I convert csyosparc Select 2D to relion star using csparcstar2.py. below is the command,
csparc2star.py --swapxy particles_selected.cs J24_passthrough_particles_selected.cs select-2D-cryosparc-relion.star --inverty. the converted star header shows something like this below,
data_optics
loop_
_rlnVoltage #1
_rlnImagePixelSize #2
_rlnSphericalAberration #3
_rlnAmplitudeContrast #4
_rlnOpticsGroup #5
_rlnImageSize #6
_rlnImageDimensionality #7
_rlnOpticsGroupName #8
300.000000 2.120000 2.700000 0.100000 1 150 2 opticsGroup1
data_particles
loop_
_rlnImageName #1
_rlnMicrographName #2
_rlnCoordinateX #3
_rlnCoordinateY #4
_rlnAnglePsi #5
_rlnOriginXAngst #6
_rlnOriginYAngst #7
_rlnDefocusU #8
_rlnDefocusV #9
_rlnDefocusAngle #10
_rlnPhaseShift #11
_rlnCtfBfactor #12
_rlnClassNumber #13
_rlnOpticsGroup #14
000001@J17/extract/000001588802743444929_FoilHole_25535974_Data_24203023_24203025_20230425_225906_fractions_patch_aligned_doseweighted_particles.mrc J2/motioncorrected/000001588802743444929_FoilHole_25535974_Data_24203023_24203025_20230425_225906_fractions_patch_aligned_doseweighted.mrc 1985 883 224.999985 -3.445000 7.579000 16945.931641 15777.030273 -81.389389 0.000000 0.000000 68 1
As mentioned in previous thread, I edited the header and link the J2/cryosparc motioncorrected mrc and J17/extract/mrc to the relion folder, below is the edited star,
data_optics
loop_
_rlnVoltage #1
_rlnImagePixelSize #2
_rlnSphericalAberration #3
_rlnAmplitudeContrast #4
_rlnOpticsGroup #5
_rlnImageSize #6
_rlnImageDimensionality #7
_rlnOpticsGroupName #8
300.000000 2.120000 2.700000 0.100000 1 150 2 opticsGroup1
data_particles
loop_
_rlnImageName #1
_rlnMicrographName #2
_rlnCoordinateX #3
_rlnCoordinateY #4
_rlnAnglePsi #5
_rlnOriginXAngst #6
_rlnOriginYAngst #7
_rlnDefocusU #8
_rlnDefocusV #9
_rlnDefocusAngle #10
_rlnPhaseShift #11
_rlnCtfBfactor #12
_rlnClassNumber #13
_rlnOpticsGroup #14
000001@cryosparc-extract/000001588802743444929_FoilHole_25535974_Data_24203023_24203025_20230425_225906_fractions_patch_aligned_doseweighted_particles.mrcs motion-sparc/000001588802743444929_FoilHole_25535974_Data_24203023_24203025_20230425_225906_fractions_patch_aligned_doseweighted.mrc 1985 883 224.999985 -3.445000 7.579000 16945.931641 15777.030273 -81.389389 0.000000 0.000000 68 1
but when i run particles extraction in relion3.1, it shows input micrograph star file has no rInMicrographName column,
I have no idea which part i did wrong. I would appreciate it if someone has suggestions