diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
index 18eb3244bbcd325f0a7cd4f8c53252e665fa0993..2b1cf48e95cf92991df3b3ba698664f516f34e0e 100644
--- a/scripts/CMakeLists.txt
+++ b/scripts/CMakeLists.txt
@@ -29,7 +29,6 @@ endif()
 set(INIT_SCRIPTS 
   init.py
   init_cl.py
-  init_iplt.py
 )
 copy_if_different("./" "${STAGE_DIR}/${LIB_DIR}/openstructure" 
                   "${INIT_SCRIPTS}" "python init scripts" ost_scripts)
diff --git a/scripts/dng_cl.in b/scripts/dng_cl.in
deleted file mode 100755
index bdffbb19a4dfb9d864615b4a7c45fe3b6e61d39a..0000000000000000000000000000000000000000
--- a/scripts/dng_cl.in
+++ /dev/null
@@ -1,110 +0,0 @@
-#!/bin/bash
-#------------------------------------------------------------------------------
-# This file is part of the OpenStructure project <www.openstructure.org>
-#
-# Copyright (C) 2008-2011 by the OpenStructure authors
-#
-# This library is free software; you can redistribute it and/or modify it under
-# the terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation; either version 3.0 of the License, or (at your option)
-# any later version.
-# This library 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 Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-#------------------------------------------------------------------------------
-
-#
-# convenience wrapper for non-gui dng
-#
-# Self detect important directories
-SCRIPT_NAME=$0
-BIN_DIR=`dirname $SCRIPT_NAME`
-export DNG_ROOT=$BIN_DIR/..
-export PATH=$BIN_DIR:$PATH
-
-# set ld_library_path and pythonhome for bundle (commented except in linux bundles)
-#export LD_LIBRARY_PATH=$DNG_ROOT/@LIBDIR@:$LD_LIBRARY_PATH
-#export PYTHONPATH=$DING_ROOT/@LIBDIR@/python2.6
-
-# retrieve absolute path to python executable
-pyexec=""
-if [ -z "$DNG_ATTACH_VALGRIND" ]; then
-  pyexec="@PYTHON_BINARY@"
-else
-  pyexec="valgrind --leak-check=full @PYTHON_BINARY@"
-fi
-
-if [ ! -f "$pyexec" ]; then 
-  echo "Error: Python executable '$pyexec' not found!"
-  exit
-fi
-
-set -o noglob
-
-# decide whether to start interactively or not
-# interactive mode can be forced by setting -i as a dng_cl option
-interactive=""
-if [ $# == 0 ];then
-  interactive="-i"
-else
-  opts=""
-  for argument in $*;do 
-    if [ $argument == "-i" ] ;then
-      interactive="-i"
-    else
-      opts=$opts" "$argument
-    fi
-  done
-fi
-# finally pass control to python instance
-exec $pyexec $interactive -c "
-import sys, os, platform
-if platform.machine()=='x86_64':
-  sys.path.insert(0, os.getenv('DNG_ROOT')+'/lib64/dng/pymod')
-else:
-  sys.path.insert(0,os.getenv('DNG_ROOT')+'/lib/dng/pymod')
-     
-from dng import io, mol, seq, gfx, SetPrefixPath
-try: 
-  from dng import img
-except ImportError:
-  pass
-SetPrefixPath(os.getenv('DNG_ROOT'))
-import os.path
-HistoryFile=os.path.expanduser('~/.dng_history')
-InGUIMode=False
-
-#try:
- # import readline, rlcompleter
-
-#  def SaveHistory(historyPath):
-#    readline.write_history_file(historyPath)
-#
-#  readline.parse_and_bind('tab: complete')
-#  if os.path.isfile(HistoryFile):
-#    readline.read_history_file(HistoryFile)
-#except ImportError:
-#  pass
-  
-gfx.set_offscreen_mode()
-sys.ps1='dng> '
-sys.ps2='..... '
-print ''
-sys.argv=sys.argv[1:]
-_dngrc=os.path.join(os.getenv('HOME'), '.dngrc')
-if os.path.exists(_dngrc):
-  try:
-    exec(open(_dngrc))
-  except Exception, e:
-    print e
-
-if(len(sys.argv)>0):
-  script=sys.argv[0]
-  execfile(script)
-"  $opts
-
diff --git a/scripts/gipltng.bat.in b/scripts/gipltng.bat.in
deleted file mode 100644
index 8c69318e475c41324115c25d96bec4de7e2bc719..0000000000000000000000000000000000000000
--- a/scripts/gipltng.bat.in
+++ /dev/null
@@ -1,30 +0,0 @@
-@ECHO OFF
-REM ------------------------------------------------------------------------------
-REM This file is part of the OpenStructure project <www.openstructure.org>
-REM
-REM Copyright (C) 2008-2011 by the OpenStructure authors
-REM
-REM This library is free software; you can redistribute it and/or modify it under
-REM the terms of the GNU Lesser General Public License as published by the Free
-REM Software Foundation; either version 3.0 of the License, or (at your option)
-REM any later version.
-REM This library is distributed in the hope that it will be useful, but WITHOUT
-REM ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-REM FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
-REM details.
-REM
-REM You should have received a copy of the GNU Lesser General Public License
-REM along with this library; if not, write to the Free Software Foundation, Inc.,
-REM 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-REM ------------------------------------------------------------------------------
-REM Windows startup script for a protein-centric user interface
-REM Author: Juergen Haas
-
-REM Self detect important directories
-set SCRIPT_NAME=%0%
-set BIN_DIR=%~dp0
-echo %BIN_DIR%
-
-set DNG_ROOT=%BIN_DIR%\..
-set PATH=%BIN_DIR%;%DNG_ROOT%\@LIBDIR@\@BUILD_TYPE@;%DNG_ROOT%\@LIBDIR@;%DNG_ROOT%\bin\@BUILD_TYPE@;%PATH%
-"%BIN_DIR%\@BUILD_TYPE@\gosty.exe" "%DNG_ROOT%\@LIBDIR@\openstructure\init_iplt.py" ost %*
diff --git a/scripts/gipltng.in b/scripts/gipltng.in
deleted file mode 100755
index 0f06c53fd219baa0a126b4dad3a374633ba8693b..0000000000000000000000000000000000000000
--- a/scripts/gipltng.in
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/bin/bash
-#------------------------------------------------------------------------------
-# This file is part of the OpenStructure project <www.openstructure.org>
-#
-# Copyright (C) 2008-2011 by the OpenStructure authors
-#
-# This library is free software; you can redistribute it and/or modify it under
-# the terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation; either version 3.0 of the License, or (at your option)
-# any later version.
-# This library 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 Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
-#------------------------------------------------------------------------------
-# Startup script for a protein-centric user interface
-# Author: Andreas Schenk, Marco Biasini
-
-# Self detect important directories
-SCRIPT_NAME=$0
-BIN_DIR=`dirname $SCRIPT_NAME`
-export DNG_ROOT=$BIN_DIR/..
-export PATH=$BIN_DIR:$PATH
-
-export LD_LIBRARY_PATH=$DNG_ROOT/@LIBDIR@:$LD_LIBRARY_PATH
-# set pythonhome for bundle (commented except in linux bundles)
-#export PYTHONHOME=$DNG_ROOT
-
-# store code in shell variable. Reduces the actuall call to gosty to just one 
-# line. If the HERE documnt is fed directly into gosty, the backtrace shows the 
-# full command in case of a segfault which is very confusing and not helpful 
-# at all
-gosty $DNG_ROOT/@LIBDIR@/openstructure/init_iplt.py img $@
diff --git a/scripts/init_iplt.py b/scripts/init_iplt.py
deleted file mode 100644
index fea91b20b2acd37cc50dba3a8be66558d7ef48dc..0000000000000000000000000000000000000000
--- a/scripts/init_iplt.py
+++ /dev/null
@@ -1,29 +0,0 @@
-from ost import gui
-import sip
-from ost.img import *
-import ost.img.alg as alg
-
-from PyQt4 import QtGui, QtCore
-from ost.gui.init_menubar import _InitMenuBar
-
-
-def Viewer(image,title=""):
-  app=gui.GostyApp.Instance()
-  viewer=app.CreateDataViewer(image)
-  app.perspective.main_area.AddWidget(title, viewer)
-  return viewer
-
-def _InitPanels(app, panels):
-  panels.AddWidgetToPool('ost.gui.PythonShell', 1)
-  if not panels.Restore("img/ui/perspective/panels"):
-    panels.AddWidget(gui.PanelPosition.BOTTOM_PANEL, app.py_shell)
-
-def _InitIPLTNextGen():
-  app=gui.GostyApp.Instance()
-  app.SetAppTitle("IPLT - Iplt Next Generation")
-  main_area=app.perspective.main_area
-  _InitPanels(app, app.perspective.panels)
-  _InitMenuBar(app.perspective.GetMenuBar())
-  app.perspective.Restore()
-
-_InitIPLTNextGen()