Problem in transferring cs 3.0 extracted particles to relion for refine

[ajian]

use relion original coordinate in CS 3.0 to extract particles after CS patachCTF, followed by 2D classification, Ab and NU, then try to transfer NU particles back to relion for polishing by csparc2star, however, the polishing results looks wired and so is the refine results. This never happened to CS 2.15, try to figure out why and found that the coordinate is largely off after check the particle position in mic, see below

anyone find similar thing?

[olibclarke]

Hi @ajian, use the --swapxy flag when converting back to star for polishing using csparc2star.py and you should be good to go.

[ajian]

That works, thank you olibclarke!