Error in model building of protein fibril

[Bhargy001]

Hi Model-angelo team,

I have a cryoEM map and sequence of protein chain which formed fibrils. I am running these to build a model.

model_angelo build -v /home/bhargy/model_angelo/cryosparc_P114_J200_004_volume_map.mrc -pf /home/bhargy/model_angelo/D-seq.fasta -o output

I keep getting the runtime error as below, not sure what is going wrong. Is the error with nucleotide model? is it required for protein structures? Is there something to be changed in above command?

error log :
File "/home/bhargy/miniforge3/envs/model_angelo/bin/model_angelo", line 7, in
sys.exit(main())
│ │ └ <function main at 0x7fc8ae9c75b0>
│ └
└ <module 'sys' (built-in)>
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/model_angelo/main.py", line 58, in main
args.func(args)
│ │ └ Namespace(volume_path='/home/bhargy/model_angelo/cryosparc_P114_J200_004_volume_map.mrc', protein_fasta='/home/bhargy/model_a...
│ └ <function main at 0x7fc774c51900>
└ Namespace(volume_path='/home/bhargy/model_angelo/cryosparc_P114_J200_004_volume_map.mrc', protein_fasta='/home/bhargy/model_a...

File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/model_angelo/apps/build.py", line 154, in main
model_bundle_path = download_and_install_model(
└ <function download_and_install_model at 0x7fc77703f400>
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/model_angelo/utils/torch_utils.py", line 468, in download_and_install_model
raise RuntimeError(

RuntimeError: Checksum of downloaded file /home/bhargy/model_angelo_weights/hub/checkpoints/model_angelo_v1.0/nucleotides.zip does not match expected checksum. Expected: ce568d75b24f8a4654f1fa2f7a89cb27, got: d9dccb0a3a8069eefd6a607816e84f79

---

Traceback (most recent call last):
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/model_angelo/apps/build.py", line 250, in main
gnn_output = gnn_infer(gnn_infer_args)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/model_angelo/gnn/inference.py", line 141, in infer
results = run_inference_on_data(
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/torch/utils/_contextlib.py", line 115, in decorate_context
return func(*args, **kwargs)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/model_angelo/utils/gnn_inference_utils.py", line 220, in run_inference_on_data
result = module(meta_input_list)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
return forward_call(*args, **kwargs)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/model_angelo/models/multi_gpu_wrapper.py", line 160, in forward
self.model(**send_dict_to_device(data, device)).to("cpu").to(torch.float32)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
return forward_call(*args, **kwargs)
File "/home/bhargy/model_angelo_weights/hub/checkpoints/model_angelo_v1.0/nucleotides/gnn/model.py", line 17, in forward
return self.ipa(*args, **kwargs)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
return forward_call(*args, **kwargs)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/model_angelo/gnn/multi_layer_ipa.py", line 153, in forward
) = self.cryo_attentions[idx](
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
return forward_call(*args, **kwargs)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/model_angelo/gnn/cryo_attention.py", line 162, in forward
bde_out = self.backbone_distance_emb(x, affines, prot_mask, edge_index, batch)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1518, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1527, in _call_impl
return forward_call(*args, **kwargs)
File "/home/bhargy/miniforge3/envs/model_angelo/lib/python3.10/site-packages/model_angelo/gnn/backbone_distance_embedding.py", line 54, in forward
edge_index = edge_index[0].reshape(len(positions), self.kz)
RuntimeError: shape '[2, 20]' is invalid for input of size 2
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