using ctffind4 from Relion 1.3

To use ctffind4 from Relion 1.3, you need to supply ctffind with the "--old-school-input" command-line flag. You also need to surround the whole command with double quotes. Here is a simplified example from the command lien:

--ctffind3_exe "/lmb/home/tmartin/programs/ctffind-4.0.7-linux64/ctffind --omp-num-threads 1 --old-school-input"

Or from the Relion GUI, replace the executable by:
"/lmb/home/tmartin/programs/ctffind-4.0.7-linux64/ctffind --omp-num-threads 1 --old-school-input"

Thanks to Sjors Sheres & co-workers, as well as Ming Sun (Frank lab) for testing this.