If you get a 'Bad Interpreter' error
It is probably due to Mountain Lion's new quarantining process. You can try this:
xattr -dr com.apple.quarantine /Applications/EMAN2
Alternatively, you may have installed the wrong EMAN2 package for your operating system. Due to different Python versions, make sure you use the correct Mac OS X 10.6 build, or the Mac OS X 10.7 / 10.8 build.
Installing EMAN2 in my home directory
If you do not have Administrator privileges on your system or want to install EMAN2 in your home directory, you will want to modify the eman2.bashrc file to reflect the correct path to EMAN2 in the EMAN2DIR variable, e.g.:
export EMAN2DIR=/Users/irees/EMAN2
Other shells
If you run tcsh as your shell, the shell init file is "~/.cshrc", and the EMAN2 init script is eman2.cshrc:
test -r /Applications/EMAN2/eman2.cshrc && source /Applications/EMAN2/eman2.cshrc