Experimental support for Relion's Bayesian polishing in csparc2star.py

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Hi Dan,

Apologies if this has already been covered in this (excellent and extremely helpful!) thread:

Does csparc2star.py account for the change in the angle of the astigmatism axis when inverting the coordinates? That is, the change in defocusU & defocusV due to the change in orientation of the mics?

The reason I ask is that we encountered a puzzling situation recently, as follows:

  • Initial processing performed using MC2 corrected mics (+Patch CTF), final resolution 2.2 Å. Some beam tilt, minimal tetrafoil aberrations noted.
  • We then performed patch motion, Patch CTF on the patch motion mics, and re-extracted after applying using csparc2star.py --inverty on the refined particle set. These particles retain the defocus values from the prior refinement by default.
  • Refinement of these particles gives a reconstruction at 2.9Å, with apparent strong tetrafoil aberrations.
  • If instead, I force-extract the CTFs from the new patch CTF job, refinement proceeds to 2.2Å, as expected, with no tetrafoil aberrations evident.
  • I think this indicates that some transformation ought to be applied to defocusU & defocusV when inverting Y; Of course this will only make much of a dfifference at high resolution, and/or in the presence of strong astigmatism.

Cheers
Oli