diff --git a/pytests/xmol/polymer/test_Atom.py b/pytests/xmol/polymer/test_Atom.py
index a187fac6..411b31a7 100644
--- a/pytests/xmol/polymer/test_Atom.py
+++ b/pytests/xmol/polymer/test_Atom.py
@@ -500,28 +500,3 @@ def test_bad_selection_construction_from_list():
         AtomSelection([ a for a in frame.asChains ])
     with pytest.raises(Exception):
         ChainSelection([ a for a in frame.asResidues ])
-
-
-
-def test_shorthands():
-    # from pyxmolpp2.polymer import AtomSelection, ChainSelection
-
-    frame = make_polyglycine([("A", 20)])
-
-    asel = frame.asAtoms
-
-    asel.geom_center()
-    asel.mass_center([1.0]*asel.size)
-    asel.inertia_tensor([1.0]*asel.size)
-    asel.geom_inertia_tensor()
-    asel.rmsd(asel)
-    asel.rmsd(asel.toCoords)
-    asel.alignment(asel)
-    asel.alignment(asel.toCoords)
-    asel.align_to(asel)
-    asel.align_to(asel.toCoords)
-
-
-
-
-
diff --git a/pytests/xmol/polymer/test_shortcuts.py b/pytests/xmol/polymer/test_shortcuts.py
new file mode 100644
index 00000000..f4eefd8b
--- /dev/null
+++ b/pytests/xmol/polymer/test_shortcuts.py
@@ -0,0 +1,68 @@
+def make_polyglycine(chain_lengths, no_reserve=True):
+    from pyxmolpp2.polymer import Frame
+    from pyxmolpp2.polymer import ChainName
+    from pyxmolpp2.polymer import AtomName
+    from pyxmolpp2.polymer import ResidueName, ResidueId
+    from pyxmolpp2.geometry import XYZ
+
+    aid = 1
+    rid = 1
+    frame = Frame(0)
+    for chainId, N in chain_lengths:
+        if no_reserve:
+            c = frame.emplace(ChainName(chainId))
+        else:
+            c = frame.emplace(ChainName(chainId), N)
+        for i in range(N):
+            if no_reserve:
+                r = c.emplace(ResidueName("GLY"), ResidueId(rid))
+            else:
+                r = c.emplace(ResidueName("GLY"), ResidueId(rid), 7)
+
+            rid += 1
+            for aname in ["N", "H", "CA", "HA2", "HA3", "C", "O"]:
+                r.emplace(AtomName(aname), aid, XYZ(1, 2, 3))
+                aid += 1
+
+    return frame
+
+
+def test_shorthands():
+    import numpy as np
+
+    from pyxmolpp2.geometry import Rotation3d, Translation3d, XYZ, Degrees, calc_alignment
+
+    frame = make_polyglycine([("A", 20)])
+    for a in frame.asAtoms:
+        a.r = XYZ(*np.random.random(3))
+    frame2 = frame.copy()
+
+    asel = frame.asAtoms
+    asel2 = frame2.asAtoms
+
+    asel.geom_center()
+    asel.mass_center([1.0] * asel.size)
+    asel.inertia_tensor([1.0] * asel.size)
+    asel.geom_inertia_tensor()
+
+    T = Translation3d(XYZ(1, 0, 0))
+    asel2.transform(T)
+
+    assert np.isclose(asel.rmsd(asel2), 1.0)
+    assert np.isclose(asel.rmsd(asel2.toCoords), 1.0)
+    assert np.isclose(asel.rmsd(asel2.toCoords.transform(T.inverted())), 0.0)
+
+    T = Translation3d(XYZ(1, 0, 0)) * Rotation3d(XYZ(1, 1, 1), Degrees(45))
+    asel.align_to(asel2)
+    assert np.isclose(asel.rmsd(asel2), 0)
+
+    asel2.transform(T)
+    asel.align_to(asel2.toCoords)
+    assert np.isclose(asel.rmsd(asel2), 0)
+
+    T = Translation3d(XYZ(1, 0, 0)) * Rotation3d(XYZ(1, 1, 1), Degrees(45))
+    asel2.transform(T)
+
+    assert np.allclose(T.matrix3d(), calc_alignment(asel2.toCoords, asel.toCoords).matrix3d())
+    assert np.allclose(T.matrix3d(), asel.alignment_to(asel2).matrix3d())
+    assert np.allclose(T.matrix3d(), asel.alignment_to(asel2.toCoords).matrix3d())
diff --git a/pyxmolpp/polymer/Atom.cpp b/pyxmolpp/polymer/Atom.cpp
index 3748040f..08634cf6 100644
--- a/pyxmolpp/polymer/Atom.cpp
+++ b/pyxmolpp/polymer/Atom.cpp
@@ -617,7 +617,7 @@ Order is preserved across manipulations with :py:class:`ChainSelection`
       .def(
           "rmsd",
           [](AtomSelection& sel, AtomSelection& ref) {
-            return xmol::geometry::calc_rmsd(sel.toCoords(),ref.toCoords());
+            return xmol::geometry::calc_rmsd(sel.toCoords(), ref.toCoords());
           },
           py::arg("ref"),
           "Returns rmsd between two selections")
@@ -631,18 +631,18 @@ Order is preserved across manipulations with :py:class:`ChainSelection`
           "Returns rmsd between selection and reference coordinates")
 
       .def(
-          "alignment",
+          "alignment_to",
           [](AtomSelection& sel, std::vector<XYZ> ref) {
-            return xmol::geometry::calc_alignment(sel.toCoords(), ref);
+            return xmol::geometry::calc_alignment(ref, sel.toCoords());
           },
           py::arg("ref"),
           "Equivalent to :code:`calc_alignment(ref.toCoords(), self.toCoords())`")
 
 
       .def(
-          "alignment",
+          "alignment_to",
           [](AtomSelection& sel, AtomSelection& ref) {
-            return xmol::geometry::calc_alignment(sel.toCoords(), ref.toCoords());
+            return xmol::geometry::calc_alignment(ref.toCoords(), sel.toCoords());
           },
           py::arg("ref"),
           "Equivalent to :code:`calc_alignment(ref.toCoords(), self.toCoords())`")
@@ -650,7 +650,8 @@ Order is preserved across manipulations with :py:class:`ChainSelection`
       .def(
           "align_to",
           [](AtomSelection& sel, std::vector<XYZ> ref) -> AtomSelection& {
-            xmol::geometry::calc_alignment(sel.toCoords(), ref);
+            auto al = xmol::geometry::calc_alignment(ref, sel.toCoords());
+            sel.for_each([&](Atom& a) { a.set_r(al.transform(a.r())); });
             return sel;
           },
           py::arg("ref"),
@@ -660,7 +661,8 @@ Order is preserved across manipulations with :py:class:`ChainSelection`
       .def(
           "align_to",
           [](AtomSelection& sel, AtomSelection& ref) -> AtomSelection& {
-            xmol::geometry::calc_alignment(sel.toCoords(), ref.toCoords());
+            auto al = xmol::geometry::calc_alignment(ref.toCoords(), sel.toCoords());
+            sel.for_each([&](Atom& a) { a.set_r(al.transform(a.r())); });
             return sel;
           },
           py::arg("ref"),