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janash committed Jul 2, 2024
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8 changes: 4 additions & 4 deletions chapters/Creating_Plots_in_Jupyter_Notebooks.html
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Expand Up @@ -465,7 +465,7 @@ <h2>Using Matplotlib.pyplot<a class="headerlink" href="#using-matplotlib-pyplot"
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Expand All @@ -481,7 +481,7 @@ <h2>Using Matplotlib.pyplot<a class="headerlink" href="#using-matplotlib-pyplot"
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10 changes: 5 additions & 5 deletions chapters/binding_site_investigation.html
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Expand Up @@ -470,7 +470,7 @@ <h2>View the structure<a class="headerlink" href="#view-the-structure" title="Li
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<p>Text here about NGLView</p>
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<p>This view looks a bit messy. MDAnalysis has a human readable <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/selections.html">selection syntax</a>
that allows us to isolate parts of our structure. We will take our MDAnalysis Universe (the variable <code class="docutils literal notranslate"><span class="pre">u</span></code>) and use the <code class="docutils literal notranslate"><span class="pre">select_atoms</span></code> function.
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<p>Upon viewing this structure, you will notice that our ligand seems to appear twice.
If you open the PDB file to investigate, you will see the following in the ligand section:</p>
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<p>When we inspect the ligand in the binding site, we notice a few things.
First, the binding site has a large hydrophobic area on the surface.
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Expand Up @@ -557,7 +557,7 @@ <h2>The Michaelis-Menten equation<a class="headerlink" href="#the-michaelis-ment
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Expand Up @@ -680,7 +680,7 @@ <h2>PDB Search API<a class="headerlink" href="#pdb-search-api" title="Link to th
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