Import particle.star Error from Relion4.0 beta2

Import and Export
1

Hello everyone,

My particles were processing first in cryosparc, and import to relion after NU-refine use cs2star,py. Then, I used Relion 4.0 Beta2 to do 3D Classification, and selected a good subset. I want to import this subset particles to cryosparc, then I got the following error:

[CPU: 710.7 MB] Traceback (most recent call last): 
File "cryosparc_master/cryosparc_compute/run.py", 
    line 85, in cryosparc_compute.run.main 
File  "/home/songdf/Downloads/cryosparc/cryosparc2_master/cryosparc_compute/jobs/imports/run.py", 
    line 452, in run_import_particles 
          fig = plotutil.plot_images_simple(dispparts, rows=4, cols=8, radwn=6, figscale=1.5) 
File "/home/songdf/Downloads/cryosparc/cryosparc2_master/cryosparc_compute/plotutil.py", 
     line 582, in plot_images_simple 
          rD = img.get_original_real_data() 
File "/home/songdf/Downloads/cryosparc/cryosparc2_master/cryosparc_compute/particles.py", 
     line 22, in get_original_real_data
          return self.blob.view().copy() 
File "/home/songdf/Downloads/cryosparc/cryosparc2_master/cryosparc_compute/blobio/mrc.py", 
     line 127, in view return 
          self.get() 
File "/home/songdf/Downloads/cryosparc/cryosparc2_master/cryosparc_compute/blobio/mrc.py", 
     line 122, in get 
        _, data, total_time = prefetch.synchronous_native_read(self.fname, idx_start = self.page, idx_limit = self.page+1) 
File "cryosparc_master/cryosparc_compute/blobio/prefetch.py", 
     line 69, in cryosparc_compute.blobio.prefetch.synchronous_native_read 
          RuntimeError: mrc_readmic (1) 479 Please report this as a bug.: Invalid argument [arguments] /data/liuh/20220114/P25/J233/imported/004401021576776425598_batch_000492_downsample_particlestack.mrcs, 0, 0, 516, 517, 2, 40

Outputs

imported_particles

particleCount: 332462

My cryosparc current version is v3.3.1+220215.

Please help. Thanks!

2

Welcome to the forum @pey123456. This error message suggests an inconsistency between input metadata and the actual data, such as a discrepancy between referenced and available indices. What input fields did you define and what were the formats and origins of these inputs?

3

The metadata format is .star

Thank you for your answer, I try to use particle.star in Select job folder, and it is work.