diff --git a/doc/source/conf.py b/doc/source/conf.py
index a35df7588..985a35740 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -94,6 +94,7 @@ def sort_authors(filename):
 mathjax_path = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
 
 site_url = "https://userguide.mdanalysis.org"
+html_baseurl = "https://userguide.mdanalysis.org/"
 sitemap_url_scheme = "{link}"
 html_use_opensearch = 'https://userguide.mdanalysis.org'
 
@@ -105,7 +106,8 @@ def sort_authors(filename):
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store',
-                    '.ipynb_checkpoints', '**/.ipynb_checkpoints', 'scripts', '.*.ipynb', '.*']
+                    '.ipynb_checkpoints', '**/.ipynb_checkpoints',
+                    'scripts', '**/.*.ipynb', '.*']
 
 # -- Options for HTML output -------------------------------------------------