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):