diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
index 9c0d1b129540617ecd1c49e385174a9051ecc7ee..dff0fb617f4c85a592a0eadb44f21475ff5581d5 100644
--- a/scripts/CMakeLists.txt
+++ b/scripts/CMakeLists.txt
@@ -1,4 +1,5 @@
-set(SUBST_DICT OST_ROOT="${OST_ROOT}" 
+set(SUBST_DICT OST_ROOT="${OST_ROOT}"
+               QMEAN_ROOT=${QMEAN_ROOT}
                LIBDIR=${LIB_DIR}
                LIBEXECPATH=${LIBEXEC_PATH}
                PYTHON_VERSION=${PYTHON_VERSION})
diff --git a/scripts/pm.in b/scripts/pm.in
index d6992a94a495835f178f676ee724a18a0804b839..cd5cbf8f913db72e364548dfb314cd3ebbae11fd 100755
--- a/scripts/pm.in
+++ b/scripts/pm.in
@@ -21,12 +21,9 @@ SCRIPT_NAME=$0
 BIN_DIR=$( cd `dirname "$SCRIPT_NAME"`; pwd)
 export PROMOD3_ROOT="$BIN_DIR/.."
 PROMOD3_EXEC_PATH="$PROMOD3_ROOT/@LIBEXECPATH@"
-export PYTHONPATH="${PROMOD3_ROOT}/@LIBDIR@/python@PYTHON_VERSION@/site-packages:${PYTHONPATH}"
+export PYTHONPATH="${PROMOD3_ROOT}/@LIBDIR@/python@PYTHON_VERSION@/site-packages:@QMEAN_ROOT@/@LIBDIR@/qmean:${PYTHONPATH}"
 export PATH="$BIN_DIR:@OST_ROOT@/bin:$PATH"
 export LD_LIBRARY_PATH="${PROMOD3_ROOT}/@LIBDIR@:$LD_LIBRARY_PATH"
-if test -n "@QMEAN_ROOT@" ; then
-  export PYTHONPATH="@QMEAN_ROOT@/@LIBDIR@/qmean:${PYTHONPATH}"
-fi
 
 ACTION="$1"
 PROMOD3_SCRIPT="${PROMOD3_EXEC_PATH}/pm-${ACTION}"