I have been quite happy with my high quality map results from doing all preprocessing (motion correction, CTF estimation) in CryoSPARC, but I now want to pull my data into Relion just to compare and see if the map resolution and quality is enhanced further. I’ve been told I need my processed micrographs, a micrograph .star file, a particle.star file of my final particle set converted from CryoSPARC .cs file, and my CryoSPARC map for an initial Relion model. I’m a little confused about how to best go about this, so here are my questions:
For the .mrc files, do I just use the output micrographs from my Patch motion correction job? Is it alright that I did Patch CTF estimation downstream of this; essentially, is this where my processed micrographs are stored?
For the converted particle file, should I use the output .cs file from my 2D Select job or from a refinement? I have heard that it can be better to use an output particles.cs file from a refinement but I’m not sure why. I also get a csparc2star.py error when I use an exported refinement output file, but not when I use the exported 2D select output file.
How do I get a micrograph.star file when I did all of my preprocessing in CryoSPARC? Can I just convert the micrographs.cs file within the exported Patch Motion Correction Job using csparc2star.py? I tired this and got failed results, so i’m wondering which exact file and csparc2star.py commands to use to properly do this, or how else I can get a micrograph.star file.
If I’m super off-base and there’s a better technique to getting further refinement in Relion going, please let me know what I need to do and/or what different set of files I need to bring into Relion.