What is the meaning of each column of the meta data (.csv) after the homogeneous refinement?

CryoSPARC Parameters
1

Dear all,

I am curious about the meaning of some of the columns in the csv file after the homogenous refinement step. Specifically, what is the meaning of “alignments.model.E,alignments.model.E_min_alpha,alignments.model.alpha,alignments.model.cross_cor”?

I also found that the three Euler angles (alignments.model.r.0,alignments.model.r.1,alignments.model.r.2) are in the range of [-3.36248588705, 3.36248588705], which is surprising for me as I expected them to be in the range of [-pi, pi].

Could anyone kindly help me figure out these questions?

Thanks and warmest regards,
Wei

2

The orientations are not stored using Euler angles, but using Rodrigues coordinates. (See Wikipedia: Axis-angle representation).

The model fields you can guess from the equations in Ali’s publications (especially the supplements), with phiC/class_posterior being most important (particle probability for class).

Check out the code for csparc2star.py if you’re curious how it works!

1 Like
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Thank you so much, I have already tried csparc2star.py and it works very well.