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<!DOCTYPE html>
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<title>Chapter 10 Data Management | A Guide to YASARA</title>
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<meta name="twitter:description" content="A guide for the visualization program YASARA and the uses of the program" />
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<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#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"><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="analysis.html"><a href="analysis.html"><i class="fa fa-check"></i><b>8</b> Analysis Macros</a><ul>
<li class="chapter" data-level="8.1" data-path="analysis.html"><a href="analysis.html#the-file-for-the-macro"><i class="fa fa-check"></i><b>8.1</b> The file for the macro</a></li>
<li class="chapter" data-level="8.2" data-path="analysis.html"><a href="analysis.html#loop"><i class="fa fa-check"></i><b>8.2</b> The <code>for</code> loop</a></li>
<li class="chapter" data-level="8.3" data-path="analysis.html"><a href="analysis.html#section"><i class="fa fa-check"></i><b>8.3</b> </a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="exercise-answers.html"><a href="exercise-answers.html"><i class="fa fa-check"></i><b>9</b> Exercise Answers</a><ul>
<li class="chapter" data-level="9.1" data-path="exercise-answers.html"><a href="exercise-answers.html#threekey"><i class="fa fa-check"></i><b>9.1</b> Chapter 3</a></li>
<li class="chapter" data-level="9.2" data-path="exercise-answers.html"><a href="exercise-answers.html#fourkey"><i class="fa fa-check"></i><b>9.2</b> Chapter 4</a></li>
<li class="chapter" data-level="9.3" data-path="exercise-answers.html"><a href="exercise-answers.html#fivekey"><i class="fa fa-check"></i><b>9.3</b> Chapter 5</a></li>
<li class="chapter" data-level="9.4" data-path="exercise-answers.html"><a href="exercise-answers.html#sixkey"><i class="fa fa-check"></i><b>9.4</b> Chapter 6</a></li>
<li class="chapter" data-level="9.5" data-path="exercise-answers.html"><a href="exercise-answers.html#sevenkey"><i class="fa fa-check"></i><b>9.5</b> Chapter 6</a></li>
<li class="chapter" data-level="9.6" data-path="exercise-answers.html"><a href="exercise-answers.html#eightkey"><i class="fa fa-check"></i><b>9.6</b> Chapter 7</a></li>
</ul></li>
<li class="chapter" data-level="10" data-path="manage.html"><a href="manage.html"><i class="fa fa-check"></i><b>10</b> Data Management</a><ul>
<li class="chapter" data-level="10.1" data-path="manage.html"><a href="manage.html#introduction-to-the-problem"><i class="fa fa-check"></i><b>10.1</b> Introduction to the problem</a></li>
<li class="chapter" data-level="10.2" data-path="manage.html"><a href="manage.html#what-are-data"><i class="fa fa-check"></i><b>10.2</b> What are Data?</a></li>
<li class="chapter" data-level="10.3" data-path="manage.html"><a href="manage.html#effective-file-naming"><i class="fa fa-check"></i><b>10.3</b> Effective File naming</a><ul>
<li class="chapter" data-level="10.3.1" data-path="manage.html"><a href="manage.html#information-to-consider-including-in-file-names"><i class="fa fa-check"></i><b>10.3.1</b> Information to consider including in file names</a></li>
</ul></li>
<li class="chapter" data-level="10.4" data-path="manage.html"><a href="manage.html#organizing-files"><i class="fa fa-check"></i><b>10.4</b> Organizing files</a><ul>
<li class="chapter" data-level="10.4.1" data-path="manage.html"><a href="manage.html#use-sub-folders"><i class="fa fa-check"></i><b>10.4.1</b> Use sub-folders</a></li>
<li class="chapter" data-level="10.4.2" data-path="manage.html"><a href="manage.html#separate-raw-data-from-analysis-files"><i class="fa fa-check"></i><b>10.4.2</b> Separate raw data from analysis files</a></li>
</ul></li>
<li class="chapter" data-level="10.5" data-path="manage.html"><a href="manage.html#data-and-file-naming-dictionary"><i class="fa fa-check"></i><b>10.5</b> Data and File Naming Dictionary</a></li>
<li class="chapter" data-level="10.6" data-path="manage.html"><a href="manage.html#data-management-plan"><i class="fa fa-check"></i><b>10.6</b> Data Management Plan</a><ul>
<li class="chapter" data-level="10.6.1" data-path="manage.html"><a href="manage.html#data-management-plan-questions-for-students-in-biochemistry-class"><i class="fa fa-check"></i><b>10.6.1</b> Data Management Plan questions for students in Biochemistry class:</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="11" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html"><i class="fa fa-check"></i><b>11</b> Errors and quirks</a><ul>
<li class="chapter" data-level="11.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#macrotext"><i class="fa fa-check"></i><b>11.1</b> .mcr –> .txt and back again</a><ul>
<li class="chapter" data-level="11.1.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix"><i class="fa fa-check"></i><b>11.1.1</b> Fix</a></li>
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<li class="chapter" data-level="11.2" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#running-in-the-downloads-folder"><i class="fa fa-check"></i><b>11.2</b> Running in the downloads folder</a><ul>
<li class="chapter" data-level="11.2.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix-1"><i class="fa fa-check"></i><b>11.2.1</b> Fix</a></li>
</ul></li>
<li class="chapter" data-level="11.3" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#admin-permission-needed"><i class="fa fa-check"></i><b>11.3</b> Admin permission needed</a><ul>
<li class="chapter" data-level="11.3.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix-2"><i class="fa fa-check"></i><b>11.3.1</b> Fix</a></li>
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<li class="chapter" data-level="11.4" 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>11.4</b> MacOS won’t allow YASARA to run because not from App Store</a><ul>
<li class="chapter" data-level="11.4.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix-3"><i class="fa fa-check"></i><b>11.4.1</b> Fix</a></li>
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<li class="chapter" data-level="11.5" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#menu-bar-disappears"><i class="fa fa-check"></i><b>11.5</b> Menu bar disappears</a><ul>
<li class="chapter" data-level="11.5.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix-4"><i class="fa fa-check"></i><b>11.5.1</b> Fix</a></li>
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<li class="chapter" data-level="11.6.1" data-path="errors-and-quirks.html"><a href="errors-and-quirks.html#fix-5"><i class="fa fa-check"></i><b>11.6.1</b> Fix</a></li>
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<div id="manage" class="section level1">
<h1><span class="header-section-number">Chapter 10</span> Data Management</h1>
<p><em>Adapted from the guides of Y. Shorish for CHEM361 by C. Berndsen</em></p>
<p>The descriptions below are a more general guide to file naming and data management using in the Biochemistry class at JMU. For YASARA specific suggestions see <a href="the-yasara-user-interface.html#datam">2.6.1</a>. For those that wish to use this in a class assignment, a suggested assignment can be found <a href="https://osf.io/d3esr/">here</a>.</p>
<div id="introduction-to-the-problem" class="section level2">
<h2><span class="header-section-number">10.1</span> Introduction to the problem</h2>
<p>We all have had the problem of saving a file and then having to find that file a year or more later. Once we find where we stored the file and what we named it, we then have to figure out what we did. While this is annoying, the rise of search engines that can search within files has reduced the time spent trying to find a file.</p>
<p>Now imagine you are trying to find a file on someone else’s computer…
The challenges would be:</p>
<ul>
<li><p>How does this person organize (or not) their files?</p></li>
<li><p>What format did they save the data in?</p></li>
<li><p>When you find the file, how is the file organized and what does it mean?</p></li>
</ul>
<p>The rise of electronic data and open data practices has led to an increase in the need for best practices when recording data. Data files should be easy to read for both humans and computers as well as should be stored and named in a fashion that is easy to follow for the experimenter but also those who might use the data at a later date.</p>
</div>
<div id="what-are-data" class="section level2">
<h2><span class="header-section-number">10.2</span> What are Data?</h2>
<p>There are many possible definitions, we will consider any structure, image, number/measurement, or observation as data.</p>
</div>
<div id="effective-file-naming" class="section level2">
<h2><span class="header-section-number">10.3</span> Effective File naming</h2>
<p>Using descriptive file names is a simple way to organize even cluttered data for you and others. At minimum, a good file name conveys the contents of the file, the creator, the version, and creation date. Other useful information can also be included as indicated below, however the key is to be consistent.</p>
<div id="information-to-consider-including-in-file-names" class="section level3">
<h3><span class="header-section-number">10.3.1</span> Information to consider including in file names</h3>
<ol style="list-style-type: decimal">
<li>Project or experiment name or acronym</li>
</ol>
<p><em>(e.g. NMR, LakotaInterview, bacteria_resist)</em></p>
<ol start="2" style="list-style-type: decimal">
<li>Researcher name/initials</li>
</ol>
<p><em>(e.g. Jones, CB, KTLV)</em></p>
<ol start="3" style="list-style-type: decimal">
<li>Date or date range of experiment</li>
</ol>
<p><em>(e.g. YYYYMMDD or YYMMDD)</em></p>
<ol start="4" style="list-style-type: decimal">
<li>Type of data</li>
</ol>
<p><em>(e.g. analysis, PCR, live_counts, density)</em></p>
<ol start="5" style="list-style-type: decimal">
<li>Version number of file</li>
</ol>
<p><em>(e.g. v1 – this is useful when multiple versions occur on the same day and the date field cannot disambiguate)</em></p>
<ol start="6" style="list-style-type: decimal">
<li>Three-letter file extension for application</li>
</ol>
<p><em>(e.g. .docx, .tiff, .pdb. Some operating systems mask this by default, which is unadvisable)</em></p>
<div id="other-tips-for-file-naming" class="section level4">
<h4><span class="header-section-number">10.3.1.1</span> Other tips for file naming</h4>
<ol style="list-style-type: decimal">
<li><p>A good format for dates is YYYYMMDD (or YYMMDD). This makes sure all your files stay in chronological order, across years.</p></li>
<li><p>Don’t make file names longer than ~10 characters; longer names do not work well with all types of software.</p></li>
<li><p>Special characters should be avoided, such as: ~! @ # $ % ^ & * ( ) ` ; < > ? , <a href="analysis.html#section"></a> { } ‘ ”</p></li>
<li><p>For sequential numbering, use leading zeroes to ensure files sort properly. For example, use “0001, 0002…1001, etc” instead of “1, 2…1001, etc.”</p></li>
<li><p>Do not use spaces; they are not recognized by some software. Instead, use underscores (file_name), dashes (file-name), no separation (filename), or camel case (FileName).</p></li>
</ol>
</div>
</div>
</div>
<div id="organizing-files" class="section level2">
<h2><span class="header-section-number">10.4</span> Organizing files</h2>
<div id="use-sub-folders" class="section level3">
<h3><span class="header-section-number">10.4.1</span> Use sub-folders</h3>
<p>Having all the data and analysis in the same folder can be overwhelming, especially on the first glance through a data folder. Creating sub-folders which organize data by experiment type is highly recommended along with further sub-sub folders by date or analysis type or sample name as shown in Figure <a href="manage.html#fig:subfolder">10.1</a>. This is only one organization approach, however any method of organization should be accessible to anyone (including future you).</p>
<div class="figure"><span id="fig:subfolder"></span>
<img src="images/sub-folders.png" alt="One way to organize data in folders" width="120%" />
<p class="caption">
Figure 10.1: One way to organize data in folders
</p>
</div>
</div>
<div id="separate-raw-data-from-analysis-files" class="section level3">
<h3><span class="header-section-number">10.4.2</span> Separate raw data from analysis files</h3>
<p>Data are precious and there should be limited or no changes to the raw files. While Excel and other programs make it easy to do plotting and math in the raw data files or to annotate directly on an image file, <strong>do not do this</strong>. Always create a separate file which is the working copy so that in the event you need to redo the analysis or the file gets corrupted, the raw data are still pristine and ready for new use.</p>
</div>
</div>
<div id="data-and-file-naming-dictionary" class="section level2">
<h2><span class="header-section-number">10.5</span> Data and File Naming Dictionary</h2>
<p>Once you have named your file, how do you guide users (sometimes including yourself!) about what your file names and abbreviations mean? This is the function of a data dictionary. This is most often a README.txt file in your directory that explains your naming convention, along with any abbreviations or codes you have used. This could be captured in a Wiki on OSF as well.</p>
<p>Another use of the Data Dictionary is to help users once the file is open. If you have a spreadsheet containing numbers, describe what each column of data show along with any other information needed to read the file. This can include units of numbers, calculations used to derive or transform information, what NA or blanks mean, and any shorthand/abbreviations that might be in the data.</p>
</div>
<div id="data-management-plan" class="section level2">
<h2><span class="header-section-number">10.6</span> Data Management Plan</h2>
<p>While described last, the data management plan should be one of the first steps in the research process as it lays out the organization of the results. Investing time on the front end of the project to think about how data will be stored and organized will save a lot of time at the end of the project when you have to start interpreting results and drawing conclusions. Trying to find the “good” results in a mess of files is not fun and can lead to lots of unnecessary stress.</p>
<p>An example data management plan for a set of biochemical and computational experiments is shown <a href="https://github.com/CEBerndsen/YASARA-guide/blob/master/docs/DataManagementPlanex.pdf">here</a>.</p>
<div id="data-management-plan-questions-for-students-in-biochemistry-class" class="section level3">
<h3><span class="header-section-number">10.6.1</span> Data Management Plan questions for students in Biochemistry class:</h3>
<div id="types-of-data" class="section level4">
<h4><span class="header-section-number">10.6.1.1</span> Types of Data</h4>
<ol style="list-style-type: decimal">
<li>What data will be generated in the research?</li>
</ol>
<pre><code>– Is it sequence data? Sensor readings? Observational data? Environmental information? Structural models?</code></pre>
<ol start="2" style="list-style-type: decimal">
<li>What data types will you be creating or capturing?</li>
</ol>
<pre><code>– Actual data types here: textual data, image data, tabular, sound, structural…
- How will you collect or create the data?
– Handwritten field notes transcribed to Excel, downloads from instruments, recorded on a device, typed into a text document, written in Python…
- If you will be using existing data, state this and include how you will obtain it.
– Are you pulling from Uniprot, Ensembl, RCSB PDB or other existing data repository?
- How will the data be processed?
– What software will you be using to process the data: Excel, YASARA, R, ATSAS, Coot, PHENIX, Hadoop, ROOT, etc.</code></pre>
</div>
<div id="standards-for-data" class="section level4">
<h4><span class="header-section-number">10.6.1.2</span> Standards for Data</h4>
<ol style="list-style-type: decimal">
<li>Which file formats will you use for your data, and why?</li>
</ol>
<pre><code>- It is best here to use non-proprietary formats. Example: CSV instead of XLSX, TXT instead of DOCX. If it is necessary to use a proprietary format, explain why.</code></pre>
<ol start="2" style="list-style-type: decimal">
<li>What form will the metadata describing/documenting your data take?</li>
</ol>
<pre><code>– This is your data dictionary and the details that you will record therein. </code></pre>
<ol start="3" style="list-style-type: decimal">
<li>How will you create or capture these details?</li>
</ol>
<pre><code>– Will this be captured as a data dictionary in a spreadsheet? As a separate file? Will each data set have a separate file, or will you create one ‘master’ README? </code></pre>
<ol start="4" style="list-style-type: decimal">
<li>What contextual details (metadata) are needed to make the data you capture or collect meaningful?</li>
</ol>
<pre><code>– Essentially what methods are necessary to reproduce your data.</code></pre>
</div>
<div id="how-will-you-share-your-data" class="section level4">
<h4><span class="header-section-number">10.6.1.3</span> How will you share your data?</h4>
<ol style="list-style-type: decimal">
<li><a href="osf.io">Open Science Framework</a></li>
</ol>
<pre><code>- This is set for this course but for other research would be dependent on standards for the field/discipline.
- In biochemistry, the [RCSB PDB](rcsb.org), [BMRB](http://www.bmrb.wisc.edu/), or [SASBDB](https://www.sasbdb.org/) are examples of data sharing platforms that are required for publication of biomolecule structure data.</code></pre>
</div>
<div id="policies-for-re-use-and-redistribution" class="section level4">
<h4><span class="header-section-number">10.6.1.4</span> Policies for re-use and redistribution</h4>
<ol style="list-style-type: decimal">
<li><p>Open access with attribution (CC-BY-4.0)
- This is set for this course but for other research would be dependent on standards for the field/discipline.</p></li>
<li><p>You can set your re-use policy depending on your feelings about sharing and the type of data involved. There are many types of licenses. See here() for details.</p></li>
</ol>
</div>
<div id="plans-for-archiving-and-preservation" class="section level4">
<h4><span class="header-section-number">10.6.1.5</span> Plans for archiving and preservation</h4>
<ol style="list-style-type: decimal">
<li>Open Science Framework</li>
</ol>
<pre><code>- This is set for this course but for other research would be dependent on standards for the field/discipline.
- Your instructor backs all data up to a second cloud-based source and a local hard drive.</code></pre>
<ol start="2" style="list-style-type: decimal">
<li>Think about how file formats change over time (example. Word doc vs. Word docx). You want to store your data in the most compatible format for use by future users. This is one reason why .csv and .txt are preferred to Microsoft formats. Microsoft may not exist in 20 years!</li>
</ol>
</div>
</div>
</div>
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