Re-extract a set of selected particles imported to Relion

Import and Export
1

Hi,

I used the csparc2star.py script to export a set of my particles from Cryosparc to Relion to use its 3D classification feature. Since using the full-size particles is very time-consuming in Relion, I decided to downscale the particles before exporting them. Now I would like to 3D refine the subset of particles chosen by the 3D classification and for that, I would like to re-extract the particles at their full size.
Is there an easy way to do this in Relion or Cryosparc?

Cheers,
Lior

2

Hey Lior,

If you want to continue using relion, the particle location info is still available in the 3D-refined subset you selected, so you can use the same micrographs you used to extract the original particles. in Relion, and run a new extraction using the size you want.
Good luck

3

You can also include your micrographs as additional input when importing the particles back into cryoSPARC, then you will be able to extract in cryoSPARC.

1 Like
4

Hi Stavros,
Thanks for your answer. I would really like to re-extract in Relion but my problem is that the only input I have for Relion is my csparc2star converted particles. Should I convert my Cryosparc processed micrographs to input the Relion extract job?
Best,
Lior

5

Sure, or use star.py --to-micrographs on your particles file (but check the pixel size in the micrographs file after).

6

Hello,
I’m trying to do a similar thing but I have the micrographs in Relion already, motion corrected and CTF estimated. Now I just want to re-extract particles associated with my 2D classes found in Cryosparc from the Relion processed micrographs.
In order to pick particles and 2D classify in Cryosparc, I had to redo the motion correction and CTF estimation in cryosparc - otherwise once I loaded the micrographs motion corrected in Relion into cryosparc and then did ctf estimation, the resolutions found were abnormally high and particle picking was not as successful.
I managed to convert the cryosparc 2D classes into a star file using csparc2star.py and import it into Relion but I can’t get re-extraction to work - no particles are found in the micrographs_ctf.star.

P148J293.cs P148J293_pass.cs, P148J293_loc.cs - put in /i/emr211/u/lr001/msp1_pro_kriosdata2_61220

module load pyem/pyem
cd /i/emr211/u/lr001/msp1_pro_kriosdata2_61220
mkdir -p J175/extract
cd J175/extract
ln -s /d/emr211/u/csparc/P148/J145/motioncorrected/*.mrc -t
cd …/…
csparc2star.py P148J293.cs P148J293_pass.cs P148J293_loc.cs P148J293.star
sed -i ’s/particles.mrc/particles.mrcs/g’ P148J293.star

However, when I try to extract the particles in relion, it doesn’t find any particles.
The y co-ordinates of the particles seem to be off the range of the micrographs.
Does anyone have any idea whats going on?
Thanks
Rebecca

7

Hi Rebecca,
Since you already had particles from Relion, why not simply import the particles .star file into cryoSPARC? Then after you process you can simply convert back and use --copy-micrograph-coordinates to recover Relion’s coordinates from your original .star file. 2D classification in CS is fast enough that I would just take this approach instead.

Still, as to your second question, when you export your cryoSPARC-picked particles, you probably need to correct the rlnMicrographName entries to a path that Relion will see. They are probably Jxxx/import/blah.mrc symlinks made by CS, and you can edit them to reflect the original path seen by Relion. You may also need --swapxy or --inverty or some combination in order to get the coordinates right from Relion’s perspective.

1 Like