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e2ctf
To get familiar with how e2ctf.py works, try separating the way you using e2ctf.py into three stages:
Auto fitting
e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit
Fine tuning
(save any changes you make with the Save Parms button)
e2ctf.py 1.img --gui
Write output
e2ctf.py 1.img --phaseflip --wiener
The output will be in the particles directory. Also, you can supply more than one image as input to e2ctf.py.
You can combine more than command would have worked if you had used a command like this:
e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit --gui