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<!DOCTYPE html>
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<title>Chapter 8 Exercise Answers | A Guide to YASARA</title>
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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="index.html"><a href="index.html"><i class="fa fa-check"></i>Index</a><ul>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html#why-read-this-book"><i class="fa fa-check"></i>Why read this book</a></li>
<li class="chapter" data-level="" data-path="index.html"><a href="index.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="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>
<li class="chapter" data-level="" data-path="index.html"><a href="index.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="index.html"><a href="index.html#questions-and-corrections"><i class="fa fa-check"></i>Questions and corrections</a></li>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html#copyright"><i class="fa fa-check"></i>Copyright</a></li>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html#acknowledgements"><i class="fa fa-check"></i>Acknowledgements</a><ul>
<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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<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>
</ul></li>
<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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<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="exercise-answers" class="section level1">
<h1><span class="header-section-number">Chapter 8</span> Exercise Answers</h1>
<div id="threekey" class="section level2">
<h2><span class="header-section-number">8.1</span> Chapter 3</h2>
<ol style="list-style-type: decimal">
<li><p>What action brings up the console in the YASARA window?</p>
<p><em>Pressing the Space Bar. A second press brings up the larger console</em></p></li>
<li><p>What console command allows you to swap a residue?</p>
<p><em>SearchDoc swap bring up the index and with some reading you will find SwapRes is the appropriate command</em></p></li>
<li><p>Where would you find the distance between to atoms?</p>
<p><em>Atom Properties in the HUD. If the two atoms are connected it will be in the “Bonds” section, if you are looking between two selections, then in the “Marked Distance” row.</em></p></li>
<li><p>How can you bring up the previous command in the console?</p>
<p><em>Up Arrow</em></p></li>
<li><p>What is potentially problematic about the following file names?</p>
<p>ubiquitin.pdb –> <em>Non-specific name. Not clear when it was made or what it might be</em></p>
<p>first model of a protein!.pdb –> <em>Spaces in the name and an !.</em></p>
<p>1_model_ubiquitin.pdb –> <em>first digit is a single digit not 01 which would be better for ordering in the file explorer</em></p></li>
</ol>
</div>
<div id="fourkey" class="section level2">
<h2><span class="header-section-number">8.2</span> Chapter 4</h2>
<ol style="list-style-type: decimal">
<li><p>If you had colored a molecule and wanted to save the model and the stylizing of the model, which file types would be best? <em>.yob or .sce will include colors in the file</em></p></li>
<li><p>What does the asterisk (*) mean in the Filename box when loading or saving a file?</p>
<p><em>The asterisk is a wild-card operator that is replaced by the appropriate file name</em></p></li>
<li><p>What is the largest level of model organization in YASARA? The smallest?</p>
<p><em>Obj>Mol>Res>Atom</em></p></li>
<li><p>What repository contains most biomolecule models?</p>
<p><em>The RCSB which is also called the PDB or Protein Data Bank</em></p></li>
<li><p>What might each of the commands below do? What do they act on?</p></li>
</ol>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="op">></span>LoadPDB 1ubq, download=yes <span class="co"># Load the PDB file from the RCSB of 1ubq</span>
<span class="op">></span>SelectAtom <span class="dv">100</span><span class="op">-</span><span class="dv">150</span> <span class="co"># Select atoms 100 to 150 in the viewing window</span>
<span class="op">></span>ColorObj <span class="dv">3</span> <span class="dv">4</span>, green <span class="co"># Color objects 3 and 4 green</span>
<span class="op">></span>CountAtom Obj <span class="dv">2</span> Ala <span class="co"># Count the number of atoms in all of the alanine residues in Obj 2</span></code></pre></div>
</div>
<div id="fivekey" class="section level2">
<h2><span class="header-section-number">8.3</span> Chapter 5</h2>
<div class="figure"><span id="fig:fiveanswers"></span>
<img src="images/teststructure.PNG" alt="Did you make it?" width="120%" />
<p class="caption">
Figure 8.1: Did you make it?
</p>
</div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co">#Load PDB</span>
<span class="op">></span>LoadPDB 1qsn, download=yes
<span class="co"># Position and Orient the molecule</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="dv">75</span>, Alpha=<span class="dv">45</span>, Beta=<span class="dv">190</span>, Gamma=<span class="dv">50</span>
<span class="co"># Make the surface </span>
<span class="op">></span>ShowSurfMol atom <span class="dv">1</span>, type=molecular, OutCol =<span class="st"> </span>red, OutAlpha =<span class="st"> </span><span class="dv">40</span>
<span class="co"># Stylize the coenzyme A</span>
<span class="op">></span>BallRes coa
<span class="co"># Show the amino acid side chains in the peptide</span>
<span class="op">></span>ShowRes Mol B
<span class="co"># Hide the enzyme secondary structure</span>
<span class="op">></span>HideSecStrMol atom <span class="dv">1</span></code></pre></div>
</div>
<div id="sixkey" class="section level2">
<h2><span class="header-section-number">8.4</span> Chapter 6</h2>
<div class="figure"><span id="fig:sixanswerfig"></span>
<img src="images/annotatetest.png" alt="A labeled figure of structure 148L" width="512" />
<p class="caption">
Figure 8.2: A labeled figure of structure 148L
</p>
</div>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Load PDB</span>
<span class="op">></span>LoadPDB 148L, download=yes
<span class="co"># Make the background white</span>
<span class="op">></span>ColorBG white
<span class="co"># Position the object</span>
<span class="op">></span>PosOriObj <span class="dv">01</span>, X=<span class="fl">1.5</span>, Y=<span class="op">-</span><span class="fl">2.5</span>, Z=<span class="dv">70</span>, Alpha=<span class="op">-</span><span class="dv">20</span>, Beta=<span class="dv">30</span>, Gamma=<span class="op">-</span><span class="dv">60</span>
<span class="co"># Remove the waters</span>
<span class="op">></span>DelRes HOH
<span class="co"># Style the enzyme</span>
<span class="op">></span>Style Ribbon
<span class="co"># Style the ligand</span>
<span class="op">></span>BallStickMol S
<span class="co"># Color the enzyme</span>
<span class="op">></span>ColorMol E, grey
<span class="co"># Make the surface</span>
<span class="op">></span>ShowSurfMol E,Type=Molecular,OutCol=cyan,OutAlpha=<span class="dv">35</span>,Specular=Yes
<span class="co"># Make the label</span>
<span class="op">></span>LabelMol S,Format=<span class="st">"N-ACETYLMURAMIC ACID"</span>,Height=<span class="fl">3.0</span>,Color=Red,X=<span class="fl">0.0</span>,Y=<span class="fl">0.0</span>,Z=<span class="fl">0.0</span>
<span class="co"># Move the label around until it is in the proper position</span></code></pre></div>
</div>
<div id="sevenkey" class="section level2">
<h2><span class="header-section-number">8.5</span> Chapter 6</h2>
<ol style="list-style-type: decimal">
<li><p><code>CountRes hoh</code> should result in 140 residues</p></li>
<li><p>14 residues contact Mol S</p></li>
</ol>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Method 1</span>
<span class="op">></span>SelectRes all with distance <span class="op"><</span><span class="dv">5</span> from Mol S
<span class="op">></span>UnselectRes <span class="op">!</span>protein
<span class="op">></span>CountRes selected
<span class="co"># Method 2</span>
<span class="op">></span>SelectRes protein with distance <span class="op"><</span><span class="dv">5</span> from Mol S
<span class="op">></span>CountRes selected</code></pre></div>
</div>
<div id="eightkey" class="section level2">
<h2><span class="header-section-number">8.6</span> Chapter 7</h2>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">LoadPDB 1UBQ, download=yes
DelRes hoh
ZoomAll Steps=<span class="dv">20</span>
BallObj <span class="dv">1</span>
AutoRotateObj <span class="dv">1</span>, Y =<span class="st"> </span><span class="dv">1</span>
ShowMessage Ball representation
Wait <span class="dv">360</span>
HideMessage
PosOriObj <span class="dv">01</span>, X=<span class="op">-</span><span class="fl">1.650</span>, Y=<span class="op">-</span><span class="fl">0.442</span>, Z=<span class="fl">35.671</span>, Alpha=<span class="fl">0.000</span>, Beta=<span class="fl">0.000</span>, Gamma=<span class="fl">0.000</span>
BallStickObj <span class="dv">1</span>
AutoRotateObj <span class="dv">1</span>, Y =<span class="st"> </span><span class="dv">1</span>
ShowMessage Ball<span class="op">-</span>Stick representation
Wait <span class="dv">360</span>
HideMessage
PosOriObj <span class="dv">01</span>, X=<span class="op">-</span><span class="fl">1.650</span>, Y=<span class="op">-</span><span class="fl">0.442</span>, Z=<span class="fl">35.671</span>, Alpha=<span class="fl">0.000</span>, Beta=<span class="fl">0.000</span>, Gamma=<span class="fl">0.000</span>
StickObj <span class="dv">1</span>
AutoRotateObj <span class="dv">1</span>, Y =<span class="st"> </span><span class="dv">1</span>
ShowMessage Stick representation
Wait <span class="dv">360</span>
HideMessage
PosOriObj <span class="dv">01</span>, X=<span class="op">-</span><span class="fl">1.650</span>, Y=<span class="op">-</span><span class="fl">0.442</span>, Z=<span class="fl">35.671</span>, Alpha=<span class="fl">0.000</span>, Beta=<span class="fl">0.000</span>, Gamma=<span class="fl">0.000</span>
Style Trace
AutoRotateObj <span class="dv">1</span>, Y =<span class="st"> </span><span class="dv">1</span>
ShowMessage Trace representation
Wait <span class="dv">360</span>
HideMessage
PosOriObj <span class="dv">01</span>, X=<span class="op">-</span><span class="fl">1.650</span>, Y=<span class="op">-</span><span class="fl">0.442</span>, Z=<span class="fl">35.671</span>, Alpha=<span class="fl">0.000</span>, Beta=<span class="fl">0.000</span>, Gamma=<span class="fl">0.000</span>
Style Tube
AutoRotateObj <span class="dv">1</span>, Y =<span class="st"> </span><span class="dv">1</span>
ShowMessage Tube representation
Wait <span class="dv">360</span>
HideMessage
PosOriObj <span class="dv">01</span>, X=<span class="op">-</span><span class="fl">1.650</span>, Y=<span class="op">-</span><span class="fl">0.442</span>, Z=<span class="fl">35.671</span>, Alpha=<span class="fl">0.000</span>, Beta=<span class="fl">0.000</span>, Gamma=<span class="fl">0.000</span>
Style Ribbon
AutoRotateObj <span class="dv">1</span>, Y =<span class="st"> </span><span class="dv">1</span>
ShowMessage Ribbon representation
Wait <span class="dv">360</span>
HideMessage
PosOriObj <span class="dv">01</span>, X=<span class="op">-</span><span class="fl">1.650</span>, Y=<span class="op">-</span><span class="fl">0.442</span>, Z=<span class="fl">35.671</span>, Alpha=<span class="fl">0.000</span>, Beta=<span class="fl">0.000</span>, Gamma=<span class="fl">0.000</span>
Style Cartoon
AutoRotateObj <span class="dv">1</span>, Y =<span class="st"> </span><span class="dv">1</span>
ShowMessage Cartoon representation
Wait <span class="dv">360</span>
HideMessage
PosOriObj <span class="dv">01</span>, X=<span class="op">-</span><span class="fl">1.650</span>, Y=<span class="op">-</span><span class="fl">0.442</span>, Z=<span class="fl">35.671</span>, Alpha=<span class="fl">0.000</span>, Beta=<span class="fl">0.000</span>, Gamma=<span class="fl">0.000</span>
Style Sidechain
AutoRotateObj <span class="dv">1</span>, Y =<span class="st"> </span><span class="dv">1</span>
ShowMessage Cartoon with sidechains representation
Wait <span class="dv">360</span>
HideMessage
PosOriObj <span class="dv">01</span>, X=<span class="op">-</span><span class="fl">1.650</span>, Y=<span class="op">-</span><span class="fl">0.442</span>, Z=<span class="fl">35.671</span>, Alpha=<span class="fl">0.000</span>, Beta=<span class="fl">0.000</span>, Gamma=<span class="fl">0.000</span></code></pre></div>
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