Pyem conversion error

Hi,

I’m using the pyem command to generate a star file for one of my refinement jobs in cryosparc since I want to carry out further processing using Relion. the particles were picked and extracted in WARP and processed in cryosparc. the command for pyem is: ~ketam/pyem/csparc2star.py J130/cryosparc_P3_J130_008_particles.cs J130/P3_J130_passthrough_particles.cs J130/cryosparc_P3_J130_008_particles_test.star --boxsize 290

The star file seems to be generated but it’s missing the information for X/Y coordinates. I then tried using the star.py command to get missing parameters but I get the following error (this is for an example dataset):

~ketanm/pyem/star.py --copy-micrograph-coordinates Warp/EIF3-2/goodparticles_BoxNet2Mask_20180918.star test_cryosparc_P3_J146_particles.star cryosparc_P3_J146_particles_with_coords_dataset2.star
/lmb/home/ketanm/pyem/pyem/star.py:531: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
df[UCSF.IMAGE_INDEX], df[UCSF.IMAGE_PATH] =
/lmb/home/ketanm/pyem/pyem/star.py:539: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
df[UCSF.IMAGE_ORIGINAL_INDEX], df[UCSF.IMAGE_ORIGINAL_PATH] =
Traceback (most recent call last):
File “/lmb/home/ketanm/pyem/star.py”, line 363, in
sys.exit(main(parser.parse_args()))
File “/lmb/home/ketanm/pyem/star.py”, line 149, in main
df = star.smart_merge(df, coord_star, fields=star.Relion.MICROGRAPH_COORDS, key=args.merge_key)
File “/lmb/home/ketanm/pyem/pyem/star.py”, line 143, in smart_merge
s2 = s2.set_index(key, drop=False)
File “/lmb/home/ketanm/miniconda3/envs/pyem/lib/python3.8/site-packages/pandas/core/frame.py”, line 4548, in set_index
raise KeyError(f"None of {missing} are in the columns")
KeyError: 'None of [None] are in the columns’

It will be helpful to know what I’m doing wrong so that I can get the coordinates back into the star file.

did you import the stack to cryoSPARC? I suspect that coordinates are not linked to the actual micrographs. You might find the answer here:

Hi Alex, Yes I uploaded the particle stack directly in the form of star file from WARP to Cryosparc. You think I need to upload the micrographs as well to get the co-ordinate information? Thanks