I am doing 3D refinement with some simulated data. I would like to find Azimuth/elevation values for each particle. I looked into the .cs file and found the alignments3D/pose, three values for each particle. What does the three value correspond to? What is the relationship between these three values and azimuth/elevation?
Also, does it get updated after 3D refinement? I can only get the alignments3D/pose in the simulation job, but the .cs in the Homogeneous Refinement job does not have the info.
The poses are Rodrigues axis-angle vectors. If you want to look at the equivalent Euler angles, I suggest you use csparc2star.py to convert them. (Or you can import the libraries from pyem if you would like to make the conversions in your own code).
Also, any kind of refinement job will have the poses, but they may have a slightly different prefix. All the possibilities are covered in the pyem code but if you just look at the .dtype.names list from the cs file you opened you should be able to find them.