I have a general question regarding Ab-initio reconstruction. Does the job take previous particle alignments (2D or 3D) into account? I am curious if particles were misaligned during 2D classification or in previous ab-initio jobs, would it affect a new ab-initio reconstruction?
No, ab initio is not affected by initial orientations.
Thank you. I would have a follow-up question, just to be sure. This is also true, if I take the particles from a refinement output (like NU-refinement)? Or does “initial orientation” describe 2D classification and ab-initio, and if I take particles that went through a refinement, it will influence future ab-initio?
Doesn’t matter. Orientation information from refinement, 2D, ab initio, will not influence subsequent ab initio runs.