Importing relion 3 particle star fails in CryoSPARC 3 (bug)


When I try to import a particle star file from a polishing job executed in relion 3.1, I get the attached error. It seems like CSPARC is trying to confirm the offsets from Angstroms to pixels and failing. If I manually change the column labels in the star file to rlnOriginX/rlnOriginY instead of rlnOriginXAngst/rlnOriginYAngst it imports correctly.


Hi @olibclarke,

Are you running cryoSPARC v3.0.1? This bug was fixed in this version.

Hi @stephan, I was not but am now, so good to know!


Hi @stephan,

I still see the same bug in 3.01 (with a slightly different error message):

Hey @olibclarke,

Can you send me your star file? It doesn’t need to be the entire thing, just one or two rows would be great. Thanks!
EDIT: Can you also send me the entire contents of the “Overview” tab?

Hi @stephan, sure thing - I will try to find the star file and DM you. Thanks!

That’d be really helpful. Thank you!

I have the same problem

Is there a solution?

[CPU: 290.4 MB] Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/”, line 84, in
File “/usr/local/cryosparc/cryosparc2_master/cryosparc_compute/jobs/imports/”, line 307, in run_import_particles[‘shift’][idx] = make_shift_rln(starrow)
ValueError: could not broadcast input array from shape (2,100000) into shape (2)

Read the first post - change rlnOriginX /rlnOriginY to rlnOriginXAngst /rlnOriginYAngst in the star file. If you really need the offsets to be right (for local refinement, for example) you may also need to do some math on the values

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Hi @olibclarke, @jiskander,

Sorry for the inconvenience, a fix for this will be released in v3.1.


Thanks I saw that and solved. It will be helpful if we did not need to do that.

@jiskander We have released a v3.1.0 update to cryoSPARC in which this issue should be resolved. Please let us know if this issue persists in v3.1.0.