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<h1>Vector field visualization of a normal mode (using Chimera)<a class="headerlink" href="#vector-field-visualization-of-a-normal-mode-using-chimera" title="Permalink to this headline">ΒΆ</a></h1>
<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
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47</pre></div></td><td class="code"><div class="highlight"><pre><span class="c"># Example: Vector field visualization of the slowest normal mode of insulin.</span>
<span class="c">#</span>
<span class="c"># This example shows the use of vector fields in the analysis and</span>
<span class="c"># visualization of collective motions. For a more elaborate application,</span>
<span class="c"># see</span>
<span class="c"># A. Thomas, K. Hinsen, M.J. Field, D. Perahia</span>
<span class="c"># Tertiary and quaternary confrmational changes in aspartate</span>
<span class="c"># transcarbamylase: a normal mode study.</span>
<span class="c"># Proteins, 34(1), 96-112 (1999)</span>
<span class="c">#</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">MMTK.Proteins</span> <span class="kn">import</span> <span class="n">Protein</span>
<span class="kn">from</span> <span class="nn">MMTK.NormalModes</span> <span class="kn">import</span> <span class="n">EnergeticModes</span>
<span class="kn">from</span> <span class="nn">MMTK.ForceFields</span> <span class="kn">import</span> <span class="n">CalphaForceField</span>
<span class="kn">from</span> <span class="nn">MMTK.Field</span> <span class="kn">import</span> <span class="n">AtomicVectorField</span>
<span class="kn">from</span> <span class="nn">MMTK.Database</span> <span class="kn">import</span> <span class="n">PDBPath</span>
<span class="kn">from</span> <span class="nn">Scientific.Visualization</span> <span class="kn">import</span> <span class="n">Chimera</span>
<span class="kn">import</span> <span class="nn">chimera</span>
<span class="c"># Load the molecule into Chimera</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">PDBPath</span><span class="p">(</span><span class="s">"insulin.pdb"</span><span class="p">)</span>
<span class="n">chimera</span><span class="o">.</span><span class="n">runCommand</span><span class="p">(</span><span class="s">"open pdb:</span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">filename</span><span class="p">)</span>
<span class="c"># Create a simulation universe containing the protein</span>
<span class="n">universe</span> <span class="o">=</span> <span class="n">InfiniteUniverse</span><span class="p">(</span><span class="n">CalphaForceField</span><span class="p">())</span>
<span class="n">universe</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">Protein</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="s">'calpha'</span><span class="p">))</span>
<span class="c"># Calculate normal modes</span>
<span class="n">modes</span> <span class="o">=</span> <span class="n">EnergeticModes</span><span class="p">(</span><span class="n">universe</span><span class="p">)</span>
<span class="c"># Create the vector field corresponding to the first non-zero mode</span>
<span class="c"># using a grid spacing of 0.5 nm.</span>
<span class="n">field</span> <span class="o">=</span> <span class="n">AtomicVectorField</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="n">modes</span><span class="p">[</span><span class="mi">6</span><span class="p">])</span>
<span class="c"># Create graphics objects for the vector fields.</span>
<span class="c"># The arrows are yellow and their lengths are multiplied by 80.</span>
<span class="c"># Only displacement vectors of lengths between 0. and 0.01 will be shown.</span>
<span class="c"># (This restriction is not necessary for this example, but used for</span>
<span class="c"># illustration.)</span>
<span class="n">graphics</span> <span class="o">=</span> <span class="n">field</span><span class="o">.</span><span class="n">graphicsObjects</span><span class="p">(</span><span class="n">color</span><span class="o">=</span><span class="s">'yellow'</span><span class="p">,</span>
<span class="n">scale</span><span class="o">=</span><span class="mf">80.</span><span class="p">,</span> <span class="nb">range</span><span class="o">=</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span> <span class="mf">0.01</span><span class="p">),</span>
<span class="n">graphics_module</span><span class="o">=</span><span class="n">Chimera</span><span class="p">)</span>
<span class="c"># Display in Chimera. The scale factor is necessary because MMTK</span>
<span class="c"># uses nm whereas Chimera works in Angstrom.</span>
<span class="n">Chimera</span><span class="o">.</span><span class="n">Scene</span><span class="p">(</span><span class="n">graphics</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s">"first mode"</span><span class="p">,</span>
<span class="n">scale</span><span class="o">=</span><span class="mf">1.</span><span class="o">/</span><span class="n">Units</span><span class="o">.</span><span class="n">Ang</span><span class="p">)</span><span class="o">.</span><span class="n">view</span><span class="p">()</span>
</pre></div>
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