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Setting-up and customizing UCSF Chimera - Part 2
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<p>This is the second post of the multi-part blog series on setting up and running UCSF Chimera.</p>
<p>The <a href="https://marpat.github.io/chimera-intro.html">previous</a> article featured a general overview, installation, and several visual examples of UCSF Chimera. Detailed instructions for installation on Windows 10 and Linux Mint were also provided. </p>
<p>In this part, we will go through <u>setup</u>, customization of <u>Tools and layout</u>, and the <u>first run</u> of the Chimera application. We will also get into the writing and using <u>scripts</u> and <u>keyboard shortcuts</u>.</p>
<h2>Customize the Chimera Launch</h2>
<p>Before running Chimera, I recommend a minor customization of options and paths such that it will launch with some features and attributes already enabled and set.</p>
<ul>
<li>right-mouse click on the Chimera's Desktop icon and select <code>Properties</code> (at the bottom)</li>
<li>append <code>--bgopacity</code> option to the <code>Target</code> field and ~/Desktop path to the <code>Start in:</code> field (see <strong>Figure 1</strong>)</li>
<li>click OK</li>
</ul>
<p>What the above steps accomplished is that, first, any exported image (tiff or png) will have a transparent background (this is optional and can be changed later during image export). Second, the Chimera will now be looking for any custom (Python) script files (e.g., <code>style.py</code>) at your Desktop. An example of such a script file is <a href="#style">below</a>.</p>
<p><div class="img-fluid" style="max-width: 100%" markdown='2'>
<img alt="Chimera icon properties" src="../images/chimera/icon-properties.png" title="Fig. 1.">
</div><br>
<p style="margin: 10px 0 30px 10px; width:100%"><em>Fig. 1. Customization of Chimera's launch options under "icon" Properties.</em> </p></p>
<p>Now, when you double-click the Chimera icon on the Desktop (or type >chimera in your terminal), the application will launch and present a window shown in <strong>Figure 2</strong>. If you do not see such a layout, click the "lightning-bolt" toggle icon in the bottom-right section. <img alt="lightning-bolt alt >" src="../images/chimera/lb-icons.png"></p>
<div class="img-fluid" style="max-width: 100%">
<p><img alt="Chimera startup interface" src="../images/chimera/firstrun.png" title="Fig. 2."></p>
</div>
<p><p style="margin: 10px 0 30px 10px; width:100%"><em>Fig. 2. Chimera's GUI layout after the first launch.</em> </p></p>
<p><a name="pka"></a></p>
<div class="alert alert-success role="alert"">
<b>CHECK YOUR SETUP:</b> as an example, go to File → Fetch by ID... and enter `1ATP` into the PBD field. Assuming that your Internet connection is working, structure of PKA kinase will be loaded into the main space.<br>
Go to File → Close Session to have the workspace back in the initial state.</div>
<p>Let's continue with basic and custom settings that will persist for all Chimera sessions.</p>
<h2>Chimera settings</h2>
<p>Chimera is highly customizable, and having a toolbar of "preset" icons, buttons, and tools becomes a great convenience. Most settings are activated from the menu item <code>Favorites → Preferences</code> located at the top of the GUI <strong>(Fig. 2</strong>). Below are the settings that I found useful in my work. Different settings panels are available from the pull-down menu next to <code>Category:</code></p>
<ul>
<li>Category: <strong>General</strong> → Initial window size: remember last</li>
<li>Category: <strong>PDB</strong> - add the path to the folder of your .pdb files (optional)</li>
<li>Category: <strong>Tools</strong> - I recommend starting with selections, as shown in <strong>Fig. 3</strong>. Also, in the <code>On Toolbar</code> column, I checked <code>2D Labels</code>, <code>PseudoBond Reader</code>, <code>FindHBond</code>, <code>Find Clashes/Contacts</code>, <code>Distances</code>, <code>ViewDock, Dock Prep, AutoDock Vina</code>, <code>AddH</code>, <code>Reply Log</code></li>
</ul>
<div class="img-fluid" style="max-width: 100%">
<p><img alt="Chimera setting preferences" src="../images/chimera/preferences.png" title="Fig. 3."></p>
</div>
<p><p style="margin: 10px 0 30px 10px; width:100%"><em>Fig. 3. The main area for setting Chimera's Tools.</em> </p></p>
<p>At this point, you should see new buttons (icons) in the toolbar. I keep it positioned on the left, although <strong>Figure 4</strong>. shows it horizontal.</p>
<div class="img-fluid" style="max-width: 100%">
<p><img alt="Chimera setting preferences" src="../images/chimera/toolbar.png" title="Fig. 4."></p>
</div>
<p><p style="margin: 10px 0 30px 10px; width:100%"><em>Fig. 4. Customized toolbar with shortcut buttons.</em> </p></p>
<p>To change the order of buttons in the Toolbar, go to ~/.chimera folder (Win10: C:\Users\USERNAME\AppData\Roaming\.chimera, Linux: $HOME/.chimera), open the <code>preferences</code> file, and manually edit the (order) numbers next to each Tool in the <code>onToolbar</code> section.</p>
<h3>Plugins</h3>
<p>At the bottom of the <code>Preferences</code> window, there is an area for entering path to Chimera plugins (<strong>Fig. 3</strong>). Plugins can be downloaded from <a href="https://www.cgl.ucsf.edu/chimera/plugins/plugins.html">various sites</a> and are typically free to use. My favorite plugins are:</p>
<ul>
<li><a href="http://insilab.org/probis-plugin/">Probis Plugin</a> - Allows prediction of binding sites and their corresponding ligands for a given protein structure. Conceptually, it is similar to <code>SiteMap</code> in the <a href="https://www.schrodinger.com/maestro">Maestro</a> module from <a href="https://www.schrodinger.com/pymol" target="_blank"> Schrödinger</a>.</li>
<li><a href="https://github.com/josan82/Chimera_BILD">Chimera-BILD</a> - An extension allowing to draw arrows, spheres, boxes, etc. with customizable colors and transparency. The plugin was build by <a href="https://github.com/josan82">José Emilio Sánchez Aparicio</a> and is available at the GitHub.</li>
</ul>
<p>A typical way of installing a plugin is to download it from the author's website (or GitHub). Download the <code>.zip</code> file and place it to a directory where you keep your Chimera plugins (in my case, F:\Computation\chimera). Unzip the downloaded file (use 'extract here'). The folder structure is shown in <strong>Figure 5</strong>. Then in <code>Favorites → Preferences: Tools</code>, click <code>Add</code> and browse to the plugin directory, select the top-level plugin folder ('bild_shapes' in <strong>Fig. 3</strong>) and click <code>Open</code>.</p>
<div class="img-fluid" style="max-width: 100%">
<p><img alt="Chimera setting preferences" src="../images/chimera/plugins.png" title="Fig. 5."></p>
</div>
<p><p style="margin: 10px 0 30px 10px; width:100%"><em>Fig. 5. A typical hierarchy of plugin files.</em> </p></p>
<p>Close and restart Chimera and make sure that the new Toolbar with buttons and Command line are visible and that Plugins are loaded.</p>
<p><a name="style"></a></p>
<p><br/></p>
<h4><font color=magenta><strong><em>Advanced custom options - midasrc and style.py script</em></strong></font></h4>
<p>I prefer including more advanced topics right into the basic description, because once you start mastering the subject, you can still review the basic material all in one place.</p>
<div class="text-center"> [<i>This whole section can be skipped if you find it too overwhelming</i>]</div>
<p><br/></p>
<p>For the Chimera initial settings, we will make use of <u>two files that store custom presets and actions</u>. The first one is <code>midasrc</code>, which has to be created first. On Windows, head to <code>C:/Users/USERNAME</code> and create a new folder <code>.chimera</code>. On the Linux system, head to <code>$HOME/.chimera</code> folder. Now, on either OS and in the folder <code>.chimera</code>, create a new text document. Save the empty document as <code>midarsrc</code>. Copy/paste the text below and save the file again.</p>
<div class="highlight"><pre><span></span><code><span class="c1"># midasrc in ~./chimera</span>
<span class="c1"># Accelerators - enable keybord shortcuts as per</span>
<span class="c1"># https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/alist.html</span>
<span class="n">ac</span>
<span class="c1"># Define an alias and then call it from Command line as >style</span>
<span class="n">alias</span> <span class="n">style</span> <span class="n">run</span> <span class="n">C</span><span class="p">:</span><span class="o">/</span><span class="n">Users</span><span class="o">/</span><span class="n">Public</span><span class="o">/</span><span class="n">Desktop</span><span class="o">/</span><span class="n">style</span><span class="o">.</span><span class="n">py</span> <span class="c1"># on Windows</span>
<span class="c1"># alias style ~/Desktop/style.py # on Linux</span>
</code></pre></div>
<p>Upon launching the Chimera, the file will be read first and options applied to our project.</p>
<div class="notetip">
Note that in the dialog Favorites → Preferences: Command Line, the default preset path to file midasrc points to ~/.chimera, which on Windows expands to C:\Users\USER\.chimera. However, during the installation, Chimera creates the .chimera folder at C:\Users\USERNAME\AppData\Roaming\.chimera. That is why, we have to create one more folder `.chimera` and place the midasrc file into it.
</div>
<p>A handy feature of Chimera, that is the keyboard shortcuts (accelerators), has now been activated. The full list is maintained <a href="https://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/accelerators/alist.html">here</a>.</p>
<p>To use those shortcuts, have a protein or model loaded in the main space, place the mouse cursor in the same area, and type the command on your keyboard as a sequence of two keystrokes. My favorite commands are:</p>
<ul>
<li><code>c2</code> (color by secondary structure)</li>
<li><code>hs</code> or <code>sf</code> (hide or show surface)</li>
<li><code>wb</code> (white background) and <code>bk</code> to get back to black background</li>
<li><code>wr</code> (wire representation), <code>bs</code> (ball and stick representation) - works also for selections</li>
</ul>
<p>To further standardize and customize the initial visualization of proteins and molecules, I use the <code>style.py</code> script. This Python script is on my Desktop - <code>C:\Users\Public\Desktop</code> (notice the option Start in: in <strong>Fig. 1</strong>) and can be called from Chimera's Command line <strong>AFTER</strong> the protein/model is loaded like so:</p>
<div class="highlight"><pre><span></span><code>>style
or
>run style.py
</code></pre></div>
<div class="note">
<div class="notetip">
Note that on Windows, the path to the desktop contains `Public` not your `USERNAME`. If you simply drag and drop the style.py on your Desktop, Chimera won't be able to read it. Use File Explorer to navigate to C:\Users\Public\Desktop and paste the file there. It will appear on the Desktop as usual. You also want to change privileges of that file for all users.
</div>
</div>
<p>Copy the script below and paste it into a new text document. Save it to your ~\Public\Desktop folder as <code>style.py</code>. Your <code>midasrc</code> alias is already set to point to it. As your tasks evolve, add more commands to the script.</p>
<div class="highlight"><pre><span></span><code><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">from</span> <span class="nn">chimera</span> <span class="kn">import</span> <span class="n">runCommand</span> <span class="k">as</span> <span class="n">rc</span> <span class="c1"># Use 'rc' as shorthand for runCommand</span>
<span class="kn">from</span> <span class="nn">chimera</span> <span class="kn">import</span> <span class="n">replyobj</span> <span class="c1"># For emitting status messages</span>
<span class="c1"># run as >read style.py or >style (if alias exists)</span>
<span class="c1"># Labels</span>
<span class="n">rc</span><span class="p">(</span><span class="s2">"labelopt resinfo %(1-letter code)s</span><span class="si">%(number)s</span><span class="s2">"</span><span class="p">)</span>
<span class="n">rc</span><span class="p">(</span><span class="s2">"color hot pink,lr"</span><span class="p">)</span>
<span class="c1">#Set visualization</span>
<span class="n">rc</span><span class="p">(</span><span class="s2">"preset apply interactive 1"</span><span class="p">)</span> <span class="c1"># change later by keyboard c2</span>
<span class="n">rc</span><span class="p">(</span><span class="s2">"~longbond"</span><span class="p">)</span> <span class="c1"># remove dotted connectors of disconnected chains</span>
<span class="c1"># Background</span>
<span class="c1">#rc("set bg_color white")</span>
<span class="c1"># Orientation</span>
<span class="n">rc</span><span class="p">(</span><span class="s2">"focus"</span><span class="p">)</span>
<span class="c1"># Rendering of ligands</span>
<span class="n">rc</span><span class="p">(</span><span class="s2">"represent wire"</span><span class="p">)</span>
<span class="n">rc</span><span class="p">(</span><span class="s2">"color byelement"</span><span class="p">)</span>
<span class="n">rc</span><span class="p">(</span><span class="s2">"setattr m stickScale 0.62"</span><span class="p">)</span>
<span class="n">rc</span><span class="p">(</span><span class="s2">"setattr m ballScale 0.15"</span><span class="p">)</span>
</code></pre></div>
<p>Re-run the PKA kinase as <a href="#pka">above</a> and type <code>style</code> to the Command line and press enter. Then type the key <code>c</code> , release, and press <code>2</code> while pointing to the main window. Visualization should change and be similar to <strong>Figure 5</strong>.</p>
<div class="img-fluid" style="max-width: 100%">
<p><img alt="Chimera setting preferences" src="../images/chimera/pka.png" title="Fig. 5."></p>
</div>
<p><p style="margin: 10px 0 30px 10px; width:100%"><em>Fig. 5. Rendering of protein kinase A (1ATP.pdb) after loading the file and applying <code>style</code> and <code>c2</code> commands.</em> </p></p>
<p>If the colors of <span class="math">\(\beta\)</span>-strands and <span class="math">\(\alpha\)</span>-helices look different from <strong>Figure 5</strong>, customize your preferred colors. Head to Tools → Depiction → Color Secondary Structure. You should now see the panel shown on the left in <strong>Figure 6</strong>. Double-click each color square, and a new dialog will open (Color Editor). My preferences are:</p>
<p>Helix, green (0, 0.81, 0, 1) (RGBA)</p>
<p>Strand, magenta (0.627, 0.125, 0.941, 1)</p>
<p>Coil, gray (0.745, 0.745, 0.745, 1)</p>
<div class="img-fluid" style="max-width: 100%">
<p><img alt="Chimera color editor" src="../images/chimera/color-editor.png" title="Fig. 6."></p>
</div>
<p><p style="margin: 10px 0 30px 10px; width:100%"><em>Fig. 6. Setting the color preferences for secondary structures.</em> </p></p>
<h3>Next</h3>
<p>After having typical settings, simple scripts, and custom presets in place, the next blog article will focus on practical examples of using Menu options and commands. </p>
<section id="bib"><h2>Notes</h2>
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<h4>Part 2 of the Mastering UCSF Chimera series</h4>
<h5>Previous articles</h5>
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<li><a href="https://marpat.github.io/chimera-intro.html">Introduction to UCSF Chimera - Part 1</a></li>
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<li><a href="https://marpat.github.io/chimera-commands.html">Mastering Menu options and commands in UCSF Chimera - Part 3</a></li>
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