I encountered a bug when trying to pick particles by generating templates from a .mrc map file.
The map was produced in Chimera from a pdb file with the command
molmap #0 15 and saved as a map file (.mrc).
Then imported into cryoSPARC (2.15.0+200513) with the “Import 3D Volumes” job.
This volume was then used to “Create Templates” job which produces the following error:
Traceback (most recent call last): File "cryosparc2_worker/cryosparc2_compute/run.py", line 85, in cryosparc2_compute.run.main File "cryosparc2_worker/cryosparc2_compute/jobs/create_templates/run.py", line 45, in cryosparc2_compute.jobs.create_templates.run.run File "cryosparc2_compute/fourier.py", line 152, in zeropad new_X[a:b,a:b,a:b] = X ValueError: could not broadcast input array from shape (33,43,41) into shape (40,40,40).
If I understand correctly, the dimensions are not a cube and/or odd which can’t be used with the current cryoSPARC script.
I found that resizing the box using Relion worked to circumvent this issue:
relion_image_handler --i input.mrc --new_box 40 --o output.mrc
I hope others find this if needed or it’s fixed in future releases.