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<!DOCTYPE html>
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<title>Chapter 1 Obtaining YASARA | A Guide to YASARA</title>
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<li><a href="./">A guide to biomolecule visualization and analysis in YASARA</a></li>
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<li class="chapter" data-level="" data-path="index.html"><a href="index.html#a-note-on-using-the-command-line"><i class="fa fa-check"></i>A note on using the command line</a></li>
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<li class="chapter" data-level="" data-path="index.html"><a href="index.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>
<li class="chapter" data-level="2.4.4" data-path="the-yasara-user-interface.html"><a href="the-yasara-user-interface.html#selmenu"><i class="fa fa-check"></i><b>2.4.4</b> Selection Menus</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#datam"><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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<li class="chapter" data-level="5" data-path="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.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="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.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="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.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="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.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="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.html#rayopt"><i class="fa fa-check"></i><b>5.1.3</b> Ray Tracing options</a></li>
</ul></li>
<li class="chapter" data-level="5.2" data-path="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.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="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.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="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.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="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.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="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.html#coloring-hydrogen-bonds"><i class="fa fa-check"></i><b>5.3.1</b> Coloring hydrogen bonds</a></li>
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<li class="chapter" data-level="5.4" data-path="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.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="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.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="adding-annotations-to-your-scene.html"><a href="adding-annotations-to-your-scene.html#knowledge-checks"><i class="fa fa-check"></i><b>5.5</b> Knowledge Checks</a></li>
</ul></li>
<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>
</ul></li>
<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>
<li class="chapter" data-level="6.6" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#align"><i class="fa fa-check"></i><b>6.6</b> Alignment</a><ul>
<li class="chapter" data-level="6.6.1" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#why-did-my-objmol-move-or-not"><i class="fa fa-check"></i><b>6.6.1</b> Why did my Obj/Mol move (or not)?</a></li>
<li class="chapter" data-level="6.6.2" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#rmsd"><i class="fa fa-check"></i><b>6.6.2</b> Root Mean Square Deviation</a></li>
</ul></li>
<li class="chapter" data-level="6.7" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#swap"><i class="fa fa-check"></i><b>6.7</b> Making amino acid or nucleotide substitutions</a><ul>
<li class="chapter" data-level="6.7.1" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#swapping-bonds"><i class="fa fa-check"></i><b>6.7.1</b> Swapping bonds</a></li>
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<li class="chapter" data-level="6.8" data-path="making-measurements-and-comparisons.html"><a href="making-measurements-and-comparisons.html#knowledge-checks-1"><i class="fa fa-check"></i><b>6.8</b> Knowledge Checks</a></li>
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<li class="chapter" data-level="7" data-path="movies.html"><a href="movies.html"><i class="fa fa-check"></i><b>7</b> Macros</a><ul>
<li class="chapter" data-level="7.1" data-path="movies.html"><a href="movies.html#text-editors"><i class="fa fa-check"></i><b>7.1</b> Text editors</a></li>
<li class="chapter" data-level="7.2" data-path="movies.html"><a href="movies.html#macro"><i class="fa fa-check"></i><b>7.2</b> Organization of a macro</a><ul>
<li class="chapter" data-level="7.2.1" data-path="movies.html"><a href="movies.html#the-as-a-way-to-help-your-reader-and-you"><i class="fa fa-check"></i><b>7.2.1</b> The <code>#</code> as a way to help your reader (and you!)</a></li>
</ul></li>
<li class="chapter" data-level="7.3" data-path="movies.html"><a href="movies.html#making-a-macro"><i class="fa fa-check"></i><b>7.3</b> Making a macro</a><ul>
<li class="chapter" data-level="7.3.1" data-path="movies.html"><a href="movies.html#commands-that-can-be-used-in-a-macro"><i class="fa fa-check"></i><b>7.3.1</b> Commands that can be used in a macro</a></li>
<li class="chapter" data-level="7.3.2" data-path="movies.html"><a href="movies.html#macrosave"><i class="fa fa-check"></i><b>7.3.2</b> Saving the macro</a></li>
<li class="chapter" data-level="7.3.3" data-path="movies.html"><a href="movies.html#macroplay"><i class="fa fa-check"></i><b>7.3.3</b> Playing the macro</a></li>
</ul></li>
<li class="chapter" data-level="7.4" data-path="movies.html"><a href="movies.html#macro-examples"><i class="fa fa-check"></i><b>7.4</b> Macro examples</a></li>
<li class="chapter" data-level="7.5" data-path="movies.html"><a href="movies.html#knowledge-checks-2"><i class="fa fa-check"></i><b>7.5</b> Knowledge Checks</a></li>
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<li class="chapter" data-level="8" data-path="exercise-answers.html"><a href="exercise-answers.html"><i class="fa fa-check"></i><b>8</b> Exercise Answers</a><ul>
<li class="chapter" data-level="8.1" data-path="exercise-answers.html"><a href="exercise-answers.html#threekey"><i class="fa fa-check"></i><b>8.1</b> Chapter 3</a></li>
<li class="chapter" data-level="8.2" data-path="exercise-answers.html"><a href="exercise-answers.html#fourkey"><i class="fa fa-check"></i><b>8.2</b> Chapter 4</a></li>
<li class="chapter" data-level="8.3" data-path="exercise-answers.html"><a href="exercise-answers.html#fivekey"><i class="fa fa-check"></i><b>8.3</b> Chapter 5</a></li>
<li class="chapter" data-level="8.4" data-path="exercise-answers.html"><a href="exercise-answers.html#sixkey"><i class="fa fa-check"></i><b>8.4</b> Chapter 6</a></li>
<li class="chapter" data-level="8.5" data-path="exercise-answers.html"><a href="exercise-answers.html#sevenkey"><i class="fa fa-check"></i><b>8.5</b> Chapter 6</a></li>
<li class="chapter" data-level="8.6" data-path="exercise-answers.html"><a href="exercise-answers.html#eightkey"><i class="fa fa-check"></i><b>8.6</b> Chapter 7</a></li>
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<li class="chapter" data-level="9" data-path="manage.html"><a href="manage.html"><i class="fa fa-check"></i><b>9</b> Data Management</a><ul>
<li class="chapter" data-level="9.1" data-path="manage.html"><a href="manage.html#introduction-to-the-problem"><i class="fa fa-check"></i><b>9.1</b> Introduction to the problem</a></li>
<li class="chapter" data-level="9.2" data-path="manage.html"><a href="manage.html#what-are-data"><i class="fa fa-check"></i><b>9.2</b> What are Data?</a></li>
<li class="chapter" data-level="9.3" data-path="manage.html"><a href="manage.html#effective-file-naming"><i class="fa fa-check"></i><b>9.3</b> Effective File naming</a><ul>
<li class="chapter" data-level="9.3.1" data-path="manage.html"><a href="manage.html#information-to-consider-including-in-file-names"><i class="fa fa-check"></i><b>9.3.1</b> Information to consider including in file names</a></li>
</ul></li>
<li class="chapter" data-level="9.4" data-path="manage.html"><a href="manage.html#data-and-file-naming-dictionary"><i class="fa fa-check"></i><b>9.4</b> Data and File Naming Dictionary</a></li>
<li class="chapter" data-level="9.5" data-path="manage.html"><a href="manage.html#data-management-plan"><i class="fa fa-check"></i><b>9.5</b> Data Management Plan</a><ul>
<li class="chapter" data-level="9.5.1" data-path="manage.html"><a href="manage.html#data-management-plan-questions-for-students-in-biochemistry-class"><i class="fa fa-check"></i><b>9.5.1</b> Data Management Plan questions for students in Biochemistry class:</a></li>
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<li class="chapter" data-level="10" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html"><i class="fa fa-check"></i><b>10</b> Errors and quirks</a><ul>
<li class="chapter" data-level="10.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#macrotext"><i class="fa fa-check"></i><b>10.1</b> .mcr –> .txt and back again</a><ul>
<li class="chapter" data-level="10.1.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix"><i class="fa fa-check"></i><b>10.1.1</b> Fix</a></li>
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<li class="chapter" data-level="10.2" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#running-in-the-downloads-folder"><i class="fa fa-check"></i><b>10.2</b> Running in the downloads folder</a><ul>
<li class="chapter" data-level="10.2.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix-1"><i class="fa fa-check"></i><b>10.2.1</b> Fix</a></li>
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<li class="chapter" data-level="10.3" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#admin-permission-needed"><i class="fa fa-check"></i><b>10.3</b> Admin permission needed</a><ul>
<li class="chapter" data-level="10.3.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix-2"><i class="fa fa-check"></i><b>10.3.1</b> Fix</a></li>
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<li class="chapter" data-level="10.4" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#macos-wont-allow-yasara-to-run-because-not-from-app-store"><i class="fa fa-check"></i><b>10.4</b> MacOS won’t allow YASARA to run because not from App Store</a><ul>
<li class="chapter" data-level="10.4.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix-3"><i class="fa fa-check"></i><b>10.4.1</b> Fix</a></li>
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<li class="chapter" data-level="10.5" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#menu-bar-disappears"><i class="fa fa-check"></i><b>10.5</b> Menu bar disappears</a><ul>
<li class="chapter" data-level="10.5.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix-4"><i class="fa fa-check"></i><b>10.5.1</b> Fix</a></li>
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<li class="chapter" data-level="10.6" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#menu-bar-or-continue-button-does-not-respond-to-clicks"><i class="fa fa-check"></i><b>10.6</b> Menu bar or Continue Button does not respond to clicks</a><ul>
<li class="chapter" data-level="10.6.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix-5"><i class="fa fa-check"></i><b>10.6.1</b> Fix</a></li>
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<div id="obtaining-yasara" class="section level1">
<h1><span class="header-section-number">Chapter 1</span> Obtaining YASARA</h1>
<div id="what-is-yasara" class="section level2">
<h2><span class="header-section-number">1.1</span> What is YASARA</h2>
<p>YASARA stands for <em>Yet Another Scientific Artificial Reality Application</em> and allows interactive viewing, manipulation, and analysis of molecular data and models. The simplest version of YASARA, YASARA<sub>view</sub>, is freely available via the internet at: <a href="http://www.yasara.org/viewdl.htm" class="uri">http://www.yasara.org/viewdl.htm</a></p>
<p>For a fee, more <a href="http://www.yasara.org/yasaradl.htm">capable versions of YASARA</a> are available. However, the majority of this book will deal with the functions in free version of YASARA, YASARA<sub>view</sub>.</p>
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<div id="download-yasaraview" class="section level2">
<h2><span class="header-section-number">1.2</span> Download YASARA<sub>view</sub></h2>
<p>Visit the <a href="http://www.yasara.org/viewdl.htm">YASARA<sub>view</sub></a> website and enter the appropriate information into the menu. If you are unsure about 32-bit or 64-bit, in Windows this information is shown by clicking on <em>This PC</em> in the Windows Explorer then System Properties. System Type will indicate 32-bit or 64-bit as shown in <a href="obtaining-yasara.html#fig:os">1.1</a> .</p>
<div class="figure"><span id="fig:os"></span>
<img src="YASARA-guide_files/figure-html/os-1.png" alt="The steps to find operating system for a Windows user" width="672" />
<p class="caption">
Figure 1.1: The steps to find operating system for a Windows user
</p>
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<p>Once you have submitted the information, you will receive an email which will let you download the YASARA program.</p>
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<div id="installing-yasara" class="section level2">
<h2><span class="header-section-number">1.3</span> Installing YASARA</h2>
<p>Move the YASARA program (Mac) or install package (Windows) to an appropriate folder. I have found that installing and running YASARA from the Downloads folder is not a good idea. On Macs, it seems that programs in the Downloads folder are not given read/write permission which can cause issues with running YASARA.</p>
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