Exporting symmetry expanded particles

Import and Export
1

after a refinement I used cryosparc to do symmetry expansion. I can’t use csparc2star because it asks for a passthrough, which isn’t the the sym expanded job folder. So instead I try to use the passthrough from the preceeding refinement job. Still no luck, I get the csparc2star error:

Length mismatch: Expected axis has 19 elements, new values have 0 elements
A passthrough file may be required (check inside the cryoSPARC 2+ job directory)

thoughts? thanks!

2

Hi @orangeboomerang, I haven’t tried this myself, but is it possible to not provide the passthrough file to csparc2star? the output of symmetry expansion should have all the fields you need, I believe (CTF, alignments, etc)

3

Hi @apunjani
I have similar problem too
My error code is just like this

  File "/opt/pyem/csparc2star.py", line 42, in main
    df = metadata.parse_cryosparc_2_cs(cs, passthroughs=args.input[1:], minphic=args.minphic, boxsize=args.boxsize, swapxy=args.swapxy)
  File "/opt/pyem/pyem/metadata.py", line 362, in parse_cryosparc_2_cs
    df = cryosparc_2_cs_model_parameters(cs, df, minphic=minphic)
  File "/opt/pyem/pyem/metadata.py", line 308, in cryosparc_2_cs_model_parameters
    [cs[names[c]][i] for i, c in enumerate(cls)]))
  File "/opt/python/3.7.5/lib/python3.7/site-packages/pandas/core/frame.py", line 3484, in __setitem__
    self._setitem_array(key, value)
  File "/opt/python/3.7.5/lib/python3.7/site-packages/pandas/core/frame.py", line 3507, in _setitem_array
    raise ValueError("Columns must be same length as key")
ValueError: Columns must be same length as key

csparc2star.py works well with NU-refinement particles ‘cryosparc_P17_J22_009_particles.cs’, but it isn’t go well with symmetry expansion particles ‘P17_J30_particles.csg’ or ‘particles_expanded.cs’
Is there any way to fix this problem?

Thank you :smiley: