diff --git a/modules/base/pymod/__init__.py.in b/modules/base/pymod/__init__.py.in
index 89316b83115438dfacae9a19500b388369187001..2676aa771852b1b4407159c47f7ca10777e80874 100644
--- a/modules/base/pymod/__init__.py.in
+++ b/modules/base/pymod/__init__.py.in
@@ -20,8 +20,8 @@
 
 __all__=['CharList','Correl', 'FileLogSink', 'FloatList', 'FloatMatrix', 'FloatMatrix3', 'FloatMatrix4', 'GetCurrentLogSink', 'GetPrefixPath', 'GetSharedDataPath', 'GetVerbosityLevel', 'Histogram', 'IntList', 'LogDebug', 'LogError', 'LogInfo', 'LogScript', 'LogSink', 'LogTrace', 'LogVerbose', 'LogWarning', 'Max', 'Mean', 'Median', 'Min', 'MultiLogSink', 'PopLogSink', 'PopVerbosityLevel', 'PushLogSink', 'PushVerbosityLevel', 'Range', 'SetPrefixPath', 'StdDev', 'StreamLogSink', 'StringList', 'StringLogSink', 'Units', 'VERSION', 'VERSION_MAJOR', 'VERSION_MINOR', 'VERSION_PATCH', 'WITH_NUMPY', 'conop', 'geom', 'io', 'mol', 'seq', 'stutil' @ALL_ADDITIONAL_MODULES@]
 
-from _ost_base import *
-from stutil import *
+from ._ost_base import *
+from .stutil import *
 
 class StreamLogSink(LogSink):
   def __init__(self, stream):
diff --git a/modules/bindings/pymod/__init__.py b/modules/bindings/pymod/__init__.py
index 4510f10ef2e9b38d26efb8f5ba14c2263eb305ff..c61b4e974e96fafe00bcdef7eeb4039e04011745 100644
--- a/modules/bindings/pymod/__init__.py
+++ b/modules/bindings/pymod/__init__.py
@@ -8,4 +8,4 @@ from ost.bindings import hbplus
 from ost.bindings import clustalw
 from ost.bindings import cadscore
 from ost.bindings import align_3dcomb
-from _ost_bindings import *
+from ._ost_bindings import *
diff --git a/modules/conop/pymod/__init__.py b/modules/conop/pymod/__init__.py
index 3b7856fe1634cd5d9ec3dfb7e22218618ae2655e..b70493ec9fab999f37eba133bea8f7f567ee1c7f 100644
--- a/modules/conop/pymod/__init__.py
+++ b/modules/conop/pymod/__init__.py
@@ -16,7 +16,7 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _ost_conop import *
+from ._ost_conop import *
 
 # The 20 standard amino acids in no particular order
 STANDARD_AMINOACIDS=(
diff --git a/modules/db/pymod/__init__.py b/modules/db/pymod/__init__.py
index d443def87175ede548bcd9ff0140f3068e391c36..38881c6df2e7965196ae75e0a007f42ff1f4850f 100644
--- a/modules/db/pymod/__init__.py
+++ b/modules/db/pymod/__init__.py
@@ -16,4 +16,4 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _ost_db import *
+from ._ost_db import *
diff --git a/modules/geom/pymod/__init__.py b/modules/geom/pymod/__init__.py
index bd4691781fd76f8e22f507b9cab9a311e8c93a29..88ad89786001f3ea45e832677700844508bf3d0f 100644
--- a/modules/geom/pymod/__init__.py
+++ b/modules/geom/pymod/__init__.py
@@ -16,4 +16,4 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _ost_geom import *
+from ._ost_geom import *
diff --git a/modules/gfx/pymod/__init__.py b/modules/gfx/pymod/__init__.py
index a0525f126bd47c2015efc0784c0472561892080b..60ad84ec66082d718c582f72a7a009ce9261c549 100644
--- a/modules/gfx/pymod/__init__.py
+++ b/modules/gfx/pymod/__init__.py
@@ -16,7 +16,7 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _ost_gfx import *
+from ._ost_gfx import *
 from .py_gfx_obj import PyGfxObj
 
 WHITE=RGB(1.0,1.0,1.0)
diff --git a/modules/gfx/pymod/py_gfx_obj.py b/modules/gfx/pymod/py_gfx_obj.py
index ac91e9073a47b061ee57145e0d3d7b6b6a51dcc5..557e645ec63ca87734ba3351024c5937d6c37098 100644
--- a/modules/gfx/pymod/py_gfx_obj.py
+++ b/modules/gfx/pymod/py_gfx_obj.py
@@ -17,7 +17,7 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
 import traceback
-from _ost_gfx import *
+from ._ost_gfx import *
 
 class PyGfxObj(GfxObj):
   def __init__(self,name):
diff --git a/modules/gui/pymod/__init__.py b/modules/gui/pymod/__init__.py
index 4343829dca4a6b7a12b3215f9f0cbbad20ca20eb..68b4a7300b8e2cf51c26397871a1a8b476a79be9 100644
--- a/modules/gui/pymod/__init__.py
+++ b/modules/gui/pymod/__init__.py
@@ -17,7 +17,7 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
 import ost.gui.trajectory_viewer
-from _ost_gui import *
+from ._ost_gui import *
 import sip
 
 
diff --git a/modules/img/alg/pymod/__init__.py b/modules/img/alg/pymod/__init__.py
index d67a8675466744d97ac320e88ed67c5cf455b079..805731f76dfdc9dbd3c2a8eea7849ff4e3b77666 100644
--- a/modules/img/alg/pymod/__init__.py
+++ b/modules/img/alg/pymod/__init__.py
@@ -16,4 +16,4 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _ost_img_alg import *
+from ._ost_img_alg import *
diff --git a/modules/img/base/pymod/__init__.py b/modules/img/base/pymod/__init__.py
index 82a290219a5d9f3097ef53ff3f0dc1a7fdd4af51..398809616fd9fac1e5930d364b86fbc4043c4342 100644
--- a/modules/img/base/pymod/__init__.py
+++ b/modules/img/base/pymod/__init__.py
@@ -16,6 +16,6 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _ost_img import *
+from ._ost_img import *
 MapHandle=ImageHandle
 from ost.img import alg
diff --git a/modules/info/pymod/__init__.py b/modules/info/pymod/__init__.py
index 4243e15ac1f0a1f129535918388d15e1c58d1b11..5d78be195ffedd4eafe2a80e146d82f82a4af1f7 100644
--- a/modules/info/pymod/__init__.py
+++ b/modules/info/pymod/__init__.py
@@ -16,7 +16,7 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _ost_info import *
+from ._ost_info import *
 
 def LoadOrCreateInfo(name):
     import os.path
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index eee7af12d9d8ea7c710f53f73b41e902ac7de2b3..85e1a325e72d2fab09c2c62216b1b4a300ba8286 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -18,7 +18,7 @@
 #------------------------------------------------------------------------------
 import os, tempfile, ftplib, http.client
 
-from _ost_io import *
+from ._ost_io import *
 from ost import mol, geom, conop, seq
 
 profiles=None
diff --git a/modules/mol/alg/pymod/__init__.py b/modules/mol/alg/pymod/__init__.py
index 73d5bd802ce28765d309e65b7eed4f65374abdfb..16127a16603e93e5f3f1c19f79dfb74bdd4031a7 100644
--- a/modules/mol/alg/pymod/__init__.py
+++ b/modules/mol/alg/pymod/__init__.py
@@ -1,5 +1,5 @@
 import os.path
-from _ost_mol_alg import *
+from ._ost_mol_alg import *
 from ost.mol.alg.superpose import *
 import ost.mol.alg.trajectory_analysis
 import ost.mol.alg.structure_analysis
diff --git a/modules/mol/base/pymod/__init__.py b/modules/mol/base/pymod/__init__.py
index 512e4daf082ef7e17f8c019dc92021ff799b6ccc..e6dd8d59a623ac409043d59d62cfdde7d4e71c1f 100644
--- a/modules/mol/base/pymod/__init__.py
+++ b/modules/mol/base/pymod/__init__.py
@@ -16,7 +16,7 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _ost_mol import *
+from ._ost_mol import *
 import ost.geom as _geom
 from ost.mol import alg
 
diff --git a/modules/mol/mm/pymod/__init__.py b/modules/mol/mm/pymod/__init__.py
index f10fd7e6b69b7e5130e165de2063830c4f0c4f61..ac671a2b6254cedf823225c7cf81939f82faa151 100644
--- a/modules/mol/mm/pymod/__init__.py
+++ b/modules/mol/mm/pymod/__init__.py
@@ -18,7 +18,7 @@
 #------------------------------------------------------------------------------
 
 import os.path
-from _ost_mol_mm import *
+from ._ost_mol_mm import *
 from . import antechamber
 import ost
 
diff --git a/modules/seq/alg/pymod/__init__.py b/modules/seq/alg/pymod/__init__.py
index 8d9b9c806e1c15adcadf4574ee4a60c49b17defc..9ce2fff112b942dd6e2a6fa1d207bae78ee6bb10 100644
--- a/modules/seq/alg/pymod/__init__.py
+++ b/modules/seq/alg/pymod/__init__.py
@@ -1,4 +1,4 @@
-from _ost_seq_alg import *
+from ._ost_seq_alg import *
 from ost.seq.alg.mat import *
 
 def ValidateSEQRESAlignment(aln, chain=None):
diff --git a/modules/seq/base/pymod/__init__.py b/modules/seq/base/pymod/__init__.py
index 1594a25530766d92b4817954e7e129f8cfaafe6d..2e45c5a10724bbb3877b7518fbded88c4ae4bd05 100644
--- a/modules/seq/base/pymod/__init__.py
+++ b/modules/seq/base/pymod/__init__.py
@@ -16,7 +16,7 @@
 # along with this library; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
-from _ost_seq import *
+from ._ost_seq import *
 from ost.seq import alg
 
 _CreateAlignment=CreateAlignment