Csparc2star.py error

Import and Export
1

Hi,

I am trying to convert particles.cs file into particles.star file to process in Relion using csparc2star.py .
I encounter following error:
python3 /data/Cryosparc_user/pyem/csparc2star.py --copy-micrograph-coordinates P4_J21_passthrough_particles_selected.cs P4_J21_passthrough_particles_selected.star
Traceback (most recent call last):
File “/data/Cryosparc_user/pyem/csparc2star.py”, line 120, in
sys.exit(main(parser.parse_args()))
File “/data/Cryosparc_user/pyem/csparc2star.py”, line 38, in main
if args.input[0].endswith(".cs"):
IndexError: list index out of range

I was wondering if someone can help me resolve this issue.

Thanks

Anamika

2

Hi @Anamika1,

in your command, the flag “–copy-micrograph-coordinates” needs to be followed with your original particles.star file that was imported in cryoSPARC. or if your particles were picked in cryoSPARC, you don’t need this flag.

3

Hi Bing,

My particles were picked in Cryosparc and if I run the command without the flag, I see different error now.
(base) [cryosparc_user@delorean J21]$ python3 /data/Cryosparc_user/pyem/csparc2star.py P4_J21_passthrough_particles_selected.cs P4_J21_passthrough_particles_selected.star

Angular alignment parameters not found

(base) [cryosparc_user@delorean J21]$

4

I guess this is just a warning, you should still get a .star file. If you want to have star file containing Angular alignment parameters, you should convert .cs file in a refinement job.

5

Thanks, yes it worked.

6

Hi Bing,

Another issue, when I import the .cs to .star converted file in relion I see following error with bunch of missing variables. Is there something I need to specify during conversion?
in: /usr/local/relion-3.1-source/src/jaz/obs_model.cpp, line 198
ERROR:
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.
=== Backtrace ===
relion_import(_ZN11RelionErrorC1ERKSsS1_l+0x47) [0x4cfd17]
relion_import() [0x44073a]
relion_import(_ZN16ObservationModel10loadSafelyESsRS_R13MetaDataTableSsib+0x437) [0x4e0577]
relion_import(_ZN17import_parameters3runEv+0x1177) [0x4a3ba7]
relion_import(main+0x35) [0x49bbc5]
/usr/lib64/libc.so.6(__libc_start_main+0xf5) [0x7fd0ac2f0555]
relion_import() [0x49e7df]

ERROR:
ERROR: not all necessary variables defined in _optics.star file: rlnPixelSize, rlnVoltage and rlnSphericalAberration. Make sure to convert older STAR files anew in version-3.1, with relion_convert_star.

7

Are you using the most recent pyem? it should write out the optics group in the star file converted, something like:

data_optics

loop_
_rlnVoltage #1
_rlnSphericalAberration #2
_rlnAmplitudeContrast #3
_rlnOpticsGroup #4
_rlnImageSize #5
_rlnImagePixelSize #6
_rlnImageDimensionality #7
300.000000 2.700000 0.100000 3 320 1.052000 2

Or you can just add this manually.

8

Hi Bing,

As you mentioned above I converted the .cs file from refinement job and now I see following defocus value not found error. Any suggestion on how to fix it?

python3 /data/Cryosparc_user/pyem/csparc2star.py --swapxy /data/Cryosparc_user/P4/J68/P4_J68_passthrough_particles.cs P4_J68_passthrough_particles_swapxy.star
Defocus values not found

9

hi @Anamika
I guess you should convert particle meta data file something like: cryosparc_P4_J68_00?_particles.cs

10

Thanks! Yup that was it, no warnings any more!