diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
index 1e5f6c17c6..f68a4b8ed9 100644
--- a/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java
@@ -538,12 +538,11 @@ public static final void transform(Atom atom, Matrix4d m) {
 	 * @param m
 	 */
 	public static final void transform(Group group, Matrix4d m) {
-		AtomIterator iter = new AtomIterator(group);
-
-		while (iter.hasNext()) {
-			Atom atom = iter.next();
+		for (Atom atom : group.getAtoms()) {
 			transform(atom, m);
-
+		}
+		for (Group altG : group.getAltLocs()) {
+			transform(altG, m);
 		}
 	}
 
@@ -556,12 +555,10 @@ public static final void transform(Group group, Matrix4d m) {
 	 * @param m
 	 */
 	public static final void transform(Structure structure, Matrix4d m) {
-		AtomIterator iter = new AtomIterator(structure);
-
-		while (iter.hasNext()) {
-			Atom atom = iter.next();
-			transform(atom, m);
-
+		for (int n=0; n<structure.nrModels();n++) {
+			for (Chain c : structure.getChains(n)) {
+				transform(c, m);
+			}
 		}
 	}
 
@@ -576,9 +573,7 @@ public static final void transform(Structure structure, Matrix4d m) {
 	public static final void transform(Chain chain, Matrix4d m) {
 
 		for (Group g : chain.getAtomGroups()) {
-			for (Atom atom : g.getAtoms()) {
-				transform(atom, m);
-			}
+			transform(g, m);
 		}
 	}
 
@@ -604,12 +599,12 @@ public static final void translate(Atom atom, Vector3d v) {
 	 * @param v
 	 */
 	public static final void translate(Group group, Vector3d v) {
-		AtomIterator iter = new AtomIterator(group);
 
-		while (iter.hasNext()) {
-			Atom atom = iter.next();
+		for (Atom atom : group.getAtoms()) {
 			translate(atom, v);
-
+		}
+		for (Group altG : group.getAltLocs()) {
+			translate(altG, v);
 		}
 	}
 
@@ -623,9 +618,7 @@ public static final void translate(Group group, Vector3d v) {
 	public static final void translate(Chain chain, Vector3d v) {
 
 		for (Group g : chain.getAtomGroups()) {
-			for (Atom atom : g.getAtoms()) {
-				translate(atom, v);
-			}
+			translate(g, v);
 		}
 	}
 
@@ -637,12 +630,11 @@ public static final void translate(Chain chain, Vector3d v) {
 	 * @param v
 	 */
 	public static final void translate(Structure structure, Vector3d v) {
-		AtomIterator iter = new AtomIterator(structure);
-
-		while (iter.hasNext()) {
-			Atom atom = iter.next();
-			translate(atom, v);
-
+		
+		for (int n=0; n<structure.nrModels();n++) {
+			for (Chain c : structure.getChains(n)) {
+				translate(c, v);
+			}
 		}
 	}
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
index 3b48a402d8..c834b22a61 100644
--- a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
+++ b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestCalc.java
@@ -24,6 +24,7 @@
 
 import javax.vecmath.Matrix4d;
 import javax.vecmath.Point3d;
+import javax.vecmath.Vector3d;
 
 import org.biojava.nbio.structure.geometry.Matrices;
 import org.biojava.nbio.structure.jama.Matrix;
@@ -157,14 +158,163 @@ public void testVecmathTransformation() {
 
 		assertEquals(expected, actual);
 	}
+	
+	/**
+	 * Issue https://github.com/biojava/biojava/issues/715
+	 */
+	@Test
+	public void testChainTransform() {
+		
+		Chain c = createDummyChain();
+		
+		Matrix4d m = new Matrix4d(1,0,0,1, 0,1,0,0, 0,0,1,0, 0,0,0,1); // shift of 1 in x axis
+ 		Calc.transform(c, m);
+ 		
+ 		Group thegroup = c.getAtomGroup(0);
+ 		Group thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		Atom atom1 = thegroup.getAtom("CA");
+ 		Atom atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shifted by 1
+ 		assertEquals(2, atom1.getX(), 0.00001);
+ 		assertEquals(1, atom1.getY(), 0.00001);
+ 		assertEquals(1, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shifted by 1
+ 		assertEquals(3, atom2.getX(), 0.00001);
+ 		assertEquals(2, atom2.getY(), 0.00001);
+ 		assertEquals(2, atom2.getZ(), 0.00001);
+
+ 		
+	}
 
-	private static Atom getAtom(double x, double y, double z) {
+	/**
+	 * Issue https://github.com/biojava/biojava/issues/715
+	 */
+	@Test
+	public void testStructureTransform() {
+		
+		Structure s = createDummyStructure();
+		
+		Matrix4d m = new Matrix4d(1,0,0,1, 0,1,0,0, 0,0,1,0, 0,0,0,1); // shift of 1 in x axis
+ 		Calc.transform(s, m);
+ 		
+ 		// testing 1st chain
+ 		Group thegroup = s.getChain("A").getAtomGroup(0);
+ 		Group thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		Atom atom1 = thegroup.getAtom("CA");
+ 		Atom atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(2, atom1.getX(), 0.00001);
+ 		assertEquals(1, atom1.getY(), 0.00001);
+ 		assertEquals(1, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(3, atom2.getX(), 0.00001);
+ 		assertEquals(2, atom2.getY(), 0.00001);
+ 		assertEquals(2, atom2.getZ(), 0.00001);
+
+ 		// testing 2nd chain
+ 		thegroup = s.getChain("B").getAtomGroup(0);
+ 		thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		atom1 = thegroup.getAtom("CA");
+ 		atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(4, atom1.getX(), 0.00001);
+ 		assertEquals(3, atom1.getY(), 0.00001);
+ 		assertEquals(3, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(5, atom2.getX(), 0.00001);
+ 		assertEquals(4, atom2.getY(), 0.00001);
+ 		assertEquals(4, atom2.getZ(), 0.00001);
+
+ 		
+	}
+	
+	@Test
+	public void testChainTranslate() {
+		Chain c = createDummyChain();
+
+		Vector3d translation = new Vector3d(1, 0, 0);
+ 		Calc.translate(c, translation);
+ 		
+ 		Group thegroup = c.getAtomGroup(0);
+ 		Group thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		Atom atom1 = thegroup.getAtom("CA");
+ 		Atom atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shifted by 1
+ 		assertEquals(2, atom1.getX(), 0.00001);
+ 		assertEquals(1, atom1.getY(), 0.00001);
+ 		assertEquals(1, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shifted by 1
+ 		assertEquals(3, atom2.getX(), 0.00001);
+ 		assertEquals(2, atom2.getY(), 0.00001);
+ 		assertEquals(2, atom2.getZ(), 0.00001);
+	}
+	
+	@Test
+	public void testStructureTranslate() {
+		Structure s = createDummyStructure();
+		
+		Vector3d translation = new Vector3d(1, 0, 0);
+ 		Calc.translate(s, translation);
+ 		
+ 		// testing 1st chain
+ 		Group thegroup = s.getChain("A").getAtomGroup(0);
+ 		Group thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		Atom atom1 = thegroup.getAtom("CA");
+ 		Atom atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(2, atom1.getX(), 0.00001);
+ 		assertEquals(1, atom1.getY(), 0.00001);
+ 		assertEquals(1, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(3, atom2.getX(), 0.00001);
+ 		assertEquals(2, atom2.getY(), 0.00001);
+ 		assertEquals(2, atom2.getZ(), 0.00001);
+
+ 		// testing 2nd chain
+ 		thegroup = s.getChain("B").getAtomGroup(0);
+ 		thealtlocgroup = thegroup.getAltLocs().get(0);
+ 		
+ 		atom1 = thegroup.getAtom("CA");
+ 		atom2 = thealtlocgroup.getAtom("CA");
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(4, atom1.getX(), 0.00001);
+ 		assertEquals(3, atom1.getY(), 0.00001);
+ 		assertEquals(3, atom1.getZ(), 0.00001);
+ 		
+ 		// x should be shitfted by 1
+ 		assertEquals(5, atom2.getX(), 0.00001);
+ 		assertEquals(4, atom2.getY(), 0.00001);
+ 		assertEquals(4, atom2.getZ(), 0.00001);
+	}
+
+	private static Atom getAtom(String name, double x, double y, double z) {
 		Atom a = new AtomImpl();
 		a.setX(x);
 		a.setY(y);
 		a.setZ(z);
+		a.setName(name);
 		return a;
 	}
+	
+	private static Atom getAtom(double x, double y, double z) {
+		return getAtom(null, x, y, z);
+	}
 
 	private static Matrix4d getSampleTransform(){
 
@@ -174,5 +324,53 @@ private static Matrix4d getSampleTransform(){
 		                                0.0,0.0,0.0,1.0});
 		return sample;
 	}
+	
+	private static Chain createDummyChain() {
+		Group g = new AminoAcidImpl();
+		Atom a = getAtom("CA", 1, 1, 1);
+		g.addAtom(a);
+		Group altLocG = new AminoAcidImpl();
+		Atom a2 = getAtom("CA", 2, 2, 2);
+		altLocG.addAtom(a2);
+		
+		g.addAltLoc(altLocG);
+		
+		Chain c = new ChainImpl();
+		c.addGroup(g);
+		return c;
+	}
+	
+	private static Structure createDummyStructure() {
+		Group g = new AminoAcidImpl();
+		Atom a = getAtom("CA", 1, 1, 1);
+		g.addAtom(a);
+		Group altLocG = new AminoAcidImpl();
+		Atom a2 = getAtom("CA", 2, 2, 2);
+		altLocG.addAtom(a2);
+		
+		g.addAltLoc(altLocG);
+		
+		Chain c1 = new ChainImpl();
+		c1.addGroup(g);
+		c1.setId("A");
+		
+		Group gc2 = new AminoAcidImpl();
+		Atom ac2 = getAtom("CA", 3, 3, 3);
+		gc2.addAtom(ac2);
+		Group altLocGc2 = new AminoAcidImpl();
+		Atom ac22 = getAtom("CA", 4, 4, 4);
+		altLocGc2.addAtom(ac22);
+		
+		gc2.addAltLoc(altLocGc2);
+		
+		Chain c2 = new ChainImpl();
+		c2.addGroup(gc2);
+		c2.setId("B");
+		
+		Structure s = new StructureImpl();
+		s.addChain(c1);
+		s.addChain(c2);
+		return s;
+	}
 
 }