Q: I forgot to invert my particles (they are black on a white background), and I've already done CTF correction. How can I fix it ?
A: The following assumes you are using bash or a similar shell. If you use zsh or csh, you may need to alter this a bit:
cd <the project directory> for i in `e2bdb.py particles -s` do e2proc2d.py $i $i --inplace --mult=-1 done
That's it. That will invert ALL of your particle data without messing up any of the CTF parameters.