Hi guys,
I am trying to import particles from relion 3.1 to cryosparc but get the particle orientations are not imported. I have tried removing the opticsgroup block and changing data_particles to data_ but ended up with the same situation. Below is a log of the import.
Any help is greatly appreciated,
Thanks a lot,
Cheers,
Arka
Loaded star with 62075 items
[CPU: 217.3 MB] star file fields:
[CPU: 217.3 MB] Index([u'rlnCoordinateX', u'rlnCoordinateY', u'rlnImageName',
u'rlnMicrographName', u'rlnCtfMaxResolution', u'rlnCtfFigureOfMerit',
u'rlnDefocusU', u'rlnDefocusV', u'rlnDefocusAngle', u'rlnCtfBfactor',
u'rlnCtfScalefactor', u'rlnPhaseShift', u'rlnAngleRot', u'rlnAngleTilt',
u'rlnAnglePsi', u'rlnClassNumber', u'rlnNormCorrection',
u'rlnLogLikeliContribution', u'rlnMaxValueProbDistribution',
u'rlnNrOfSignificantSamples', u'rlnParticleSelectZScore',
u'rlnOpticsGroup', u'rlnOriginXAngst', u'rlnOriginYAngst',
u'rlnGroupNumber', u'rlnImageOriginalName'],
dtype='object')
[CPU: 217.3 MB] Reading particle data locations...
[CPU: 217.3 MB] Reading rlnImageName to get indices and paths..
[CPU: 222.5 MB] Warning: Parameter particle_blob_path was set, which overrides rlnImageName despite the latter being present in the input star file.
[CPU: 222.5 MB] Parameter particle_blob_path was set and is a directory, so will be used as the search base for finding referenced data paths in the star file.
[CPU: 222.5 MB] Searching for linked data files...
[CPU: 222.5 MB] Compiling CTF information...
[CPU: 222.6 MB] Warning: No micrographs were connected as inputs, so correspondences cannot be found, so output will not contain pick locations for particles.
[CPU: 222.6 MB] Warning: The input star file does not contain rlnAngleRot, rlnAngleTilt, rlnAnglePsi, rlnOriginX, rlnOriginY, rlnRandomSubset. Output will not contain particle orientations.
[CPU: 222.6 MB] --------------------------------------------------------------
[CPU: 222.6 MB] Particle information has now been imported for 62075 particles, creating outputs...
[CPU: 222.6 MB] Found references to 9 unique data files
[CPU: 222.6 MB] Import paths were unique at level -1
[CPU: 222.6 MB] Example imported relative path:
J27/imported/subtracted_rank10_opticsgroup1.mrcs
[CPU: 222.8 MB] Reading MRC file headers to check shape...
[CPU: 222.8 MB] Done importing.
[CPU: 222.8 MB] --------------------------------------------------------------
[CPU: 222.8 MB] ===========================================================
[CPU: 222.8 MB] Loaded 62075 particles.
[CPU: 222.8 MB] Common fields:
[CPU: 222.8 MB] ctf/accel_kv : set([300.0])
[CPU: 222.9 MB] ctf/cs_mm : set([2.7])
[CPU: 222.9 MB] ctf/amp_contrast : set([0.1])
[CPU: 222.9 MB] ctf/exp_group_id : set([5])
[CPU: 222.9 MB] blob/psize_A : set([1.1])
[CPU: 222.9 MB] blob/shape : [400 400]
[CPU: 222.9 MB] ===========================================================
[CPU: 222.9 MB] Making plots...