Exporting particles to relion

Troubleshooting
1

Hi all as new user I am going through some struggles. For me cryosparc particle picking worked good. So I did few rounds of 2D classifications. I want to run 2D classification in relion as well. I wanted export my particles of the into relion. I used following method. ```
cd relion-project
mkdir -p J22/extract
cd J22/extract
ln -s /path/to/cryosparc/P1/J22/extract/*.mrc -t .
rename .mrc .mrcs *.mrc
cd …/…
csparc2star.py path/to/cryosparc/P10/J315/cryosparc_P10_J315_009_particles.cs from_csparc.star
sed -i ‘s/particles.mrc/particles.mrcs/g’ from_csparc.star

conversion and transfer worked. in relion I imported my parcles.star file. that worked as well.
When I tried to run the 2D classification using this particles.star file relion giving an error message .mrcs file does not exist.
so to verify I opened my particles.star file in text editor. this is the content I have

particlesinfo
particlesinfo1906×893 165 KB

This was the error message I got in relion
errormessage
errormessage802×367 35.9 KB

any one please guide me
Thank you

2

Hi Venkata, did you verify that the rename command worked for your J22/extract/*mrc links? I have not seen it used like that but I am not well versed in its use. I usually change my mrc to mrcs with “rename s/\mrc/\mrcs/ *”

3

Hi Venkata， I also have the same problem. How do you relove your problem

4

Hi Yiwu,
Unfortunately I couldn’t resolve. I am waiting for some suggestions from this forum.

5

Hi Venkata,

It looks like the relative path to the extracted particles is not accessible. You could check this by running header (or any other operation on the file) from the directory where you opened relion on one of the relative paths shown in your relion error. If the paths do not point to the files correctly you can either change the paths in the star file or link the mrc/mrcs in your relion project.