I was wondering if you might incorporate this new feature into future versions of CTFFind?
I think it would be a big aid if calling the program with something like -h/--h/-help/--help would output a full list of required and optional parameters and switches.
Currently in CTFFind 4.1.8 I receive this when I attempt that:
$ ./ctffind help
Usage: ctffind [--old-school-input] [--old-school-input-ctffind4] [--amplitude-spectrum-input] [--filtered-amplitude-spectrum-input] [--fast] [controller_address] [controller_port] [job_code]
--old-school-input Pretend this is ctffind3 (for compatibility with old scripts and programs)
--old-school-input-ctffind4 Accept parameters from stdin, like ctffind3, but with extra lines for ctffind4-specific options (movie processing and phase shift estimation
--amplitude-spectrum-input The input image is an amplitude spectrum, not a real-space image
--filtered-amplitude-spectrum-input The input image is filtered (background-subtracted) amplitude spectrum
--fast Skip computation of fit statistics as well as spectrum contrast enhancement
Which has some switches but does not say what is required and I don't think this is a complete list of possible parameters.
Please let me know if you'd like me to elaborate on this suggestion