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diff --git a/.doctrees/develop/class/class_avogadro_1_1_core_1_1_molecule.doctree b/.doctrees/develop/class/class_avogadro_1_1_core_1_1_molecule.doctree
diff --git a/.doctrees/develop/class/class_avogadro_1_1_qt_gui_1_1_molecule.doctree b/.doctrees/develop/class/class_avogadro_1_1_qt_gui_1_1_molecule.doctree
diff --git a/.doctrees/docs/getting-started/index.doctree b/.doctrees/docs/getting-started/index.doctree
diff --git a/.doctrees/docs/getting-started/saving-files.doctree b/.doctrees/docs/getting-started/saving-files.doctree
diff --git a/.doctrees/docs/index.doctree b/.doctrees/docs/index.doctree
diff --git a/.doctrees/docs/tutorials/naming-a-molecule.doctree b/.doctrees/docs/tutorials/naming-a-molecule.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/_images/Analysis-MoleculeProperties.png b/_images/Analysis-MoleculeProperties.png
diff --git a/_images/Ligand-CentroidMenu.png b/_images/Ligand-CentroidMenu.png
diff --git a/_images/NamingEthane.png b/_images/NamingEthane.png
diff --git a/_images/NamingSubstituted.png b/_images/NamingSubstituted.png
diff --git a/_images/OtherFunctionalGroup.png b/_images/OtherFunctionalGroup.png
diff --git a/_images/Template-LigandPerpendicular.png b/_images/Template-LigandPerpendicular.png
diff --git a/_images/media_1340251460215.png b/_images/media_1340251460215.png
diff --git a/_images/media_1340251491638.png b/_images/media_1340251491638.png
diff --git a/_images/media_1340251768869.png b/_images/media_1340251768869.png
diff --git a/_images/tutorial-save.png b/_images/tutorial-save.png
diff --git a/_sources/docs/getting-started/index.md.txt b/_sources/docs/getting-started/index.md.txt
@@ -3,6 +3,7 @@
 * [Introduction](introduction)
 * [Drawing Molecules](drawing-molecules)
 * [Making Selections](making-selections)
+* [Saving Files](saving-files)
 
 ```{toctree}
 ---
@@ -13,4 +14,5 @@ hidden: true
 introduction
 drawing-molecules
 making-selections
+saving-files
 ```
diff --git a/_sources/docs/getting-started/saving-files.md.txt b/_sources/docs/getting-started/saving-files.md.txt
@@ -0,0 +1,20 @@
+# Saving Files
+
+By default, Avogadro saves files to "native" formats CJSON (Chemical JSON) and CML (Chemical Markup Language), which store as much chemical information as possible.
+
+![Screenshot indicating File => Save and Save As menu items](../../_static/tutorial-save.png)
+
+In particular the default [Chemical JSON](https://github.com/OpenChemistry/chemicaljson) format will retain atoms, bond orders, formal charges, unit cell parameters, space group information, surfaces, orbitals, vibrations and other spectra, selections, custom colors, etc.
+
+## Exporting to Other Formats
+
+If you wish to **export** to other formats (e.g., XYZ, PDB, SDF, etc.) use
+File => Export => Molecule…
+
+![Screenshot indicating File => Export => Molecule menu item](../../_static/FileExportMolecule.png)
+
+Avogadro uses support for [Open Babel](https://openbabel.org/) to write to over 100 different chemical file formats.
+
+```{tip} **New in 2.0**
+We separated the "export" to other formats into a new command because users would be surprised when saving to some formats (e.g., XYZ, PDB) and bond orders or other information would be lost.
+```
diff --git a/_sources/docs/index.md.txt b/_sources/docs/index.md.txt
@@ -1,8 +1,6 @@
 (Guide)=
 
-# User Guide
-
-## Avogadro: Molecular Editor and Visualization
+# Introduction
 
 Avogadro is a free, open source molecular editor and visualization tool, designed for use on Mac, Windows, and Linux in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.
 

diff --git a/_sources/docs/tutorials/naming-a-molecule.md.txt b/_sources/docs/tutorials/naming-a-molecule.md.txt
@@ -2,14 +2,14 @@
 
 Avogadro includes support for naming compounds using the PubChem database, which includes over 112 million compounds. Since these are deposited by chemical suppliers, pharmaceutical companies, etc. the database may not cover _**every**_ molecule you may build, but includes a broad selection of compounds.
 
-![](../../_static/media\_1340251460215.png)
+Open up the Molecule Properties window, under the Analysis menu.
 
-Open up the Molecule Properties window, under the View menu.
-
-![](../../_static/media\_1340251491638.png)
+![](../../_static/Analysis-MoleculeProperties.png)
 
 The IUPAC name will initially show as (pending) while the server returns the name, (unknown) if the molecule is not found in the resolver, or (unavailable) if your network connection is down or the resolver service is otherwise unreachable.
 
-![](../../_static/media\_1340251768869.png)
+![](../../_static/NamingEthane.png)
+
+As you modify the molecule (e.g., adding a Br atom or two), the name will update automatically with the other properties, albeit while temporarily showing (pending)
 
-As you modify the molecule (e.g., adding a Cl atom), the name will update automatically with the other properties, albeit while temporarily showing (pending)
+![](../../_static/NamingSubstituted.png)
diff --git a/_static/Analysis-MoleculeProperties.png b/_static/Analysis-MoleculeProperties.png
diff --git a/_static/Ligand-CentroidMenu.png b/_static/Ligand-CentroidMenu.png
diff --git a/_static/NamingEthane.png b/_static/NamingEthane.png
diff --git a/_static/NamingSubstituted.png b/_static/NamingSubstituted.png
diff --git a/_static/OtherFunctionalGroup.png b/_static/OtherFunctionalGroup.png
diff --git a/_static/Template-LigandPerpendicular.png b/_static/Template-LigandPerpendicular.png
diff --git a/_static/scripts/pydata-sphinx-theme.js b/_static/scripts/pydata-sphinx-theme.js
diff --git a/_static/scripts/pydata-sphinx-theme.js.map b/_static/scripts/pydata-sphinx-theme.js.map
diff --git a/_static/styles/pydata-sphinx-theme.css b/_static/styles/pydata-sphinx-theme.css
diff --git a/_static/styles/pydata-sphinx-theme.css.map b/_static/styles/pydata-sphinx-theme.css.map
diff --git a/_static/tutorial-save.png b/_static/tutorial-save.png
diff --git a/_static/webpack-macros.html b/_static/webpack-macros.html
@@ -4,28 +4,28 @@
 -->
 {# Load FontAwesome icons #}
 {% macro head_pre_icons() %}
-  <link href="{{ pathto('_static/vendor/fontawesome/6.1.2/css/all.min.css', 1) }}?digest=365ca57ee442770a23c6" rel="stylesheet" />
+  <link href="{{ pathto('_static/vendor/fontawesome/6.1.2/css/all.min.css', 1) }}?digest=5b4479735964841361fd" rel="stylesheet" />
   <link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.1.2/webfonts/fa-solid-900.woff2', 1) }}" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2', 1) }}" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2', 1) }}" />
 {% endmacro %}
 
 {% macro head_pre_assets() %}
   <!-- Loaded before other Sphinx assets -->
-  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=365ca57ee442770a23c6" rel="stylesheet" />
-<link href="{{ pathto('_static/styles/bootstrap.css', 1) }}?digest=365ca57ee442770a23c6" rel="stylesheet" />
-<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=365ca57ee442770a23c6" rel="stylesheet" />
+  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=5b4479735964841361fd" rel="stylesheet" />
+<link href="{{ pathto('_static/styles/bootstrap.css', 1) }}?digest=5b4479735964841361fd" rel="stylesheet" />
+<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=5b4479735964841361fd" rel="stylesheet" />
 {% endmacro %}
 
 {% macro head_js_preload() %}
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=365ca57ee442770a23c6" />
-<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=365ca57ee442770a23c6" />
-  <script src="{{ pathto('_static/vendor/fontawesome/6.1.2/js/all.min.js', 1) }}?digest=365ca57ee442770a23c6"></script>
+  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=5b4479735964841361fd" />
+<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=5b4479735964841361fd" />
+  <script src="{{ pathto('_static/vendor/fontawesome/6.1.2/js/all.min.js', 1) }}?digest=5b4479735964841361fd"></script>
 {% endmacro %}
 
 {% macro body_post() %}
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=365ca57ee442770a23c6"></script>
-<script src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=365ca57ee442770a23c6"></script>
+  <script src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=5b4479735964841361fd"></script>
+<script src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=5b4479735964841361fd"></script>
 {% endmacro %}
diff --git a/contrib/code-docs.html b/contrib/code-docs.html
@@ -2,7 +2,7 @@
 <!DOCTYPE html>
 
 
-<html lang="en" >
+<html lang="en" data-content_root="../" >
 
   <head>
     <meta charset="utf-8" />
@@ -18,12 +18,12 @@
   </script>
 
   <!-- Loaded before other Sphinx assets -->
-  <link href="../_static/styles/theme.css?digest=365ca57ee442770a23c6" rel="stylesheet" />
-<link href="../_static/styles/bootstrap.css?digest=365ca57ee442770a23c6" rel="stylesheet" />
-<link href="../_static/styles/pydata-sphinx-theme.css?digest=365ca57ee442770a23c6" rel="stylesheet" />
+  <link href="../_static/styles/theme.css?digest=5b4479735964841361fd" rel="stylesheet" />
+<link href="../_static/styles/bootstrap.css?digest=5b4479735964841361fd" rel="stylesheet" />
+<link href="../_static/styles/pydata-sphinx-theme.css?digest=5b4479735964841361fd" rel="stylesheet" />
 
 
-  <link href="../_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=365ca57ee442770a23c6" rel="stylesheet" />
+  <link href="../_static/vendor/fontawesome/6.1.2/css/all.min.css?digest=5b4479735964841361fd" rel="stylesheet" />
   <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-solid-900.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" />
@@ -34,9 +34,9 @@
     <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=ee427ece" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=365ca57ee442770a23c6" />
-<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6" />
-  <script src="../_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=365ca57ee442770a23c6"></script>
+  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=5b4479735964841361fd" />
+<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=5b4479735964841361fd" />
+  <script src="../_static/vendor/fontawesome/6.1.2/js/all.min.js?digest=5b4479735964841361fd"></script>
 
     <script src="../_static/documentation_options.js?v=17258b5a"></script>
     <script src="../_static/doctools.js?v=888ff710"></script>
@@ -113,6 +113,7 @@
   <div class="col-lg-3 navbar-header-items__start">
 
       <div class="navbar-item">
+
 
 
 <a class="navbar-brand logo" href="../index.html">
@@ -132,7 +133,8 @@
 
     <div class="me-auto navbar-header-items__center">
 
-        <div class="navbar-item"><nav class="navbar-nav">
+        <div class="navbar-item">
+<nav class="navbar-nav">
   <p class="sidebar-header-items__title"
      role="heading"
      aria-level="1"
@@ -150,7 +152,7 @@
 
                     <li class="nav-item">
                       <a class="nav-link nav-internal" href="../docs/index.html">
-                        User Guide
+                        Introduction
                       </a>
                     </li>
 
@@ -192,6 +194,7 @@
 
         <div class="navbar-item navbar-persistent--container">
 
+
  <script>
  document.write(`
    <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
@@ -205,6 +208,7 @@
 
 
         <div class="navbar-item">
+
 <script>
 document.write(`
   <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
@@ -261,6 +265,7 @@
 
 
     <div class="navbar-persistent--mobile">
+
  <script>
  document.write(`
    <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
@@ -294,7 +299,8 @@
 
       <div class="sidebar-header-items__center">
 
-          <div class="navbar-item"><nav class="navbar-nav">
+          <div class="navbar-item">
+<nav class="navbar-nav">
   <p class="sidebar-header-items__title"
      role="heading"
      aria-level="1"
@@ -312,7 +318,7 @@
 
                     <li class="nav-item">
                       <a class="nav-link nav-internal" href="../docs/index.html">
-                        User Guide
+                        Introduction
                       </a>
                     </li>
 
@@ -354,6 +360,7 @@
       <div class="sidebar-header-items__end">
 
           <div class="navbar-item">
+
 <script>
 document.write(`
   <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
@@ -409,7 +416,8 @@
   </div>
 
     <div class="sidebar-primary-items__start sidebar-primary__section">
-        <div class="sidebar-primary-item"><nav class="bd-docs-nav bd-links"
+        <div class="sidebar-primary-item">
+<nav class="bd-docs-nav bd-links"
      aria-label="Section Navigation">
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><p aria-level="2" class="caption" role="heading"><span class="caption-text">Contributing</span></p>
@@ -573,7 +581,7 @@
 
 
                 <footer class="prev-next-footer">
-                  <!-- Previous / next buttons -->
+
 <div class="prev-next-area">
     <a class="left-prev"
        href="style.html"
@@ -603,6 +611,7 @@
                 <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
 
   <div class="sidebar-secondary-item">
+
   <div class="page-toc tocsection onthispage">
     <i class="fa-solid fa-list"></i> On this page
   </div>
@@ -614,6 +623,7 @@
   </nav></div>
 
   <div class="sidebar-secondary-item">
+
 
   <div class="tocsection editthispage">
     <a href="https://github.com/avogadro/two.avogadro.cc/edit/main/source/contrib/code-docs.md">
@@ -641,8 +651,8 @@
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script src="../_static/scripts/bootstrap.js?digest=365ca57ee442770a23c6"></script>
-<script src="../_static/scripts/pydata-sphinx-theme.js?digest=365ca57ee442770a23c6"></script>
+  <script src="../_static/scripts/bootstrap.js?digest=5b4479735964841361fd"></script>
+<script src="../_static/scripts/pydata-sphinx-theme.js?digest=5b4479735964841361fd"></script>
 
   <footer class="bd-footer">
 <div class="bd-footer__inner bd-page-width">
@@ -660,6 +670,7 @@
         </p></div>
 
         <div class="footer-item">
+
   <p class="sphinx-version">
     Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     <br/>
@@ -672,8 +683,9 @@
 
     <div class="footer-items__end">
 
-        <div class="footer-item"><p class="theme-version">
-  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.14.3.
+        <div class="footer-item">
+<p class="theme-version">
+  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.14.4.
 </p></div>
 
     </div>