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<!DOCTYPE html>
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<title>Chapter 2 The YASARA user interface | 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>
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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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<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="the-yasara-user-interface" class="section level1">
<h1><span class="header-section-number">Chapter 2</span> The YASARA user interface</h1>
<p>Open YASARA and you should see a screen that looks similar to <a href="the-yasara-user-interface.html#fig:opening">2.1</a>.</p>
<div class="figure"><span id="fig:opening"></span>
<img src="images/opening.PNG" alt="The initial YASARA screen" width="120%" />
<p class="caption">
Figure 2.1: The initial YASARA screen
</p>
</div>
<p>When a file is loaded it will appear in the center of the display in one of the various visualiation styles to be covered in a section <a href="manipulate.html#style">4.2</a>. So far we have not learned to load a molecule or to select anything, <em>so do not panic!</em> This chapter is one to read to start and then read again after you have read through Chapters 4 to 7.</p>
<p>The next sections will orient you to the Heads-up Display (<a href="the-yasara-user-interface.html#HUD">2.1</a>), the command line console <a href="the-yasara-user-interface.html#console">2.2</a>, the top Menu <a href="the-yasara-user-interface.html#Menu">2.4</a>, and the file organization (<a href="the-yasara-user-interface.html#files">2.6</a>), and includes a section on where to find help (<a href="the-yasara-user-interface.html#help">2.5</a>).</p>
<div id="HUD" class="section level2">
<h2><span class="header-section-number">2.1</span> Heads Up Display (HUD)</h2>
<p>The <em>Heads-up Display or HUD</em> in YASARA<sub>view</sub> consists of two main pieces: the <strong>Atom Properties</strong> list and the <strong>Scene Content</strong> <a href="the-yasara-user-interface.html#fig:hud">2.2</a>.</p>
<div class="figure"><span id="fig:hud"></span>
<img src="YASARA-guide_files/figure-html/hud-1.png" alt="Heads-Up Display in YASARA. The Atom properties area is shown inside the yellow box, while the Scene Content table is shown in the red box" width="747" />
<p class="caption">
Figure 2.2: Heads-Up Display in YASARA. The Atom properties area is shown inside the yellow box, while the Scene Content table is shown in the red box
</p>
</div>
<div id="atom-properties" class="section level3">
<h3><span class="header-section-number">2.1.1</span> Atom Properties</h3>
<p>The <strong>Atom Properties</strong> list describes the characteristics of a selected atom. These characteristics include the identifying traits such as element, what residue:Mol:Object it is a part of, and where it is located. Further characteristics place it within the context of the molecule being displayed under the section <em>Bonds</em>. Finally, there is a section containing 3 items: <em>Marked Distance, Marked Angle</em>, and <em>Marked Dihedral</em>. These are types of measurements we will use in Chapter <a href="making-measurements-and-comparisons.html#measure">6.2</a>.</p>
</div>
<div id="content" class="section level3">
<h3><span class="header-section-number">2.1.2</span> Scene Content</h3>
<p>The <strong>Scene Content</strong> table shows what models<a href="#fn1" class="footnoteRef" id="fnref1"><sup>1</sup></a> are loaded into the system. There are 5 columns in this table: <em>Obj, Name, Vis, Act</em>, and <em>Atom</em>.</p>
<ul>
<li><p><strong>Obj</strong>: Numerical assignment of the Obj. This is a useful indentifier for commands to maniupulate the Obj.</p></li>
<li><p><strong>Name</strong>: Indicates the name of the model. Typically this is the <a href="https://www.rcsb.org/pdb/staticHelp.do?p=help/advancedsearch/pdbIDs.html">PDB ID</a>, however you can rename the Object.</p></li>
<li><p><strong>Vis</strong>: Stands for “Visible”. When a file is loaded, this will default “Yes”. Left-clicking with the mouse on “Yes”, will change it to “No” and the model will disappear<a href="#fn2" class="footnoteRef" id="fnref2"><sup>2</sup></a>.</p></li>
<li><p><strong>Act</strong>: Stands for “Active”. When a file is loaded, this will default to “Yes”. A file that is active can be manipulated and is included in the view screen if <strong>Vis</strong> is set to “Yes. To change this to”No" the Object must be removed from the screen <a href="file-types-and-how-to-work-with-them-in-yasara.html#remove">3.7</a>.</p></li>
<li><p><strong>Atom</strong>: This column shows the number of the first atom in the Object. Like <strong>Obj</strong> this number can be useful for manipulating the view and other commands.</p></li>
</ul>
</div>
<div id="hiding-the-hud" class="section level3">
<h3><span class="header-section-number">2.1.3</span> Hiding the HUD</h3>
<p>The HUD can be hid or revealed by pressing the “Insert” key. This will be important when taking screenshots or making figures as covered in Chapter <a href="file-types-and-how-to-work-with-them-in-yasara.html#save">3.6</a>.</p>
</div>
</div>
<div id="console" class="section level2">
<h2><span class="header-section-number">2.2</span> The Console</h2>
<p>You can manipulate the view and perform analysis of the molecules in YASARA through two methods: the <strong>Console</strong> and the <strong>Menu system</strong> (<a href="the-yasara-user-interface.html#Menu">2.4</a>).</p>
<p>The console can be accessed by pressing the Space Bar. The console will appear at the bottom of the program window as shown in Figure <a href="the-yasara-user-interface.html#fig:console">2.3</a>. Pressing the Space Bar a second time will result in a larger console window. To hide the console, click your mouse in the program window somewhere outside of the console area.</p>
<div class="figure"><span id="fig:console"></span>
<img src="images/littleconsole.PNG" alt="The console in YASARA, just another name for the command line." width="801" />
<p class="caption">
Figure 2.3: The console in YASARA, just another name for the command line.
</p>
</div>
<p>Commands are typed directly into the console in the YASARA command system or Python. You can also copy and paste into the console using the Ctrl+C followed by Ctrl+V keys. Additionally you can copy console text by hightlighting and pressing Ctrl+C. The latter activity will be a useful tool when we get to the chapter on Making Movies (<a href="movies.html#movies">7</a>).</p>
<div id="up-arrow" class="section level3">
<h3><span class="header-section-number">2.2.1</span> Up Arrow!</h3>
<p>If you want to repeat or edit a command that you have already executed, whether in the console or using the interactive GUI or the menus, pressing Space Bar followed by the Up Arrow copies the previous command and allows you to repeat or edit the command to tweak the outcome. In YASARA<sub>view</sub> this is limited to the previous <em>ten commands</em> so if you know you are going to use a complex command again, copy it out before it is lost!</p>
</div>
<div id="tangent-on-using-the-command-line-and-the-interactive-menus" class="section level3">
<h3><span class="header-section-number">2.2.2</span> Tangent on using the command line and the interactive menus</h3>
<p>Users who are new to YASARA are often hesitant to use the console to perform tasks. For my students, they report this is due to inexperience with non-GUI interfaces and a fear of not knowing what to do. <strong><em>I get it</em></strong>. It took me nearly 3 years of using YASARA before I became comfortable opening the console regularly and even today, I still have issues to get the command line to work every time and to find the correct commands.</p>
<p><strong>BUT</strong></p>
<p>knowing <em>how</em> the program makes changes to the contents of the window is valuable for understanding what happened if it is not readily apparent and if you need help, having a sense of the command that is causing problems will make finding aid easier. As you become more experienced, you might begin to find command line is more versatile and even faster (assuming you type efficiently).</p>
<p><strong>For beginners</strong>, start by using the menus and checking the console for the command. Then start using the console to refine choices after using the menus to make the command. Finally, as you feel confident do as much as you can using the console.</p>
<p>Given the importance of computers to many scientific careers, experience working with command line will only make you more marketable and flexible in many situations.</p>
</div>
</div>
<div id="seq" class="section level2">
<h2><span class="header-section-number">2.3</span> Sequence Bar</h2>
<p>Hidden toward the bottom of the screen is the Sequence bar (<a href="the-yasara-user-interface.html#fig:seqbar">2.4</a>). Moving the cursor toward the bottom of the screen brings the bar up. You can click on the amino acids and scroll through the sequence of the model using this bar. This is an easy way to navigate through the model and find the specific part that you are interested. The bar can be pinned on the screen by clicking the blue button on the top left side.</p>
<div class="figure"><span id="fig:seqbar"></span>
<img src="images/sequencebar.PNG" alt="The initial YASARA screen" width="120%" />
<p class="caption">
Figure 2.4: The initial YASARA screen
</p>
</div>
</div>
<div id="Menu" class="section level2">
<h2><span class="header-section-number">2.4</span> Menu System</h2>
<p>In addition to the console, YASARA can be controlled using the Menu System which has three parts: the <em>Top Menu</em>, the <em>Top Row Buttons</em>, and the <em>Pop-up Menus</em>.</p>
<div id="top-menu" class="section level3">
<h3><span class="header-section-number">2.4.1</span> Top Menu</h3>
<p>The <strong>Top Menu</strong> will look familiar to users who use the Microsoft suite of programs or most modern productivity software. The 8 top-level categories are shown in the green box in Figure <a href="the-yasara-user-interface.html#fig:menutree">2.5</a>. We will explore several of this categories in more depth in later chapters. One note to make now is that the <em>Analyze</em> category is inaccessible until a molecule is loaded. This is shown as being in light grey, compared to the black of other categories. In general, if a menu category or option cannot be used under the current conditions, it will be colored grey.</p>
<div class="figure"><span id="fig:menutree"></span>
<img src="YASARA-guide_files/figure-html/menutree-1.png" alt="Menu Bar of YASARA showing the Top Menu inside the green box and the Top row buttons inside the light blue box" width="747" />
<p class="caption">
Figure 2.5: Menu Bar of YASARA showing the Top Menu inside the green box and the Top row buttons inside the light blue box
</p>
</div>
</div>
<div id="toprow" class="section level3">
<h3><span class="header-section-number">2.4.2</span> Top row buttons</h3>
<p>The <strong>Top row buttons</strong> are quick ways to perform tasks such as center the view or open a new scene. The buttons are indicated by the light blue box in Figure <a href="the-yasara-user-interface.html#fig:menutree">2.5</a>. The buttons will vary depending what version of YASARA being used however there are a few common and useful ones, which are highlighted below.</p>
<ul>
<li><p><img src="images/boxsel.PNG" alt="box-select" /> : This button allows you to select parts of a model in a box</p></li>
<li><p><img src="images/areasel.PNG" alt="area-select" /> : This button allows you to select parts of a model in an arbitrary area which is somewhat circular. This is similar to the lasso tool seen in other programs.</p></li>
<li><p><img src="images/clear.PNG" alt="clear" /> : This button clears everything out of the YASARA window. Typically you will get a warning to avoid inadvertant loss of data.</p></li>
<li><p><img src="images/center.PNG" alt="center" /> : This button centers the active models in the window. This really useful early on until you gain experience orienting molecules.</p></li>
<li><p><img src="images/rotate.PNG" alt="rotate" /> : This button rotates all the active models in the window. This button is often a source of frustrating for you when things start rotating unexpectedly.</p></li>
</ul>
</div>
<div id="pop-up-menu" class="section level3">
<h3><span class="header-section-number">2.4.3</span> Pop-up menu</h3>
<div class="figure"><span id="fig:pop"></span>
<img src="images/Pop-menu.png" alt="Example of the pop-up menu in YASARA" width="958" />
<p class="caption">
Figure 2.6: Example of the pop-up menu in YASARA
</p>
</div>
<p>In addition to the visible command options and readouts of YASARA like the Top Menu (<a href="the-yasara-user-interface.html#Menu">2.4</a>) and the HUD (<a href="the-yasara-user-interface.html#HUD">2.1</a>), there are ways to access commands on a selection. Referred to here as the pop-up menu (<a href="the-yasara-user-interface.html#fig:pop">2.6</a>), this menu can be accessed after a selection has been made by clicking on the selection using the right mouse button. Many of the options in the pop-up menu are found with some digging through the top menu, so this pop-up menu is a fast, easy way to find some of the most used commands. The pop-up menu is only accessible with a model loaded into YASARA.</p>
</div>
<div id="selmenu" class="section level3">
<h3><span class="header-section-number">2.4.4</span> Selection Menus</h3>
<p>When using the menu system, a box like that shown in Figure <a href="the-yasara-user-interface.html#fig:threemen">2.7</a> asking for input. The three columns can be used alone or in combination to precisely pick the Obj/Mol/Res/Atom or parts thereof you are interested in manipulating or analyzing.</p>
<ul>
<li><p><strong>Sequence</strong> – Selections in this box are the most specific and allow for the selection of one or more Obj/Mol/Res/Atoms. To make multiple selections hold down the CTRL key and left click on your selection.</p></li>
<li><p><strong>Name</strong> – Selections in this box pick broad types of Obj/Mol/Res/Atoms with the same name. As shown in Figure <a href="the-yasara-user-interface.html#fig:threemen">2.7</a>, the names of the individual amino acids are shown. For Obj or Mol, this would have the name of the Obj/Mol, while atoms will have the atom designation both simple (e.g. O for oxygen) and more specific (e.g. Ca for the <span class="math inline">\(\alpha\)</span> carbon).</p></li>
<li><p><strong>Belongs to or has</strong> – Selections here are the least specific and are aimed at broad categories such as Obj/Mol/Res/Atom in the backbone of the biomolecule or those that have certain structures like <span class="math inline">\(\alpha\)</span> helix.</p></li>
</ul>
<div class="figure"><span id="fig:threemen"></span>
<img src="images/selmenuexplain.PNG" alt="Example of the selection menu in YASARA" width="85%" />
<p class="caption">
Figure 2.7: Example of the selection menu in YASARA
</p>
</div>
</div>
</div>
<div id="help" class="section level2">
<h2><span class="header-section-number">2.5</span> Where to find help</h2>
<p><strong><em>HELP!!!!</em></strong></p>
<p>This is probably the most requested piece of information. The reason for putting this underneath all the orientation is to make getting help easier. YASARA has a specific set of words and phrases. Knowing the “jargon” of YASARA makes limiting the amount of information during a help request easier.</p>
<div id="searchdoc" class="section level3">
<h3><span class="header-section-number">2.5.1</span> SearchDoc</h3>
<p>The SearchDoc function can be found two ways:</p>
<p>Help>Search User Manual<a href="#fn3" class="footnoteRef" id="fnref3"><sup>3</sup></a></p>
<p><strong>OR</strong></p>
<p>Press the Space Bar to open the console and type <code>SearchDoc</code> followed by the inquiry word or command. See code chunk below for examples.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="co"># Search for every help page containing the word color</span>
<span class="op">></span>SearchDoc color
<span class="co"># Search for every help page referencing the word PDB</span>
<span class="op">></span>SearchDoc PDB</code></pre></div>
<p>The help page will open as a webpage in your default web browser (<a href="the-yasara-user-interface.html#fig:helpind">2.8</a>). This page will list every time that word or phrase appears in the YASARA documentation.</p>
<div class="figure"><span id="fig:helpind"></span>
<img src="images/helpindex.PNG" alt="Results of using SearchDoc part 1: Initial search results" width="415" />
<p class="caption">
Figure 2.8: Results of using SearchDoc part 1: Initial search results
</p>
</div>
<p>Clicking on any of the blue links will take you to the page for the command as shown in <a href="the-yasara-user-interface.html#fig:helppage">2.9</a>. These pages have 3 parts:</p>
<ol style="list-style-type: decimal">
<li><p>The box showing information on the command</p></li>
<li><p>A brief text description of the command and purpose</p></li>
<li><p>Examples of how to use the command in the console or in a macro.</p></li>
</ol>
<div class="figure"><span id="fig:helppage"></span>
<img src="images/helppage1.PNG" alt="Results of using SearchDoc part 2: The help page for the ColorBG command" width="578" />
<p class="caption">
Figure 2.9: Results of using SearchDoc part 2: The help page for the ColorBG command
</p>
</div>
<p>Like this reference, the <em>Menu</em> row in the box describes where in the Menus this command is found. This is most useful early on and as you learn more about YASARA, the examples become useful too. Often you can compare what happened in your console to the examples to make sure that you are looking at the right command and using the correct arguments.</p>
</div>
<div id="help-movies" class="section level3">
<h3><span class="header-section-number">2.5.2</span> Help Movies</h3>
<p>While not formally part of the help system, users can click on the <em>Help</em> category in the top menu and then choose <em>Play Help Movie</em> (Help>Play Help Movie) to access YASARA rendered movies introducing users to a variety of topics. The movies are interactive and useful for first-time users, however they are not searchable and can take a while to find a specific topic. Therefore, I recommend going through the help movies once or twice early on, but using <code>SearchDoc</code> as you become more experienced.</p>
</div>
</div>
<div id="files" class="section level2">
<h2><span class="header-section-number">2.6</span> File system</h2>
<div class="figure"><span id="fig:filetree"></span>
<img src="images/filetree.PNG" alt="File folders created upon installing YASARA in Windows" width="101" />
<p class="caption">
Figure 2.10: File folders created upon installing YASARA in Windows
</p>
</div>
<p>Upon installing windows, YASARA creates a series of folders similar to that shown in <a href="the-yasara-user-interface.html#fig:filetree">2.10</a>. The number and types of folders will depend on your YASARA version, however there will be several constant folders. Unless you have another data management system, I recommend using the YASARA system to start out. When you save a file, it will go into a folder corresponding to that file type, which can save a number of beginner headaches.</p>
<div id="datam" class="section level3">
<h3><span class="header-section-number">2.6.1</span> Naming files and Data Management</h3>
<p>While not specific to YASARA, having a good system to name and keep track of files that you create can save you many future issues. File names should be readable not only by a human but also the computer, especially if you are making a movie or executing a macro which iterates over a series of files. Therefore, some useful hints:</p>
<ol style="list-style-type: decimal">
<li><p><em>Use a single string when naming a file</em> – 01_model_ubiquitin.pdb or 01_ModelUbiquitin.pdb not this is a file with ubiquitin.pdb You can read spaces, but they can do funny things in a program.</p></li>
<li><p><em>Avoid punctuation in file names</em> – the only punctuation should be between the name and the file type 01_model_ubiquitin.pdb not 1:model/ubiquitin{today}.pdb Exceptions to this rule can be underscores (_) or dashes (-).</p></li>
<li><p><em>Dates or numbers can help organize your progress</em> – 01_model_ubiquitin.pdb or 2018-08-01_model_ubiquitin.pdb If you use numbers make sure you use two digits even for numbers less than 10. It helps keep files in order in the file viewer. Dates can be in any format but YYYY-MM-DD is most common internationally.</p></li>
<li><p><em>Keep a key or notebook</em> – This is will help you remember what you did along the way, but also help others who may work with or after you on the project. If you are using <a href="https://osf.io/">Open Science Framework (OSF)</a> or <a href="https://github.com/">Github</a> to help with your project management, then the Wiki in OSF or the Readme in GitHub are great places to provide some insight into what your files are.</p></li>
<li><p><em>Never be afraid to start over</em> – Sometimes you will dig a hole in your work and not be able to get out. It is okay to start over and try again. Data management takes a while to become routine, but should be a skill that you exercise often.</p></li>
</ol>
<p>In-depth details on file naming and data management can be found in <a href="manage.html#manage">9</a></p>
</div>
</div>
<div id="knowledge-self-checks" class="section level2">
<h2><span class="header-section-number">2.7</span> Knowledge Self-Checks</h2>
<p>Answers to questions are found in the Answers chapter under the Chapter Three header (<a href="exercise-answers.html#threekey">8.1</a>)</p>
<ol style="list-style-type: decimal">
<li><p>What action brings up the console in the YASARA window?</p></li>
<li><p>What console command allows you to swap a residue?</p></li>
<li><p>Where would you find the distance between to atoms?</p></li>
<li><p>How can you bring up the previous command in the console?</p></li>
<li><p>What is potentially problematic about each of the following file names?</p>
<p>ubiquitin.pdb</p>
<p>first model of a protein!.pdb</p>
<p>1_model_ubiquitin.pdb</p></li>
</ol>
</div>
</div>
<div class="footnotes">
<hr />
<ol start="1">
<li id="fn1"><p>When I say <strong>Model</strong> I am referring to a file that is loaded in YASARA that displays as a molecule. The main file types that do this are .pdb, .sce, and .yob and will be covered more extensively in the next chapter<a href="the-yasara-user-interface.html#fnref1">↩</a></p></li>
<li id="fn2"><p>While the model will disappear any commands that you execute will apply the model!<a href="the-yasara-user-interface.html#fnref2">↩</a></p></li>
<li id="fn3"><p>Remember that menu commands will be designated as Menu Category>Sub-option>Sub-sub-option>…<a href="the-yasara-user-interface.html#fnref3">↩</a></p></li>
</ol>
</div>
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</div>
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