From 3e152ef4e2a689b1edcae9f429dcd4807b1b3d87 Mon Sep 17 00:00:00 2001
From: janash <janash@users.noreply.github.com>
Date: Tue, 2 Jul 2024 23:01:23 +0000
Subject: [PATCH] deploy: 658063f07bc57f4e0d9ef4f619f76cfabc008e6f

---
 ...47111ad4d11dc5acab0479ef51e2b280a83398.png | Bin 0 -> 23097 bytes
 ...f53fa6c362f0e4dda61f34fff77d7fca88a748.png | Bin 25391 -> 0 bytes
 ...ced6358be44b366ddd21b896699eebb23e7172.png | Bin 0 -> 48195 bytes
 ...5c0c313bb65e946e426bbbeb940cbe6f70f91d.png | Bin 48246 -> 0 bytes
 .../Creating_Plots_in_Jupyter_Notebooks.html  |   8 +-
 chapters/MolVis_with_iCN3D.html               | 144 +++++++++---------
 chapters/binding_site_investigation.html      |  46 ++++--
 chapters/nonlinear_regression_part_2.html     |   2 +-
 chapters/rcsb_api.html                        |   4 +-
 .../binding_site_investigation.err.log        |  42 +++++
 searchindex.js                                |   2 +-
 11 files changed, 157 insertions(+), 91 deletions(-)
 create mode 100644 _images/88c52027db529de7c3ae7d423a47111ad4d11dc5acab0479ef51e2b280a83398.png
 delete mode 100644 _images/a3c950784f486b8b28dce3de97f53fa6c362f0e4dda61f34fff77d7fca88a748.png
 create mode 100644 _images/a951e6aad5e398bb17cba2a433ced6358be44b366ddd21b896699eebb23e7172.png
 delete mode 100644 _images/bd02bcab94c68d2fa2388a53115c0c313bb65e946e426bbbeb940cbe6f70f91d.png
 create mode 100644 reports/chapters/binding_site_investigation.err.log

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zqdrM4gDJbVD<0tay7^ik<rm_qiwMjeO}7xo+;FT>tE55&zx0pj`Y%;={%cZh=Rf_Y
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diff --git a/chapters/Creating_Plots_in_Jupyter_Notebooks.html b/chapters/Creating_Plots_in_Jupyter_Notebooks.html
index bf0329c..bd14109 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 0x7fae3b0f3ed0&gt;
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;matplotlib.collections.PathCollection at 0x7f7ce4593f90&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 0x7fae3b190f10&gt;]
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7f7ce45a2bd0&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/a3c950784f486b8b28dce3de97f53fa6c362f0e4dda61f34fff77d7fca88a748.png" src="../_images/a3c950784f486b8b28dce3de97f53fa6c362f0e4dda61f34fff77d7fca88a748.png" />
+<img alt="../_images/88c52027db529de7c3ae7d423a47111ad4d11dc5acab0479ef51e2b280a83398.png" src="../_images/88c52027db529de7c3ae7d423a47111ad4d11dc5acab0479ef51e2b280a83398.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/bd02bcab94c68d2fa2388a53115c0c313bb65e946e426bbbeb940cbe6f70f91d.png" src="../_images/bd02bcab94c68d2fa2388a53115c0c313bb65e946e426bbbeb940cbe6f70f91d.png" />
+<img alt="../_images/a951e6aad5e398bb17cba2a433ced6358be44b366ddd21b896699eebb23e7172.png" src="../_images/a951e6aad5e398bb17cba2a433ced6358be44b366ddd21b896699eebb23e7172.png" />
 </div>
 </div>
 <div class="key admonition">
diff --git a/chapters/MolVis_with_iCN3D.html b/chapters/MolVis_with_iCN3D.html
index 9fe2cb7..06db495 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="icn3dviewer17199555991957593" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199555991957593" 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="icn3dviewer1719961261366333" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning1719961261366333" 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 viewer17199555991957593 = null;
-var warn = document.getElementById("icn3dwarning17199555991957593");
+var viewer1719961261366333 = null;
+var warn = document.getElementById("icn3dwarning1719961261366333");
 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: "icn3dviewer17199555991957593", idname: "pdbid", idvalue: "1a0j", pdbid: "1a0j", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '', };
-viewer17199555991957593 = new icn3d.iCn3DUI(cfg);
-viewer17199555991957593.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer1719961261366333", idname: "pdbid", idvalue: "1a0j", pdbid: "1a0j", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '', };
+viewer1719961261366333 = new icn3d.iCn3DUI(cfg);
+viewer1719961261366333.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7f799c3b1710&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fb55cc7bcd0&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="icn3dviewer17199555992020545" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199555992020545" 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="icn3dviewer17199612613725157" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199612613725157" 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 viewer17199555992020545 = null;
-var warn = document.getElementById("icn3dwarning17199555992020545");
+var viewer17199612613725157 = null;
+var warn = document.getElementById("icn3dwarning17199612613725157");
 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: "icn3dviewer17199555992020545", idname: "pdbid", idvalue: "8gch", pdbid: "8gch", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '', };
-viewer17199555992020545 = new icn3d.iCn3DUI(cfg);
-viewer17199555992020545.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199612613725157", idname: "pdbid", idvalue: "8gch", pdbid: "8gch", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: '', };
+viewer17199612613725157 = new icn3d.iCn3DUI(cfg);
+viewer17199612613725157.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7f799c1d3490&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fb55cc9d590&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="icn3dviewer17199555992109554" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199555992109554" 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="icn3dviewer17199612613815706" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199612613815706" 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 viewer17199555992109554 = null;
-var warn = document.getElementById("icn3dwarning17199555992109554");
+var viewer17199612613815706 = null;
+var warn = document.getElementById("icn3dwarning17199612613815706");
 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: "icn3dviewer17199555992109554", idname: "pdbid", idvalue: "1mbo", pdbid: "1mbo", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'style proteins cylinder and plate', };
-viewer17199555992109554 = new icn3d.iCn3DUI(cfg);
-viewer17199555992109554.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199612613815706", idname: "pdbid", idvalue: "1mbo", pdbid: "1mbo", width: "640px", height: "480px", mobilemenu: 1, notebook: 1, command: 'style proteins cylinder and plate', };
+viewer17199612613815706 = new icn3d.iCn3DUI(cfg);
+viewer17199612613815706.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7f799c1de850&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fb55ce5f450&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="icn3dviewer17199555992167323" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199555992167323" 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="icn3dviewer1719961261386881" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning1719961261386881" 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 viewer17199555992167323 = null;
-var warn = document.getElementById("icn3dwarning17199555992167323");
+var viewer1719961261386881 = null;
+var warn = document.getElementById("icn3dwarning1719961261386881");
 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: "icn3dviewer17199555992167323", 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', };
-viewer17199555992167323 = new icn3d.iCn3DUI(cfg);
-viewer17199555992167323.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer1719961261386881", 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', };
+viewer1719961261386881 = new icn3d.iCn3DUI(cfg);
+viewer1719961261386881.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7f799c1e1650&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fb55cca1ed0&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="icn3dviewer17199555992227745" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199555992227745" 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="icn3dviewer1719961261392985" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning1719961261392985" 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 viewer17199555992227745 = null;
-var warn = document.getElementById("icn3dwarning17199555992227745");
+var viewer1719961261392985 = null;
+var warn = document.getElementById("icn3dwarning1719961261392985");
 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: "icn3dviewer17199555992227745", 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', };
-viewer17199555992227745 = new icn3d.iCn3DUI(cfg);
-viewer17199555992227745.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer1719961261392985", 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', };
+viewer1719961261392985 = new icn3d.iCn3DUI(cfg);
+viewer1719961261392985.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7f799c1e2650&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fb55cca3cd0&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="icn3dviewer17199555992284958" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199555992284958" 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="icn3dviewer17199612613985746" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199612613985746" 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 viewer17199555992284958 = null;
-var warn = document.getElementById("icn3dwarning17199555992284958");
+var viewer17199612613985746 = null;
+var warn = document.getElementById("icn3dwarning17199612613985746");
 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: "icn3dviewer17199555992284958", 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', };
-viewer17199555992284958 = new icn3d.iCn3DUI(cfg);
-viewer17199555992284958.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199612613985746", 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', };
+viewer17199612613985746 = new icn3d.iCn3DUI(cfg);
+viewer17199612613985746.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7f799c1e4110&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fb55cca2650&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="icn3dviewer17199555992342067" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199555992342067" 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="icn3dviewer17199612614038188" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199612614038188" 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 viewer17199555992342067 = null;
-var warn = document.getElementById("icn3dwarning17199555992342067");
+var viewer17199612614038188 = null;
+var warn = document.getElementById("icn3dwarning17199612614038188");
 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: "icn3dviewer17199555992342067", 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"}}', };
-viewer17199555992342067 = new icn3d.iCn3DUI(cfg);
-viewer17199555992342067.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199612614038188", 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"}}', };
+viewer17199612614038188 = new icn3d.iCn3DUI(cfg);
+viewer17199612614038188.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7f799c1e6910&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fb55cca7550&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="icn3dviewer17199555992401986" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning17199555992401986" 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="icn3dviewer1719961261409527" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning1719961261409527" 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 viewer17199555992401986 = null;
-var warn = document.getElementById("icn3dwarning17199555992401986");
+var viewer1719961261409527 = null;
+var warn = document.getElementById("icn3dwarning1719961261409527");
 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: "icn3dviewer17199555992401986", 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"}}', };
-viewer17199555992401986 = new icn3d.iCn3DUI(cfg);
-viewer17199555992401986.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer1719961261409527", 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"}}', };
+viewer1719961261409527 = new icn3d.iCn3DUI(cfg);
+viewer1719961261409527.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7f799c1de750&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fb55cc756d0&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="icn3dviewer1719955599249877" style="position: relative; width: 640px; min-height: 530px; height: auto">
-        <p id="icn3dwarning1719955599249877" 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="icn3dviewer17199612614189866" style="position: relative; width: 640px; min-height: 530px; height: auto">
+        <p id="icn3dwarning17199612614189866" 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 viewer1719955599249877 = null;
-var warn = document.getElementById("icn3dwarning1719955599249877");
+var viewer17199612614189866 = null;
+var warn = document.getElementById("icn3dwarning17199612614189866");
 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: "icn3dviewer1719955599249877", 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"}}', };
-viewer1719955599249877 = new icn3d.iCn3DUI(cfg);
-viewer1719955599249877.show3DStructure(cfg.pdb);
+cfg = {divid: "icn3dviewer17199612614189866", 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"}}', };
+viewer17199612614189866 = new icn3d.iCn3DUI(cfg);
+viewer17199612614189866.show3DStructure(cfg.pdb);
 });
-</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7f799c1c7250&gt;
+</script></div><div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>&lt;icn3dpy.view at 0x7fb55cc86e50&gt;
 </pre></div>
 </div>
 </div>
diff --git a/chapters/binding_site_investigation.html b/chapters/binding_site_investigation.html
index a335470..bd61a96 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">{"model_id": "b99491671e01419ea6e9dd4d41e4527f", "version_major": 2, "version_minor": 0}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "1c0a1db552e24401b76ab762e90bcce1"}</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">{"model_id": "2401aa6c72574b7daf42ea1fa5b8be4b", "version_major": 2, "version_minor": 0}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "f4bf0df4e8374061a847a80ef8387aeb"}</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">{"model_id": "e76e61ee77e54089b97cc13e88d4ba18", "version_major": 2, "version_minor": 0}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "57cc534d74ca4c49bd4b86168af63d12"}</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">{"model_id": "39f72e25876f4a59a5451baa0beb88fd", "version_major": 2, "version_minor": 0}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "380e3bce47be44c28bb972fd2df092b2"}</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">{"model_id": "86508b08ae76439f89976b8e570328a8", "version_major": 2, "version_minor": 0}</script></div>
+<script type="application/vnd.jupyter.widget-view+json">{"version_major": 2, "version_minor": 0, "model_id": "a171ea6d7db146da9e45b1b966d34e29"}</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.
@@ -577,7 +577,7 @@ <h2>Making a Map of Ligand Contacts<a class="headerlink" href="#making-a-map-of-
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/home/janash/miniconda3/envs/iqb-2024/lib/python3.11/site-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: &#39;formalcharges&#39; Using default value of &#39;0&#39;
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: &#39;formalcharges&#39; Using default value of &#39;0&#39;
   warnings.warn(&quot;Found no information for attr: &#39;{}&#39;&quot;
 </pre></div>
 </div>
@@ -603,7 +603,9 @@ <h3>Structure Preparation<a class="headerlink" href="#structure-preparation" tit
 INFO:Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
 INFO:Checking and transforming input arguments.
 INFO:Loading topology files.
-INFO:Loading molecule: pdb/protein_2zq2.pdb
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>INFO:Loading molecule: pdb/protein_2zq2.pdb
 ERROR:Error parsing line: invalid literal for int() with base 10: &#39;&#39;
 ERROR:&lt;REMARK     2&gt;
 ERROR:Truncating remaining errors for record type:REMARK
@@ -666,7 +668,9 @@ <h3>Structure Preparation<a class="headerlink" href="#structure-preparation" tit
 WARNING:Multiple occupancies found in GLN A 240. At least one of the instances is being ignored.
 INFO:Setting termini states for biomolecule chains.
 INFO:Loading forcefield.
-INFO:Loading hydrogen topology definitions.
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>INFO:Loading hydrogen topology definitions.
 WARNING:Missing atom CG in residue LYS A 222
 WARNING:Missing atom CD in residue LYS A 222
 WARNING:Missing atom CE in residue LYS A 222
@@ -687,9 +691,15 @@ <h3>Structure Preparation<a class="headerlink" href="#structure-preparation" tit
 INFO:Updating disulfide bridges.
 INFO:Debumping biomolecule.
 INFO:Adding hydrogens to biomolecule.
-INFO:Debumping biomolecule (again).
-INFO:Optimizing hydrogen bonds
-INFO:Applying force field to biomolecule states.
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>INFO:Debumping biomolecule (again).
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>INFO:Optimizing hydrogen bonds
+</pre></div>
+</div>
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>INFO:Applying force field to biomolecule states.
 INFO:Regenerating headers.
 INFO:Regenerating PDB lines.
 WARNING:Ignoring 390 header lines in output.
@@ -722,6 +732,20 @@ <h3>Structure Preparation<a class="headerlink" href="#structure-preparation" tit
 </pre></div>
 </div>
 </div>
+<div class="cell_output docutils container">
+<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
+<span class="ne">OSError</span><span class="g g-Whitespace">                                   </span>Traceback (most recent call last)
+<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">14</span><span class="p">],</span> <span class="n">line</span> <span class="mi">5</span>
+<span class="g g-Whitespace">      </span><span class="mi">1</span> <span class="kn">from</span> <span class="nn">rdkit</span> <span class="kn">import</span> <span class="n">Chem</span>
+<span class="g g-Whitespace">      </span><span class="mi">3</span> <span class="kn">from</span> <span class="nn">rdkit.Chem.AllChem</span> <span class="kn">import</span> <span class="n">AssignBondOrdersFromTemplate</span>
+<span class="ne">----&gt; </span><span class="mi">5</span> <span class="n">template</span> <span class="o">=</span> <span class="n">Chem</span><span class="o">.</span><span class="n">MolFromMol2File</span><span class="p">(</span><span class="s2">&quot;ligands/13U_ideal.mol2&quot;</span><span class="p">)</span>
+<span class="g g-Whitespace">      </span><span class="mi">6</span> <span class="n">pdb_ligand</span> <span class="o">=</span> <span class="n">Chem</span><span class="o">.</span><span class="n">MolFromPDBFile</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;pdb/ligand_A.pdb&quot;</span><span class="p">)</span>
+<span class="g g-Whitespace">      </span><span class="mi">8</span> <span class="n">template</span> <span class="o">=</span> <span class="n">Chem</span><span class="o">.</span><span class="n">RemoveAllHs</span><span class="p">(</span><span class="n">template</span><span class="p">)</span>
+
+<span class="ne">OSError</span>: Bad input file ligands/13U_ideal.mol2
+</pre></div>
+</div>
+</div>
 </div>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
diff --git a/chapters/nonlinear_regression_part_2.html b/chapters/nonlinear_regression_part_2.html
index d76a4f2..c8c0898 100644
--- a/chapters/nonlinear_regression_part_2.html
+++ b/chapters/nonlinear_regression_part_2.html
@@ -557,7 +557,7 @@ <h2>The Michaelis-Menten equation<a class="headerlink" href="#the-michaelis-ment
 </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 0x7fcddd22e6d0&gt;]
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>[&lt;matplotlib.lines.Line2D at 0x7efd3ce69790&gt;]
 </pre></div>
 </div>
 <img alt="../_images/ed2e8a80cd568b164f79f3c9cf21556ba7d5baac33497c50cc6db1e0744d85e0.png" src="../_images/ed2e8a80cd568b164f79f3c9cf21556ba7d5baac33497c50cc6db1e0744d85e0.png" />
diff --git a/chapters/rcsb_api.html b/chapters/rcsb_api.html
index 9fcd865..9a41767 100644
--- a/chapters/rcsb_api.html
+++ b/chapters/rcsb_api.html
@@ -680,7 +680,7 @@ <h2>PDB Search API<a class="headerlink" href="#pdb-search-api" title="Link to th
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;query_id&#39;: &#39;bc667b42-9091-4a62-af30-c23666e5e7ba&#39;,
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;query_id&#39;: &#39;817f2b57-9670-4609-9431-50845964fd08&#39;,
  &#39;result_type&#39;: &#39;entry&#39;,
  &#39;total_count&#39;: 668,
  &#39;result_set&#39;: [{&#39;identifier&#39;: &#39;2BMM&#39;, &#39;score&#39;: 1.0},
@@ -802,7 +802,7 @@ <h2>PDB Search API<a class="headerlink" href="#pdb-search-api" title="Link to th
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;query_id&#39;: &#39;f987c8a2-8c6f-487d-96af-dd0b32e8a43d&#39;,
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;query_id&#39;: &#39;dc4f4404-d744-4a64-9bda-67402b963e68&#39;,
  &#39;result_type&#39;: &#39;entry&#39;,
  &#39;total_count&#39;: 571,
  &#39;result_set&#39;: [{&#39;identifier&#39;: &#39;1MBN&#39;, &#39;score&#39;: 1.0},
diff --git a/reports/chapters/binding_site_investigation.err.log b/reports/chapters/binding_site_investigation.err.log
new file mode 100644
index 0000000..9f70f5d
--- /dev/null
+++ b/reports/chapters/binding_site_investigation.err.log
@@ -0,0 +1,42 @@
+Traceback (most recent call last):
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+    executenb(
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/nbclient/client.py", line 1314, in execute
+    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
+    return loop.run_until_complete(inner)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete
+    return future.result()
+           ^^^^^^^^^^^^^^^
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/nbclient/client.py", line 709, in async_execute
+    await self.async_execute_cell(
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/nbclient/client.py", line 1062, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
+    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
+nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
+------------------
+from rdkit import Chem
+
+from rdkit.Chem.AllChem import AssignBondOrdersFromTemplate
+
+template = Chem.MolFromMol2File("ligands/13U_ideal.mol2")
+pdb_ligand = Chem.MolFromPDBFile(f"pdb/ligand_A.pdb")
+
+template = Chem.RemoveAllHs(template)
+------------------
+
+
+---------------------------------------------------------------------------
+OSError                                   Traceback (most recent call last)
+Cell In[14], line 5
+      1 from rdkit import Chem
+      3 from rdkit.Chem.AllChem import AssignBondOrdersFromTemplate
+----> 5 template = Chem.MolFromMol2File("ligands/13U_ideal.mol2")
+      6 pdb_ligand = Chem.MolFromPDBFile(f"pdb/ligand_A.pdb")
+      8 template = Chem.RemoveAllHs(template)
+
+OSError: Bad input file ligands/13U_ideal.mol2
+
diff --git a/searchindex.js b/searchindex.js
index 4412631..c242a73 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"1D arrays": [[8, "d-arrays"], [12, "d-arrays"]], "2D arrays": [[8, "id1"], [12, "id1"]], "3D arrays": [[8, "id2"], [12, "id2"]], "A final note about regular expressions": [[2, "a-final-note-about-regular-expressions"]], "A final note about string formatting": [[6, "a-final-note-about-string-formatting"]], "A note about jupyter notebooks": [[11, "a-note-about-jupyter-notebooks"]], "Absolute and relative paths": [[2, "absolute-and-relative-paths"]], "Add the column to the dataframe": [[3, "add-the-column-to-the-dataframe"]], "Adding commands to the icn3dpy.view function": [[5, "adding-commands-to-the-icn3dpy-view-function"]], "Analyzing MMCIF Files using Biopython": [[10, "analyzing-mmcif-files-using-biopython"]], "Answer": [[2, null], [2, null]], "Applying the power of python": [[5, "applying-the-power-of-python"]], "Assigning multiple variables at once": [[11, "assigning-multiple-variables-at-once"]], "Assigning variables and data types": [[11, "assigning-variables-and-data-types"]], "Calculate the Slopes": [[12, "calculate-the-slopes"]], "Calculate the initial velocity": [[12, "calculate-the-initial-velocity"]], "Calculating the initial velocity": [[12, "calculating-the-initial-velocity"]], "Challenge - Repeat analysis for a Zinc Finger": [[10, "challenge-repeat-analysis-for-a-zinc-finger"]], "Check Your Understanding": [[2, null], [2, null], [6, null]], "Check your Understanding": [[0, null], [2, null]], "Check your understanding": [[6, null], [8, null], [11, null], [12, null]], "Common errors": [[13, "common-errors"]], "Converting the 2D ligand structures to 3D structures for use in docking": [[4, "converting-the-2d-ligand-structures-to-3d-structures-for-use-in-docking"]], "Create the Equation": [[3, "create-the-equation"]], "Creating Functions": [[13, "creating-functions"]], "Creating Plots in Jupyter Notebooks": [[0, "creating-plots-in-jupyter-notebooks"]], "Creating functions based on preferred command sets generated from iCN3D web pages": [[5, "creating-functions-based-on-preferred-command-sets-generated-from-icn3d-web-pages"]], "Creating the pandas dataframe": [[12, "creating-the-pandas-dataframe"]], "Data Fitting": [[13, "data-fitting"]], "Data types": [[11, "data-types"]], "Datatype": [[12, "datatype"]], "Digital Representation of Molecules": [[4, "digital-representation-of-molecules"]], "Downloading all of the ligands using a for loop": [[1, "downloading-all-of-the-ligands-using-a-for-loop"]], "Downloading the Structure": [[9, "downloading-the-structure"]], "Eliminating values outside the calibration curve (optional)": [[3, "eliminating-values-outside-the-calibration-curve-optional"]], "Enzyme Commission Class with Ligands": [[1, "enzyme-commission-class-with-ligands"]], "Exercise": [[0, null], [1, "exercise"], [3, null], [5, null], [8, null], [11, null], [13, null], [13, null]], "Exerise on file parsing": [[2, null]], "Extracting the output from curve_fit": [[13, "extracting-the-output-from-curve-fit"]], "File Download using Biopython": [[14, "file-download-using-biopython"]], "File Parsing": [[2, "file-parsing"]], "Finding information in a dataframe": [[8, "finding-information-in-a-dataframe"]], "Finding the ligands": [[1, "finding-the-ligands"]], "Getting Started": [[11, "getting-started"]], "Hint": [[2, null], [3, null], [6, null], [12, null]], "How do we download the ligand files?": [[1, "how-do-we-download-the-ligand-files"]], "Importing data with pandas": [[3, "importing-data-with-pandas"]], "Importing libraries": [[6, "importing-libraries"]], "Importing python libraries": [[8, "importing-python-libraries"]], "Importing the Data": [[12, "importing-the-data"]], "Importing the data with pandas": [[8, "importing-the-data-with-pandas"]], "Inspect the data": [[12, "inspect-the-data"]], "Install nglview": [[15, "install-nglview"]], "Installing Python through Anaconda": [[15, "installing-python-through-anaconda"]], "Introduction": [[11, "introduction"]], "Investigation the Binding Site": [[9, "investigation-the-binding-site"]], "Key Points": [[0, null], [2, null], [3, null], [6, null], [8, null]], "Libraries for the IQB workshop": [[1, "libraries-for-the-iqb-workshop"]], "Libraries you will need": [[3, "libraries-you-will-need"]], "Linear Regression": [[3, "linear-regression"]], "Linear Regression with SciPy": [[3, "linear-regression-with-scipy"]], "Lists": [[11, "lists"]], "Loading the iCN3D library": [[5, "loading-the-icn3d-library"]], "Locating the data": [[8, "locating-the-data"]], "Making a Map of Ligand Contacts": [[9, "making-a-map-of-ligand-contacts"]], "Making choices: Logic Statements": [[11, "making-choices-logic-statements"]], "Making queries": [[1, "making-queries"]], "Measuring 3D Properties - Ligand Neighbors": [[10, "measuring-3d-properties-ligand-neighbors"]], "Modifying Ligands in Python": [[4, "modifying-ligands-in-python"]], "Modifying a ligand that is known to bind to trypsin": [[4, "modifying-a-ligand-that-is-known-to-bind-to-trypsin"]], "Modifying the ligand molecule": [[4, "modifying-the-ligand-molecule"]], "Molecular Visualization with iCN3D": [[5, "molecular-visualization-with-icn3d"]], "Nonlinear Regression Part 1": [[12, "nonlinear-regression-part-1"]], "Nonlinear Regression Part 2": [[13, "nonlinear-regression-part-2"]], "Obtain lesson materials": [[15, "obtain-lesson-materials"]], "Overview": [[0, null], [1, null], [2, null], [3, null], [5, null], [6, null], [8, null], [10, null], [11, null], [12, null], [13, null], [14, null]], "PDB Data API": [[14, "pdb-data-api"]], "PDB Search API": [[14, "pdb-search-api"]], "Plotting the data": [[13, "plotting-the-data"]], "Preparing to Plot": [[0, "preparing-to-plot"]], "Printing to a File": [[6, "printing-to-a-file"]], "Processing Multiple Files and Writing Files": [[6, "processing-multiple-files-and-writing-files"]], "Processing multiple files": [[6, "processing-multiple-files"]], "Programmatic Access of APIs": [[14, "programmatic-access-of-apis"]], "Project": [[6, null]], "Pulling collections of commands from an iCN3D web page": [[5, "pulling-collections-of-commands-from-an-icn3d-web-page"]], "Questions": [[4, "questions"]], "Reading MMCIF Files": [[10, "reading-mmcif-files"]], "Reading a file": [[2, "reading-a-file"]], "Reading multiple files with nested for loops": [[6, "reading-multiple-files-with-nested-for-loops"]], "Repeating an operation many times: for loops": [[11, "repeating-an-operation-many-times-for-loops"]], "Results for Glucose and ATP": [[4, "results-for-glucose-and-atp"]], "Retrieving Information from the PDB using the Web API": [[14, "retrieving-information-from-the-pdb-using-the-web-api"]], "Review of f string printing": [[13, "review-of-f-string-printing"]], "Scatter Plots with Seaborn": [[0, "scatter-plots-with-seaborn"]], "Searching for a particular line number in your file": [[2, "searching-for-a-particular-line-number-in-your-file"]], "Searching for a pattern in your file": [[2, "searching-for-a-pattern-in-your-file"]], "Selected ligands": [[1, "selected-ligands"]], "Set Up": [[15, "set-up"]], "Setting up your Jupyter notebooks": [[11, "setting-up-your-jupyter-notebooks"]], "Slices": [[11, "slices"]], "Smoothing the plot": [[13, "smoothing-the-plot"]], "Solution": [[0, null], [0, null], [2, null], [2, null], [3, null], [5, null], [6, null], [6, null], [6, null], [8, null], [8, null], [11, null], [11, null], [12, null], [13, null], [13, null], [13, null]], "Solving for protein concentrations in samples": [[3, "solving-for-protein-concentrations-in-samples"]], "Sorting data with pandas": [[8, "sorting-data-with-pandas"]], "Stages of this module": [[3, "stages-of-this-module"]], "Start a Jupyter notebook": [[15, "start-a-jupyter-notebook"]], "Structure Preparation": [[9, "structure-preparation"]], "Take Home Exercise": [[5, "take-home-exercise"], [13, null]], "Teasing apart the command set from the iCN3D page for PDB ID 1ETS": [[5, "teasing-apart-the-command-set-from-the-icn3d-page-for-pdb-id-1ets"]], "The 7 Enzyme Classes": [[1, "the-7-enzyme-classes"]], "The Michaelis-Menten equation": [[13, "the-michaelis-menten-equation"]], "Things to Do for this Notebook": [[4, "things-to-do-for-this-notebook"]], "Use pandas to import the csv data into a dataframe": [[3, "use-pandas-to-import-the-csv-data-into-a-dataframe"]], "Using Biopython to Analyze Search Results": [[14, "using-biopython-to-analyze-search-results"]], "Using Matplotlib.pyplot": [[0, "using-matplotlib-pyplot"]], "Using curve_fit": [[13, "using-curve-fit"]], "View the structure": [[9, "view-the-structure"]], "Viewing Small Molecules in iCN3D": [[7, "viewing-small-molecules-in-icn3d"]], "Viewing a PDB structure": [[5, "viewing-a-pdb-structure"]], "Visualizing the Binding Site": [[9, "visualizing-the-binding-site"]], "What is pandas and why do we use it?": [[8, "what-is-pandas-and-why-do-we-use-it"], [12, "what-is-pandas-and-why-do-we-use-it"]], "Where can 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