multimer model error:config_dict.py", line 903, in __getitem__ field = self._fields[key] KeyError: 'data'

Hi,

I am able to predict a protein file but when I try the multimer model, I use: /home/qiushi/localcolabfold/colabfold_batch/bin/colabfold_batch \ > --amber \ > --templates \ > --num-recycle 1 \ > --model-type AlphaFold2-multimer \ > /home/qiushi/RESC6/complex.fasta \ > /home/qiushi/RESC6/complexdir

I got this error:

If you require more MSAs, please host your own API and pass it to --host-url 2022-03-06 18:21:09,433 Running colabfold 1.2.0 (46ae46946d771af1745d55c2c40050e8f54f5e17) 2022-03-06 18:21:09,434 Found 8 citations for tools or databases 2022-03-06 18:21:16,481 Query 1/2: T1084 (length 73) 2022-03-06 18:21:17,725 Sleeping for 9s. Reason: PENDING COMPLETE: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 150/150 [elapsed: 00:12 remaining: 00:00]2022-03-06 18:21:29,021 Sequence 0 found no templates 2022-03-06 18:21:29,021 Running model_3 Traceback (most recent call last): File “/home/qiushi/localcolabfold/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/ml_collections/config_dict/config_dict.py”, line 903, in getitem field = self._fields[key] KeyError: ‘data’ During handling of the above exception, another exception occurred: Traceback (most recent call last): File “/home/qiushi/localcolabfold/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/ml_collections/config_dict/config_dict.py”, line 827, in getattr return self[attribute] File “/home/qiushi/localcolabfold/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/ml_collections/config_dict/config_dict.py”, line 909, 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/qiushi/localcolabfold/colabfold_batch/colabfold-conda/bin/colabfold_batch”, line 8, in <module> sys.exit(main()) File “/home/qiushi/localcolabfold/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/colabfold/batch.py”, line 1386, in main save_pair_representations=args.save_pair_representations, File “/home/qiushi/localcolabfold/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/colabfold/batch.py”, line 1102, in run prediction_callback=prediction_callback, File “/home/qiushi/localcolabfold/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/colabfold/batch.py”, line 198, in predict_structure use_templates, File “/home/qiushi/localcolabfold/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/colabfold/batch.py”, line 132, in batch_input eval_cfg = model_config.data.eval File “/home/qiushi/localcolabfold/colabfold_batch/colabfold-conda/lib/python3.7/site-packages/ml_collections/config_dict/config_dict.py”, line 829, in getattr raise AttributeError(e) AttributeError: “‘data’”

any idea how to make it work?

THanks

[JohnJPaul]

Hi Had the same problem and I solved it by creating a fasta file containing both of the sequences and separated by : . Worked for me , hope it will does for you

Hi John, So, like my input file used to look like:

>T1083
GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED
>T1084
MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH

Then you mean add a : for these fasta:

>T1083
GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED:
>T1084
MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH

like this?

HI echard write the write syntax of the fasta file . The main problem is that 2 different lines start with > and collabfold can’t accept it.

If I am not mistaken the type of input fasta that you used is accepted but the AlphaFold2 or used to be accepted

Hope that will work for you Cheers JJ

[eckhard-hofmann]

Hi Qiushi, no, you have to have only one entry in the fasta file (only one header line starting with “>”, and then the sequences separated by “:”

Complex T1083 and T1084 GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED:

MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH

No trailing “:” either … 😉 Cheers, Eckhard

Am 20.03.22 um 11:40 schrieb Qiushi Liu:

Hi

Had the same problem and I solved it by creating a fasta file
containing both of the sequences and separated by : . Worked for me
, hope it will does for you

Hi John, So, like my input file used to look like:

|>T1083 GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED

T1084 MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH |

Then you mean add a : for these fasta:

|>T1083 GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED:

T1084 MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH |

like this?

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