This is a new problem that I believe did not occur in version 3. When importing a particle stack from relion, which was extracted or polished in relion and contains particle locations, cryosparc does not keep these locations, unless the micrographs are linked. I want to symmetry expand my particles for 3D classification and then unexpand the subsets for refinement with symmetry applied.
Initial issue- particles imported give error: Warning: No micrographs were connected as inputs, so correspondences cannot be found, so output will not contain pick locations for particles.
Despite star file containing: ‘rlnMicrographName’, ‘rlnCoordinateX’, ‘rlnCoordinateY’
This is what I have tried:
Micrographs are imported at J308/imported/uid_micrograph_enn_frames.mrc
Patch CTF job is J309 and linked for particle import
Import with source micrographs linked (patch ctf job). I realize I needed to check remove the leading uid
Example source micrograph filename: uid_micrograph_frames.mrc
Example query micrograph filename: micrograph_frames.mrc
Traceback (most recent call last):
File "cryosparc_master/cryosparc_compute/run.py", line 96, in cryosparc_compute.run.main
File "/home/cryosparc_user/software/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py", line 224, in run_import_particles
assert qname in inv_index_source, "Could not find match for %s" % qname
AssertionError: Could not find match for micrograph_frames.mrc
Import with source micrographs linked (patch ctf job) and Remove leading UID in input micrograph file name
Compiling particle location information...
Attempting to find corresponding filenames in rlnMicrographName and connected input micrographs..
Example source micrograph filename: micrograph_frames.mrc
Example query micrograph filename: micrograph_frames.mrc
So it looks like it worked. I already ran symmetry expansion and 3D classification on particles imported without micrographs linked. I now attempt to unexpand with remove duplicates, link particle locations from the lower level output of the import with source micrographs job, gives error:
Traceback (most recent call last):
File "cryosparc_master/cryosparc_compute/run.py", line 96, in cryosparc_compute.run.main
File "/home/cryosparc_user/software/cryosparc/cryosparc_master/cryosparc_compute/jobs/utilities/run_remove_duplicates.py", line 31, in run
rc.log('Loaded particle stack with %d items' % len(particles_dset))
TypeError: object of type 'NoneType' has no len()