Phase plate CTF Estimation¶

Low defocus CTF estimation can be done with CTFFind4 and gCTF. With a few critical changes of the default parameters:

Nominal Defocus¶

Set this to be slightly higher than the defocus used, otherwise the algorithm tend to fit it with lower defocus values and high phase shift.

Defocus Search Range¶

Set the step of search range smaller so that it does not extend to very low defocus for the same reason above.

Lowest Resolution for Search¶

Because of the much higher contrast from specimen structural factor at low resolution, CTF estimation programs tend to bias phase shift estimation at this edge.
Enter a value at higher resolution than any of these. See the above screenshot as an example.

Activate phase shift estimation¶

Activate "Do phase shift"

Phase Shift Intial Search Range¶

If the maximal phase shift is known, this value should be adjusted.