diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 91b70493ed4aa8916512fc0791f554eee65cfeee..0ddaf784291fbc80e914c18046b4f282e2162afb 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -510,7 +510,7 @@ class HHblits:
                 self.working_dir = tmp_dir.dirname
                 self.filename = tmp_dir.files[0]
 
-    def BuildQueryMSA(self, nrdb, options={}, a3m_file=None, assign_ss=False):
+    def BuildQueryMSA(self, nrdb, options={}, a3m_file=None, assign_ss=True):
         """Builds the MSA for the query sequence.
 
         This function directly uses hhblits of hhtools. While in theory it would