Issue on Coordinates import

Import and Export
1

Hi, I find something suprising. After importing coordinates or particles stack into cryosparc, I used “Manually Curate Exposures” to check and find all particles are assigned to one micrograph rather to their own micrographs. Why this happens? I checked carefully that particles in the relion star file are assigned to their own micrographs.

Thank you!
Jianhao

2

Hi @jianhaoc,

Can you report what version of cryoSPARC you’re running?
Also, can you show us the output of the Import Particles job?

3

Hi @stephan,

The version of cryoSPARC is v3.2.0. Below is the output of the Import Particles job.

License is valid.

Running job on master node

[CPU: 67.7 MB]   Project P27 Job J55 Started

[CPU: 67.8 MB]   Master running v3.2.0, worker running v3.2.0

[CPU: 67.8 MB]   Running on lane default

[CPU: 67.8 MB]   Resources allocated: 

[CPU: 67.8 MB]     Worker:  zhanglab

[CPU: 67.8 MB]   --------------------------------------------------------------

[CPU: 67.8 MB]   Importing job module for job type import_particles...

[CPU: 207.0 MB]  Job ready to run

[CPU: 207.0 MB]  ***************************************************************

[CPU: 207.0 MB]  Importing particles from  /data/test-cryolo/ptcl-ctf-mic-gctf_x2.star

[CPU: 207.0 MB]  File extension is  star

[CPU: 207.0 MB]  Importing star file.

[CPU: 316.8 MB]  --------------------------------------------------------------

[CPU: 316.8 MB]  Loaded star file with 214152 items

[CPU: 316.8 MB]  Fields loaded from star file:  ['rlnOpticsGroup', 'rlnOpticsGroupName', 'rlnAmplitudeContrast', 'rlnSphericalAberration', 'rlnVoltage', 'rlnMicrographOriginalPixelSize', 'rlnImagePixelSize', 'rlnImageSize', 'rlnImageDimensionality', 'rlnCoordinateX', 'rlnCoordinateY', 'rlnAnglePsi', 'rlnClassNumber', 'rlnAutopickFigureOfMerit', 'rlnImageName', 'rlnMicrographName', 'rlnCtfFigureOfMerit', 'rlnDefocusU', 'rlnDefocusV', 'rlnDefocusAngle', 'rlnCtfBfactor', 'rlnCtfScalefactor', 'rlnPhaseShift']

[CPU: 316.8 MB]  --------------------------------------------------------------

[CPU: 316.8 MB]  Reading particle data locations...

[CPU: 316.8 MB]    Reading rlnImageName to get indices and paths..

[CPU: 387.3 MB]    Warning: Parameter particle_blob_path was set, which overrides rlnImageName despite the latter being present in the input star file.

[CPU: 387.3 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: 387.3 MB]  Searching for linked data files...

[CPU: 387.3 MB]  --------------------------------------------------------------

[CPU: 387.3 MB]  Compiling CTF information...

[CPU: 387.3 MB]  --------------------------------------------------------------

[CPU: 387.3 MB]  Compiling particle location information...

[CPU: 387.3 MB]    Attempting to find corresponding filenames in rlnMicrographName and connected input micrographs..

[CPU: 387.4 MB]    Example source micrograph filename: 

[CPU: 387.4 MB]       

[CPU: 387.4 MB]    Example query micrograph filename: 

[CPU: 387.4 MB]       

[CPU: 387.4 MB]  Warning: Output will not contain particle orientations since the input star file does not contain: rlnAngleRot, rlnAngleTilt, either {'rlnOriginX', 'rlnOriginY'} or {'rlnOriginXAngst', 'rlnOriginYAngst'}, 'rlnRandomSubset'

[CPU: 387.4 MB]  Note: Use the 'Ignore half-set split if missing' parameter if you want to re-split the particles since the 'rlnRandomSubset' field is missing from the star file.

[CPU: 387.4 MB]  --------------------------------------------------------------

[CPU: 387.4 MB]  Particle information has now been imported for 214152 particles, creating outputs...

[CPU: 387.4 MB]  Found references to 100 unique data files

[CPU: 387.4 MB]  Import paths were unique at level -1

[CPU: 387.4 MB]  Example imported relative path:
 J55/imported/stack_00000.mrcs

[CPU: 387.4 MB]  Reading MRC file headers to check shape...

[CPU: 430.2 MB]  --------------------------------------------------------------

[CPU: 430.2 MB]  Loaded 214152 particles.

[CPU: 430.2 MB]    Common fields: 

[CPU: 430.2 MB]            ctf/accel_kv :  {300.0}

[CPU: 430.2 MB]               ctf/cs_mm :  {2.7}

[CPU: 430.2 MB]        ctf/amp_contrast :  {0.1}

[CPU: 430.2 MB]        ctf/exp_group_id :  {1}

[CPU: 430.2 MB]            blob/psize_A :  {1.0694}

[CPU: 430.2 MB]              blob/shape :  [128 128]

[CPU: 430.2 MB]  --------------------------------------------------------------

[CPU: 430.2 MB]  Making plots...

Lowpass Filtered Images:  [png]  [pdf] 
Lowpass Filtered Images: 

Raw Images:  [png]  [pdf] 
Raw Images: 

[CPU: 475.6 MB]  --------------------------------------------------------------

[CPU: 475.6 MB]  Compiling job outputs...

[CPU: 480.9 MB]  Updating job size...

[CPU: 480.9 MB]  Exporting job and creating csg files...

[CPU: 480.9 MB]  ***************************************************************
[CPU: 480.9 MB]  Job complete. Total time 14.80s
4

Interesting how this bit is blank- was this an artefact of the copy+paste? Or is it blank for you too?
Did you connect your micrographs to this job? Did you Import the Micrographs, or create them using Patch Motion Correction?

5

I imported micrographs then imported particles stack with imported micrographs connected. Yes, these 2 lines are blank in the output.