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<!DOCTYPE html>
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<title>Chapter 10 Errors and quirks | A Guide to YASARA</title>
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<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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<section class="normal" id="section-">
<div id="errors-and-quirks" class="section level1">
<h1><span class="header-section-number">Chapter 10</span> Errors and quirks</h1>
<div id="macrotext" class="section level2">
<h2><span class="header-section-number">10.1</span> .mcr –> .txt and back again</h2>
<p>When downloading a macro from Canvas, Dropbox, OSF or other cloud-based sources, sometimes the file extension (.mcr) gets changed to .txt. This is especially common with MacOS users. Alternatively, the extension gets modified to .mcr.txt. In both cases, YASARA may reject or ignore the file.</p>
<div id="fix" class="section level3">
<h3><span class="header-section-number">10.1.1</span> Fix</h3>
<p>Rename the file and use only .mcr in the file name. You may get a warning saying that changing file extensions can cause problems, (which is what the system did) however in this instance changing the file extension is fine.</p>
</div>
</div>
<div id="running-in-the-downloads-folder" class="section level2">
<h2><span class="header-section-number">10.2</span> Running in the downloads folder</h2>
<p>After downloading YASARA, the program does not load or start. If the program is still in the downloads folder, the security settings for MacOS and sometimes Windows do not allow programs to write if they are stored in the downloads folder.</p>
<div id="fix-1" class="section level3">
<h3><span class="header-section-number">10.2.1</span> Fix</h3>
<p>Move the YASARA application or YASARA program folder to the Applications directory on a Mac or into Program Files on a Windows computer.</p>
</div>
</div>
<div id="admin-permission-needed" class="section level2">
<h2><span class="header-section-number">10.3</span> Admin permission needed</h2>
<p>YASARA loads but then fails because it cannot write the start-up file. This may be because the program has not been allowed to write to the current directory.</p>
<div id="fix-2" class="section level3">
<h3><span class="header-section-number">10.3.1</span> Fix</h3>
<p>Right click on the YASARA program to bring up the menu and then click “Run as administrator”. You may be asked for your password afterwards.</p>
</div>
</div>
<div id="macos-wont-allow-yasara-to-run-because-not-from-app-store" class="section level2">
<h2><span class="header-section-number">10.4</span> MacOS won’t allow YASARA to run because not from App Store</h2>
<p>This is a common issue on modern Apple computers. When trying to start YASARA, a warning appears saying that the application may not be trustworthy.</p>
<div id="fix-3" class="section level3">
<h3><span class="header-section-number">10.4.1</span> Fix</h3>
<p>To fix this problem, you should follow the instructions under the question mark to change the security settings for the computer or shown <a href="https://support.apple.com/kb/ph25088?locale=en_US">here</a> or <a href="https://appleinsider.com/articles/16/04/13/how-to-install-and-run-mac-apps-that-dont-come-from-the-mac-app-store">here</a>.</p>
</div>
</div>
<div id="menu-bar-disappears" class="section level2">
<h2><span class="header-section-number">10.5</span> Menu bar disappears</h2>
<p>When the window is maximized sometimes the menu bar disappears.</p>
<div id="fix-4" class="section level3">
<h3><span class="header-section-number">10.5.1</span> Fix</h3>
<p>This is a screen resolution or size issue. Go to Window>Screen Size, then select a smaller size or lower resolution. There is a bit of trial and error here and multiple attempts may be required.</p>
</div>
</div>
<div id="menu-bar-or-continue-button-does-not-respond-to-clicks" class="section level2">
<h2><span class="header-section-number">10.6</span> Menu bar or Continue Button does not respond to clicks</h2>
<p>When trying to click on the Menu bar or the Continue button, it is necessary to click below the button or menu to get it to respond.</p>
<div id="fix-5" class="section level3">
<h3><span class="header-section-number">10.6.1</span> Fix</h3>
<p>his is a screen resolution or size issue. Go to Window>Screen Size, then select a smaller size or lower resolution. There is a bit of trial and error here and multiple attempts may be required.</p>
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