Extraction error by Manual picker

Particle Picking
1

Hi everyone,

I am a beginner for cryoSPARC and I am suffering from an error of manual picking and extraction.
Import movies, Motion correction and CTF estimation worked nicely in cryoSPARC v2.8.3.
Then I picked several hundreds of particles by Manual picker and tried to extract them.
“Done picking! Extract Particles” failed to run, and I received following error message,

Traceback (most recent call last): File “cryosparc2_master/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_master/cryosparc2_compute/run.c:3954) File “cryosparc2_compute/jobs/manual_picker/run.py”, line 700, in run_manual_picker do_extract_particles_from_micrographs(state[‘box_size_pix’], state[‘bin_size_pix’]) File “cryosparc2_compute/jobs/manual_picker/run.py”, line 480, in do_extract_particles_from_micrographs scale_const, overall_normalizer, bg_fwhm_A = 200, has_ctf=state[‘has_ctf’]) File “cryosparc2_compute/jobs/extract/extraction.py”, line 105, in do_extract_particles_single_mic particles_out = ctf_utils.extract_ctf(particles_out, micrograph) File “cryosparc2_compute/jobs/ctf_estimation/ctf_utils.py”, line 15, in extract_ctf micshape = particles_in.data[‘location/micrograph_shape’][0] ValueError: no field of name location/micrograph_shape

I tried different conditions before Manual picker, but all results were same.
Do you have any idea??

Thanks!

Tasuku

2

Hi @Tasuku,

This bug has been fixed in the latest version of cryoSPARC, v2.9.0.

3

Hi Sarulthasan,

Thanks! We will try it.

4

Hi, team cryoSPARC,
I am trying to process the negatively stained dataset with cryosparc version 2.11.0. I picked ~3000 particles manually with my preferred box size (125 pixels). After some time, when I reopened the cryosSPARC, accidentally I clicked on “Done Picking! Extract particles” with a default box size of 256 px. Now, I see two particles adjacent to each other in a single class. Can I rerun the job (while saving the manually picked particles) with a different box size?
Thanks.