introToProtStructWithChimeraBuddCT2014.html

<h1 id="embo-practical-course-on-computational-analysis-of-protein-protein-interactions-from-sequences-to-networks">EMBO Practical Course on Computational analysis of protein-protein interactions: From sequences to networks</h1>
<h2 id="september---3-october-2014-uct-cape-town-south-africa">28 September - 3 October 2014, UCT, Cape Town, South Africa</h2>
<h2 id="aidan-budd-embl-heidelberg">Aidan Budd, EMBL, Heidelberg</h2>
<h2 id="presentation"><a href="./presentations/introToProtStructBuddCTSept2014.pdf">Presentation</a></h2>
<h3 id="introduction-to-protein-structure-with-chimera-tuesday-30th-september-2014">Introduction to protein structure with Chimera, Tuesday 30th September 2014</h3>
<h4 id="useful-links-for-working-with-chimera">Useful links for working with Chimera</h4>
<ul class="incremental">
<li>The <a href="https://www.cgl.ucsf.edu/chimera/">Chimera homepage</a></li>
<li>Chimera's &quot;Getting Started&quot; page <a href="https://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html0">on the Chimera website</a> and a <a href="./staticVersionsOfRemotePages/2014_09_27_GettingStartedWithChimera.html">local copy</a></li>
<li>Chimera <a href="./staticVersionsOfRemotePages/chimera_quickref.pdf">&quot;Quick Reference&quot;</a></li>
<li>There is also documentation bundled with the Chimera version you're running on your computer - to quite <a href="https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/">this page in the Chimera User Guide</a>: &quot; Chimera documentation, including the User's Guide, is bundled with each download. Your local copy of the documentation can be accessed and searched from the Chimera Help menu. We recommend using the bundled documentation because it is synchronized with your installed version of Chimera. Latest production release and development versions of the User's Guide are available from the Chimera home page documentation index. Please see the Chimera home page for other types of information. &quot;</li>
</ul>
<h4 id="chimera-demo">Chimera demo</h4>
<p>We'll demo for you how to do the following things in Chimera</p>
<ul class="incremental">
<li>load structures into Chimera</li>
<li>change colour and representation and orientation and zoom level of structures</li>
<li>select, and then visualise differently, different polypeptide chains differently so the PPIs can be easily seen</li>
<li>show backbone and surface at the same time, with transparent surface</li>
<li>indicate H-bonds between the peptide chains</li>
</ul>
<h4 id="chierma-exercises">Chierma exercises</h4>
<p>Use the PDB website to identify and download locally PDB files containing:</p>
<ul class="incremental">
<li>a single polypeptide chain</li>
<li>multiple polypeptide chains</li>
<li>at least one phosphorylated aminoacid residue</li>
<li>only alpha-helices, no beta strands</li>
<li>only beta-strands, no alpha-helices</li>
</ul>
<p>Create figures that illustrate these different things nicely.</p>