Protein residue modification issues

[kanghw0325]

Thank you for the great job and I have some issues in protein residue modification.

Here is my json file

[
    {
        "sequences": [
            {
                "proteinChain": {
                    "sequence": "MFERFTDRARRVVVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKSLESLGISLEGVRSQVEEIIGQGQQAPSGHIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVAAQVLVKLGAELTRVRQQVIQLLSGYKLAAALEHHHHHH",
                    "count": 1,
                    "modifications": []
                }
            },
            {
                "proteinChain": {
                    "sequence": "WLYALLK",
                    "count": 1,
                    "modifications": [
                        {
                            "ptmType": "CCD_F7P",
                            "ptmPosition": 1
                        },
                        {
                            "ptmType": "CCD_MLE",
                            "ptmPosition": 2
                        },
                        {
                            "ptmType": "CCD_NIY",
                            "ptmPosition": 3
                        },
                        {
                            "ptmType": "CCD_F7S",
                            "ptmPosition": 5
                        },
                        {
                            "ptmType": "CCD_F7V",
                            "ptmPosition": 7
                        }
                    ]
                }
            }
        ],
        "name": "6CN8"
    }

Then, I got Assert error like this.

2025-01-21 15:10:57,493 [/workdir_efs/hwkang/.conda/envs/protenix0.3.9/lib/python3.12/site-packages/runner/inference.py:232] INFO runner.inference: :
Traceback (most recent call last):
  File "/workdir_efs/hwkang/.conda/envs/protenix0.3.9/lib/python3.12/site-packages/protenix/data/infer_data_pipeline.py", line 211, in __getitem__
    data, atom_array, _ = self.process_one(
                          ^^^^^^^^^^^^^^^^^
  File "/workdir_efs/hwkang/.conda/envs/protenix0.3.9/lib/python3.12/site-packages/protenix/data/infer_data_pipeline.py", line 114, in process_one
    InferenceMSAFeaturizer.make_msa_feature(
  File "/workdir_efs/hwkang/.conda/envs/protenix0.3.9/lib/python3.12/site-packages/protenix/data/msa_featurizer.py", line 1144, in make_msa_feature
    msa_feats = InferenceMSAFeaturizer.get_inference_prot_msa_features_for_assembly(
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/workdir_efs/hwkang/.conda/envs/protenix0.3.9/lib/python3.12/site-packages/protenix/data/msa_featurizer.py", line 1083, in get_inference_prot_msa_features_for_assembly
    sequence_feat = InferenceMSAFeaturizer.process_prot_single_sequence(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/workdir_efs/hwkang/.conda/envs/protenix0.3.9/lib/python3.12/site-packages/protenix/data/msa_featurizer.py", line 969, in process_prot_single_sequence
    sequence_features = process_single_sequence(
                        ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/workdir_efs/hwkang/.conda/envs/protenix0.3.9/lib/python3.12/site-packages/protenix/data/msa_featurizer.py", line 797, in process_single_sequence
    msa_features = load_and_process_msa(
                   ^^^^^^^^^^^^^^^^^^^^^
  File "/workdir_efs/hwkang/.conda/envs/protenix0.3.9/lib/python3.12/site-packages/protenix/data/msa_utils.py", line 558, in load_and_process_msa
    msa_data = parse_msa_data(
               ^^^^^^^^^^^^^^^
  File "/workdir_efs/hwkang/.conda/envs/protenix0.3.9/lib/python3.12/site-packages/protenix/data/msa_utils.py", line 450, in parse_msa_data
    return parse_prot_msa_data(raw_msa_paths, seq_limits)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/workdir_efs/hwkang/.conda/envs/protenix0.3.9/lib/python3.12/site-packages/protenix/data/msa_utils.py", line 518, in parse_prot_msa_data
    assert all([len(seq) == len(aligned_sequences[0]) for seq in aligned_sequences])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError

100%|██████████| 1/1 [00:06<00:00,  6.77s/it]

is there anything wrong with my json file? I could make other files with my json files and got write outputs.

[zhangyuxuann]

Hi @kanghw0325, This has been fixed after v0.3.6. can you remove the output dir containing MSA, and update protenix to v0.4.1 and retry. I run successfully using your json.

[kanghw0325]

Thank you for kind response!