diff --git a/modules/bindings/tests/test_hhblits.py b/modules/bindings/tests/test_hhblits.py
index 4bc61f45575e750218bc44bd44e18463c8e7b44a..f1d2d404291238aed9fd2492db5dc8ad06808369 100644
--- a/modules/bindings/tests/test_hhblits.py
+++ b/modules/bindings/tests/test_hhblits.py
@@ -118,12 +118,12 @@ class TestHHblitsBindings(unittest.TestCase):
         print "A3M"
         with open(a3m) as fh:
             for line in fh:
-                line = line.split()
+                line = line.strip()
                 print line
         print "TESTFILE"
         with open("testfiles/testali.a3m") as fh:
             for line in fh:
-                line = line.split()
+                line = line.strip()
                 print line
         self.assertTrue(filecmp.cmp(a3m, "testfiles/testali.a3m"))