How to find the input coordinates for relion particle extraction from picking done by cryosparc

Hi everyone,
After looking several similar discussion, I still did not make it work. I initiated single particle processing in Crysparc, from patch motion Corr to templated-picker. After several round 2D/3D Classification, I want to re-extract selected particles into relion for polishing. For this aim, I conducted motionCorrection in relion and used csparc2star.py (-inverty) to convert the particles star files from a non-uniform refinement from cryosparc. I edit the rlhMicrgraphName to the corresponding mrc files from Motioncorr in relion. I use this file as ‘imput coordinates’ in relion, the job yields with 0 particles. I hope I explained the scenario clear and appreciate any comments.

Here is the example of my star file: (J41 is symbolic to the extraction folder in cryosparc)
loop_
_rlnOpticsGroupName #1
_rlnOpticsGroup #2
_rlnMtfFileName #3
_rlnMicrographOriginalPixelSize #4
_rlnVoltage #5
_rlnSphericalAberration #6
_rlnAmplitudeContrast #7
_rlnImagePixelSize #8
_rlnImageSize #9
_rlnImageDimensionality #10
_rlnCtfDataAreCtfPremultiplied #11
opticsGroup1 1 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup2 2 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup3 3 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup4 4 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup5 5 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup6 6 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup7 7 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup8 8 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup9 9 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup10 10 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup11 11 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup12 12 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup13 13 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup14 14 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup15 15 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup16 16 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup17 17 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup18 18 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup19 19 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup20 20 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0
opticsGroup21 21 mtf_falcon4EC_200kV.star 0.860000 200.000000 2.700000 0.070000 0.860000 288 2 0

data_particles

loop_
_rlnImageName #1
_rlnMicrographName #2
_rlnCoordinateX #3
_rlnCoordinateY #4
_rlnAngleRot #5
_rlnAngleTilt #6
_rlnAnglePsi #7
_rlnOriginXAngst #8
_rlnOriginYAngst #9
_rlnDefocusU #10
_rlnDefocusV #11
_rlnDefocusAngle #12
_rlnPhaseShift #13
_rlnCtfBfactor #14
_rlnOpticsGroup #15
_rlnRandomSubset #16
_rlnClassNumber #17
000001@J41/extract/000000860335196052099_FoilHole_14566558_Data_14506611_7_20241015_021708_Fractions_patch_aligned_doseweighted_particles.mrcs MotionCorr/job016/Micrographs/FoilHole_14566558_Data_14506611_7_20241015_021708_Fractions.mrc 2646 2301 -2.355675 71.078903 -125.754158 0.896281 0.896281 6626.966309 5460.039062 82.864311 -1.530396 0.000000 8 2 1

the job.star from relion:

version 50001

data_joboptions_values

loop_
_rlnJobOptionVariable #1
_rlnJobOptionValue #2
bg_diameter -1
black_dust -1
coords_suffix J54_particles_editted.star
do_cut_into_segments Yes
do_extract_helical_tubes Yes
do_extract_helix No
do_float16 Yes
do_fom_threshold No
do_invert Yes
do_norm Yes
do_queue Yes
do_recenter No
do_reextract No
do_rescale No
do_reset_offsets No
extract_size 288
fndata_reextract “”
helical_bimodal_angular_priors Yes
helical_nr_asu 1
helical_rise 1
helical_tube_outer_diameter 200
min_dedicated 1
minimum_pick_fom 0
nr_mpi 20
other_args “”
qsub sbatch
qsub_extra1 account
qsub_extra2 16:00:00
qsub_extra3 230GB
qsub_extra4 rocky
qsub_extra5 gpu:2
qsubscript relion5_CPU_anywhere.bash
queuename openmpi
recenter_x 0
recenter_y 0
recenter_z 0
rescale 64
star_mics MotionCorr/job016/corrected_micrographs.star
white_dust -1

Hi,

In your specific workflow, the particle star file should be supplied as a Refined particles STAR file, not as Input coordinates. That might be where it’s falling down.

Cheers,
Yang

Hi Yang,
Thank you for this comment. It works perfect now.
cheers
JSON