diff --git a/configure b/configure
index 5a6e3fe334..48127ef87e 100755
--- a/configure
+++ b/configure
@@ -655,6 +655,7 @@ CPPFLAGS
 LDFLAGS
 CXXFLAGS
 CXX
+CYTHON_FOUND
 PYTHON_CFLAGS
 PYTHON_LDFLAGS
 PYBIND11_CFLAGS
@@ -3251,6 +3252,7 @@ fi
 
 
 
+
 # by default use -O flag
 # we override the autoconf default (-g) because in release build we do not want to
 # include symbol information (obj files are huge)
@@ -8973,44 +8975,9 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_FFTW" >&2;}
 
 fi
 
-if test $pycv = true  ; then
-  if test -n "$PYTHON_BIN"
-  then
-    { $as_echo "$as_me:${as_lineno-$LINENO}: Python executable is $PYTHON_BIN" >&5
-$as_echo "$as_me: Python executable is $PYTHON_BIN" >&6;}
-    { $as_echo "$as_me:${as_lineno-$LINENO}: checking pycv: support for required python modules (python3, pybind11, numpy)" >&5
-$as_echo_n "checking pycv: support for required python modules (python3, pybind11, numpy)... " >&6; }
-testimport="
-import numpy
-import pybind11
-#no need to check for python3, if you have python2, you don't have pybind11 (and vice-versa)
-"
-    if echo "$testimport" | "$PYTHON_BIN" 1>/dev/null 2>/dev/null;  then
-       { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
-       pyver=$($PYTHON_BIN -c "import sysconfig;print(sysconfig.get_config_var('VERSION'))")
-       python_config=python${pyver}-config
-       PYBIND11_CFLAGS="$($PYTHON_BIN -m pybind11 --includes) -fvisibility=hidden"
-       PYTHON_CFLAGS=$(${python_config} --cflags --embed)
-       PYTHON_LDFLAGS=$(${python_config} --ldflags --embed)
-       #TODO: conda_fixup
-       PLUMED_CAN_PYCV=yes
-    else
-       { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-       { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable pycv" >&5
-$as_echo "$as_me: WARNING: cannot enable pycv" >&2;}
-    fi
-  else
-    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable pycv" >&5
-$as_echo "$as_me: WARNING: cannot enable pycv" >&2;}
-  fi
-fi
-
-if test $python = true  ; then
 # if PYTHON_BIN is defined, it is expected to be the full path to python
 # Otherwise, search from a list of names:
-  if test -z "$PYTHON_BIN" ; then
+if test -z "$PYTHON_BIN" ; then
     for ac_prog in python
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
@@ -9053,14 +9020,43 @@ fi
   test -n "$PYTHON_BIN" && break
 done
 
-  fi
-  if test -n "$PYTHON_BIN"
-  then
+fi
+if test -n "$PYTHON_BIN" ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: Python executable is $PYTHON_BIN" >&5
 $as_echo "$as_me: Python executable is $PYTHON_BIN" >&6;}
+  if test $pycv = true  ; then
+    { $as_echo "$as_me:${as_lineno-$LINENO}: checking pycv: support for required python modules (python3, pybind11, numpy)" >&5
+$as_echo_n "checking pycv: support for required python modules (python3, pybind11, numpy)... " >&6; }
+  testimport="
+import numpy
+import pybind11
+#no need to check for python3, if you have python2, you don't have pybind11 (and vice-versa)
+"
+    if echo "$testimport" | "$PYTHON_BIN" 1>/dev/null 2>/dev/null;  then
+       { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+       pyver=$($PYTHON_BIN -c "import sysconfig;print(sysconfig.get_config_var('VERSION'))")
+       python_config=python${pyver}-config
+       PYBIND11_CFLAGS="$($PYTHON_BIN -m pybind11 --includes) -fvisibility=hidden"
+       PYTHON_CFLAGS=$(${python_config} --cflags --embed)
+       PYTHON_LDFLAGS=$(${python_config} --ldflags --embed)
+       #TODO: conda_fixup
+       PLUMED_CAN_PYCV=yes
+    else
+       { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+       { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable pycv" >&5
+$as_echo "$as_me: WARNING: cannot enable pycv" >&2;}
+    fi
+  else
+    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable pycv" >&5
+$as_echo "$as_me: WARNING: cannot enable pycv" >&2;}
+  fi
+
+  if test $python = true  ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: checking support for required python modules (python3, setuptools, cython)" >&5
 $as_echo_n "checking support for required python modules (python3, setuptools, cython)... " >&6; }
-testimport="
+    testimport="
 from setuptools import setup
 from setuptools import Extension
 from Cython.Build import cythonize
@@ -9073,12 +9069,12 @@ if sys.version_info < (3,):
 $as_echo "yes" >&6; }
        $as_echo "#define __PLUMED_HAS_PYTHON 1" >>confdefs.h
 
+       CYTHON_FOUND=yes
     else
        { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
 $as_echo "no" >&6; }
        { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable python interface" >&5
 $as_echo "$as_me: WARNING: cannot enable python interface" >&2;}
-       PYTHON_BIN=
     fi
   else
     { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable python interface" >&5
@@ -9086,6 +9082,11 @@ $as_echo "$as_me: WARNING: cannot enable python interface" >&2;}
   fi
 fi
 
+if test "${PLUMED_CAN_PYCV}" != yes &&  test "${CYTHON_FOUND}" != yes; then
+  #this deactivate python bin if no package was found
+  PYTHON_BIN=
+fi
+
 if test "$af_ocl" = true ; then
 
     found=ko
diff --git a/configure.ac b/configure.ac
index 44dfac3d8e..7c65c52008 100644
--- a/configure.ac
+++ b/configure.ac
@@ -844,12 +844,16 @@ if test $fftw = true ; then
   PLUMED_CHECK_PACKAGE([fftw3.h],[fftw_execute],[__PLUMED_HAS_FFTW],[fftw3])
 fi
 
-if test $pycv = true  ; then
-  if test -n "$PYTHON_BIN"
-  then
+# if PYTHON_BIN is defined, it is expected to be the full path to python
+# Otherwise, search from a list of names:  
+if test -z "$PYTHON_BIN" ; then
+    AC_CHECK_PROGS([PYTHON_BIN],[python])
+fi
+if test -n "$PYTHON_BIN" ; then
     AC_MSG_NOTICE([Python executable is $PYTHON_BIN])
+  if test $pycv = true  ; then
     AC_MSG_CHECKING([pycv: support for required python modules (python3, pybind11, numpy)])
-testimport="
+  testimport="
 import numpy
 import pybind11
 #no need to check for python3, if you have python2, you don't have pybind11 (and vice-versa)
@@ -870,19 +874,10 @@ import pybind11
   else
     AC_MSG_WARN([cannot enable pycv])
   fi
-fi
 
-if test $python = true  ; then
-# if PYTHON_BIN is defined, it is expected to be the full path to python
-# Otherwise, search from a list of names:
-  if test -z "$PYTHON_BIN" ; then
-    AC_CHECK_PROGS([PYTHON_BIN],[python])
-  fi
-  if test -n "$PYTHON_BIN"
-  then
-    AC_MSG_NOTICE([Python executable is $PYTHON_BIN])
+  if test $python = true  ; then
     AC_MSG_CHECKING([support for required python modules (python3, setuptools, cython)])
-testimport="
+    testimport="
 from setuptools import setup
 from setuptools import Extension
 from Cython.Build import cythonize
@@ -903,6 +898,11 @@ if sys.version_info < (3,):
   fi
 fi
 
+if test "${PLUMED_CAN_PYCV}" != yes &&  test "${CYTHON_FOUND}" != yes; then
+  #this deactivate python bin if no package was found
+  PYTHON_BIN=
+fi
+
 if test "$af_ocl" = true ; then
   PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afopencl])
   PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE_OCL],[afopencl])