@@ -414,12 +414,12 @@ public void actionPerformed(ActionEvent ae) {
 				// Kimura, Structural and Fractional Dissimilarity Score
 				Phylogeny kimura = MultipleAlignmentTools
 						.getKimuraTree(multAln);
-				Phylogeny hsdm = MultipleAlignmentTools
-						.getHSDMTree(multAln);
+				Phylogeny sdm = MultipleAlignmentTools
+						.getSDMTree(multAln);
 				// Phylogeny structural = MultipleAlignmentTools
 				//		.getStructuralTree(multAln);
 
-				Archaeopteryx.createApplication(new Phylogeny[] { kimura,hsdm });
+				Archaeopteryx.createApplication(new Phylogeny[] { kimura, sdm });
 			}
 		} catch (Exception e) {
 			logger.error("Could not complete display option.", e);
 
@@ -66,7 +66,9 @@ public static MultipleAlignmentJmol displayRepeats(CeSymmResult symm)
 			throws StructureException {
 
 		MultipleAlignment repeats = SymmetryTools.toRepeatsAlignment(symm);
-		return MultipleAlignmentJmolDisplay.display(repeats);
+		MultipleAlignmentJmol jmol = MultipleAlignmentJmolDisplay.display(repeats);
+		jmol.setTitle(getSymmTitle(symm));
+		return jmol;
 	}
 
 	/**
@@ -84,6 +86,7 @@ public static MultipleAlignmentJmol displayFull(CeSymmResult symm)
 
 		MultipleAlignmentJmol jmol = MultipleAlignmentJmolDisplay.display(full);
 		jmol.setColorByBlocks(true);
+		jmol.setTitle(getSymmTitle(symm));
 
 		return jmol;
 	}
 
@@ -26,6 +26,7 @@
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
+import org.biojava.nbio.structure.align.gui.jmol.AbstractAlignmentJmol;
 import org.biojava.nbio.structure.align.gui.jmol.MultipleAlignmentJmol;
 import org.biojava.nbio.structure.symmetry.internal.CeSymmResult;
 import org.slf4j.Logger;
@@ -74,8 +75,9 @@ public void actionPerformed(ActionEvent ae) {
 
 			} else if (cmd.equals("Optimal Self Alignment")) {
 				Atom[] cloned = StructureTools.cloneAtomArray(symm.getAtoms());
-				StructureAlignmentDisplay.display(symm.getSelfAlignment(),
-						symm.getAtoms(), cloned);
+				AbstractAlignmentJmol jmol = StructureAlignmentDisplay.display(
+						symm.getSelfAlignment(), symm.getAtoms(), cloned);
+				jmol.setTitle(jmol.getTitle() + " Optimal Self-Alignment");
 
 			} else if (cmd.equals("Show Symmetry Group")) {
 				String script = SymmetryDisplay.printSymmetryGroup(symm);
 
@@ -867,7 +867,7 @@ public static Phylogeny getKimuraTree(MultipleAlignment msta)
 
 	/**
 	 * Calculate a phylogenetic tree of the MultipleAlignment using
-	 * dissimilarity scores (DS), based in HSDM Substitution Matrix (ideal for
+	 * dissimilarity scores (DS), based in SDM Substitution Matrix (ideal for
 	 * distantly related proteins, structure-derived) and the Neighbor Joining
 	 * algorithm from forester.
 	 * 
@@ -877,15 +877,15 @@ public static Phylogeny getKimuraTree(MultipleAlignment msta)
 	 * @throws CompoundNotFoundException
 	 * @throws IOException
 	 */
-	public static Phylogeny getHSDMTree(MultipleAlignment msta)
+	public static Phylogeny getSDMTree(MultipleAlignment msta)
 			throws CompoundNotFoundException, IOException {
 		MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa = MultipleAlignmentTools
 				.toProteinMSA(msta);
 		BasicSymmetricalDistanceMatrix distmat = (BasicSymmetricalDistanceMatrix) DistanceMatrixCalculator
-				.dissimilarityScore(msa, SubstitutionMatrixHelper.getAminoAcidSubstitutionMatrix("PRLA000102"));
+				.dissimilarityScore(msa, SubstitutionMatrixHelper.getAminoAcidSubstitutionMatrix("PRLA000101"));
 		Phylogeny tree = TreeConstructor.distanceTree(distmat,
 				TreeConstructorType.NJ);
-		tree.setName("HSDM Tree");
+		tree.setName("SDM Tree");
 		return tree;
 	}
Original file line number	Diff line number	Diff line change
`@@ -66,7 +66,9 @@ public static MultipleAlignmentJmol displayRepeats(CeSymmResult symm)`
`66`	`66`	`throws StructureException {`
`67`	`67`
`68`	`68`	`MultipleAlignment repeats = SymmetryTools.toRepeatsAlignment(symm);`
`69`		`- return MultipleAlignmentJmolDisplay.display(repeats);`
	`69`	`+ MultipleAlignmentJmol jmol = MultipleAlignmentJmolDisplay.display(repeats);`
	`70`	`+ jmol.setTitle(getSymmTitle(symm));`
	`71`	`+ return jmol;`
`70`	`72`	`}`
`71`	`73`
`72`	`74`	`/**`
`@@ -84,6 +86,7 @@ public static MultipleAlignmentJmol displayFull(CeSymmResult symm)`
`84`	`86`
`85`	`87`	`MultipleAlignmentJmol jmol = MultipleAlignmentJmolDisplay.display(full);`
`86`	`88`	`jmol.setColorByBlocks(true);`
	`89`	`+ jmol.setTitle(getSymmTitle(symm));`
`87`	`90`
`88`	`91`	`return jmol;`
`89`	`92`	`}`