Hello! Would it be possible to add an option to Volume Alignment Tools to flip a volume and its particles through the Z axis? Or is there a different way to change the handedness of particles in addition to the volume?
The particle images don’t have any inherent handedness as they are projections I think? What is the goal of flipping the particles? Or do you mean adjusting the particle orientations to match the z-flipped volume so you can do local refinement or something without redoing global refinement?
I believe what you’re describing is an option in the Homogeneous Reconstruct Only job as the “Flip the reconstruction hand” parameter, which reflects the output reconstruction volume through the xy plane and corrects the particles’ alignments to agree with that reflection (but this definitely also makes sense as an addition to Volume Alignment Tools too).
Ah, thank you, missed that option!