Configure EMAN2

1. Go to 'build' and type 

ccmake ../eman2

2. Link all libraries properly.

When using Homebrew, this phase takes a little more care to get right. I suggest comparing your screen to the one I've pasted below (using OS X 10.8): 

BOOST_INCLUDE_PATH               /usr/local/include
 BOOST_LIBRARY                    /usr/local/lib/libboost_python.dylib
 CMAKE_BUILD_TYPE
 CMAKE_OSX_ARCHITECTURES
 CMAKE_OSX_DEPLOYMENT_TARGET
 CMAKE_OSX_SYSROOT                /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platf
 CMAKE_VERBOSE_MAKEFILE           OFF
 EMAN_INSTALL_PREFIX              /Users/jmbell/EMAN2
 ENABLE_AUTODOC                   OFF
 ENABLE_BOUNDS_CHECKING           OFF
 ENABLE_DEBUG                     OFF
 ENABLE_EMAN_CUDA                 OFF
 ENABLE_FFTW2                     OFF
 ENABLE_FFTW3                     ON
 ENABLE_FFTW_PLAN_CACHING         ON
 ENABLE_FFT_CACHING               OFF
 ENABLE_FTGL                      ON
 ENABLE_HDF5                      ON
 ENABLE_IOCACHE                   OFF
 ENABLE_JPEG                      ON
 ENABLE_MEMDEBUG                  OFF
 ENABLE_MEMDEBUG2                 OFF
 ENABLE_NATIVE_FFT                OFF
 ENABLE_NFFT2                     OFF
 ENABLE_OPENGL                    ON
 ENABLE_OPTIMIZE_MACHINE          ON
 ENABLE_OPTIMIZE_MOUNTAIN_LION    OFF
 ENABLE_OPTIMIZE_WINDOWS_VC       OFF
 ENABLE_OPTIMIZE_X86_64           OFF
 ENABLE_OPTPP                     OFF
 ENABLE_PNG                       ON
 ENABLE_PROFILE                   OFF
 ENABLE_RT                        ON
 ENABLE_SPARX_CUDA                OFF
 ENABLE_TIFF                      ON
 ENABLE_V4L2                      OFF
 FFTW3_INCLUDE_PATH               /usr/local/include
 FFTW3_LIBRARY                    /usr/local/lib/libfftw3f.dylib
 FREETYPE_INCLUDE_PATH            /usr/local/include/freetype2
 FREETYPE_LIBRARY                 /usr/local/lib/libfreetype.dylib
 FTGL_INCLUDE_PATH                /usr/local/include
 FTGL_LIBRARY                     /usr/local/lib/libftgl.dylib
 GSL_CBLAS_INCLUDE_PATH           /usr/local/include
 GSL_CBLAS_LIBRARY                /usr/local/lib/libgslcblas.dylib
 GSL_INCLUDE_PATH                 /usr/local/include
 GSL_LIBRARY                      /usr/local/lib/libgsl.dylib
 HDF5_INCLUDE_PATH                /usr/local/include
 HDF5_LIBRARY                     /usr/local/lib/libhdf5.dylib
 JPEG_INCLUDE_PATH                /Library/Frameworks/UnixImageIO.framework/Headers
 JPEG_LIBRARY                     /usr/local/lib/libjpeg.dylib
 NUMPY_INCLUDE_PATH               /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/l
 PNG_INCLUDE_PATH                 /Library/Frameworks/UnixImageIO.framework/Headers
 PNG_LIBRARY                      /usr/local/lib/libpng.dylib
 PYTHON_INCLUDE_PATH              /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platf
 PYTHON_LIBRARY                   /usr/lib/libpython2.7.dylib
 TIFF_INCLUDE_PATH                /Library/Frameworks/UnixImageIO.framework/Headers
 TIFF_LIBRARY                     /usr/local/lib/libtiff.dylib
 ZLIB_LIBRARY                     /usr/lib/libz.dylib