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Trouble converting exported .cs file #124
Description
Hello! I have an issue with using csparc2star. I enter the following commands:
conda activate pyem
(pyem) csparc2star.py --boxsize 150 --copy-micrograph-coordinates path J26_particles_exported.cs J26_particles_exported.star
Traceback (most recent call last):
File "/home/sofia.ievleva/miniconda3/bin/csparc2star.py", line 33, in
sys.exit(load_entry_point('pyem', 'console_scripts', 'csparc2star.py')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sofia.ievleva/pyem/pyem/cli/csparc2star.py", line 185, in main
sys.exit(main(parser.parse_args()))
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sofia.ievleva/pyem/pyem/cli/csparc2star.py", line 122, in main
df = star.smart_merge(df, coord_star, fields=fields, key=key)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sofia.ievleva/pyem/pyem/star/star.py", line 209, in smart_merge
s2 = s2.set_index(key, drop=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/sofia.ievleva/miniconda3/lib/python3.12/site-packages/pandas/core/frame.py", line 6122, in set_index
raise KeyError(f"None of {missing} are in the columns")
KeyError: 'None of [None] are in the columns'
I have downloaded everything including miniforge3 in hopes that it can help but this error still occurs. What can be done to fix this error? Thank you.
Activity
[-]Downloaded pyem and miniconda3 but csparc2star.py still is not working[/-][+]Downloaded pyem and miniconda3 but csparc2star.py still not working[/+]asarnow commentedon Oct 17, 2024
Looks like the image names don't match between the star file and the exported particles.
SI18 commentedon Oct 17, 2024
Thank you for your response! Could you please share what image names I need to change and how I can do that? I currently have .cs file and micrograph coordinates extracted from Relion as particles.star but I cannot seem to open .cs file and no matter what I do, I cannot convert it to .star.
[-]Downloaded pyem and miniconda3 but csparc2star.py still not working[/-][+]Trouble converting exported .cs file[/+]asarnow commentedon Oct 17, 2024
Start by converting the .cs file on its own and take a look. Then you can see if there is some mismatch in the image file names such that the ones in your old star file don't match anymore.
andreanans commentedon Nov 22, 2024
You probably need to add --strip-uid to your command. Try this:
csparc2star.py --strip-uid --boxsize 150 --copy-micrograph-coordinates path J26_particles_exported.cs J26_particles_exported.star