EMAN2 use [http://www.boost.org/libs/python/doc/ Boost.python] to wrap c++ function to Python. [http://www.boost.org/libs/python/pyste/ Pyste] is a Boost.Python code generator. In EMAN2 there is a script create_boost_python in /eman2/libpyEM directory call [http://www.boost.org/libs/python/pyste/ Pyste] to create c++ wrapping files libpy***.cpp. Then the c++ compiler will create libraries which contain all the Python function call of EMAN2. Current release of [http://www.boost.org/libs/python/pyste/ Pyste] has a dificit for the default argument handling. So please replace two of your Pyste files in Python site-packages with attached files.