The difference between the two is that in Phase only correction
only the phase of the CTF is flipped whereas in Phase and Amplitude
correction, Wiener filtering is done to correct both phase and
amplitude. If the envelope function and noise spectrum parameters
are not available then phase only correction is recommended.
For example if the parameters calculated from far from focus images
are used to correct near to focus images (after adjusting for the
defocus difference), the envelope function and noise spectrum
parameter estimates of far from focus images are not reliable for
near to focus images.