Importing particle picks from cryosparc to Relion

Import and Export
1

Hello,

I picked particles using cryolo, imported the picks and the motion corrected micrographs to cryosparc. After 2D classification, I would like to import them back to Relion 3 but having new issues I have not seen before. I have previously imported the picks with the remove UID option and would run this command to generate the star files and the remainder of my pipeline went smoothly:

csparc2star.py particles_selected Jxx_passthrough_particles_selected.cs test.star --micrograph-path MotionCorr/jobxxx/Frames --swapxy

This would strip the UID from micrographs because of the selected “remove UID option” while importing the picks. In the past, I have not had to pass the --strip-uid flag. With the new changes, I included --strip-uid flag as I noticed micrograph filename containing having UID without this flag and removed the --swapxy flag based on recent responses by developers here. I ran this command and performed a test classification after extraction in Relion:

csparc2star.py particles_selected Jxx_passthrough_particles_selected.cs test.star --micrograph-path MotionCorr/jobxxx/Frames --strip-uid

Neverthless, the picks in Relion are in the wrong regions of the micrograph. Let me know if you have thoughts on how to fix this.

2

Hi,

Contemporary versions of pyem initiate an inverty operation in the background. At a guess, this probably has to be undone in your case, i.e. by specifying an explicit --inverty flag, in order to maintain the same output coordinates.

Cheers,
Yang