2" data-path="manipulate.html"><a href="manipulate.html#style"><i class="fa fa-check"></i><b>4.2</b> Changing how the model looks</a><ul>
<li class="chapter" data-level="4.2.1" data-path="manipulate.html"><a href="manipulate.html#stylizing-individual-amino-acids"><i class="fa fa-check"></i><b>4.2.1</b> Stylizing individual amino acids</a></li>
<li class="chapter" data-level="4.2.2" data-path="manipulate.html"><a href="manipulate.html#hide"><i class="fa fa-check"></i><b>4.2.2</b> Showing and Hiding Atoms and Amino Acids</a></li>
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<li class="chapter" data-level="4.3" data-path="manipulate.html"><a href="manipulate.html#colors"><i class="fa fa-check"></i><b>4.3</b> Setting the Colors of the Model</a><ul>
<li class="chapter" data-level="4.3.1" data-path="manipulate.html"><a href="manipulate.html#color-wheel"><i class="fa fa-check"></i><b>4.3.1</b> Color Wheel</a></li>
<li class="chapter" data-level="4.3.2" data-path="manipulate.html"><a href="manipulate.html#color-by-element-and-other-features"><i class="fa fa-check"></i><b>4.3.2</b> Color by Element and other features</a></li>
<li class="chapter" data-level="4.3.3" data-path="manipulate.html"><a href="manipulate.html#changing-the-color-scheme"><i class="fa fa-check"></i><b>4.3.3</b> Changing the color scheme</a></li>
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<li class="chapter" data-level="4.4" data-path="manipulate.html"><a href="manipulate.html#surfaces"><i class="fa fa-check"></i><b>4.4</b> Adding a surface</a><ul>
<li class="chapter" data-level="4.4.1" data-path="manipulate.html"><a href="manipulate.html#hiding-a-surface"><i class="fa fa-check"></i><b>4.4.1</b> Hiding a surface</a></li>
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<li class="chapter" data-level="4.5" data-path="manipulate.html"><a href="manipulate.html#knowledge-self-check"><i class="fa fa-check"></i><b>4.5</b> Knowledge Self-Check</a></li>
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<li class="chapter" data-level="5" data-path="anno.html"><a href="anno.html"><i class="fa fa-check"></i><b>5</b> Adding annotations to your scene</a><ul>
<li class="chapter" data-level="5.1" data-path="anno.html"><a href="anno.html#png"><i class="fa fa-check"></i><b>5.1</b> Saving an image</a><ul>
<li class="chapter" data-level="5.1.1" data-path="anno.html"><a href="anno.html#background"><i class="fa fa-check"></i><b>5.1.1</b> Change the background color</a></li>
<li class="chapter" data-level="5.1.2" data-path="anno.html"><a href="anno.html#hidehud"><i class="fa fa-check"></i><b>5.1.2</b> Hide the HUD!</a></li>
<li class="chapter" data-level="5.1.3" data-path="anno.html"><a href="anno.html#rayopt"><i class="fa fa-check"></i><b>5.1.3</b> Ray Tracing options</a></li>
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<li class="chapter" data-level="5.2" data-path="anno.html"><a href="anno.html#labels"><i class="fa fa-check"></i><b>5.2</b> Labels</a><ul>
<li class="chapter" data-level="5.2.1" data-path="anno.html"><a href="anno.html#labpar"><i class="fa fa-check"></i><b>5.2.1</b> Label parameters</a></li>
<li class="chapter" data-level="5.2.2" data-path="anno.html"><a href="anno.html#removing-a-label"><i class="fa fa-check"></i><b>5.2.2</b> Removing a label</a></li>
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<li class="chapter" data-level="5.3" data-path="anno.html"><a href="anno.html#bonds"><i class="fa fa-check"></i><b>5.3</b> Adding Hydrogen Bonds</a><ul>
<li class="chapter" data-level="5.3.1" data-path="anno.html"><a href="anno.html#coloring-hydrogen-bonds"><i class="fa fa-check"></i><b>5.3.1</b> Coloring hydrogen bonds</a></li>
</ul></li>
<li class="chapter" data-level="5.4" data-path="anno.html"><a href="anno.html#figurelessons"><i class="fa fa-check"></i><b>5.4</b> Making good figures</a><ul>
<li class="chapter" data-level="5.4.1" data-path="anno.html"><a href="anno.html#considerations-when-making-a-biomolecule-figure"><i class="fa fa-check"></i><b>5.4.1</b> Considerations when making a biomolecule figure</a></li>
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<li class="chapter" data-level="5.5" data-path="anno.html"><a href="anno.html#knowledge-checks"><i class="fa fa-check"></i><b>5.5</b> Knowledge Checks</a></li>
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<li class="chapter" data-level="6" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html"><i class="fa fa-check"></i><b>6</b> Making measurements and comparisons</a><ul>
<li class="chapter" data-level="6.1" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#select"><i class="fa fa-check"></i><b>6.1</b> Making Selections</a><ul>
<li class="chapter" data-level="6.1.1" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#making-multiple-selections"><i class="fa fa-check"></i><b>6.1.1</b> Making multiple selections</a></li>
<li class="chapter" data-level="6.1.2" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#how-to-manipulate-selections"><i class="fa fa-check"></i><b>6.1.2</b> How to manipulate selections</a></li>
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<li class="chapter" data-level="6.2" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#measure"><i class="fa fa-check"></i><b>6.2</b> Measuring Distance</a><ul>
<li class="chapter" data-level="6.2.1" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#labdist"><i class="fa fa-check"></i><b>6.2.1</b> Labeling distances</a></li>
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<li class="chapter" data-level="6.3" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#mangle"><i class="fa fa-check"></i><b>6.3</b> Measuring Angles</a></li>
<li class="chapter" data-level="6.4" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#dihedral"><i class="fa fa-check"></i><b>6.4</b> Measurings Dihedrals</a></li>
<li class="chapter" data-level="6.5" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#count"><i class="fa fa-check"></i><b>6.5</b> Counting Atoms/Residues</a></li>
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<li class="chapter" data-level="7.1" data-path="exercise-answers.html"><a href="exercise-answers.html#threekey"><i class="fa fa-check"></i><b>7.1</b> Chapter 3</a></li>
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<li class="chapter" data-level="7.5" data-path="exercise-answers.html"><a href="exercise-answers.html#sevenkey"><i class="fa fa-check"></i><b>7.5</b> Chapter 6</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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<section class="normal" id="section-">
<div id="anno" class="section level1">
<h1><span class="header-section-number">Chapter 5</span> Adding annotations to your scene</h1>
<p>With the various manipulations covered in Chapter <a href="manipulate.html#manipulate">4</a>, we can now start making figures to display biomolecule structures. This chapter will cover the basics of annotation and conclude with some tips on making good figures (<a href="anno.html#figurelessons">5.4</a>). We will start with making a basic image of a protein and then add layers of annotation.</p>
<p>As a note, many of the annotations added here, can be added via standard illustration or photo manipulation software as well. Therefore, do not see this as the only way to make a figure using structural data, just one way.</p>
<div id="png" class="section level2">
<h2><span class="header-section-number">5.1</span> Saving an image</h2>
<p>The first step in making a figure is to know how to save an image of your model. Thus far, I have described how to save the model itself, but not how to take an image. There are two levels of image quality when saving, the standard screen shot and <code>RayTrace</code>. The latter is the preferred method however, the standard screen shot works in most cases (see <a href="anno.html#hidehud">5.1.2</a> for caveat).</p>
<p>To save an image via the menu: File>Save As>Normal Screenshot, then choose your filename and destination.</p>
<p>For a raytraced image via the menu: File>Save As>Ray traced hisres screenshot, then set your options (<a href="anno.html#rayopt">5.1.3</a>) and click OK, then select your destination and image dimensions and click OK.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Load PDB file</span>
<span class="op">></span>LoadPDB 1crn
<span class="co"># Save an image of the model in PNG format</span>
<span class="op">></span>SavePNG png\test.png
<span class="co"># Saving a ray traced image in PNG format</span>
<span class="op">></span>RayTrace png\test.png,X=<span class="dv">1024</span>,Y=<span class="dv">00541</span>,Zoom=<span class="fl">1.0</span>,Atoms=Balls,LabelShadow=No,SecAlpha=<span class="dv">100</span>,Display=Yes,Outline=<span class="fl">0.0</span>,Background=No</code></pre></div>
<p>I don’t recommend saving images via the command line, especially ray traced images and all the options. The ability to alter the background texture and image size however are great advantages of using <code>RayTrace</code> over <code>SavePNG</code>.</p>
<div id="background" class="section level3">
<h3><span class="header-section-number">5.1.1</span> Change the background color</h3>
<p>The background color is changed via the <code>ColorBG</code> command followed by the color of choice. White is the typical value however it depends on your medium. You can also set the background to be a gradient between two colors.</p>
<p>To change the color via menus:</p>
<p>View>Color>Background, then select your color and click OK.</p>
<p>If you choosing a gradient, then click Continue with Bottom Color and then selecting a color and clicking OK. In the command line this appears as below.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Color background a single color</span>
<span class="op">></span>ColorBG green
<span class="co"># Color background as a two-color gradient</span>
<span class="op">></span>ColorBG green, blue</code></pre></div>
</div>
<div id="hidehud" class="section level3">
<h3><span class="header-section-number">5.1.2</span> Hide the HUD!</h3>
<p>If you use the <code>SavePNG</code> command to take a normal screenshot, everything in the scene including the HUD will appear in the image. To hide the HUD, press the Insert key or type <code>HUD off</code> in the command line. This will save you having the text of the HUD appear and gives you more image space to occupy with your biomolecule.</p>
</div>
<div id="rayopt" class="section level3">
<h3><span class="header-section-number">5.1.3</span> Ray Tracing options</h3>
<p>Ray tracing requires downloading POV-Ray from www.povray.org and installing it in the pov folder of YASARA. In some versions of YASARA, this can be done via menus by:</p>
<p>Help>Install>POVRay</p>
<p>More details of installing POV-Ray can be found by using <code>SearchDoc</code> for the command <code>RayTrace</code>. The page on the <code>RayTrace</code> command also describes all the options for ray tracing in detail and I will summarize the key ones here.</p>
<ul>
<li><p><strong>Transparent Background</strong> – When this box is checked or Background=No, then everything that is not model will be transparent. This is a great feature for when making images for articles or presentations as it saves cropping of the background out of the image later.</p></li>
<li><p><strong>Label Shadow</strong> – If checked or set to Yes, then any labels that you add (see section <a href="anno.html#labels">5.2</a>), will have shadows. This is a neat effect for presentations, but not something I would use in a figure in a paper.</p></li>
<li><p><strong>X and Y values</strong> – This is the size in pixels of the final output from the ray tracing. To make a high resolution image for a paper or article, I recommend increasing these values by 2 to 5-fold and then shrinking the image size after inserting it. This reduces the pixelation issue that haunts structural biologists. Increasing these values will make for a larger file size so do not go crazy.</p></li>
</ul>
</div>
</div>
<div id="labels" class="section level2">
<h2><span class="header-section-number">5.2</span> Labels</h2>
<p>Labels are useful for explicitly marking atoms, distances, molecules, and other aspects of the scene contents. Labels can be positioned freely once they are made and maintain their orientation to the viewer throughout rotations of the scene.</p>
<p>To add a label via the menus:</p>
<p>Effects>Label><em>Pick your option</em>, then select what will be labeled and click OK, then define the label parameters (<a href="anno.html#labpar">5.2.1</a>) and then select the color OR click OK.</p>
<p>The command to add a label is <code>Label</code> followed by the level of organization or distance (<code>Dis</code>). There are a number of parameters to be set afterwards (see Section <a href="anno.html#labpar">5.2.1</a> for more details.</p>
<p>The code below shows how to make the image in Figure <a href="anno.html#fig:labelpic">5.1</a>.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Load PDB file</span>
LoadPDB 1crn, download=yes
<span class="co"># Position the model for viewing and labeling</span>
<span class="op">></span>PosOriObj <span class="dv">01</span>, X=<span class="fl">0.000</span>, Y=<span class="fl">0.000</span>, Z=<span class="fl">50.000</span>, Alpha=<span class="op">-</span><span class="dv">5</span>, Beta=<span class="dv">280</span>, Gamma=<span class="op">-</span><span class="dv">15</span>
<span class="co"># Stylize the molecule and scene area</span>
<span class="op">></span>ColorBG White
<span class="op">></span>Style Ribbon
<span class="op">></span>Style Sidechain=stick
<span class="op">></span>ColorObj <span class="dv">1</span>, grey
<span class="co"># Color Arg 17 blue and show in Ball style</span>
<span class="op">></span>ColorRes <span class="dv">17</span>, blue
<span class="op">></span>BallRes <span class="dv">17</span>
<span class="co"># Make a blue label showing Arg 17 and have it be to the right of the target</span>
<span class="op">></span>LabelRes Arg <span class="dv">17</span>,Format=RESNAME RESNUM,Height=<span class="fl">2.0</span>,Color=Blue,X=<span class="fl">10.0</span>,Y=<span class="op">-</span><span class="dv">1</span>,Z=<span class="fl">0.0</span></code></pre></div>
<div class="figure"><span id="fig:labelpic"></span>
<img src="images/labelone.png" alt="Resulting image of labeling code" width="125%" />
<p class="caption">
Figure 5.1: Resulting image of labeling code
</p>
</div>
<div id="labpar" class="section level3">
<h3><span class="header-section-number">5.2.1</span> Label parameters</h3>
<ul>
<li><p><strong>Scene/Obj/Res/Mol/Atom/Distance</strong> – These options are under the Effects>Label menu. With the exception of Distance, all of them describe a level of organization. Distance will calculate the distance between the selection and display that number.</p></li>
<li><p><strong>Format</strong> – This option describes what aspect will be labeled. RESNAME is the three letter code for the residue, RESNUM is the residue number. You can also put arbitrary text in this space.</p></li>
<li><p><strong>Height</strong> – This defines how tall the text will be in Angstroms, which is 10<sup>-10</sup> meters. This is really small compared to a human but is the standard unit of measurement for biomolecules. The text in Figure <a href="anno.html#fig:labelpic">5.1</a> is 2 angstroms tall for reference.</p></li>
<li><p><strong>Color</strong> – Defines the color. Can be chosen using words or numbers as in section <a href="manipulate.html#colors">4.3</a>.</p></li>
<li><p><strong>X, Y, Z</strong> – Indicates where the label is placed relative to the target of the label. The units are in angstroms. Placing the label is the trickest part of labeling part of a scene.</p></li>
</ul>
<p>After you have created the label, if you want to move it to a new location, left-click on the label and you can freely move it around the screen using the mouse commands described in <a href="manipulate.html#tab:mousetable">4.1</a>. This is very useful when making figures.</p>
</div>
<div id="removing-a-label" class="section level3">
<h3><span class="header-section-number">5.2.2</span> Removing a label</h3>
<p>To remove a label, you can left-click on the label and press delete. Alternative use the command <code>Unlabel</code>. Typing <code>UnlabelResAll</code> removes all amino acid labels.</p>
</div>
</div>
<div id="bonds" class="section level2">
<h2><span class="header-section-number">5.3</span> Adding Hydrogen Bonds</h2>
<p><a href="https://www.ncbi.nlm.nih.gov/books/NBK22567/">Hydrogen bonds</a> are important weak interactions found throughout biochemistry. Hydrogen bonds hold <span class="math inline">\(\alpha\)</span> helices together, connect <span class="math inline">\(\beta\)</span> strands to form sheets, and can have dramatic effects on protein activity. Showing hydrogen bonds explicitly can show the role that these important interactions play in your biomolecule of interest.</p>
<p>In the scene we have created, it would be nice to show the role of Arg 17 in the structure of the protein. The side chain of the protein makes one or more hydrogen bonds with other parts of the protein so let’s show them. First you need to add hydrogens if they are not already in the molecule using the <code>AddHyd</code> command. Then use the <code>ShowHBo</code> along with your selection to show the hydrogen bonds.</p>
<p>From the menu:</p>
<p>View>Show Interactions>Hydrogen bonds of><em>Pick your option</em>, then select your Obj/Mol/Res/Atom to show hydrogen bonds and then specify if you only want to show hydrogen bonds <em>within</em> your selection or all the hydrogen bonds that your selection makes. This is the Extend command shown in the code chunk below.</p>
<p>You can also add hydrogen bonds by selecting an atom and bringing up the pop-up menu. Within the pop-up menu choose Show>Hydrogen Bonds><em>Pick your option</em>. The menu thereafter will relate to the Extend command described in the previous paragraph.</p>
<p>From the command line:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Load PDB file</span>
<span class="op">></span>LoadPDB 1crn, download=yes
<span class="co"># Position the model for viewing and labeling</span>
<span class="op">></span>PosOriObj <span class="dv">01</span>, X=<span class="fl">0.000</span>, Y=<span class="fl">0.000</span>, Z=<span class="fl">50.000</span>, Alpha=<span class="op">-</span><span class="dv">5</span>, Beta=<span class="dv">280</span>, Gamma=<span class="op">-</span><span class="dv">15</span>
<span class="co"># Stylize the molecule and scene area</span>
<span class="op">></span>ColorBG White
<span class="op">></span>Style Ribbon
<span class="op">></span>Style Sidechain=stick
<span class="op">></span>ColorObj <span class="dv">1</span>, grey
<span class="co"># Color Arg 17 blue and show in Ball style</span>
<span class="op">></span>ColorRes <span class="dv">17</span>, blue
<span class="op">></span>BallRes <span class="dv">17</span>
<span class="co"># Make a blue label showing Arg 17 and have it be to the right of the target</span>
<span class="op">></span>LabelRes <span class="dv">17</span>,Format=RESNAME RESNUM,Height=<span class="fl">2.0</span>,Color=Blue,X=<span class="fl">10.0</span>,Y=<span class="op">-</span><span class="dv">1</span>,Z=<span class="fl">0.0</span>
<span class="co"># Add hydrogens to 1crn</span>
<span class="op">></span>AddHyd all
<span class="co"># Add hydrogen bonds to Arg 17</span>
<span class="op">></span>ShowHBoRes <span class="dv">17</span>,Extend=Yes</code></pre></div>
<div class="figure"><span id="fig:hbopic"></span>
<img src="images/hbo1.png" alt="Resulting image of code adding hydrogen bonds to Arg 17" width="125%" />
<p class="caption">
Figure 5.2: Resulting image of code adding hydrogen bonds to Arg 17
</p>
</div>
<p>You will notice that 3 hydrogen bonds appear, although one is hidden by the side chain and requires rotation of the image to view.</p>
<div id="coloring-hydrogen-bonds" class="section level3">
<h3><span class="header-section-number">5.3.1</span> Coloring hydrogen bonds</h3>
<p>You can change the color of hydrogen bonds using the <code>ColorHBo</code> command as shown in the code chunk below. You must specify the color, the transparency (Alpha), and whether the bond inherits the color from the bounding atoms. This latter option is useful if you have certain hydrogen bound atoms colored the same and you want the bonds to be that same color.</p>
<p>From the menu:</p>
<p>View>Color>Hydrogen bonds, then select your color, transparency (alpha), and whether it inherits atom colors.</p>
<p>From the command line:</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Change hydrogen bond color to blue with 50% transparency and do not inherit atom colors</span>
<span class="op">></span>ColorHBo Color=Blue,Alpha=<span class="dv">50</span>,Inherit=No</code></pre></div>
</div>
</div>
<div id="figurelessons" class="section level2">
<h2><span class="header-section-number">5.4</span> Making good figures</h2>
<p>A good figure can convey more than the text ever could, while a bad figure can confuse the reader. Therefore it is important to keep a few considerations in mind when making figures of biomolecules. These ideas can apply to other types of figures and data but we are focused on biomolecule figures. Other tips on making figures can be found <a href="https://ceberndsen.github.io/CEBerndsen.github.io/Data_Fitting.html">here</a>. Additionally, a good illustration or graphics program is useful when combining figures. I recommend <a href="https://inkscape.org/en/">Inkscape</a> or Google Drawings which is found within the <a href="https://www.google.com/docs/about/">Google Drive</a> framework. Both are free and pretty easy to use.</p>
<div id="considerations-when-making-a-biomolecule-figure" class="section level3">
<h3><span class="header-section-number">5.4.1</span> Considerations when making a biomolecule figure</h3>
<ol style="list-style-type: decimal">
<li><p><strong>Why am I making the figure?</strong> – Don’t make a picture because you can, have a purpose and a point.</p></li>
<li><p><strong>What am I trying to convey with this figure?</strong> – What are the two or three main ideas that the figure needs to convey. If upon making the figure, these aren’t obvious. Then further work is needed.</p></li>
<li><p><strong>Don’t be messy</strong> – Remove unecessary parts of the molecule, try to crop the figure appropriately, and don’t go overboard. As in consideration #1, don’t show something because you can, show it because it matters.</p></li>
<li><p><strong>Use labels, colors, and representations</strong> – This chapter has shown how to add annotations to figures, so use these to your advantage.</p></li>
<li><p><strong>Make text legible</strong> – If you think the text is too small, then it probably is. If you think it is just right, then it is probably still too small. Claus Wilke’s excellent <a href="https://serialmentor.com/dataviz/small-axis-labels.html">book on data visualization</a> shows this principle very well.</p></li>
<li><p><strong>Have a figure legend</strong> – Where possible use text to help the reader sort through the figure and the meaning.</p></li>
</ol>
<p>Let’s look back at Figure <a href="anno.html#fig:hbopic">5.2</a> and you will notice that it violates principles 2, 3, 4, possibly 5 and 6. Now look at a revised figure (Figure <a href="anno.html#fig:better">5.3</a>). The unecessary side chains are gone and labels have been added to amino acids that interact with Arg 17. Additionally, the amino acids that are shown are colored by element with hydrogen bonds. So now we not only see the hydrogen bonds made by Arg 17, we also see the hydrogen bonding partners and the types of chemical groups involved. This figure still has an issue: the label for Arg 17 blocks the structure. Moving it away might confuse the reader, so why not save an image of the molecule and move to another program to add an arrow.</p>
<div class="figure"><span id="fig:better"></span>
<img src="images/better.png" alt="Better(?) figure of 1CRN showing interactions with Arg 17" width="125%" />
<p class="caption">
Figure 5.3: Better(?) figure of 1CRN showing interactions with Arg 17
</p>
</div>
<p>Figure <a href="anno.html#fig:betterarrow">5.4</a> shows the figure after moving the Arg 17 label over and adding an arrow in Google Drawings to indicate what the label refers to. You will notice I left the size of the Arg 17 label larger and in blue compared to the other labels. This was intentional to help my reader focus on Arg 17. Also notice I made an informative figure legend.</p>
<div class="figure"><span id="fig:betterarrow"></span>
<img src="images/betterarrow.png" alt="Model of structure 1crn showing how Arg 17 (shown by arrow in ball and stick representation) hydrogen bonds within the protein. Hydrogen bonds are shown as dotted red lines between donor and acceptor atoms. Amino acid side chains are colored by element with carbon colored cyan, nitrogen colored blue, oxygen colored red, and hydrogen colored grey." width="125%" />
<p class="caption">
Figure 5.4: Model of structure 1crn showing how Arg 17 (shown by arrow in ball and stick representation) hydrogen bonds within the protein. Hydrogen bonds are shown as dotted red lines between donor and acceptor atoms. Amino acid side chains are colored by element with carbon colored cyan, nitrogen colored blue, oxygen colored red, and hydrogen colored grey.
</p>
</div>
<p>If you are still struggling, show your figure to a peer or mentor and get feedback. I also recommend reading <a href="https://serialmentor.com/dataviz/index.html">Fundamentals of Data Visualization</a> by Claus Wilke to get a sense of best practices for other types of data. While not aimed at biomolecules, some of the principles and ideas in this book can help with figures in general.</p>
</div>
</div>
<div id="knowledge-checks" class="section level2">
<h2><span class="header-section-number">5.5</span> Knowledge Checks<a href="#fn6" class="footnoteRef" id="fnref6"><sup>6</sup></a></h2>
<ol style="list-style-type: decimal">
<li>Try to re-create the image in Figure <a href="anno.html#fig:sixtest">5.5</a> using PDB <a href="https://www.rcsb.org/structure/148l">148L</a>. You will use commands from this chapter as well as the previous chapters to make the figure. List the commands.</li>
</ol>
<div class="figure"><span id="fig:sixtest"></span>
<img src="images/annotatetest.png" alt="Your challenge" width="125%" />
<p class="caption">
Figure 5.5: Your challenge
</p>
</div>
</div>
</div>
<div class="footnotes">
<hr />
<ol start="6">
<li id="fn6"><p>Answers can be found <a href="exercise-answers.html#sixkey">7.4</a><a href="anno.html#fnref6">↩</a></p></li>
</ol>
</div>
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