Hi,
Align3D currently outputs a rotation matrix and translational shift for each alignment.
Would it be possible to output this transformation in terms of a set of euler angles and an adjusted center, so that we can apply the same transformation using volume alignment tools (or I guess alllow VAT to take a rotation matrix & translation as input)?
This would allow compatibility with cryosparc tools scripts which use data from volume alignment tools, e.g. https://discuss.cryosparc.com/t/adjust-per-particle-defocus-of-subparticles-in-volume-alignment-tools, for situations where just recentering a mask is insufficient, e.g. cases of non-point group symmetry?
Cheers
Oli
EDIT: In the meantime I found a work around - use VAT to recenter the volumes and particle sets, then use these VAT jobs for defocus adjustment. Run Align3D on the recentered volumes to match orientations, then replace the CTF slot with the adjusted one from after the appropriate VAT job.
