IndexError: arrays used as indices must be of integer (or boolean) type

[mmucsf]

Hello,
I am trying to use ModelAngelo from within the Relion 5.1-beta_cu12.2 GUI. I input a sharpened map from cryosparc and a fasta file downloaded from the PDB. I get the following error in the model_angelo.log. It seems that an array is non-integer, but I don't know how to fix this. Any advice would be very much appreciated. Thanks.

2024-11-19 at 11:45:53 | INFO | ModelAngelo with args: {'volume_path': 'J106_007_volume_map_sharp.mrc', 'protein_fasta': 'rcsb_pdb_4XHL.fasta', 'rna_fasta': None, 'dna_fasta': None, 'output_dir': 'ModelAngelo/job052', 'mask_path': None, 'device': '0', 'config_path': None, 'model_bundle_name': 'nucleotides', 'model_bundle_path': None, 'keep_intermediate_results': False, 'pipeline_control': 'ModelAngelo/job052/', 'func': <function main at 0x14ae5f54ab00>}
2024-11-19 at 11:45:54 | INFO | Initial C-alpha prediction with args: {'model_checkpoint': 'chkpt.torch', 'bfactor': 0, 'batch_size': 4, 'box_size': 64, 'stride': 16, 'dont_mask_input': True, 'threshold': 0.05, 'save_real_coordinates': False, 'save_cryo_em_grid': False, 'do_nucleotides': True, 'save_backbone_trace': False, 'save_output_grid': False, 'crop': 6, 'log_dir': '/programs/share/relion/hub/checkpoints/model_angelo_v1.0/nucleotides/c_alpha', 'map_path': 'J106_007_volume_map_sharp.mrc', 'output_path': 'ModelAngelo/job052/see_alpha_output', 'mask_path': None, 'device': '0', 'auto_mask': False}
2024-11-19 at 11:45:54 | INFO | Using model file /programs/share/relion/hub/checkpoints/model_angelo_v1.0/nucleotides/c_alpha/model.py
2024-11-19 at 11:45:54 | INFO | Using checkpoint file /programs/share/relion/hub/checkpoints/model_angelo_v1.0/nucleotides/c_alpha/chkpt.torch
2024-11-19 at 11:46:06 | INFO | Input structure has shape: (296, 296, 296)
2024-11-19 at 11:46:06 | INFO | Running with these arguments:
2024-11-19 at 11:46:06 | INFO | {'model_checkpoint': 'chkpt.torch', 'bfactor': 0, 'batch_size': 4, 'box_size': 64, 'stride': 16, 'dont_mask_input': True, 'threshold': 0.05, 'save_real_coordinates': False, 'save_cryo_em_grid': False, 'do_nucleotides': True, 'save_backbone_trace': False, 'save_output_grid': False, 'crop': 6, 'log_dir': '/programs/share/relion/hub/checkpoints/model_angelo_v1.0/nucleotides/c_alpha', 'map_path': 'J106_007_volume_map_sharp.mrc', 'output_path': 'ModelAngelo/job052/see_alpha_output', 'mask_path': None, 'device': '0', 'auto_mask': False}
2024-11-19 at 12:02:28 | INFO | Model prediction done, took 981.89 seconds for 3375 sliding windows
2024-11-19 at 12:02:28 | INFO | Average time is 290.931 ms
2024-11-19 at 12:02:28 | INFO | Starting Cα grid to points...
2024-11-19 at 12:02:28 | INFO | Have 3092 Cα points before pruning and 409 after pruning
2024-11-19 at 12:02:28 | INFO | Starting P grid to points...
2024-11-19 at 12:02:29 | INFO | Have 0 P points before pruning and 0 after pruning
2024-11-19 at 12:02:29 | INFO | Finished inference!
2024-11-19 at 12:02:29 | INFO | GNN model refinement round 1 with args: {'num_rounds': 3, 'crop_length': 200, 'repeat_per_residue': 1, 'esm_model': 'esm1b_t33_650M_UR50S', 'aggressive_pruning': True, 'seq_attention_batch_size': 200, 'fp16': False, 'batch_size': 1, 'voxel_size': 1.0, 'map': 'J106_007_volume_map_sharp.mrc', 'protein_fasta': 'rcsb_pdb_4XHL.fasta', 'rna_fasta': None, 'dna_fasta': None, 'struct': 'ModelAngelo/job052/see_alpha_output/see_alpha_merged_output.cif', 'output_dir': 'ModelAngelo/job052/gnn_output_round_1', 'model_dir': '/programs/share/relion/hub/checkpoints/model_angelo_v1.0/nucleotides/gnn', 'device': '0', 'write_hmm_profiles': False, 'refine': False}
2024-11-19 at 12:02:29 | INFO | Loaded module from step: 483863
2024-11-19 at 12:03:25 | ERROR | Error in ModelAngelo
Traceback (most recent call last):

File "", line 1, in
File "/programs/x86_64-linux/relion/5.0-beta_cu12.2/relion_extlib/miniconda3-4.10.3-orl6/envs/relion-5.0/lib/python3.10/site-packages/model_angelo/main.py", line 58, in main
args.func(args)
│ │ └ Namespace(volume_path='J106_007_volume_map_sharp.mrc', protein_fasta='rcsb_pdb_4XHL.fasta', rna_fasta=None, dna_fasta=None, o...
│ └ <function main at 0x14ae5f54ab00>
└ Namespace(volume_path='J106_007_volume_map_sharp.mrc', protein_fasta='rcsb_pdb_4XHL.fasta', rna_fasta=None, dna_fasta=None, o...

File "/programs/x86_64-linux/relion/5.0-beta_cu12.2/relion_extlib/miniconda3-4.10.3-orl6/envs/relion-5.0/lib/python3.10/site-packages/model_angelo/apps/build.py", line 242, in main
gnn_output = gnn_infer(gnn_infer_args)
│ └ {'num_rounds': 3, 'crop_length': 200, 'repeat_per_residue': 1, 'esm_model': 'esm1b_t33_650M_UR50S', 'aggressive_pruning': Tru...
└ <function infer at 0x14ae5fbbd900>
File "/programs/x86_64-linux/relion/5.0-beta_cu12.2/relion_extlib/miniconda3-4.10.3-orl6/envs/relion-5.0/lib/python3.10/site-packages/model_angelo/gnn/inference.py", line 184, in infer
final_results_to_cif(
└ <function final_results_to_cif at 0x14ae5f54a3b0>
File "/programs/x86_64-linux/relion/5.0-beta_cu12.2/relion_extlib/miniconda3-4.10.3-orl6/envs/relion-5.0/lib/python3.10/site-packages/model_angelo/gnn/flood_fill.py", line 331, in final_results_to_cif
fix_chains_output = prune_and_connect_chains(
└ <function prune_and_connect_chains at 0x14ae5f549d80>
File "/programs/x86_64-linux/relion/5.0-beta_cu12.2/relion_extlib/miniconda3-4.10.3-orl6/envs/relion-5.0/lib/python3.10/site-packages/model_angelo/utils/hmm_sequence_align.py", line 552, in prune_and_connect_chains
chains, best_match_output = sort_chains(best_match_output, chains, ca_pos,)
│ │ │ │ └ array([[291.27365, 230.41208, 163.59029],
│ │ │ │ [292.82507, 227.35979, 165.11305],
│ │ │ │ [292.67972, 232.7009 , 165.25647],...
│ │ │ └ []
│ │ └ <model_angelo.utils.match_to_sequence.MatchToSequence object at 0x14ae5d2bcb80>
│ └ <function sort_chains at 0x14ae5f5497e0>
└ []
File "/programs/x86_64-linux/relion/5.0-beta_cu12.2/relion_extlib/miniconda3-4.10.3-orl6/envs/relion-5.0/lib/python3.10/site-packages/model_angelo/utils/hmm_sequence_align.py", line 371, in sort_chains
chain_start_pos = ca_positions[chain_starts]
│ └ array([], dtype=float64)
└ array([[291.27365, 230.41208, 163.59029],
[292.82507, 227.35979, 165.11305],
[292.67972, 232.7009 , 165.25647],...

IndexError: arrays used as indices must be of integer (or boolean) type