Particle Import to Relion from cryoSPARC error- optics group "" does not exist in micrograph STAR file

Troubleshooting
1

Hi All,
I had picked and cleaned particles in cryosparc from images motion-corrected in relion. Now I want to re-extract these particles in relion. Thanks to @DanielAsarnow I converted the cryosparc files to particle.star file. After editing the output to point to motion-corrected micrographs in relion I am able to import the files in relion and run a re-extract job which seem to work with swapXY coordinates (normal conversion gave error “particle coordinates outside the micrograph” ). However, at the very end of the run, the job fails with the error - optics group “” does not exist in micrograph STAR file."
I am attaching screen-shots of start of the edited particle star file

Swapxy_Edited_Star_file
Swapxy_Edited_Star_file1630×1116 137 KB
and same file after import
Imported_Swapxy_Edited_Star_file
Imported_Swapxy_Edited_Star_file1982×1278 273 KB
, the microgaph star file
micrograph_ctf.star
micrograph_ctf.star1986×1222 281 KB
and the error message
error_message
error_message1560×592 30.9 KB
. Any input is highly appreciated.
Best,
Kapil

1 Like
2

you just need manually add the _rlnOpticsGroupName (e.g. opticsGroup1 )

3 Likes
3

thanks, that did it.

4

Looks like a Relion bug, I guess if _rlnOpticsGroupName is not in the .star file, then it is added to the optics table, and then their code then uses that field for the particles even if it is missing there. Of course, _rlnOpticsGroup is there in both tables throughout.

3 Likes
6

It works for me, many thanks!

7

add to where? the particle.star or micrograph.star?

8

In my experience with relion 3, both particles.star and micrograph.star needed _rlnOpticsGroupName and opticsGroup1 in their optics tables.

Best,
Kookjoo

1 Like
9

Thanks a lot! That works!