Dear all,
I exported the picked particles from Relion 4, then imported them to CryoSPARC for 2D classification to do the clean-up. Now, I would like to export the selected 2D particles from CS, and then re-import them to Relion, but the pyem didn’t work well.
I know there have been multiple similar articles discussed before. However, I still cannot address the issue of my case.
That would be great if someone could give me some advice. Thank you all!!!
TJ
[Command what I used for data conversion]
csparc2star.py particles_selected.cs J34_passthrough_particles_selected.cs from_P17J34.star --copy-micrograph-coordinates …/J29/particles.star --loglevel debug
J34 : “Select 2D” job
J29: “Import Particles” job (particles.star is from the “Extract job” of Relion 4)
[Error messages]
Detected CryoSPARC 2+ .cs file
Reading primary file
Assigning parameters 2D classes or single 3D class
Assigning skew angle from 2D classification
Reading auxiliary file J34_passthrough_particles_selected.cs
Classification parameters not found
Trying to merge: ctf/type, ctf/exp_group_id, ctf/accel_kv, ctf/cs_mm, ctf/amp_contrast, ctf/df1_A, ctf/df2_A, ctf/df_angle_rad, ctf/phase_shift_rad, ctf/scale, ctf/scale_const, ctf/shift_A, ctf/tilt_A, ctf/trefoil_A, ctf/tetra_A, ctf/anisomag, ctf/bfactor, pick_stats/ncc_score, pick_stats/power, pick_stats/template_idx, pick_stats/angle_rad
Merging: rlnPhaseShift, rlnDefocusU, rlnAmplitudeContrast, rlnDefocusAngle, rlnSphericalAberration, rlnOpticsGroup, rlnVoltage, rlnCtfBfactor, rlnDefocusV
Directly copied fields: rlnDetectorPixelSize, ucsfImagePath, ucsfImageIndex, ucsfUid, rlnRandomSubset, rlnOriginX, rlnOriginY, rlnAnglePsi, rlnClassNumber, rlnPhaseShift, rlnDefocusU, rlnAmplitudeContrast, rlnDefocusAngle, rlnSphericalAberration, rlnOpticsGroup, rlnVoltage, rlnCtfBfactor, rlnDefocusV, rlnMagnification
Converting DEFOCUSANGLE from degrees to radians
Converting PHASESHIFT from degrees to radians
Changing RANDOMSUBSET to 1-based index
Changing CLASS to 1-based index
Converting ANGLEPSI from degrees to radians
Traceback (most recent call last):
File “/mpcdf/soft/local/pyem-0.5/csparc2star.py”, line 105, in
sys.exit(main(parser.parse_args()))
File “/mpcdf/soft/local/pyem-0.5/csparc2star.py”, line 59, in main
coord_star = pd.concat(
File “/mpcdf/soft/local/anaconda3/envs/pyem/lib/python3.8/site-packages/pandas/core/reshape/concat.py”, line 271, in concat
op = _Concatenator(
File “/mpcdf/soft/local/anaconda3/envs/pyem/lib/python3.8/site-packages/pandas/core/reshape/concat.py”, line 326, in init
objs = list(objs)
File “/mpcdf/soft/local/pyem-0.5/csparc2star.py”, line 60, in
(star.parse_star(inp, keep_index=False, augment=True) for inp in
File “/home/system/soft.2018-08-22/local/pyem-0.5/pyem/star.py”, line 282, in parse_star
df = pd.read_csv(starfile, skiprows=ln, delimiter=‘\s+’, header=None, nrows=nrows)
File “/mpcdf/soft/local/anaconda3/envs/pyem/lib/python3.8/site-packages/pandas/io/parsers.py”, line 676, in parser_f
return _read(filepath_or_buffer, kwds)
File “/mpcdf/soft/local/anaconda3/envs/pyem/lib/python3.8/site-packages/pandas/io/parsers.py”, line 454, in _read
data = parser.read(nrows)
File “/mpcdf/soft/local/anaconda3/envs/pyem/lib/python3.8/site-packages/pandas/io/parsers.py”, line 1133, in read
ret = self._engine.read(nrows)
File “/mpcdf/soft/local/anaconda3/envs/pyem/lib/python3.8/site-packages/pandas/io/parsers.py”, line 2037, in read
data = self._reader.read(nrows)
File “pandas/_libs/parsers.pyx”, line 859, in pandas._libs.parsers.TextReader.read
File “pandas/_libs/parsers.pyx”, line 874, in pandas._libs.parsers.TextReader._read_low_memory
File “pandas/_libs/parsers.pyx”, line 928, in pandas._libs.parsers.TextReader._read_rows
File “pandas/_libs/parsers.pyx”, line 915, in pandas._libs.parsers.TextReader._tokenize_rows
File “pandas/_libs/parsers.pyx”, line 2070, in pandas._libs.parsers.raise_parser_error
pandas.errors.ParserError: Error tokenizing data. C error: Expected 9 fields in line 40, saw 16