Hi Daniel,
I tried your latest version of pyem, it does produce files with helical tube ID. That is good, but I am getting completely different orientations with the new version compared to the older one (20210407). Rot, Tilt, and Psi are 6.466606, 62.377716, 167.797440 in the version of 20210729, and the previous version gave me -100.316521, 89.302757, 61.014317. Those angles were compatible with Relion, the new ones are not. Do you apply a transformation now and if yes, what kind? Is it possible to go back to the previous version with angles?
Forgot to tell you that when I tried to use csparc2star.py with exported cs file, it crashed:
csparc2star.py …/cryosparc/P59/exports/groups/P59_J214_particles/P59_J214_particles_exported.cs jnk_ltst.star
/opt/apps/PyEM/20210729/pyem/pyem/metadata.py:334: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify ‘dtype=object’ when creating the ndarray.
df[model[k]] = pd.DataFrame(np.array(
Columns must be same length as key
Traceback (most recent call last):
File “/opt/apps/PyEM/20210729/pyem/csparc2star.py”, line 42, in main
df = metadata.parse_cryosparc_2_cs(cs, passthroughs=args.input[1:], minphic=args.minphic,
File “/opt/apps/PyEM/20210729/pyem/pyem/metadata.py”, line 415, in parse_cryosparc_2_cs
df = cryosparc_2_cs_model_parameters(cs, df, minphic=minphic)
File “/opt/apps/PyEM/20210729/pyem/pyem/metadata.py”, line 334, in cryosparc_2_cs_model_parameters
df[model[k]] = pd.DataFrame(np.array(
File “/opt/apps/PyEM/20210729/lib/python3.9/site-packages/pandas/core/frame.py”, line 3597, in setitem
self._setitem_array(key, value)
File “/opt/apps/PyEM/20210729/lib/python3.9/site-packages/pandas/core/frame.py”, line 3634, in _setitem_array
check_key_length(self.columns, key, value)
File “/opt/apps/PyEM/20210729/lib/python3.9/site-packages/pandas/core/indexers.py”, line 428, in check_key_length
raise ValueError(“Columns must be same length as key”)
ValueError: Columns must be same length as key
Required fields could not be mapped. Are you using the right input file(s)?
Without exporting everything works well.
Thanks,
Michael