IndexError: list index out of range during local CTF refinement

CTF Refinement
1

Dear all,

I am trying to run a local CTF refinement job, but after the particle processing for split B starts, I run into this error message:

[CPU: 827.5 MB] Traceback (most recent call last):
File “cryosparc_worker/cryosparc_compute/run.py”, line 85, in cryosparc_compute.run.main
File “cryosparc_worker/cryosparc_compute/jobs/ctf_refinement/run_local.py”, line 148, in cryosparc_compute.jobs.ctf_refinement.run_local.run
File “cryosparc_worker/cryosparc_compute/jobs/ctf_refinement/run_local.py”, line 217, in cryosparc_compute.jobs.ctf_refinement.run_local.full_defocus_refine
File “cryosparc_worker/cryosparc_compute/jobs/ctf_refinement/run_local.py”, line 325, in cryosparc_compute.jobs.ctf_refinement.run_local.do_defocus_refine
IndexError: list index out of range

I have no clue what this could mean, and how I could fix it. Global CTF refinement was successful

Thank you for any advice,
Marton

2

Please can you post

  • additional lines from that log so we may know how far the job has proceeded
  • the text from the job’s job.json
3

Where can I find that file?

4

Near the top (“Show from top”) of the log where you observed the error, there should be a line
“Working in directory:”. That is where you would find the relevant job.json.
On v4+, an equivalent job_document_*.json is included in the error report.

5

Thank you for the reply.

What I posted above is the complete error message. The messages above the error message are below, and for the sake of better visibility, the text from the job.json file will be in my next reply:

[CPU: 275.4 MB] Loaded particle stack metadata.

[CPU: 275.6 MB] Mask input was not connected, but volume input has mask_refine slot connected. Will apply this mask to references before comparison with images

[CPU: 278.6 MB] Loading input halfmaps…

[CPU: 332.6 MB] Finished loading halfmaps.

[CPU: 332.6 MB] Computing FSC…

[CPU: 454.0 MB] Using full box size 192, downsampled box size 96, with low memory mode disabled.

[CPU: 454.0 MB] Computing FFTs on GPU.

[CPU: 536.0 MB] Done in 1.02s

[CPU: 536.0 MB] Half-maps have FSC=0.5 at 2.65A resolution, which is 94.50 Fourier shells.
[CPU: 536.0 MB] Half-maps have FSC=0.143 at 2.65A resolution, which is 94.50 Fourier shells.

[CPU: 537.3 MB] Half-maps will be FSC-filtered before being used as references.

[CPU: 738.1 MB] Maximum fit resolution was set manually to 3.00A

[CPU: 738.1 MB] Loaded volumes.

[CPU: 738.1 MB] Reading particle stack…

[CPU: 738.1 MB] Windowing particles

[CPU: 738.1 MB] Done.

[CPU: 738.1 MB] SSD cache : cache successfuly synced in_use

[CPU: 740.2 MB] SSD cache : cache successfuly synced, found 3078855.70MB of files on SSD.

[CPU: 739.7 MB] SSD cache : cache successfuly requested to check 20602 files.

[CPU: 740.7 MB] SSD cache : cache requires 0.00MB more on the SSD for files to be downloaded.

[CPU: 740.7 MB] SSD cache : cache has enough available space.

[CPU: 740.7 MB] SSD cache : cache starting transfers to SSD.

[CPU: 746.1 MB] SSD cache : complete, all requested files are available on SSD.

[CPU: 797.4 MB] Will process 88294 particles

[CPU: 797.4 MB] Splitting particles into half-sets…

[CPU: 797.4 MB] Split A has 88294 particles.
[CPU: 797.7 MB] Split B has 0 particles.

[CPU: 804.0 MB] Starting Local CTF Refinement =====================

[CPU: 804.0 MB] --------------------------------------

[CPU: 804.0 MB] Fitting parameters…

[CPU: 804.0 MB] Fit min resolution: 12.000A

[CPU: 804.0 MB] Fit max resolution: 3.000A

[CPU: 806.4 MB] GPU batch size auto-fit is 1000

[CPU: 806.4 MB] Starting particle processing for split A…
[CPU: 806.6 MB] batch 89 of 89

[CPU: 1.25 GB] Starting particle processing for split B…

6

Job.json text is the following:

{
    "project_uid": "P86",
    "uid": "J1200",
    "workspace_uids": [
        "W24"
    ],
    "version": "v3.3.2+220518",
    "job_type": "ctf_refine_local",
    "type": "ctf_refine_local",
    "deleted": false,
    "run_as_user": null,
    "title": "New Job J1200",
    "description": "Enter a description.",
    "params_secs": {
        "prepare": {
            "title": "Particle preprocessing",
            "desc": "",
            "order": 0
        },
        "ctf_ref_local": {
            "title": "Local CTF Refinement",
            "desc": "",
            "order": 1
        },
        "compute_settings": {
            "title": "Compute settings",
            "desc": "",
            "order": 2
        }
    },
    "params_base": {
        "prepare_window_dataset": {
            "type": "boolean",
            "value": true,
            "title": "Window dataset (real-space)",
            "desc": "",
            "order": 0,
            "section": "prepare",
            "advanced": false,
            "hidden": false
        },
        "prepare_window_inner_radius": {
            "type": "number",
            "value": 0.85,
            "title": "Window inner radius",
            "desc": "",
            "order": 1,
            "section": "prepare",
            "advanced": true,
            "hidden": false
        },
        "prepare_window_outer_radius": {
            "type": "number",
            "value": 0.99,
            "title": "Window outer radius",
            "desc": "",
            "order": 2,
            "section": "prepare",
            "advanced": true,
            "hidden": false
        },
        "crl_N": {
            "type": "number",
            "value": null,
            "title": "Refinement box size (Voxels)",
            "desc": "Size of reconstruction/image to use for refinement. Blank means to use the particle box size (upsampling input maps as needed).",
            "order": 3,
            "section": "ctf_ref_local",
            "advanced": false,
            "hidden": true
        },
        "crl_num_plots": {
            "type": "number",
            "value": 50,
            "title": "Num. particles to plot",
            "desc": "Number of particles to make plots for. After this many, stop plotting to save time.",
            "order": 4,
            "section": "ctf_ref_local",
            "advanced": false,
            "hidden": false
        },
        "crl_min_res_A": {
            "type": "number",
            "value": 20,
            "title": "Minimum Fit Res (A)",
            "desc": "The minimum resolution to use during refinement of image aberrations.",
            "order": 5,
            "section": "ctf_ref_local",
            "advanced": false,
            "hidden": false
        },
        "crl_max_res_A": {
            "type": "number",
            "value": null,
            "title": "Maximum Fit Res (A)",
            "desc": "The maximum resolution to use during refinement of image aberrations. If blank, use input half-maps to compute FSC and set max to FSC=0.5",
            "order": 6,
            "section": "ctf_ref_local",
            "advanced": false,
            "hidden": false
        },
        "crl_df_range": {
            "type": "number",
            "value": 2000,
            "title": "Defocus Search Range (A +/-)",
            "desc": "Defocus search range in Angstroms, searching both above and below the input defocus by this amount",
            "order": 7,
            "section": "ctf_ref_local",
            "advanced": false,
            "hidden": false
        },
        "crl_do_ews_correct": {
            "type": "boolean",
            "value": false,
            "title": "Account for EWS curvature",
            "desc": "Whether or not to correct for the curvature of the Ewald Sphere",
            "order": 8,
            "section": "ctf_ref_local",
            "advanced": false,
            "hidden": false
        },
        "crl_ews_zsign": {
            "type": "enum",
            "value": "negative",
            "title": "EWS curvature sign",
            "desc": "Whether to use positive or negative curvature in Ewald Sphere correction.",
            "order": 9,
            "section": "ctf_ref_local",
            "advanced": false,
            "hidden": false,
            "enum_keys": [
                "positive",
                "negative"
            ],
            "enum_dict": {
                "positive": 1,
                "negative": -1
            }
        },
        "compute_use_ssd": {
            "type": "boolean",
            "value": true,
            "title": "Cache particle images on SSD",
            "desc": "",
            "order": 10,
            "section": "compute_settings",
            "advanced": false,
            "hidden": false
        },
        "compute_gpu_batch_size": {
            "type": "number",
            "value": null,
            "title": "GPU batch size of images",
            "desc": "",
            "order": 11,
            "section": "compute_settings",
            "advanced": true,
            "hidden": false
        }
    },
    "params_spec": {
        "crl_max_res_A": {
            "value": 3
        },
        "crl_min_res_A": {
            "value": 12
        }
    },
    "input_slot_groups": [
        {
            "type": "particle",
            "name": "particles",
            "title": "Particle stacks",
            "description": "Particle stacks to use. Multiple stacks will be concatenated.",
            "count_min": 1,
            "count_max": Infinity,
            "repeat_allowed": false,
            "slots": [
                {
                    "type": "particle.blob",
                    "name": "blob",
                    "title": "Particle data blobs",
                    "description": "",
                    "optional": false
                },
                {
                    "type": "particle.ctf",
                    "name": "ctf",
                    "title": "Particle ctf parameters",
                    "description": "",
                    "optional": false
                },
                {
                    "type": "particle.alignments3D",
                    "name": "alignments3D",
                    "title": "Particle alignments3D parameters",
                    "description": "",
                    "optional": false
                }
            ],
            "connections": [
                {
                    "job_uid": "J1077",
                    "group_name": "particles_class_3",
                    "slots": [
                        {
                            "slot_name": "blob",
                            "job_uid": "J1077",
                            "group_name": "particles_class_3",
                            "result_name": "blob",
                            "result_type": "particle.blob",
                            "version": "F"
                        },
                        {
                            "slot_name": "ctf",
                            "job_uid": "J1077",
                            "group_name": "particles_class_3",
                            "result_name": "ctf",
                            "result_type": "particle.ctf",
                            "version": "F"
                        },
                        {
                            "slot_name": "alignments3D",
                            "job_uid": "J1077",
                            "group_name": "particles_class_3",
                            "result_name": "alignments3D",
                            "result_type": "particle.alignments3D",
                            "version": "F"
                        },
                        {
                            "slot_name": null,
                            "job_uid": "J1077",
                            "group_name": "particles_class_3",
                            "result_name": "alignments2D",
                            "result_type": "particle.alignments2D",
                            "version": "F"
                        },
                        {
                            "slot_name": null,
                            "job_uid": "J1077",
                            "group_name": "particles_class_3",
                            "result_name": "location",
                            "result_type": "particle.location",
                            "version": "F"
                        },
                        {
                            "slot_name": null,
                            "job_uid": "J1077",
                            "group_name": "particles_class_3",
                            "result_name": "pick_stats",
                            "result_type": "particle.pick_stats",
                            "version": "F"
                        }
                    ]
                }
            ]
        },
        {
            "type": "volume",
            "name": "volume",
            "title": "Input volume",
            "description": "",
            "count_min": 1,
            "count_max": 1,
            "repeat_allowed": false,
            "slots": [
                {
                    "type": "volume.blob",
                    "name": "map",
                    "title": "Refined volume",
                    "description": "",
                    "optional": true
                },
                {
                    "type": "volume.blob",
                    "name": "map_half_A",
                    "title": "Halfmap A",
                    "description": "",
                    "optional": false
                },
                {
                    "type": "volume.blob",
                    "name": "map_half_B",
                    "title": "Halfmap B",
                    "description": "",
                    "optional": false
                },
                {
                    "type": "volume.blob",
                    "name": "mask_refine",
                    "title": "Refinement mask",
                    "description": "",
                    "optional": true
                }
            ],
            "connections": [
                {
                    "job_uid": "J1077",
                    "group_name": "volume_class_3",
                    "slots": [
                        {
                            "slot_name": "map",
                            "job_uid": "J1077",
                            "group_name": "volume_class_3",
                            "result_name": "map",
                            "result_type": "volume.blob",
                            "version": "F"
                        },
                        {
                            "slot_name": "map_half_A",
                            "job_uid": "J1077",
                            "group_name": "volume_class_3",
                            "result_name": "map",
                            "result_type": "volume.blob",
                            "version": "F"
                        },
                        {
                            "slot_name": "map_half_B",
                            "job_uid": "J1077",
                            "group_name": "volume_class_3",
                            "result_name": "map",
                            "result_type": "volume.blob",
                            "version": "F"
                        },
                        {
                            "slot_name": "mask_refine",
                            "job_uid": "J1077",
                            "group_name": "volume_class_3",
                            "result_name": "map",
                            "result_type": "volume.blob",
                            "version": "F"
                        }
                    ]
                }
            ]
        },
        {
            "type": "mask",
            "name": "mask",
            "title": "Static mask",
            "description": "",
            "count_min": 0,
            "count_max": 1,
            "repeat_allowed": false,
            "slots": [
                {
                    "type": "volume.blob",
                    "name": "mask",
                    "title": "Mask",
                    "description": "",
                    "optional": false
                }
            ],
            "connections": []
        }
    ],
    "output_result_groups": [
        {
            "uid": "J1200-G0",
            "type": "particle",
            "name": "particles",
            "title": "All particles",
            "description": "All particles that were processed, including alignments",
            "contains": [
                {
                    "uid": "J1200-R0",
                    "type": "particle.ctf",
                    "group_name": "particles",
                    "name": "ctf",
                    "passthrough": false
                },
                {
                    "uid": "J1200-R1",
                    "type": "particle.blob",
                    "group_name": "particles",
                    "name": "blob",
                    "passthrough": true
                },
                {
                    "uid": "J1200-R2",
                    "type": "particle.alignments3D",
                    "group_name": "particles",
                    "name": "alignments3D",
                    "passthrough": true
                },
                {
                    "uid": "J1200-R3",
                    "type": "particle.alignments2D",
                    "group_name": "particles",
                    "name": "alignments2D",
                    "passthrough": true
                },
                {
                    "uid": "J1200-R4",
                    "type": "particle.location",
                    "group_name": "particles",
                    "name": "location",
                    "passthrough": true
                },
                {
                    "uid": "J1200-R5",
                    "type": "particle.pick_stats",
                    "group_name": "particles",
                    "name": "pick_stats",
                    "passthrough": true
                }
            ],
            "passthrough": "particles",
            "num_items": 0,
            "summary": {}
        }
    ],
    "output_results": [
        {
            "uid": "J1200-R0",
            "type": "particle.ctf",
            "group_name": "particles",
            "name": "ctf",
            "title": "Particle CTF parameters",
            "description": "Particle CTF parameters",
            "min_fields": [
                [
                    "type",
                    "O"
                ],
                [
                    "exp_group_id",
                    "u4"
                ],
                [
                    "accel_kv",
                    "f4"
                ],
                [
                    "cs_mm",
                    "f4"
                ],
                [
                    "amp_contrast",
                    "f4"
                ],
                [
                    "df1_A",
                    "f4"
                ],
                [
                    "df2_A",
                    "f4"
                ],
                [
                    "df_angle_rad",
                    "f4"
                ],
                [
                    "phase_shift_rad",
                    "f4"
                ],
                [
                    "scale",
                    "f4"
                ],
                [
                    "scale_const",
                    "f4"
                ],
                [
                    "shift_A",
                    "2f4"
                ],
                [
                    "tilt_A",
                    "2f4"
                ],
                [
                    "trefoil_A",
                    "2f4"
                ],
                [
                    "tetra_A",
                    "4f4"
                ],
                [
                    "anisomag",
                    "4f4"
                ],
                [
                    "bfactor",
                    "f4"
                ]
            ],
            "versions": [],
            "metafiles": [],
            "num_items": [],
            "passthrough": false
        },
        {
            "uid": "J1200-R1",
            "type": "particle.blob",
            "group_name": "particles",
            "name": "blob",
            "title": "Passthrough blob",
            "description": "Passthrough from input particles.blob (slot_name)",
            "min_fields": [
                [
                    "path",
                    "O"
                ],
                [
                    "idx",
                    "u4"
                ],
                [
                    "shape",
                    "2u4"
                ],
                [
                    "psize_A",
                    "f4"
                ],
                [
                    "sign",
                    "f4"
                ],
                [
                    "import_sig",
                    "u8"
                ]
            ],
            "versions": [],
            "metafiles": [],
            "num_items": [],
            "passthrough": true
        },
        {
            "uid": "J1200-R2",
            "type": "particle.alignments3D",
            "group_name": "particles",
            "name": "alignments3D",
            "title": "Passthrough alignments3D",
            "description": "Passthrough from input particles.alignments3D (slot_name)",
            "min_fields": [
                [
                    "split",
                    "u4"
                ],
                [
                    "shift",
                    "2f4"
                ],
                [
                    "pose",
                    "3f4"
                ],
                [
                    "psize_A",
                    "f4"
                ],
                [
                    "error",
                    "f4"
                ],
                [
                    "error_min",
                    "f4"
                ],
                [
                    "resid_pow",
                    "f4"
                ],
                [
                    "slice_pow",
                    "f4"
                ],
                [
                    "image_pow",
                    "f4"
                ],
                [
                    "cross_cor",
                    "f4"
                ],
                [
                    "alpha",
                    "f4"
                ],
                [
                    "alpha_min",
                    "f4"
                ],
                [
                    "weight",
                    "f4"
                ],
                [
                    "pose_ess",
                    "f4"
                ],
                [
                    "shift_ess",
                    "f4"
                ],
                [
                    "class_posterior",
                    "f4"
                ],
                [
                    "class",
                    "u4"
                ],
                [
                    "class_ess",
                    "f4"
                ]
            ],
            "versions": [],
            "metafiles": [],
            "num_items": [],
            "passthrough": true
        },
        {
            "uid": "J1200-R3",
            "type": "particle.alignments2D",
            "group_name": "particles",
            "name": "alignments2D",
            "title": "Passthrough alignments2D",
            "description": "Passthrough from input particles.alignments2D (result_name)",
            "min_fields": [
                [
                    "split",
                    "u4"
                ],
                [
                    "shift",
                    "2f4"
                ],
                [
                    "pose",
                    "f4"
                ],
                [
                    "psize_A",
                    "f4"
                ],
                [
                    "error",
                    "f4"
                ],
                [
                    "error_min",
                    "f4"
                ],
                [
                    "resid_pow",
                    "f4"
                ],
                [
                    "slice_pow",
                    "f4"
                ],
                [
                    "image_pow",
                    "f4"
                ],
                [
                    "cross_cor",
                    "f4"
                ],
                [
                    "alpha",
                    "f4"
                ],
                [
                    "alpha_min",
                    "f4"
                ],
                [
                    "weight",
                    "f4"
                ],
                [
                    "pose_ess",
                    "f4"
                ],
                [
                    "shift_ess",
                    "f4"
                ],
                [
                    "class_posterior",
                    "f4"
                ],
                [
                    "class",
                    "u4"
                ],
                [
                    "class_ess",
                    "f4"
                ]
            ],
            "versions": [],
            "metafiles": [],
            "num_items": [],
            "passthrough": true
        },
        {
            "uid": "J1200-R4",
            "type": "particle.location",
            "group_name": "particles",
            "name": "location",
            "title": "Passthrough location",
            "description": "Passthrough from input particles.location (result_name)",
            "min_fields": [
                [
                    "micrograph_uid",
                    "u8"
                ],
                [
                    "exp_group_id",
                    "u4"
                ],
                [
                    "micrograph_path",
                    "O"
                ],
                [
                    "micrograph_shape",
                    "2u4"
                ],
                [
                    "center_x_frac",
                    "f4"
                ],
                [
                    "center_y_frac",
                    "f4"
                ]
            ],
            "versions": [],
            "metafiles": [],
            "num_items": [],
            "passthrough": true
        },
        {
            "uid": "J1200-R5",
            "type": "particle.pick_stats",
            "group_name": "particles",
            "name": "pick_stats",
            "title": "Passthrough pick_stats",
            "description": "Passthrough from input particles.pick_stats (result_name)",
            "min_fields": [
                [
                    "ncc_score",
                    "f4"
                ],
                [
                    "power",
                    "f4"
                ],
                [
                    "template_idx",
                    "u4"
                ],
                [
                    "angle_rad",
                    "f4"
                ]
            ],
            "versions": [],
            "metafiles": [],
            "num_items": [],
            "passthrough": true
        }
    ],
    "output_group_images": {},
    "ui_tile_images": [],
    "errors_build_params": {},
    "errors_build_inputs": {},
    "errors_run": [],
    "status": "building",
    "created_at": {
        "$date": 1667551637613
    },
    "queued_at": null,
    "launched_at": null,
    "started_at": null,
    "running_at": null,
    "waiting_at": null,
    "completed_at": null,
    "killed_at": null,
    "failed_at": null,
    "heartbeat_at": null,
    "tokens_acquired_at": null,
    "tokens_requested_at": null,
    "last_scheduled_at": null,
    "last_accessed": {
        "name": "m.liziczai@bioc.uzh.ch",
        "accessed_at": {
            "$date": 1667824482282
        }
    },
    "priority": 0,
    "resources_needed": {
        "slots": {
            "CPU": 4,
            "GPU": 1,
            "RAM": 2
        },
        "fixed": {
            "SSD": true
        }
    },
    "resources_allocated": {},
    "run_on_master_direct": false,
    "queued_to_lane": "",
    "queue_index": null,
    "queue_status": null,
    "queue_message": null,
    "queued_job_hash": null,
    "interactive": false,
    "interactive_hostname": "",
    "interactive_port": null,
    "PID_monitor": null,
    "PID_main": null,
    "PID_workers": [],
    "cluster_job_id": null,
    "parents": [
        "J1077"
    ],
    "children": [],
    "created_by_user_id": "607fc7d4bf2cceea8d589803",
    "created_by_job_uid": null,
    "cloned_from": null,
    "is_experiment": false,
    "job_dir": "J1200",
    "job_dir_size": 0,
    "experiment_worker_path": null,
    "ui_tile_width": 2,
    "ui_tile_height": 1,
    "enable_bench": false,
    "bench": {},
    "completed_count": 0,
    "instance_information": {},
    "project_uid_num": 86,
    "uid_num": 1200,
    "ui_layouts": {},
    "last_exported": {
        "$date": 1667824580558
    },
    "queued_to_hostname": null,
    "queued_to_gpu": null,
    "no_check_inputs_ready": false,
    "num_tokens": null,
    "job_sig": null,
    "status_num": 40,
    "progress": []
}
7

This split is unusual. Please can you post job.json for the upstream job J1077 also.

8

Thank you for looking into it so quickly. The job.json for J1077 is huge, and will be posted in several replies.

{
    "project_uid": "P86",
    "uid": "J1077",
    "workspace_uids": [
        "W24"
    ],
    "version": "v3.3.2+220518",
    "job_type": "homo_abinit",
    "type": "homo_abinit",
    "deleted": false,
    "run_as_user": null,
    "title": "New Job J1077",
    "description": "Enter a description.",
    "params_secs": {
        "prepare": {
            "title": "Particle preprocessing",
            "desc": "",
            "order": 0
        },
        "abinit": {
            "title": "Ab-Initio reconstruction",
            "desc": "",
            "order": 1
        },
        "random": {
            "title": "Random Seeds",
            "desc": "",
            "order": 2
        },
        "compute_settings": {
            "title": "Compute settings",
            "desc": "",
            "order": 3
        }
    },
    "params_base": {
        "prepare_window_dataset": {
            "type": "boolean",
            "value": true,
            "title": "Window dataset (real-space)",
            "desc": "",
            "order": 0,
            "section": "prepare",
            "advanced": false,
            "hidden": false
        },
        "prepare_window_inner_radius": {
            "type": "number",
            "value": 0.85,
            "title": "Window inner radius",
            "desc": "",
            "order": 1,
            "section": "prepare",
            "advanced": true,
            "hidden": false
        },
        "prepare_window_outer_radius": {
            "type": "number",
            "value": 0.99,
            "title": "Window outer radius",
            "desc": "",
            "order": 2,
            "section": "prepare",
            "advanced": true,
            "hidden": false
        },
        "abinit_K": {
            "type": "number",
            "value": 1,
            "title": "Number of Ab-Initio classes",
            "desc": "The number of classes. Each class will be randomly initialized independently, unless an initial structure was provided, in which case each class will be a random variant of the initial structure",
            "order": 3,
            "section": "abinit",
            "advanced": false,
            "hidden": false
        },
        "abinit_num_particles": {
            "type": "number",
            "value": null,
            "title": "Num particles to use",
            "desc": "The number of particles to use in optimization. Only this many particles will be read and classified, starting from the beginning of the particle stack. The output of this job will only contain this many particles as well.",
            "order": 4,
            "section": "abinit",
            "advanced": false,
            "hidden": false
        },
        "abinit_max_res": {
            "type": "number",
            "value": 12.0,
            "title": "Maximum resolution (Angstroms)",
            "desc": "Maximum frequency to consider",
            "order": 5,
            "section": "abinit",
            "advanced": false,
            "hidden": false
        },
        "abinit_init_res": {
            "type": "number",
            "value": 35.0,
            "title": "Initial resolution (Angstroms)",
            "desc": "Starting frequency to consider",
            "order": 6,
            "section": "abinit",
            "advanced": false,
            "hidden": false
        },
        "abinit_num_init_iters": {
            "type": "number",
            "value": 200,
            "title": "Number of initial iterations",
            "desc": "Number of initial iterations before annealing starts",
            "order": 7,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_num_final_iters": {
            "type": "number",
            "value": 300,
            "title": "Number of final iterations",
            "desc": "Number of final iterations after annealing ends",
            "order": 8,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_radwn_step": {
            "type": "number",
            "value": 0.04,
            "title": "Fourier radius step",
            "desc": "Increase in Fourier radius a each iteration",
            "order": 9,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_window": {
            "type": "boolean",
            "value": true,
            "title": "Window structures in real space",
            "desc": "Softly window the reconstructions in real space at each iteration",
            "order": 10,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_center": {
            "type": "boolean",
            "value": true,
            "title": "Center structures in real space",
            "desc": "Center the reconstructions in real space at each iteration",
            "order": 11,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_scale_mg_correct": {
            "type": "boolean",
            "value": false,
            "title": "Correct for per-micrograph optimal scales",
            "desc": "(Experimental) Estimate and compute optimal scales per micrograph",
            "order": 12,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_scale_compute": {
            "type": "boolean",
            "value": false,
            "title": "Compute per-image optimal scales",
            "desc": "(Experimental) Estimate and compute optimal scales per image",
            "order": 13,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_mom": {
            "type": "number",
            "value": 0,
            "title": "SGD Momentum",
            "desc": "Momentum for stochastic gradient descent",
            "order": 14,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_sparsity": {
            "type": "number",
            "value": 0,
            "title": "Sparsity prior",
            "desc": "",
            "order": 15,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_minisize_init": {
            "type": "number",
            "value": 90,
            "title": "Initial minibatch size",
            "desc": "Number of images per minibatch at the beginning. Set to zero to autotune. Autotune sets the initial minibatch size to 300 if the particle is small (box extent is less than 220A) or symmetry order is greater than 4.",
            "order": 16,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_minisize": {
            "type": "number",
            "value": 300,
            "title": "Final minibatch size",
            "desc": "Final number of images per minibatch. Set to zero to autotune. Autotune sets the minibatch size to 1000 if the particle is small (box extent is less than 220A) or symmetry order is greater than 4.",
            "order": 17,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_minisize_epsilon": {
            "type": "number",
            "value": 0.05,
            "title": "Abinit minisize epsilon",
            "desc": "Parameter that controls batch size when autotuning minibatch size. Set closer to zero for larger batches",
            "order": 18,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_minisize_minp": {
            "type": "number",
            "value": 0.01,
            "title": "Abinit minisize minp",
            "desc": "Parameter that controls how the batch size adjusts to low probability classes when autotuning minibatch sizes",
            "order": 19,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_minisize_num_init_iters": {
            "type": "number",
            "value": 300,
            "title": "Initial minibatch size num iters",
            "desc": "When to switch to final number of images per minibatch",
            "order": 20,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_noise_model": {
            "type": "string",
            "value": "symmetric",
            "title": "Noise model (white, symmetric or coloured)",
            "desc": "Noise model to use. Valid options are white, coloured or symmetric. Symmetric is the default, meaning coloured with radial symmetry",
            "order": 21,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_noise_priorw": {
            "type": "number",
            "value": 50,
            "title": "Noise priorw",
            "desc": "Weight of the prior for estimating noise (units of # of images)",
            "order": 22,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_noise_initw": {
            "type": "number",
            "value": 5000,
            "title": "Noise initw",
            "desc": "Weight of the initial noise estimate (units of # of images)",
            "order": 23,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_noise_init_sigmascale": {
            "type": "number",
            "value": null,
            "title": "Noise initial sigma-scale",
            "desc": "Scale factor initially applied to the base noise estimate, set to null to auto-estimate based on ESS target",
            "order": 24,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_class_anneal_beta": {
            "type": "number",
            "value": 0.1,
            "title": "Class similarity",
            "desc": "Expected similarity of structures from different classes. A number between 0 and 1. 0 means classes are independent, 1 means classes are very similar",
            "order": 25,
            "section": "abinit",
            "advanced": false,
            "hidden": false
        },
        "abinit_class_anneal_start": {
            "type": "number",
            "value": 300,
            "title": "Class similarity anneal start iter",
            "desc": "Start point for annealing the similarity factor",
            "order": 26,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_class_anneal_end": {
            "type": "number",
            "value": 350,
            "title": "Class similarity anneal end iter",
            "desc": "Finish point for annealing the similarity factor",
            "order": 27,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_target_initial_ess_fraction": {
            "type": "number",
            "value": 0.011,
            "title": "Target 3D ESS Fraction",
            "desc": "Fraction of poses at the first iteration that should have significant probability (used for auto-tuning initial noise sigma-scale)",
            "order": 28,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_symmetry": {
            "type": "string",
            "value": "C1",
            "title": "Symmetry",
            "desc": "Symmetry enforced (C, D, I, O, T). Eg. C1, D7, C4 etc. Enforcing symmetry above C1 is not recommended for ab-initio reconstruction",
            "order": 29,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_r_grid": {
            "type": "number",
            "value": 25,
            "title": "Abinit_r_grid",
            "desc": "",
            "order": 30,
            "section": "abinit",
            "advanced": true,
            "hidden": true
        },
        "abinit_high_lr_duration": {
            "type": "number",
            "value": 100,
            "title": "Initial learning rate duration",
            "desc": "How long to apply the initial learning rate",
            "order": 31,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_high_lr": {
            "type": "number",
            "value": 0.4,
            "title": "Initial learning rate",
            "desc": "Learning rate (step size) used at the start of optimization to help make rapid progress",
            "order": 32,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_nonneg": {
            "type": "boolean",
            "value": true,
            "title": "Enforce non-negativity",
            "desc": "Enforce non-negativity of structures in real space during optimization. Non-negativity is recommended for ab-initio reconstruction",
            "order": 33,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_ignore_dc": {
            "type": "boolean",
            "value": true,
            "title": "Ignore DC component",
            "desc": "Ignore the DC component of images. Should be true",
            "order": 34,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_seed_init": {
            "type": "number",
            "value": null,
            "title": "Initial structure random seed",
            "desc": "Random seed for generating initial structures. Set to null for each run to use a different seed based off the dataset random seed",
            "order": 35,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_init_radwn_cutoff": {
            "type": "number",
            "value": 7,
            "title": "Initial structure lowpass (Fourier radius)",
            "desc": "Lowpass filter cutoff in Fourier radius for initial random structures",
            "order": 36,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "abinit_search_start_iter": {
            "type": "number",
            "value": 200,
            "title": "Abinit_search_start_iter",
            "desc": "",
            "order": 37,
            "section": "abinit",
            "advanced": true,
            "hidden": true
        },
        "abinit_use_engine": {
            "type": "boolean",
            "value": true,
            "title": "Use fast codepaths",
            "desc": "",
            "order": 38,
            "section": "abinit",
            "advanced": true,
            "hidden": false
        },
        "intermediate_plots": {
            "type": "boolean",
            "value": true,
            "title": "Show plots from intermediate steps",
            "desc": "",
            "order": 39,
            "section": "abinit",
            "advanced": false,
            "hidden": false
        },
        "random_seed": {
            "type": "number",
            "value": null,
            "title": "Random seed",
            "desc": "Set to null to auto generate.",
            "order": 40,
            "section": "random",
            "advanced": true,
            "hidden": false
        },
        "compute_use_ssd": {
            "type": "boolean",
            "value": true,
            "title": "Cache particle images on SSD",
            "desc": "",
            "order": 41,
            "section": "compute_settings",
            "advanced": false,
            "hidden": false
        }
    },
    "params_spec": {
        "abinit_K": {
            "value": 4
        },
        "abinit_max_res": {
            "value": 6
        },
        "abinit_init_res": {
            "value": 7
        },
        "abinit_num_init_iters": {
            "value": 1500
        },
        "abinit_num_final_iters": {
            "value": 1000
        },
        "abinit_minisize_init": {
            "value": 1000
        },
        "abinit_minisize": {
            "value": 1000
        },
        "abinit_minisize_num_init_iters": {
            "value": 1500
        }
    },
    "input_slot_groups": [
        {
            "type": "particle",
            "name": "particles",
            "title": "Particle stacks",
            "description": "Particle stacks to use. Multiple stacks will be concatenated.",
            "count_min": 1,
            "count_max": Infinity,
            "repeat_allowed": false,
            "slots": [
                {
                    "type": "particle.blob",
                    "name": "blob",
                    "title": "Particle data blobs",
                    "description": "",
                    "optional": false
                },
                {
                    "type": "particle.ctf",
                    "name": "ctf",
                    "title": "Particle ctf parameters",
                    "description": "",
                    "optional": false
                },
                {
                    "type": "particle.filament",
                    "name": "filament",
                    "title": "Particle filament info",
                    "description": "",
                    "optional": true
                }
            ],
            "connections": [
                {
                    "job_uid": "J1076",
                    "group_name": "particles_selected",
                    "slots": [
                        {
                            "slot_name": "blob",
                            "job_uid": "J1076",
                            "group_name": "particles_selected",
                            "result_name": "blob",
                            "result_type": "particle.blob",
                            "version": "F"
                        },
                        {
                            "slot_name": "ctf",
                            "job_uid": "J1076",
                            "group_name": "particles_selected",
                            "result_name": "ctf",
                            "result_type": "particle.ctf",
                            "version": "F"
                        },
                        {
                            "slot_name": null,
                            "job_uid": "J1076",
                            "group_name": "particles_selected",
                            "result_name": "alignments2D",
                            "result_type": "particle.alignments2D",
                            "version": "F"
                        },
                        {
                            "slot_name": null,
                            "job_uid": "J1076",
                            "group_name": "particles_selected",
                            "result_name": "location",
                            "result_type": "particle.location",
                            "version": "F"
                        },
                        {
                            "slot_name": null,
                            "job_uid": "J1076",
                            "group_name": "particles_selected",
                            "result_name": "pick_stats",
                            "result_type": "particle.pick_stats",
                            "version": "F"
                        }
                    ]
                }
            ]
        }
    ],
9 
"output_result_groups": [
        {
            "uid": "J1077-G0",
            "type": "particle",
            "name": "particles_all_classes",
            "title": "All particles",
            "description": "All particles that were processed, including alignments across all classes.",
            "contains": [
                {
                    "uid": "J1077-R0",
                    "type": "particle.blob",
                    "group_name": "particles_all_classes",
                    "name": "blob",
                    "passthrough": false
                },
                {
                    "uid": "J1077-R1",
                    "type": "particle.ctf",
                    "group_name": "particles_all_classes",
                    "name": "ctf",
                    "passthrough": false
                },
                {
                    "uid": "J1077-R2",
                    "type": "particle.alignments3D",
                    "group_name": "particles_all_classes",
                    "name": "alignments_class_0",
                    "passthrough": false
                },
                {
                    "uid": "J1077-R10",
                    "type": "particle.alignments3D",
                    "group_name": "particles_all_classes",
                    "name": "alignments_class_1",
                    "passthrough": false
                },
                {
                    "uid": "J1077-R18",
                    "type": "particle.alignments3D",
                    "group_name": "particles_all_classes",
                    "name": "alignments_class_2",
                    "passthrough": false
                },
                {
                    "uid": "J1077-R26",
                    "type": "particle.alignments3D",
                    "group_name": "particles_all_classes",
                    "name": "alignments_class_3",
                    "passthrough": false
                },
                {
                    "uid": "J1077-R34",
                    "type": "particle.alignments2D",
                    "group_name": "particles_all_classes",
                    "name": "alignments2D",
                    "passthrough": true
                },
                {
                    "uid": "J1077-R35",
                    "type": "particle.location",
                    "group_name": "particles_all_classes",
                    "name": "location",
                    "passthrough": true
                },
                {
                    "uid": "J1077-R36",
                    "type": "particle.pick_stats",
                    "group_name": "particles_all_classes",
                    "name": "pick_stats",
                    "passthrough": true
                }
            ],
            "passthrough": "particles",
            "num_items": 287066,
            "summary": {
                "blob/shape": [
                    192,
                    192
                ],
                "blob/psize_A": 1.3020000457763672,
                "blob/sign": -1.0,
                "ctf/type": "spline",
                "ctf/accel_kv": 300.0,
                "ctf/cs_mm": 2.700000047683716,
                "ctf/amp_contrast": 0.10000000149011612,
                "ctf/phase_shift_rad": 0.0,
                "ctf/scale": 1.0,
                "ctf/shift_A": [
                    0.0,
                    0.0
                ],
                "ctf/tilt_A": [
                    0.0,
                    0.0
                ],
                "ctf/trefoil_A": [
                    0.0,
                    0.0
                ],
                "ctf/tetra_A": [
                    0.0,
                    0.0,
                    0.0,
                    0.0
                ],
                "ctf/anisomag": [
                    0.0,
                    0.0,
                    0.0,
                    0.0
                ],
                "ctf/bfactor": 0.0,
                "alignments_class_0/psize_A": 1.9530000686645508,
                "alignments_class_1/psize_A": 1.9530000686645508,
                "alignments_class_2/psize_A": 1.9530000686645508,
                "alignments_class_3/psize_A": 1.9530000686645508,
                "alignments2D/psize_A": 1.9530000686645508,
                "location/micrograph_shape": [
                    4092,
                    5760
                ]
            }
        },
        {
            "uid": "J1077-G1",
            "type": "particle",
            "name": "particles_class_0",
            "title": "Particles class 0",
            "description": "Particles that belong maximally to class 0",
            "contains": [
                {
                    "uid": "J1077-R3",
                    "type": "particle.blob",
                    "group_name": "particles_class_0",
                    "name": "blob",
                    "passthrough": false
                },
                {
                    "uid": "J1077-R4",
                    "type": "particle.ctf",
                    "group_name": "particles_class_0",
                    "name": "ctf",
                    "passthrough": false
                },
                {
                    "uid": "J1077-R5",
                    "type": "particle.alignments3D",
                    "group_name": "particles_class_0",
                    "name": "alignments3D",
                    "passthrough": false
                },
                {
                    "uid": "J1077-R6",
                    "type": "particle.alignments2D",
                    "group_name": "particles_class_0",
                    "name": "alignments2D",
                    "passthrough": true
                },
                {
                    "uid": "J1077-R7",
                    "type": "particle.location",
                    "group_name": "particles_class_0",
                    "name": "location",
                    "passthrough": true
                },
                {
                    "uid": "J1077-R8",
                    "type": "particle.pick_stats",
                    "group_name": "particles_class_0",
                    "name": "pick_stats",
                    "passthrough": true
                }
            ],
            "passthrough": "particles",
            "num_items": 73695,
            "summary": {
                "blob/shape": [
                    192,
                    192
                ],
                "blob/psize_A": 1.3020000457763672,
                "blob/sign": -1.0,
                "ctf/type": "spline",
                "ctf/accel_kv": 300.0,
                "ctf/cs_mm": 2.700000047683716,
                "ctf/amp_contrast": 0.10000000149011612,
                "ctf/phase_shift_rad": 0.0,
                "ctf/scale": 1.0,
                "ctf/shift_A": [
                    0.0,
                    0.0
                ],
                "ctf/tilt_A": [
                    0.0,
                    0.0
                ],
                "ctf/trefoil_A": [
                    0.0,
                    0.0
                ],
                "ctf/tetra_A": [
                    0.0,
                    0.0,
                    0.0,
                    0.0
                ],
                "ctf/anisomag": [
                    0.0,
                    0.0,
                    0.0,
                    0.0
                ],
                "ctf/bfactor": 0.0,
                "alignments3D/psize_A": 1.9530000686645508,
                "alignments2D/psize_A": 1.9530000686645508,
                "location/micrograph_shape": [
                    4092,
                    5760
                ]
            }
        },
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            "message": "Done iteration 1400 ",
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            "message": "Done iteration 1500 ",
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            "message": "Done iteration 1600 ",
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            "message": "Done iteration 1700 ",
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            "message": "Done iteration 1800 ",
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            "message": "Done iteration 2100 ",
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            "message": "Done iteration 2200 ",
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            "message": "Done iteration 2300 ",
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            "message": "Done iteration 2400 ",
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            "message": "Done iteration 2500 ",
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            "message": "Done iteration 2600 ",
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            "message": "Done iteration 2700 ",
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            "message": "Done iteration 2800 ",
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            "message": "Done iteration 2934 ",
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}
15

Thank you for this information. The input particles and volume came from an ab initio, not a refinement job, and therefore lack the expected gold-standard FSC split into particle half sets and density half maps. You may want to retry local CTF refinement with inputs of a volume and corresponding particles from homogeneous or non-uniform refinement. For example, you might

  1. “feed” particles and ab initio volumes into a heterogeneous refinement
  2. connect the volume and particles of a selected class from heterogeneous refinement to homogeneous refinement
  3. connect volume and particles from homogeneous refinement to a local CTF refinement job
1 Like
16

Thank you very much. Using volume and particles from a refinement made it work.