ConorFWild
commented
2 years ago Yeah, I thought I might have broken high_res_random ^^" I'm just checking it on the most recent commit and will let you know when a fix is merged!
Open KristianStoedkilde opened 2 years ago
ConorFWild
commented
2 years ago Yeah, I thought I might have broken high_res_random ^^" I'm just checking it on the most recent commit and will let you know when a fix is merged!
ConorFWild
commented
2 years ago @KristianStoedkilde Fix merged to master! If it works for you I'll close ^^
KristianStoedkilde
commented
2 years ago Seems to be working. Feel free to close :-)
Syntax: python analyse.py --data_dirs all_data --out_dir all_data_output --pdb_regex="final.pdb" --mtz_regex="final.mtz" --autobuild=False --rank_method="size" --comparison_strategy="high_res_random"
Getting this error during the "Processing resolution shells" step.
Full json log: { "Start time": 1650371914.5108826, "The arguments to the main function and their values": { "data_dirs": "all_data", "out_dir": "all_data_output", "pdb_regex": "final.pdb", "mtz_regex": "final.mtz", "ligand_dir_regex": "compound", "ligand_cif_regex": ".cif", "ligand_pdb_regex": ".pdb", "ligand_smiles_regex": "*.smiles", "statmaps": "False", "low_memory": "False", "ground_state_datasets": "None", "exclude_from_z_map_analysis": "None", "exclude_from_characterisation": "None", "only_datasets": "None", "ignore_datasets": "None", "dynamic_res_limits": "True", "high_res_upper_limit": "1.0", "high_res_lower_limit": "4.0", "high_res_increment": "0.05", "max_shell_datasets": "60", "min_characterisation_datasets": "25", "structure_factors": "None", "all_data_are_valid_values": "True", "low_resolution_completeness": "4.0", "sample_rate": "3.0", "max_rmsd_to_reference": "1.5", "max_rfree": "0.4", "max_wilson_plot_z_score": "0.4", "same_space_group_only": "False", "similar_models_only": "False", "resolution_factor": "0.25", "grid_spacing": "0.5", "padding": "3.0", "density_scaling": "True", "outer_mask": "8.0", "inner_mask": "2.0", "inner_mask_symmetry": "2.0", "contour_level": "2.5", "negative_values": "False", "min_blob_volume": "10.0", "min_blob_z_peak": "3.0", "clustering_cutoff": "1.5", "cluster_cutoff_distance_multiplier": "1.5", "max_site_distance_cutoff": "1.732", "min_bdc": "0.0", "max_bdc": "0.95", "increment": "0.05", "output_multiplier": "2.0", "comparison_strategy": "high_res_random", "comparison_res_cutoff": "0.5", "comparison_min_comparators": "30", "comparison_max_comparators": "30", "known_apos": "None", "exclude_local": "5", "cluster_selection": "close", "local_processing": "ray", "local_cpus": "6", "global_processing": "serial", "memory_availability": "low", "job_params_file": "None", "distributed_scheduler": "SGE", "distributed_queue": "medium.q", "distributed_project": "labxchem", "distributed_num_workers": "12", "distributed_cores_per_worker": "12", "distributed_mem_per_core": "10", "distributed_resource_spec": "m_mem_free=10G", "distributed_tmp": "/tmp", "distributed_job_extra": "[\"--exclusive\", ]", "distributed_walltime": "30:00:00", "distributed_watcher": "False", "distributed_slurm_partition": "False", "autobuild": "False", "autobuild_strategy": "rhofit", "rhofit_coord": "False", "cif_strategy": "elbow", "rank_method": "size", "debug": "False" }, "FS model building time": 2.484349489212036, "Reference Dtag": "XXX-AU10-CPS-6888-pos7", "Time to perform b factor smoothing": 44.83301091194153, "trace": "Traceback (most recent call last):\n File \"/media/hauptman/Data/x-ray_data/Pandda/../../../../../../home/hauptman/Desktop/pandda2/pandda_2_gemmi/pandda_gemmi/analyse.py\", line 604, in process_pandda\n shells: ShellsInterface = get_shells(\n File \"/home/hauptman/Desktop/pandda2/pandda_2_gemmi/pandda_gemmi/pandda_functions.py\", line 1812, in get_shells\n for dtag, comparison_dtags in comparators.items():\nAttributeError: 'tuple' object has no attribute 'items'\n", "exception": "'tuple' object has no attribute 'items'" }