diff --git a/modelling/tests/data/gly_on_top.pdb b/modelling/tests/data/gly_on_top.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..34bd74759383a80d3e4270c57e19cfb656249122
--- /dev/null
+++ b/modelling/tests/data/gly_on_top.pdb
@@ -0,0 +1,81 @@
+ATOM      1  N   GLY A   1     -11.301  11.863  12.812  1.00 46.35           N  
+ATOM      2  CA  GLY A   1     -10.174  12.241  13.713  1.00 45.84           C  
+ATOM      3  C   GLY A   1      -9.595  11.051  14.465  1.00 44.35           C  
+ATOM      4  O   GLY A   1     -10.219   9.989  14.526  1.00 46.54           O  
+ATOM      9  N   GLY A   2      -8.383  11.240  14.995  1.00 42.02           N  
+ATOM     10  CA  GLY A   2      -7.611  10.243  15.755  1.00 39.04           C  
+ATOM     11  C   GLY A   2      -7.093   9.042  14.960  1.00 35.73           C  
+ATOM     12  O   GLY A   2      -7.875   8.322  14.336  1.00 35.25           O  
+ATOM     18  N   GLY A   3      -5.757   8.838  14.934  1.00 32.59           N  
+ATOM     19  CA  GLY A   3      -5.167   7.704  14.210  1.00 30.22           C  
+ATOM     20  C   GLY A   3      -5.475   6.389  14.924  1.00 28.03           C  
+ATOM     21  O   GLY A   3      -5.774   6.389  16.125  1.00 25.91           O  
+ATOM     25  N   GLY A   4      -5.434   5.288  14.176  1.00 26.73           N  
+ATOM     26  CA  GLY A   4      -5.705   3.960  14.726  1.00 26.95           C  
+ATOM     27  C   GLY A   4      -4.622   3.524  15.706  1.00 27.12           C  
+ATOM     28  O   GLY A   4      -3.426   3.545  15.366  1.00 27.18           O  
+ATOM     35  N   GLY A   5      -5.020   3.161  16.948  1.00 27.05           N  
+ATOM     36  CA  GLY A   5      -4.064   2.725  17.976  1.00 26.49           C  
+ATOM     37  C   GLY A   5      -3.515   1.307  17.792  1.00 25.98           C  
+ATOM     38  O   GLY A   5      -2.801   0.795  18.659  1.00 26.77           O  
+ATOM     42  N   GLY A   6      -3.807   0.705  16.641  1.00 23.73           N  
+ATOM     43  CA  GLY A   6      -3.371  -0.650  16.363  1.00 22.05           C  
+ATOM     44  C   GLY A   6      -2.311  -0.858  15.292  1.00 21.12           C  
+ATOM     45  O   GLY A   6      -1.814  -1.970  15.124  1.00 19.47           O  
+ATOM     56  N   GLY A   7      -1.980   0.191  14.544  1.00 22.58           N  
+ATOM     57  CA  GLY A   7      -0.962   0.055  13.501  1.00 20.39           C  
+ATOM     58  C   GLY A   7       0.393   0.457  14.047  1.00 22.27           C  
+ATOM     59  O   GLY A   7       0.645   1.639  14.340  1.00 22.00           O  
+ATOM     67  N   GLY A   8       1.271  -0.539  14.140  1.00 21.40           N  
+ATOM     68  CA  GLY A   8       2.612  -0.344  14.678  1.00 21.91           C  
+ATOM     69  C   GLY A   8       2.612  -0.344  14.678  1.00 22.34           C  
+ATOM     70  O   GLY A   8       4.910  -0.258  13.998  1.00 24.21           O  
+ATOM     78  N   GLY A   9       3.365  -0.539  12.371  1.00 20.22           N  
+ATOM     79  CA  GLY A   9       4.342  -0.585  11.293  1.00 20.67           C  
+ATOM     80  C   GLY A   9       5.264  -1.780  11.345  1.00 20.79           C  
+ATOM     81  O   GLY A   9       4.834  -2.874  11.700  1.00 19.22           O  
+ATOM     82  N   GLY A  10       6.545  -1.555  11.072  1.00 20.29           N  
+ATOM     83  CA  GLY A  10       7.521  -2.635  11.071  1.00 22.16           C  
+ATOM     84  C   GLY A  10       8.055  -3.014  12.464  1.00 23.01           C  
+ATOM     85  O   GLY A  10       9.266  -3.098  12.676  1.00 23.84           O  
+ATOM     91  N   GLY A  11       7.141  -3.248  13.409  1.00 24.30           N  
+ATOM     92  CA  GLY A  11       7.527  -3.666  14.757  1.00 23.54           C  
+ATOM     93  C   GLY A  11       7.811  -5.171  14.643  1.00 23.07           C  
+ATOM     94  O   GLY A  11       7.027  -5.913  14.030  1.00 23.44           O  
+ATOM     99  N   GLY A  12       9.005  -5.608  15.082  1.00 23.03           N  
+ATOM    100  CA  GLY A  12       9.328  -7.039  15.000  1.00 23.30           C  
+ATOM    101  C   GLY A  12       8.373  -7.936  15.805  1.00 22.52           C  
+ATOM    102  O   GLY A  12       7.733  -7.476  16.760  1.00 21.80           O  
+ATOM    106  N   GLY A  13       8.271  -9.196  15.382  1.00 22.06           N  
+ATOM    107  CA  GLY A  13       7.433 -10.219  16.020  1.00 22.83           C  
+ATOM    108  C   GLY A  13       7.699 -10.347  17.529  1.00 24.10           C  
+ATOM    109  O   GLY A  13       6.768 -10.261  18.334  1.00 23.86           O  
+ATOM    117  N   GLY A  14       8.974 -10.480  17.898  1.00 22.59           N  
+ATOM    118  CA  GLY A  14       9.386 -10.612  19.299  1.00 23.66           C  
+ATOM    119  C   GLY A  14       9.109  -9.356  20.121  1.00 23.97           C  
+ATOM    120  O   GLY A  14       8.824  -9.445  21.320  1.00 21.85           O  
+ATOM    122  N   GLY A  15       9.149  -8.199  19.455  1.00 23.41           N  
+ATOM    123  CA  GLY A  15       8.880  -6.917  20.103  1.00 25.09           C  
+ATOM    124  C   GLY A  15       7.378  -6.717  20.320  1.00 23.56           C  
+ATOM    125  O   GLY A  15       6.968  -6.064  21.278  1.00 23.45           O  
+ATOM    131  N   GLY A  16       6.569  -7.318  19.442  1.00 21.80           N  
+ATOM    132  CA  GLY A  16       5.106  -7.272  19.532  1.00 20.39           C  
+ATOM    133  C   GLY A  16       4.711  -8.157  20.718  1.00 20.37           C  
+ATOM    134  O   GLY A  16       3.856  -7.788  21.511  1.00 18.06           O  
+ATOM    136  N   GLY A  17       5.429  -9.273  20.876  1.00 20.11           N  
+ATOM    137  CA  GLY A  17       5.215 -10.213  21.983  1.00 21.59           C  
+ATOM    138  C   GLY A  17       5.492  -9.561  23.332  1.00 22.42           C  
+ATOM    139  O   GLY A  17       4.665  -9.622  24.238  1.00 23.01           O  
+ATOM    145  N   GLY A  18       6.639  -8.890  23.414  1.00 24.69           N  
+ATOM    146  CA  GLY A  18       7.114  -8.182  24.603  1.00 26.91           C  
+ATOM    147  C   GLY A  18       6.147  -7.077  25.056  1.00 26.71           C  
+ATOM    148  O   GLY A  18       5.800  -7.000  26.231  1.00 27.59           O  
+ATOM    154  N   GLY A  19       5.683  -6.273  24.099  1.00 25.69           N  
+ATOM    155  CA  GLY A  19       4.764  -5.161  24.348  1.00 25.99           C  
+ATOM    156  C   GLY A  19       3.375  -5.643  24.772  1.00 23.81           C  
+ATOM    157  O   GLY A  19       2.828  -5.155  25.769  1.00 24.09           O  
+ATOM    162  N   GLY A  20       2.830  -6.601  24.019  1.00 19.41           N  
+ATOM    163  CA  GLY A  20       1.496  -7.148  24.282  1.00 21.16           C  
+ATOM    164  C   GLY A  20       1.366  -8.006  25.540  1.00 20.66           C  
+ATOM    165  O   GLY A  20       0.301  -8.035  26.151  1.00 20.51           O  
+END
\ No newline at end of file
diff --git a/modelling/tests/test_modelling.py b/modelling/tests/test_modelling.py
index f7169d4d60577dddc3fd54429d67627e49765343..204854b886edd2a2da55e72ba3ae46594a532646 100644
--- a/modelling/tests/test_modelling.py
+++ b/modelling/tests/test_modelling.py
@@ -174,6 +174,17 @@ class ModellingTests(unittest.TestCase):
         mhandle = modelling.BuildRawModel(aln)
         self.assertEqual(len(mhandle.gaps), 4)
 
+    def testOnTop(self):
+        # do we clean up atoms that are on top of each other?
+        # ResNum 8 has CA-pos == C-pos
+        tpl = io.LoadPDB('data/gly_on_top.pdb')
+        aln = io.LoadAlignment('data/seq.fasta')
+        aln.AttachView(1, tpl.CreateFullView())
+        result = modelling.BuildRawModel(aln)
+        self.assertEqual(len(result.gaps), 1)
+        self.assertEqual(result.gaps[0].before.number.num, 7)
+        self.assertEqual(result.gaps[0].after.number.num, 9)
+
     #######################################################################
 
     def testModellingHandleOperations(self):