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

olibclarke · December 24, 2020, 11:51am

Hi,

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.

Cheers
Oli

stephan · December 27, 2020, 2:16am

Hi @olibclarke,

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

olibclarke · December 27, 2020, 2:23am

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

Oli

olibclarke · December 27, 2020, 12:24pm

Hi @stephan,

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

stephan · January 15, 2021, 5:09pm

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?

olibclarke · January 15, 2021, 5:53pm

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

stephan · January 15, 2021, 5:54pm

That’d be really helpful. Thank you!

jiskander · January 19, 2021, 4:33am

I have the same problem

Is there a solution?

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

olibclarke · January 19, 2021, 2:05pm

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

stephan · January 20, 2021, 5:36pm

Hi @olibclarke, @jiskander,

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

jiskander · January 21, 2021, 7:03am

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

spunjani · January 29, 2021, 9:29pm

@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.