Importing particles from Relion4.0


I was trying to import particles from Relion4.0 to CryoSPARC v3.3.1 using ‘Import Particle Stack’ and ‘Particles meta path’ option. It worked just ok with previous versions and not sure what the error means. Anyone have an idea?

Min Woo Sung

License is valid.Running job on master node[CPU: 67.9 MB] Project P1 Job J20 Started [CPU: 67.9 MB] Master running v3.3.1, worker running v3.3.1 [CPU: 67.9 MB] Working in directory: /data/Him/protein-Me/CryoSPARC/P1/J20 [CPU: 67.9 MB] Running on lane default [CPU: 67.9 MB] Resources allocated: [CPU: 67.9 MB] Worker: egpu6 [CPU: 67.9 MB] -------------------------------------------------------------- [CPU: 67.9 MB] Importing job module for job type import_particles… [CPU: 206.9 MB] Job ready to run [CPU: 206.9 MB] *************************************************************** [CPU: 206.9 MB] Importing particles from /data/Him/protein-Me/Him-test/Extract/83k-rs160-forCS/ [CPU: 206.9 MB] File extension is star [CPU: 206.9 MB] Importing star file. [CPU: 266.2 MB] -------------------------------------------------------------- [CPU: 266.2 MB] Loaded star file with 83488 items [CPU: 266.2 MB] Fields loaded from star file: [‘rlnOpticsGroupName’, ‘rlnOpticsGroup’, ‘rlnMicrographOriginalPixelSize’, ‘rlnVoltage’, ‘rlnSphericalAberration’, ‘rlnAmplitudeContrast’, ‘rlnImagePixelSize’, ‘rlnImageSize’, ‘rlnImageDimensionality’, ‘rlnCoordinateX’, ‘rlnCoordinateY’, ‘rlnClassNumber’, ‘rlnAutopickFigureOfMerit’, ‘rlnAnglePsi’, ‘rlnImageName’, ‘rlnMicrographName’, ‘rlnCtfMaxResolution’, ‘rlnCtfFigureOfMerit’, ‘rlnDefocusU’, ‘rlnDefocusV’, ‘rlnDefocusAngle’, ‘rlnCtfBfactor’, ‘rlnCtfScalefactor’, ‘rlnPhaseShift’, ‘rlnAngleRot’, ‘rlnAngleTilt’, ‘rlnOriginXAngst’, ‘rlnOriginYAngst’, ‘rlnNormCorrection’, ‘rlnLogLikeliContribution’, ‘rlnMaxValueProbDistribution’, ‘rlnNrOfSignificantSamples’, ‘rlnGroupNumber’, ‘rlnRandomSubset’] [CPU: 266.2 MB] -------------------------------------------------------------- [CPU: 266.2 MB] Reading particle data locations… [CPU: 266.2 MB] Reading rlnImageName to get indices and paths… [CPU: 292.9 MB] Searching for linked data files… [CPU: 292.9 MB] -------------------------------------------------------------- [CPU: 292.9 MB] Compiling CTF information… [CPU: 293.0 MB] Warning: No micrographs were connected as inputs, so correspondences cannot be found, so output will not contain pick locations for particles. [CPU: 293.0 MB] -------------------------------------------------------------- [CPU: 293.0 MB] Compiling particle pose information… [CPU: 293.0 MB] Converting euler angles… [CPU: 293.0 MB] Converting rlnOriginXAngst to pixels using parameter psize_A [CPU: 314.1 MB] -------------------------------------------------------------- [CPU: 314.1 MB] Particle information has now been imported for 83488 particles, creating outputs… [CPU: 314.3 MB] Found references to 9632 unique data files [CPU: 317.6 MB] Import paths were unique at level -1 [CPU: 317.6 MB] Example imported relative path: J20/imported/017913876916102559764_20210806_proteinP53_Grid2_0005.mrcs [CPU: 318.2 MB] Reading MRC file headers to check shape… [CPU: 319.8 MB] -------------------------------------------------------------- [CPU: 319.8 MB] Loaded 83488 particles. [CPU: 319.8 MB] Common fields: [CPU: 319.8 MB] ctf/accel_kv : {300.0} [CPU: 319.8 MB] ctf/cs_mm : {2.7} [CPU: 319.8 MB] ctf/amp_contrast : {0.1} [CPU: 319.8 MB] ctf/exp_group_id : {1} [CPU: 319.8 MB] blob/psize_A : {1.396} [CPU: 319.8 MB] blob/shape : [160 160] [CPU: 319.8 MB] -------------------------------------------------------------- [CPU: 319.8 MB] Making plots… [CPU: 338.2 MB] Traceback (most recent call last): File “cryosparc_master/cryosparc_compute/”, line 85, in File “/opt/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/”, line 452, in run_import_particles fig = plotutil.plot_images_simple(dispparts, rows=4, cols=8, radwn=6, figscale=1.5) File “/opt/cryosparc/cryosparc_master/cryosparc_compute/”, line 588, in plot_images_simple rD = img.get_original_real_data() File “/opt/cryosparc/cryosparc_master/cryosparc_compute/”, line 22, in get_original_real_data return self.blob.view().copy() File “/opt/cryosparc/cryosparc_master/cryosparc_compute/blobio/”, line 127, in view return self.get() File “/opt/cryosparc/cryosparc_master/cryosparc_compute/blobio/”, line 122, in get _, data, total_time = prefetch.synchronous_native_read(self.fname, idx_start =, idx_limit = File “cryosparc_master/cryosparc_compute/blobio/”, line 67, in cryosparc_compute.blobio.prefetch.synchronous_native_read RuntimeError: dtype_to_bytes 462: Invalid argument [arguments] /data/Him/protein-Me/CryoSPARC/P1/J20/imported/005760266825950795707_20210806_proteinP53_Grid2_7348.mrcs, 0, 0, 12, 13, 2, 40

Hi Min,

Were your particles extracted in Relion using float16?



Hi Ryan,

Yes, I just realized that there is ‘float16’ option and it was ‘yes’ by default. Was that the issue? I’ll try it w/o the option.

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Thanks! 'float16 - ‘no’ was resolved the issue. I’ve got particles in CS now. Thanks!

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