id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14771	AlphaFold2 colab notebook error	bregman3@…	Tom Goddard	"{{{
Hello
I've been trying to use the colab on ChimeraX, and I used it previously this week and it worked perfectly fine. I'm now getting the following error
2024-03-14 18:44:43,264 Starting prediction on 2024-03-14 UTC time
2024-03-14 18:44:43,264 Installing ColabFold on Google Colab virtual machine.
Using Tesla T4 graphics processor
2024-03-14 18:44:43,493 Running on GPU
2024-03-14 18:44:43,496 Found 5 citations for tools or databases
2024-03-14 18:44:43,497 Query 1/1: af42 (length 42)
COMPLETE: 100%|██████████| 150/150 [elapsed: 00:01 remaining: 00:00]
2024-03-14 18:44:44,734 Could not generate input features af42: Invalid character in the sequence:  
Traceback (most recent call last):
  File ""/usr/local/lib/python3.10/dist-packages/colabfold/batch.py"", line 1512, in run
    = generate_input_feature(query_seqs_unique, query_seqs_cardinality, unpaired_msa, paired_msa,
  File ""/usr/local/lib/python3.10/dist-packages/colabfold/batch.py"", line 1039, in generate_input_feature
    feature_dict = build_monomer_feature(
  File ""/usr/local/lib/python3.10/dist-packages/colabfold/batch.py"", line 892, in build_monomer_feature
    **pipeline.make_sequence_features(
  File ""/usr/local/lib/python3.10/dist-packages/alphafold/data/pipeline.py"", line 40, in make_sequence_features
    features['aatype'] = residue_constants.sequence_to_onehot(
  File ""/usr/local/lib/python3.10/dist-packages/alphafold/common/residue_constants.py"", line 580, in sequence_to_onehot
    raise ValueError(f'Invalid character in the sequence: {aa_type}')
ValueError: Invalid character in the sequence:  
2024-03-14 18:44:44,736 Done
Downloading structure predictions to directory Downloads/ChimeraX/AlphaFold
cp: cannot stat '*_relaxed_rank_001_*.pdb': No such file or directory
cp: cannot stat '*_scores_rank_001_*.json': No such file or directory

when I put the same sequence into the colab not through ChimeraX, it works. I've tried restarting everything, trying different amino acid sequences and I just get the same error. 
Here is the actual amino acid input sequence: MTTTLPEGVSHRVGFKPHLRVEIVRGEAVYLLSERGTTALQ
I'm not sure how to go about fixing this. 
Thank you
Miriam Bregman
}}}
"	defect	closed	normal		Structure Prediction		not a bug						all	ChimeraX