Export particles coordinates to relion for re-extraction

closed

#1

Hi Dear cryosparc community,

I extracted binned 2 particles in relion and imported them into cryoSparc, did 2D classification and would like to re-extracted the selected particles in relion for futher 3D-reconstrction. I am wondering how to do it correctly: which files do I need to use to create the star file and in relion import, what is the import file option I need to choose (eg. 2D/3D coordinates etc) What I tried so far is:
I used to pyem to combine particles.cs and passthrough_particles.cs file to create a particles_combine.cs file. The output seems all right. But it could not be imported into relion and used to do the extraction.
Thank you.

Jing

data_images

loop_
_rlnImageName #1
_rlnAnglePsi #2
_rlnOriginX #3
_rlnOriginY #4
_rlnVoltage #5
_rlnMagnification #6
_rlnDetectorPixelSize #7
_rlnDefocusU #8
_rlnDefocusV #9
_rlnDefocusAngle #10
_rlnSphericalAberration #11
_rlnPhaseShift #12
_rlnAmplitudeContrast #13
_rlnClassNumber #14
_rlnRandomSubset #15
000004@J10/imported/…_22_04_51.mrcs 234.183655 2.925000 2.275000 300.000000 1$
000005@J10/imported/…22_04_51.mrcs 22.959183 -2.925000 1.625000 300.000000 1$
000006@J10/imported/…22_04_51.mrcs 197.448975 0.975000 -0.975


#2

Hi Jing,
Try this
csparc2star.py --copy-micrograph-coordinates particles.star your.cs your .star
particles.star is the one you imported into cryosparc
Good luck
Yibin


#3

Thanks, I found that I made a very stupid mistake. I am working with cryolo and relion particle pciking with the same data set, and I mistakenly using particle.star file from cryolo to the .cs file from relion job to make the star file. The command works perfectly. And the problem is solved. Thank you very much.

Updated, I say so too early. There is still a problem. I am supposed to extract ~400k particles, but by running the command I listed below, I only have ~280K particles in the star file I created. I tried to just combine the two .cs to .star file, and the line number is correct. I am not sure what is wrong. Thanks again.
Thanks for the reply, Yibin. It works this time as you suggested. I used
csparc2star.py --copy-micrograph-coordinates particles.star particles.cs passthrough_particles_selected.cs particles4reextract.star
the two .cs file are from the selected 2D.
The new star file then contains the orignal image name and the original X,Y and I can use it directly in the relion for re-extraction.
The cryosparc version is V2.9