Nothing in the half-maps after refinement 2.0

Dear colleagues,

I faced a similar issue with the half-maps.
Nothing in the half-maps after refinement - Troubleshooting - CryoSPARC Discuss

They are nothing but dust.

Any suggestion is appreciated.

Thank you.

Kind regards,

Updates - that happens when using 3D Homogeneous refinements and Local resolution refinement.

The half-maps in NU-refinement is ok.

Cryosparc 4.4.1 + 240110

Kind regards,

@Dmitry Please can you post additional information:

  1. The filename of the map that you showed in your first post.
  2. The output of the following command, with the correct project and job IDs specified, for the job that produced that map:
    cryosparcm cli "get_job('P912', 'J934',  'job_type', 'version', 'params_spec', 'input_slot_groups')"
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Hello @wtempel,

  1. cryosparc_P13_J128_013_volume_map.mrc
  2. Please see the output of the following command

cryosparcm cli "get_job('P13', 'J128', 'job_type', 'version', 'params_spec', 'input_slot_groups')"


cryosparcm cli "get_job('P13', 'J128', 'job_type', 'version', 'params_spec', 'input_slot_groups')"

{'_id': '663bacc09d2d40135037ff92', 'input_slot_groups': [{'connections': [{'group_name': 'particles_0', 'job_uid': 'J109', 'slots': [{'group_name': 'particles_0', 'job_uid': 'J109', 'result_name': 'blob', 'result_type': 'particle.blob', 'slot_name': 'blob', 'version': 'F'}, {'group_name': 'particles_0', 'job_uid': 'J109', 'result_name': 'ctf', 'result_type': 'particle.ctf', 'slot_name': 'ctf', 'version': 'F'}, {'group_name': 'particles_0', 'job_uid': 'J109', 'result_name': 'alignments3D', 'result_type': 'particle.alignments3D', 'slot_name': 'alignments3D', 'version': 'F'}, {'group_name': 'particles_0', 'job_uid': 'J109', 'result_name': 'motion', 'result_type': 'particle.motion', 'slot_name': None, 'version': 'F'}, {'group_name': 'particles_0', 'job_uid': 'J109', 'result_name': 'location', 'result_type': 'particle.location', 'slot_name': None, 'version': 'F'}]}], 'count_max': inf, 'count_min': 1, 'description': 'Particle stacks to use. Multiple stacks will be concatenated.', 'name': 'particles', 'repeat_allowed': False, 'slots': [{'description': '', 'name': 'blob', 'optional': False, 'title': 'Particle data blobs', 'type': 'particle.blob'}, {'description': '', 'name': 'ctf', 'optional': False, 'title': 'Particle ctf parameters', 'type': 'particle.ctf'}, {'description': '', 'name': 'alignments3D', 'optional': True, 'title': 'Particle 3D alignments (optional)', 'type': 'particle.alignments3D'}], 'title': 'Particle stacks', 'type': 'particle'}, {'connections': [{'group_name': 'volume', 'job_uid': 'J111', 'slots': [{'group_name': 'volume', 'job_uid': 'J111', 'result_name': 'map', 'result_type': 'volume.blob', 'slot_name': 'map', 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J111', 'result_name': 'map_sharp', 'result_type': 'volume.blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J111', 'result_name': 'map_half_A', 'result_type': 'volume.blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J111', 'result_name': 'map_half_B', 'result_type': 'volume.blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J111', 'result_name': 'mask_refine', 'result_type': 'volume.blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J111', 'result_name': 'mask_fsc', 'result_type': 'volume.blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J111', 'result_name': 'mask_fsc_auto', 'result_type': 'volume.blob', 'slot_name': None, 'version': 'F'}, {'group_name': 'volume', 'job_uid': 'J111', 'result_name': 'precision', 'result_type': 'volume.blob', 'slot_name': None, 'version': 'F'}]}], 'count_max': 1, 'count_min': 1, 'description': '', 'name': 'volume', 'repeat_allowed': False, 'slots': [{'description': '', 'name': 'map', 'optional': False, 'title': 'Initial volume raw data', 'type': 'volume.blob'}], 'title': 'Initial volume', 'type': 'volume'}, {'connections': [{'group_name': 'mask', 'job_uid': 'J111', 'slots': [{'group_name': 'mask', 'job_uid': 'J111', 'result_name': 'mask_refine', 'result_type': 'volume.blob', 'slot_name': 'mask', 'version': 'F'}]}], 'count_max': 1, 'count_min': 0, 'description': '', 'name': 'mask', 'repeat_allowed': False, 'slots': [{'description': '', 'name': 'mask', 'optional': False, 'title': 'Static mask', 'type': 'volume.blob'}], 'title': 'Static mask', 'type': 'mask'}], 'job_type': 'homo_refine_new', 'params_spec': {'refine_ctf_global_refine': {'value': True}, 'refine_num_final_iterations': {'value': 2}, 'refine_scale_min': {'value': True}}, 'project_uid': 'P13', 'uid': 'J128', 'version': 'v4.5.0'}

Hi @Dmitry! For the jobs with the empty half-maps, does the full map have anything in it, or is it also empty?

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hello @rposert yes, the full map is ok. :slight_smile:

Thanks for the info @Dmitry, that’s interesting…

Could you please share a bit more info about the half maps?

  • It would be interesting to see the voxel histogram for one of the half maps and for the full map (like below)

  • If you contour down your half map, does the noise fill up the entire box (like below)? If so, can you see anything inside the box using the Graphics > Side View panel to “cut into” it?