Thank you!
I will try this out. A little question already: After symmetry expansion and before recentering I already did a local refinement of the protomer of interest (yielding a high resolution). I reextracted at a boxsize of 400 px after re-centering (initial boxsize 576 px) with “recenter using aligned shifts” enabled. A box size large enough to extract the whole protein complex. I did a sanity check using “homolog. reconstruct only” which led to a terrible resolution of 19 Å. What could have gone wrong? It is very much related to Alignments degrade after re-extracting particles - #8 by cbeck
Best regards, Tristan