Input format of complexes while running locally with colabfold_batch

[marcmk6]

Hi, With the Colab notebook AlphaFold2_mmseqs2 I can use a colon : to specify inter-protein chainbreaks as per instruction. I'm wondering what should I do when running with colabfold_batch locally.

Specifically I tried writing the following

>sp|Q9UI25|YP002_HUMAN Putative uncharacterized protein PRO0461 OS=Homo sapiens OX=9606 GN=PRO0461 PE=5 SV=1 MEEMSYGENSGTHVGSFSCSPQPSQQMKVLFVGNSFLLTPVLHRQPHLQPCNFGPEVVAP QRL

into a fasta file inside directory tmp and run colabfold_batch --model-type AlphaFold2-multimer tmp tmp_output but got an error.

Here is the error log:

Traceback (most recent call last): File "/home/jovyan/.conda/envs/colabfold_test_env/lib/python3.8/site-packages/ml_collections/config_dict/config_dict.py", line 883, in getitem field = self._fields[key] KeyError: 'data'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/jovyan/.conda/envs/colabfold_test_env/lib/python3.8/site-packages/ml_collections/config_dict/config_dict.py", line 807, in getattr return self[attribute] File "/home/jovyan/.conda/envs/colabfold_test_env/lib/python3.8/site-packages/ml_collections/config_dict/config_dict.py", line 889, in getitem raise KeyError(self._generate_did_you_mean_message(key, str(e))) KeyError: "'data'"

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/jovyan/.conda/envs/colabfold_test_env/bin/colabfold_batch", line 8, in sys.exit(main()) File "/home/jovyan/.conda/envs/colabfold_test_env/lib/python3.8/site-packages/colabfold/batch.py", line 1209, in main run( File "/home/jovyan/.conda/envs/colabfold_test_env/lib/python3.8/site-packages/colabfold/batch.py", line 998, in run outs, model_rank = predict_structure( File "/home/jovyan/.conda/envs/colabfold_test_env/lib/python3.8/site-packages/colabfold/batch.py", line 184, in predict_structure input_features = batch_input( File "/home/jovyan/.conda/envs/colabfold_test_env/lib/python3.8/site-packages/colabfold/batch.py", line 122, in batch_input eval_cfg = model_config.data.eval File "/home/jovyan/.conda/envs/colabfold_test_env/lib/python3.8/site-packages/ml_collections/config_dict/config_dict.py", line 809, in getattr raise AttributeError(e) AttributeError: "'data'"

[konstin]

Hi, could you please post the error and the log?

[marcmk6]

Hi, could you please post the error and the log?

Hi, I've added the log to the post.

[liuqs1990]

Hi, could you please post the error and the log?

Hi Konstin,

I have almost the same problem when running the localcolabfold. The error is described here: https://github.com/YoshitakaMo/localcolabfold/issues/69

I am able to run with a single protein locally but always have error when trying to predict the complex structure.

any suggestions would be grateful.