[3dem] Importing Particles from Cryosparc into Relion for Processing

[Lauren Pellows]

Hi all,

I am new to cryoEM field and have been working in Cryosparc for all my processing. I am now wanting to use Relion and have been trying to figure out how to import the particles I extracted in cryosparc into relion. I wanted to reprocess my raw micrographs in relion so I imported those ran motion correction and CTF estimation on those. After that I ran csparc2spar on my cryosparc data and now have my particles in a .star file. I also have gone into the particle.star file made sure the _rlnMicrographName in the star file to match the relion processes images. I have now imported the particles.star file into relion but when I run the extraction job I don't get any extracted particles.

I have been reading online and can't find anything conclusive on if I need to run the extraction job. I have read that I dont need run the extraction job since the particles.star file should have all the metadata on the particles, and I can just use the particles.star to run my jobs. I also read that I can rerun the extraction job using the particle coordinates from cryosparc. Since these feel counter intuitive and I keep getting errors I am not sure what to do next. I know that this is a very typically workflow that people do so im hoping this is a pretty straightforward question. Any help or advice anyone has would be a great help!!

Thank you so much,

Lauren Pellows, PhD

Postdoctoral Fellow
Dukovic Lab
University of Colorado, Boulder

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