Phacon
Phase contrast portion for CTF correction [phacon]
allows to specify the amount of Phase Contrast in the image. This information is used for the correction of the Contrast Transfer Function in ctfapply. The Phase Contrast portion is corrected as elastically scattered, and its CTF is calculated as the sinus of the phaseshift of the beam in the sample. The amplitude contrast due to inelastically scattered electrons instead contributes to the CTF as the cosinus of the phaseshift. The amplitude contrast portion is calculated from the phase contrast portion by assuming that:
AmplitudeContrast = SQRT( 1 - PhaseContrast^2 )
Usually the value for phacon is 0.9975, which corresponds to 7% amplitude contrast.