try to export CS 3.0 particle (after patch CTF) to relion for 2D and 3D process by the csparc2.star, use command below:
csparc2star.py P1/J17/extracted_particles.cs cs_j17_extracted_particles.star --boxsize 280 --copy-micrograph-coordinates Extract/job009/particles.star
found the output star file is extremely big (28G), and relion can not handle it
any one find similar ?
Hi @ajian,
Nothing has changed in terms of .cs files - how many particles do you have? You can paste the first few lines of the star file so others can see if anything is strange in it.
here is the size of the file :
-rw-rw-r–. 1 lrss lrss 29531131024 Dec 15 19:23 cs_j17_extracted_particles.star
and here is the first few line of star file:
loop_
_rlnVoltage #1
_rlnSphericalAberration #2
_rlnAmplitudeContrast #3
_rlnOpticsGroup #4
_rlnImagePixelSize #5
_rlnImageDimensionality #6
300.000000 2.700000 0.100000 1 1.100000 2
data_particles
loop_
_rlnImageName #1
_rlnMicrographName #2
_rlnCoordinateX #3
_rlnCoordinateY #4
_rlnDefocusU #5
_rlnDefocusV #6
_rlnDefocusAngle #7
_rlnPhaseShift #8
_rlnCtfBfactor #9
_rlnOpticsGroup #10
000001@Extract/job009/movies/HYZ20201207-07Ti_spuer_0003.mrcs MotionCorr/job002/movies/HYZ20201207-07Ti_spuer_0003.mrc 3582.500000 3562.500000 29303.527344 28536.794922 45.388657 0.000000 0.000000 1
000002@Extract/job009/movies/HYZ20201207-07Ti_spuer_0003.mrcs MotionCorr/job002/movies/HYZ20201207-07Ti_spuer_0003.mrc 2055.000000 3516.000000 29303.527344 28536.794922 45.388657 0.000000 0.000000 1
000003@Extract/job009/movies/HYZ20201207-07Ti_spuer_0003.mrcs MotionCorr/job002/movies/HYZ20201207-07Ti_spuer_0003.mrc 2571.500000 3499.000000 29303.527344 28536.794922 45.388657 0.000000 0.000000 1
000004@Extract/job009/movies/HYZ20201207-07Ti_spuer_0003.mrcs MotionCorr/job002/movies/HYZ20201207-07Ti_spuer_0003.mrc 2877.000000 3493.000000 29303.527344 28536.794922 45.388657 0.000000 0.000000 1
000005@Extract/job009/movies/HYZ20201207-07Ti_spuer_0003.mrcs MotionCorr/job002/movies/HYZ20201207-07Ti_spuer_0003.mrc 1818.000000 3427.500000 29303.527344 28536.794922 45.388657 0.000000 0.000000 1
000006@Extract/job009/movies/HYZ20201207-07Ti_spuer_0003.mrcs MotionCorr/job002/movies/HYZ20201207-07Ti_spuer_0003.mrc 1956.500000 3364.000000 29303.527344 28536.794922 45.388657 0.000000 0.000000 1
000007@Extract/job009/movies/HYZ20201207-07Ti_spuer_0003.mrcs MotionCorr/job002/movies/HYZ20201207-07Ti_spuer_0003.mrc 1677.500000 3341.000000 29303.527344 28536.794922 45.388657 0.000000 0.000000 1
000008@Extract/job009/movies/HYZ20201207-07Ti_spuer_0003.mrcs MotionCorr/job002/movies/HYZ20201207-07Ti_spuer_0003.mrc 2162.500000 3287.000000 29303.527344 28536.794922 45.388657 0.000000 0.000000 1
000009@Extract/job009/movies/HYZ20201207-07Ti_spuer_0003.mrcs MotionCorr/job002/movies/HYZ20201207-07Ti_spuer_0003.mrc 1305.000000 3164.000000 29303.527344 28536.794922 45.388657 0.000000 0.000000 1
000010@Extract/job009/movies/HYZ20201207-07Ti_spuer_0003.mrcs MotionCorr/job002/movies/HYZ20201207-07Ti_spuer_0003.mrc 1859.000000 3144.000000 29303.527344 28536.794922 45.388657 0.000000 0.000000 1
:
another issue, when i try to use csparc2star to export particle from NU job to relion,
csparc2star.py cryosparc_P3_J36_009_particles.cs cryosparc_P3_J36_009_particles.star --boxsize 256 --copy-micrograph-coordinates selcect_j15_particles.star
/home/lrss/softwares/pyem/pyem/star.py:531: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
df[UCSF.IMAGE_INDEX], df[UCSF.IMAGE_PATH] =
/home/lrss/softwares/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 “/home/lrss/softwares/pyem/csparc2star.py”, line 120, in
sys.exit(main(parser.parse_args()))
File “/home/lrss/softwares/pyem/csparc2star.py”, line 71, in main
df = star.smart_merge(df, coord_star, fields=fields, key=key)
File “/home/lrss/softwares/pyem/pyem/star.py”, line 143, in smart_merge
s2 = s2.set_index(key, drop=False)
File “/home/lrss/EMAN2/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’
figured it out, not need “-copy-micrograph-coordinates” option.