Hi @olibclarke,
To your first question, the soft windowing on the particle images is actually applied before the CTF is used. That meaning, particles are windowed at the start, then are used for alignment/reconstruction along with the previously estimated CTF values.
For your second question, windowing is applied relative to the original center of the extracted particles, rather than the fulcrum. Right now, local refinement doesn’t recenter particles on the fulcrum, instead it modifies the shifts to achieve the same effect (as doing rotations around the fulcrum).
Best,
Michael