diff --git a/doxygen/make-docs.py b/doxygen/make-docs.py
index 3db8515..f09eb23 100755
--- a/doxygen/make-docs.py
+++ b/doxygen/make-docs.py
@@ -85,6 +85,8 @@ def make_doxyfile(tags):
                 line = 'GENERATE_LATEX = NO\n'
             elif line.startswith('USE_MATHJAX '):
                 line = 'USE_MATHJAX = YES\n'
+            elif line.startswith('MATHJAX_RELPATH '):
+                line = 'MATHJAX_RELPATH = //integrativemodeling.org/mathjax\n'
             elif line.startswith('TAGFILES '):
                 line = 'TAGFILES = %s\n' % tagfiles
             fh.write(line)
diff --git a/notebook/process_notebook.py b/notebook/process_notebook.py
index 6ef874d..e51b2d6 100755
--- a/notebook/process_notebook.py
+++ b/notebook/process_notebook.py
@@ -596,6 +596,8 @@ def make_doxyfile(root, tags):
                 line = 'GENERATE_LATEX = NO\n'
             elif line.startswith('USE_MATHJAX '):
                 line = 'USE_MATHJAX = YES\n'
+            elif line.startswith('MATHJAX_RELPATH '):
+                line = 'MATHJAX_RELPATH = //integrativemodeling.org/mathjax\n'
             elif line.startswith('AUTOLINK_SUPPORT '):
                 # Don't make links from the text (only from code samples)
                 line = 'AUTOLINK_SUPPORT = NO\n'