Particle re-extract cryosparc to relion

Troubleshooting
1

Hi all,
After “select 2D” in cryosparc, I use “csparc2star.py particles_selected.cs particles.star” to get the star file.Here is the particles.star file with the correct columns

data_images
loop_
_rlnAmplitudeContrast #1 
_rlnCoordinateX #2 
_rlnCoordinateY #3 
_rlnDefocusAngle #4 
_rlnDefocusU #5 
_rlnDefocusV #6 
_rlnMagnification #7 
_rlnMicrographName #8 
_rlnPhaseShift #9 
_rlnSphericalAberration #10 
_rlnVoltage #11

Then I import the star file into relion and re-extract the particle. I got the error:

ERROR: 
Preprocessing::initialise ERROR: input _data.star should contain rlnMagnification and rlnDetectorPixelSize.
/data/software/relion-3.0.4/bin/relion_preprocess_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x427771]
/data/software/relion-3.0.4/bin/relion_preprocess_mpi(_ZN13Preprocessing26getCoordinateMetaDataTableE8FileName+0x2c2) [0x4456d2]
/data/software/relion-3.0.4/bin/relion_preprocess_mpi(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x29f) [0x44e7ff]
/data/software/relion-3.0.4/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x34c) [0x45e9ac]
/data/software/relion-3.0.4/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x25) [0x45ee15]
/data/software/relion-3.0.4/bin/relion_preprocess_mpi(main+0x3b) [0x41ee9b]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2b29c05dbc05]
/data/software/relion-3.0.4/bin/relion_preprocess_mpi() [0x41f57f]

Does anyone know how to solve this problem?

Thanks,
Shasha

2

Others will be able to respond better than me, but here’s my quick answer.
Have you tried using the extract passthrough file after particles_selected.cs?
I recall trying to use different particles.cs files from 2d output to get it to work in relion and I don’t remember which one worked.
You can manually add the needed parameters in a text editor and make a data_optics section so your star file looks like this. I don’t think relion has ever asked me for rlnMagnification.
data_optics
loop_
_rlnVoltage #1
_rlnSphericalAberration #2
_rlnAmplitudeContrast #3
_rlnOpticsGroup #4
_rlnImagePixelSize #5
_rlnImageDimensionality #6
_rlnImageSize #7
300.000000 2.652304 0.100000 1 0.830000 2 480

data_particles

loop_
_rlnImageName #1
…