Process particles from cryolo


I’m trying to pick particles in cryolo and importing them into cryoSPARC for further steps. The extraction from micrograph job worked but when performing 2D classifications, it raised errors as following:
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/”, line 95, in
File “cryosparc_master/cryosparc_compute/jobs/class2D/”, line 57, in
AssertionError: CTF parameters must be connected to perform CTF correction.

I use the Patch CTF estimated micrographs as input in Extraction job.

cryosparc version 4.4
cryolo version 1.9.8

Thanks a lot.

Hi @Lai,

How are you getting the particles/picks into CS? Are you using crYOLO in a standalone setting and importing a .star file or are you using CS-tools to pick particles in crYOLO as described here?



I use crYOLO GUI to pick particles and it generated four outputs, one of them is CRYOSPARC/ The result looks like :


_rlnMicrographName #1
_rlnCoordinateX #2
_rlnCoordinateY #3
_rlnAutopickFigureOfMerit #4
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 490.93841552734375 3937.248825073242 0.35988849401474
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 1771.45556640625 3947.5416717529297 0.5496110320091248
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 2919.79345703125 3952.607681274414 0.3419470489025116
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 3558.08447265625 3927.53369140625 0.7469070553779602
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 3787.430419921875 3940.988815307617 0.6527037620544434
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 3420.403564453125 3877.25341796875 0.729738175868988
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 2337.649658203125 3808.981689453125 0.2347775101661682
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 2644.262939453125 3810.0367126464844 0.20469319820404053
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 3181.429931640625 3800.4844970703125 0.2900577187538147
FoilHole_26960797_Data_26960480_26960482_20230926_153345_EER.mrc 3681.886962890625 3805.6930236816406 0.3370276093482971


Hi @Lai,

Did you perform the steps for importing particles from crYOLO following the ones outlined in this post?


Hi @kstachowski ,

Thanks very much! It works now.
I did check the “ignore raw data” and “ignore pose data” as in the post you mentioned. I did not give the microscope parameters. And it finally works after giving those parameters. Those parameters ensure it use micrograph CTF as particle CTF when extracting as I only give the coordinates.

Thanks again.


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