Changing the euler angles to manually align a small part of the molecule


My molecule has a stable >> 150KD domain, and a small rigid domain <<50KD that rotates / oscillates around a hinge point as shown from focused classification without alignment.

I can fit the different classes of the small domain into each other in Chimera with ~ 97% correlation, so I was wondering how I can calculate and apply these transformations to the euler angles of each class to be able to manually align and average all the classes together.

Thanks a lot.