diff --git a/docs/conf.py b/docs/conf.py
index 5c69e75d..83bfd1c5 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -26,29 +26,30 @@
 
 extensions = [
     "sphinx.ext.napoleon",
-    "sphinx.ext.autodoc",
-    "sphinx.ext.autosummary",
+    #"sphinx.ext.autodoc",
+    #"sphinx.ext.autosummary",
     "sphinx.ext.todo",
     "sphinx.ext.viewcode",
-    #"sphinxext.rediraffe",
-    #"sphinx_design",
-    #"sphinx_copybutton",
+    "sphinxext.rediraffe",
+    "sphinx_design",
+    "sphinx_copybutton",
     #"autoapi.extension",
     #"_extension.gallery_directive",
     # For extension examples and demos
-    #"ablog",
-    #"jupyter_sphinx",
-    #"matplotlib.sphinxext.plot_directive",
+    "ablog",
+    "jupyter_sphinx",
+    "matplotlib.sphinxext.plot_directive",
     #"myst_nb",
-    #"sphinxcontrib.youtube",
+    # "sphinxcontrib.youtube",
     # "nbsphinx",  # Uncomment and comment-out MyST-NB for local testing purposes.
-    #"numpydoc",
-    #"sphinx_togglebutton",
+    "numpydoc",
+    "sphinx_togglebutton",
     #"jupyterlite_sphinx",
-    #"sphinx_favicon",
-    #"myst_parser",
+    "sphinx_favicon",
+    "myst_parser",
 ]
 
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -75,7 +76,7 @@
 # -- MyST options ------------------------------------------------------------
 
 # This allows us to use ::: to denote directives, useful for admonitions
-myst_enable_extensions = ["colon_fence", "linkify", "substitution"]
+myst_enable_extensions = ["colon_fence", "substitution"]
 myst_heading_anchors = 2
 myst_substitutions = {"rtd": "[Read the Docs](https://readthedocs.org/)"}
 
@@ -131,21 +132,9 @@
         },
         {
             "name": "GitHub",
-            "url": "https://github.com/pydata/pydata-sphinx-theme",
+            "url": "https://github.com/conradry/proteome",
             "icon": "fa-brands fa-github",
         },
-        {
-            "name": "PyPI",
-            "url": "https://pypi.org/project/pydata-sphinx-theme",
-            "icon": "fa-custom fa-pypi",
-        },
-        {
-            "name": "PyData",
-            "url": "https://pydata.org",
-            "icon": "_static/pydata-logo.png",
-            "type": "local",
-            "attributes": {"target": "_blank"},
-        },
     ],
     # alternative way to set twitter and github header icons
     # "github_url": "https://github.com/pydata/pydata-sphinx-theme",
@@ -247,14 +236,13 @@
 
 # -- Options for autoapi -------------------------------------------------------
 autoapi_type = "python"
-autoapi_dirs = ["../src/pydata_sphinx_theme"]
+autoapi_dirs = ["../proteome"]
 autoapi_keep_files = True
 autoapi_root = "api"
 autoapi_member_order = "groupwise"
 
 # -- application setup -------------------------------------------------------
 
-
 def setup_to_main(
     app: Sphinx, pagename: str, templatename: str, context, doctree
 ) -> None:
diff --git a/docs/index.md b/docs/index.md
index c1f58931..87e02d41 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,4 +1,22 @@
-prtm
--------
+---
+myst:
+  html_meta:
+    "description lang=en": |
+      Top-level documentation for pydata-sphinx theme, with links to the rest
+      of the site..
+html_theme.sidebar_secondary.remove: true
+---
 
-`prtm` is the library for state-of-the-art protein models.
\ No newline at end of file
+# prtm
+
+`prtm` is the library for state-of-the-art protein models.
+
+## User Guide
+
+Information about using, configuration, and customizing this theme.
+
+```{toctree}
+:maxdepth: 2
+
+user_guide/index
+```
\ No newline at end of file
diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md
new file mode 100644
index 00000000..d22e27a0
--- /dev/null
+++ b/docs/user_guide/index.md
@@ -0,0 +1,23 @@
+---
+myst:
+  html_meta:
+    "description lang=en": |
+      Documentation for users who wish to build sphinx sites with
+      pydata-sphinx-theme.
+---
+
+# User Guide
+
+You can configure the behavior, look, and feel of the theme in many ways.
+The remaining pages in the user guide cover various ways of doing so.
+
+```{danger}
+This theme is still under active development, and we make no promises
+about the stability of any specific HTML structure, CSS variables, etc.
+Make these customizations at your own risk, and pin versions if you're
+worried about breaking changes!
+```
+
+There are a number of options for configuring your site's look and feel.
+All configuration options are passed with the `html_theme_options` variable in your `conf.py` file.
+This is a dictionary with `key: val` pairs that you can configure in various ways.
\ No newline at end of file