From 438479d9a6448756a44b6185806b5567dfafca73 Mon Sep 17 00:00:00 2001
From: janash <janash@users.noreply.github.com>
Date: Tue, 2 Jul 2024 20:45:05 +0000
Subject: [PATCH] deploy: 1b3b7d52e507dd844226f1343d3ef6b6ca75b803

---
 ...fa7eac8bb03bc68d73d250a2960282cbabfdf5.png | Bin 39452 -> 0 bytes
 ...0921582d686f681160f65fe0c5f8e819d19d96.png | Bin 26097 -> 0 bytes
 ...85d516ae31773f65ba0ba8861e8f33591effd8.png | Bin 0 -> 47962 bytes
 ...26fbcc03e4832803205f2b3d8c36c971e45e48.png | Bin 0 -> 26099 bytes
 .../Creating_Plots_in_Jupyter_Notebooks.html  |   8 +-
 chapters/MolVis_with_iCN3D.html               | 144 +++++++++---------
 chapters/binding_site_investigation.html      |  10 +-
 chapters/nonlinear_regression_part_2.html     |   2 +-
 chapters/rcsb_api.html                        |   4 +-
 searchindex.js                                |   2 +-
 10 files changed, 85 insertions(+), 85 deletions(-)
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diff --git a/chapters/Creating_Plots_in_Jupyter_Notebooks.html b/chapters/Creating_Plots_in_Jupyter_Notebooks.html
index 415d59b..a92e1f6 100644
--- a/chapters/Creating_Plots_in_Jupyter_Notebooks.html
+++ b/chapters/Creating_Plots_in_Jupyter_Notebooks.html
@@ -465,7 +465,7 @@ <h2>Using Matplotlib.pyplot<a class="headerlink" href="#using-matplotlib-pyplot"
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;matplotlib.collections.PathCollection at 0x7fec32370310&gt;
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;matplotlib.collections.PathCollection at 0x7fe8181dcbd0&gt;
 </pre></div>
 </div>
 <img alt="../_images/ceaaf9ece89b08454dd7707908e35945d376737045e460c49eebbcadd1df23cf.png" src="../_images/ceaaf9ece89b08454dd7707908e35945d376737045e460c49eebbcadd1df23cf.png" />
@@ -481,7 +481,7 @@ <h2>Using Matplotlib.pyplot<a class="headerlink" href="#using-matplotlib-pyplot"
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7fec3239e310&gt;]
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7fe8181e9510&gt;]
 </pre></div>
 </div>
 <img alt="../_images/720b0e757eaaa9fb1a4f291e9abd2db1cede159aac7a370b4b02faa4ef0066e2.png" src="../_images/720b0e757eaaa9fb1a4f291e9abd2db1cede159aac7a370b4b02faa4ef0066e2.png" />
@@ -579,7 +579,7 @@ <h2>Scatter Plots with Seaborn<a class="headerlink" href="#scatter-plots-with-se
 <div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;Axes: xlabel=&#39;Protein Concentration (mg/mL)&#39;, ylabel=&#39;A595&#39;&gt;
 </pre></div>
 </div>
-<img alt="../_images/8371472862b2f922bb59a0c77e0921582d686f681160f65fe0c5f8e819d19d96.png" src="../_images/8371472862b2f922bb59a0c77e0921582d686f681160f65fe0c5f8e819d19d96.png" />
+<img alt="../_images/bc36ef4c8e3d0ad87b6d00f65e26fbcc03e4832803205f2b3d8c36c971e45e48.png" src="../_images/bc36ef4c8e3d0ad87b6d00f65e26fbcc03e4832803205f2b3d8c36c971e45e48.png" />
 </div>
 </div>
 <div class="exercise admonition">
@@ -628,7 +628,7 @@ <h2>Scatter Plots with Seaborn<a class="headerlink" href="#scatter-plots-with-se
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../_images/51cf05d799f955c6bc97abcf6bfa7eac8bb03bc68d73d250a2960282cbabfdf5.png" src="../_images/51cf05d799f955c6bc97abcf6bfa7eac8bb03bc68d73d250a2960282cbabfdf5.png" />
+<img alt="../_images/8df5c7f39f20f1dee3db00356185d516ae31773f65ba0ba8861e8f33591effd8.png" src="../_images/8df5c7f39f20f1dee3db00356185d516ae31773f65ba0ba8861e8f33591effd8.png" />
 </div>
 </div>
 <div class="key admonition">
diff --git a/chapters/MolVis_with_iCN3D.html b/chapters/MolVis_with_iCN3D.html
index 7ef7bc0..8228ea0 100644
--- a/chapters/MolVis_with_iCN3D.html
+++ b/chapters/MolVis_with_iCN3D.html
@@ -424,8 +424,8 @@ <h2>Viewing a PDB structure<a class="headerlink" href="#viewing-a-pdb-structure"
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_html"><div id="icn3dviewer1719952653731664" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning1719952653731664" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
+<div class="output text_html"><div id="icn3dviewer17199530845083816" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199530845083816" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
         <tt>jupyter labextension install jupyterlab_3dmol</tt></p>
         </div>
 <script>
@@ -464,8 +464,8 @@ <h2>Viewing a PDB structure<a class="headerlink" href="#viewing-a-pdb-structure"
   css2 = loadCssAsync("https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css");
 }
 
-var viewer1719952653731664 = null;
-var warn = document.getElementById("icn3dwarning1719952653731664");
+var viewer17199530845083816 = null;
+var warn = document.getElementById("icn3dwarning17199530845083816");
 if(warn) {
     warn.parentNode.removeChild(warn);
 }
@@ -474,11 +474,11 @@ <h2>Viewing a PDB structure<a class="headerlink" href="#viewing-a-pdb-structure"
 .then(function() { return css2; })
 .then(function() { return js; })
 .then(function() {
-cfg = {divid: "icn3dviewer1719952653731664", idname: "pdbid", idvalue: "1a0j", pdbid: "1a0j", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '', };
-viewer1719952653731664 = new icn3d.iCn3DUI(cfg);
-viewer1719952653731664.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199530845083816", idname: "pdbid", idvalue: "1a0j", pdbid: "1a0j", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '', };
+viewer17199530845083816 = new icn3d.iCn3DUI(cfg);
+viewer17199530845083816.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fad347d9850&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fd36c6d74d0&gt;
 </pre></div>
 </div>
 </div>
@@ -502,8 +502,8 @@ <h2>Applying the power of python<a class="headerlink" href="#applying-the-power-
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_html"><div id="icn3dviewer17199526537377582" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199526537377582" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
+<div class="output text_html"><div id="icn3dviewer17199530845144548" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199530845144548" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
         <tt>jupyter labextension install jupyterlab_3dmol</tt></p>
         </div>
 <script>
@@ -542,8 +542,8 @@ <h2>Applying the power of python<a class="headerlink" href="#applying-the-power-
   css2 = loadCssAsync("https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css");
 }
 
-var viewer17199526537377582 = null;
-var warn = document.getElementById("icn3dwarning17199526537377582");
+var viewer17199530845144548 = null;
+var warn = document.getElementById("icn3dwarning17199530845144548");
 if(warn) {
     warn.parentNode.removeChild(warn);
 }
@@ -552,11 +552,11 @@ <h2>Applying the power of python<a class="headerlink" href="#applying-the-power-
 .then(function() { return css2; })
 .then(function() { return js; })
 .then(function() {
-cfg = {divid: "icn3dviewer17199526537377582", idname: "pdbid", idvalue: "8gch", pdbid: "8gch", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '', };
-viewer17199526537377582 = new icn3d.iCn3DUI(cfg);
-viewer17199526537377582.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199530845144548", idname: "pdbid", idvalue: "8gch", pdbid: "8gch", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '', };
+viewer17199530845144548 = new icn3d.iCn3DUI(cfg);
+viewer17199530845144548.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fad346203d0&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fd36c6f0e90&gt;
 </pre></div>
 </div>
 </div>
@@ -581,8 +581,8 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_html"><div id="icn3dviewer17199526537467322" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199526537467322" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
+<div class="output text_html"><div id="icn3dviewer17199530845240011" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199530845240011" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
         <tt>jupyter labextension install jupyterlab_3dmol</tt></p>
         </div>
 <script>
@@ -621,8 +621,8 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
   css2 = loadCssAsync("https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css");
 }
 
-var viewer17199526537467322 = null;
-var warn = document.getElementById("icn3dwarning17199526537467322");
+var viewer17199530845240011 = null;
+var warn = document.getElementById("icn3dwarning17199530845240011");
 if(warn) {
     warn.parentNode.removeChild(warn);
 }
@@ -631,11 +631,11 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
 .then(function() { return css2; })
 .then(function() { return js; })
 .then(function() {
-cfg = {divid: "icn3dviewer17199526537467322", idname: "pdbid", idvalue: "1mbo", pdbid: "1mbo", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'style proteins cylinder and plate', };
-viewer17199526537467322 = new icn3d.iCn3DUI(cfg);
-viewer17199526537467322.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199530845240011", idname: "pdbid", idvalue: "1mbo", pdbid: "1mbo", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'style proteins cylinder and plate', };
+viewer17199530845240011 = new icn3d.iCn3DUI(cfg);
+viewer17199530845240011.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fad3462fe90&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fd36c6fd910&gt;
 </pre></div>
 </div>
 </div>
@@ -649,8 +649,8 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_html"><div id="icn3dviewer17199526537524993" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199526537524993" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
+<div class="output text_html"><div id="icn3dviewer17199530845298953" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199530845298953" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
         <tt>jupyter labextension install jupyterlab_3dmol</tt></p>
         </div>
 <script>
@@ -689,8 +689,8 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
   css2 = loadCssAsync("https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css");
 }
 
-var viewer17199526537524993 = null;
-var warn = document.getElementById("icn3dwarning17199526537524993");
+var viewer17199530845298953 = null;
+var warn = document.getElementById("icn3dwarning17199530845298953");
 if(warn) {
     warn.parentNode.removeChild(warn);
 }
@@ -699,11 +699,11 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
 .then(function() { return css2; })
 .then(function() { return js; })
 .then(function() {
-cfg = {divid: "icn3dviewer17199526537524993", idname: "pdbid", idvalue: "1mbo", pdbid: "1mbo", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'style proteins cylinder and plate; style chemicals ball and stick', };
-viewer17199526537524993 = new icn3d.iCn3DUI(cfg);
-viewer17199526537524993.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199530845298953", idname: "pdbid", idvalue: "1mbo", pdbid: "1mbo", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'style proteins cylinder and plate; style chemicals ball and stick', };
+viewer17199530845298953 = new icn3d.iCn3DUI(cfg);
+viewer17199530845298953.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fad34631690&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fd36c700bd0&gt;
 </pre></div>
 </div>
 </div>
@@ -720,8 +720,8 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_html"><div id="icn3dviewer17199526537582283" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199526537582283" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
+<div class="output text_html"><div id="icn3dviewer17199530845362904" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199530845362904" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
         <tt>jupyter labextension install jupyterlab_3dmol</tt></p>
         </div>
 <script>
@@ -760,8 +760,8 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
   css2 = loadCssAsync("https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css");
 }
 
-var viewer17199526537582283 = null;
-var warn = document.getElementById("icn3dwarning17199526537582283");
+var viewer17199530845362904 = null;
+var warn = document.getElementById("icn3dwarning17199530845362904");
 if(warn) {
     warn.parentNode.removeChild(warn);
 }
@@ -770,11 +770,11 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
 .then(function() { return css2; })
 .then(function() { return js; })
 .then(function() {
-cfg = {divid: "icn3dviewer17199526537582283", idname: "pdbid", idvalue: "1mbo", pdbid: "1mbo", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '; style proteins cylinder and plate; style chemicals ball and stick', };
-viewer17199526537582283 = new icn3d.iCn3DUI(cfg);
-viewer17199526537582283.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199530845362904", idname: "pdbid", idvalue: "1mbo", pdbid: "1mbo", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '; style proteins cylinder and plate; style chemicals ball and stick', };
+viewer17199530845362904 = new icn3d.iCn3DUI(cfg);
+viewer17199530845362904.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fad34633dd0&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fd36c703cd0&gt;
 </pre></div>
 </div>
 </div>
@@ -792,8 +792,8 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_html"><div id="icn3dviewer17199526537636948" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199526537636948" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
+<div class="output text_html"><div id="icn3dviewer17199530845423124" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199530845423124" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
         <tt>jupyter labextension install jupyterlab_3dmol</tt></p>
         </div>
 <script>
@@ -832,8 +832,8 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
   css2 = loadCssAsync("https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css");
 }
 
-var viewer17199526537636948 = null;
-var warn = document.getElementById("icn3dwarning17199526537636948");
+var viewer17199530845423124 = null;
+var warn = document.getElementById("icn3dwarning17199530845423124");
 if(warn) {
     warn.parentNode.removeChild(warn);
 }
@@ -842,11 +842,11 @@ <h2>Adding commands to the icn3dpy.view function<a class="headerlink" href="#add
 .then(function() { return css2; })
 .then(function() { return js; })
 .then(function() {
-cfg = {divid: "icn3dviewer17199526537636948", idname: "pdbid", idvalue: "4hhb", pdbid: "4hhb", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '; style proteins cylinder and plate; style chemicals ball and stick', };
-viewer17199526537636948 = new icn3d.iCn3DUI(cfg);
-viewer17199526537636948.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199530845423124", idname: "pdbid", idvalue: "4hhb", pdbid: "4hhb", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '; style proteins cylinder and plate; style chemicals ball and stick', };
+viewer17199530845423124 = new icn3d.iCn3DUI(cfg);
+viewer17199530845423124.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fad34636250&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fd36c706110&gt;
 </pre></div>
 </div>
 </div>
@@ -876,8 +876,8 @@ <h1>Pulling collections of commands from an iCN3D web page<a class="headerlink"
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_html"><div id="icn3dviewer17199526537694244" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199526537694244" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
+<div class="output text_html"><div id="icn3dviewer1719953084548066" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning1719953084548066" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
         <tt>jupyter labextension install jupyterlab_3dmol</tt></p>
         </div>
 <script>
@@ -916,8 +916,8 @@ <h1>Pulling collections of commands from an iCN3D web page<a class="headerlink"
   css2 = loadCssAsync("https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css");
 }
 
-var viewer17199526537694244 = null;
-var warn = document.getElementById("icn3dwarning17199526537694244");
+var viewer1719953084548066 = null;
+var warn = document.getElementById("icn3dwarning1719953084548066");
 if(warn) {
     warn.parentNode.removeChild(warn);
 }
@@ -926,11 +926,11 @@ <h1>Pulling collections of commands from an iCN3D web page<a class="headerlink"
 .then(function() { return css2; })
 .then(function() { return js; })
 .then(function() {
-cfg = {divid: "icn3dviewer17199526537694244", idname: "mmdbafid", idvalue: "1ETS", mmdbafid: "1ETS", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'load mmdb 1ets | parameters &mmdbid=1ets&bu=1; defined sets; select sets chemicals; set background white; style chemicals ball and stick; set surface wireframe on; set surface wireframe on; style proteins cylinder and plate; style proteins cylinder and plate; defined sets; select sets 1ETS; style proteins cylinder and plate; color secondary structure yellow|||{"factor":"1.000","mouseChange":{"x":"0.000","y":"0.000"},"quaternion":{"_x":"0.000","_y":"0.000","_z":"0.000","_w":"1.000"}}', };
-viewer17199526537694244 = new icn3d.iCn3DUI(cfg);
-viewer17199526537694244.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer1719953084548066", idname: "mmdbafid", idvalue: "1ETS", mmdbafid: "1ETS", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'load mmdb 1ets | parameters &mmdbid=1ets&bu=1; defined sets; select sets chemicals; set background white; style chemicals ball and stick; set surface wireframe on; set surface wireframe on; style proteins cylinder and plate; style proteins cylinder and plate; defined sets; select sets 1ETS; style proteins cylinder and plate; color secondary structure yellow|||{"factor":"1.000","mouseChange":{"x":"0.000","y":"0.000"},"quaternion":{"_x":"0.000","_y":"0.000","_z":"0.000","_w":"1.000"}}', };
+viewer1719953084548066 = new icn3d.iCn3DUI(cfg);
+viewer1719953084548066.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fad34637a50&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fd36c8a8e10&gt;
 </pre></div>
 </div>
 </div>
@@ -955,8 +955,8 @@ <h2>Teasing apart the command set from the <a class="reference external" href="h
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_html"><div id="icn3dviewer17199526537752697" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199526537752697" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
+<div class="output text_html"><div id="icn3dviewer17199530845536928" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199530845536928" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
         <tt>jupyter labextension install jupyterlab_3dmol</tt></p>
         </div>
 <script>
@@ -995,8 +995,8 @@ <h2>Teasing apart the command set from the <a class="reference external" href="h
   css2 = loadCssAsync("https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css");
 }
 
-var viewer17199526537752697 = null;
-var warn = document.getElementById("icn3dwarning17199526537752697");
+var viewer17199530845536928 = null;
+var warn = document.getElementById("icn3dwarning17199530845536928");
 if(warn) {
     warn.parentNode.removeChild(warn);
 }
@@ -1005,11 +1005,11 @@ <h2>Teasing apart the command set from the <a class="reference external" href="h
 .then(function() { return css2; })
 .then(function() { return js; })
 .then(function() {
-cfg = {divid: "icn3dviewer17199526537752697", idname: "mmdbafid", idvalue: "8gch", mmdbafid: "8gch", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'load mmdb8gch| parameters &mmdbid=8gch&bu=1; defined sets; select sets chemicals; set background white; style chemicals ball and stick; set surface wireframe on; set surface wireframe on; style proteins cylinder and plate; style proteins cylinder and plate; defined sets; select sets 1ETS; style proteins cylinder and plate; color secondary structure yellow|||{"factor":"1.000","mouseChange":{"x":"0.000","y":"0.000"},"quaternion":{"_x":"0.000","_y":"0.000","_z":"0.000","_w":"1.000"}}', };
-viewer17199526537752697 = new icn3d.iCn3DUI(cfg);
-viewer17199526537752697.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199530845536928", idname: "mmdbafid", idvalue: "8gch", mmdbafid: "8gch", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'load mmdb8gch| parameters &mmdbid=8gch&bu=1; defined sets; select sets chemicals; set background white; style chemicals ball and stick; set surface wireframe on; set surface wireframe on; style proteins cylinder and plate; style proteins cylinder and plate; defined sets; select sets 1ETS; style proteins cylinder and plate; color secondary structure yellow|||{"factor":"1.000","mouseChange":{"x":"0.000","y":"0.000"},"quaternion":{"_x":"0.000","_y":"0.000","_z":"0.000","_w":"1.000"}}', };
+viewer17199530845536928 = new icn3d.iCn3DUI(cfg);
+viewer17199530845536928.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fad34604dd0&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fd36c6f4c50&gt;
 </pre></div>
 </div>
 </div>
@@ -1045,8 +1045,8 @@ <h1>Creating functions based on preferred command sets generated from iCN3D web
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_html"><div id="icn3dviewer1719952653785767" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning1719952653785767" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
+<div class="output text_html"><div id="icn3dviewer17199530845631418" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199530845631418" style="background-color:#ffcccc;color:black">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason).  You need to install the extension: <br>
         <tt>jupyter labextension install jupyterlab_3dmol</tt></p>
         </div>
 <script>
@@ -1085,8 +1085,8 @@ <h1>Creating functions based on preferred command sets generated from iCN3D web
   css2 = loadCssAsync("https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.css");
 }
 
-var viewer1719952653785767 = null;
-var warn = document.getElementById("icn3dwarning1719952653785767");
+var viewer17199530845631418 = null;
+var warn = document.getElementById("icn3dwarning17199530845631418");
 if(warn) {
     warn.parentNode.removeChild(warn);
 }
@@ -1095,11 +1095,11 @@ <h1>Creating functions based on preferred command sets generated from iCN3D web
 .then(function() { return css2; })
 .then(function() { return js; })
 .then(function() {
-cfg = {divid: "icn3dviewer1719952653785767", idname: "mmdbafid", idvalue: "1ETS", mmdbafid: "1ETS", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'load mmdb1ETS| parameters &mmdbid=1ETS&bu=1; defined sets; select sets chemicals; set background white; style chemicals ball and stick; set surface wireframe on; set surface wireframe on; style proteins cylinder and plate; style proteins cylinder and plate; defined sets; select sets 1ETS; style proteins cylinder and plate; color secondary structure yellow|||{"factor":"1.000","mouseChange":{"x":"0.000","y":"0.000"},"quaternion":{"_x":"0.000","_y":"0.000","_z":"0.000","_w":"1.000"}}', };
-viewer1719952653785767 = new icn3d.iCn3DUI(cfg);
-viewer1719952653785767.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199530845631418", idname: "mmdbafid", idvalue: "1ETS", mmdbafid: "1ETS", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'load mmdb1ETS| parameters &mmdbid=1ETS&bu=1; defined sets; select sets chemicals; set background white; style chemicals ball and stick; set surface wireframe on; set surface wireframe on; style proteins cylinder and plate; style proteins cylinder and plate; defined sets; select sets 1ETS; style proteins cylinder and plate; color secondary structure yellow|||{"factor":"1.000","mouseChange":{"x":"0.000","y":"0.000"},"quaternion":{"_x":"0.000","_y":"0.000","_z":"0.000","_w":"1.000"}}', };
+viewer17199530845631418 = new icn3d.iCn3DUI(cfg);
+viewer17199530845631418.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fad3461ab90&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fd36c6e79d0&gt;
 </pre></div>
 </div>
 </div>
diff --git a/chapters/binding_site_investigation.html b/chapters/binding_site_investigation.html
index 49ca487..b39e00f 100644
--- a/chapters/binding_site_investigation.html
+++ b/chapters/binding_site_investigation.html
@@ -470,7 +470,7 @@ <h2>View the structure<a class="headerlink" href="#view-the-structure" title="Li
 </div>
 </div>
 <div class="cell_output docutils container">
-<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "626b47a88ff44a8ba9904b8395296b28"}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "78aa81479dd74049a15a1ea7444cb16b"}</script></div>
 </div>
 <p>Text here about NGLView</p>
 <div class="cell docutils container">
@@ -481,7 +481,7 @@ <h2>View the structure<a class="headerlink" href="#view-the-structure" title="Li
 </div>
 </div>
 <div class="cell_output docutils container">
-<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "7e4ba5b126ce4877b950fedc58643cc8"}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "e2cb084d744c4db0ba2808149697a171"}</script></div>
 </div>
 <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.
@@ -505,7 +505,7 @@ <h2>View the structure<a class="headerlink" href="#view-the-structure" title="Li
 </div>
 </div>
 <div class="cell_output docutils container">
-<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "667cc174ad924093acb7bbf186cdd2f8"}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "6436183840db4b0db8587ce05c7d4b77"}</script></div>
 </div>
 <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>
@@ -543,7 +543,7 @@ <h2>View the structure<a class="headerlink" href="#view-the-structure" title="Li
 </div>
 </div>
 <div class="cell_output docutils container">
-<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "2f2718bf8c74478a8f0987b464c3124a"}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "ce732a0453974a1d837b2b1f655551a1"}</script></div>
 </div>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
@@ -552,7 +552,7 @@ <h2>View the structure<a class="headerlink" href="#view-the-structure" title="Li
 </div>
 </div>
 <div class="cell_output docutils container">
-<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "a2584e683a8246c88657c9594897ceeb"}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "ce37fff02a684a31b11ee4fad106a846"}</script></div>
 </div>
 <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.
diff --git a/chapters/nonlinear_regression_part_2.html b/chapters/nonlinear_regression_part_2.html
index a8db1cb..a0683db 100644
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