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diff --git a/test/jalview/io/ImportHomologyModelTest.java b/test/jalview/io/ImportHomologyModelTest.java
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+++ b/test/jalview/io/ImportHomologyModelTest.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class ImportHomologyModelTest
+{
+
+  public static String base = "examples/testdata/phyre2/";
+
+  public static String profile_msa = base + "query.jal",
+          profile_annot = base + "query.jal.ann";
+
+  public static String templaten[] = new String[] { "c1o1nA_", "c3pt8B_",
+      "d1scta_" };
+
+  AlignmentI al;
+  AlignFrame af;
+
+  /**
+   * Ensure 'process secondary structure from PDB and add annotations' are set
+   * in preferences, and load PDB example file 1gaq
+   * 
+   * @throws Exception
+   */
+  @BeforeMethod(alwaysRun = true)
+  public void setup() throws Exception
+  {
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
+    FileLoader loader = new FileLoader(false);
+    af = loader.LoadFileWaitTillLoaded(profile_msa,
+            FormatAdapter.FILE);
+    Desktop.addInternalFrame(af, "homology models", 800, 500);
+    al = af.getViewport().getAlignment();
+    af.loadJalviewDataFile(profile_annot, FormatAdapter.FILE, null, null);
+    // if file was loaded, the view should have a reference sequence set
+    Assert.assertTrue(al.hasSeqrep());
+  }
+
+
+  @Test(groups = { "Functional" })
+  public void testModelsAssociated()
+  {
+    for (String template : templaten)
+    {
+      SequenceI templseq = al.findName(template);
+      Assert.assertNotNull("Couldn't find template sequence for "
+              + template, templseq);
+      PDBEntry querymdl = al.getSeqrep().getPDBEntry(template);
+      PDBEntry templmdl = templseq.getPDBEntry(template);
+      Assert.assertEquals(querymdl.getFile(), templmdl.getFile());
+    }
+  }
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @BeforeClass(alwaysRun = true)
+  public static void setUpBeforeClass() throws Exception
+  {
+    jalview.bin.Jalview.main(new String[] { "-props",
+        "test/jalview/io/testProps.jvprops" });
+  }
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @AfterClass(alwaysRun = true)
+  public static void tearDownAfterClass() throws Exception
+  {
+    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+
+}