Error in google colab

[aaaniich]

Hi! I try to analyse my sequence with google colab, but i have this error. Can you help me? Thank you

IndexError Traceback (most recent call last) in 7 with open(fasta_file, "w") as f: 8 f.write(">:H\n{}\n>:L\n{}\n".format(heavy_sequence, light_sequence)) ----> 9 cst_defs = get_cst_defs(model, fasta_file, device=device) 10 11 pred_pdb = build_structure(model,

1 frames /content/deepab/deepab/constraints/write_constraints.py in get_constraint_residue_pairs(model, fasta_file, constraint_bin_value_dict, mask_distant_orientations, use_logits, device) 94 95 if constraint_type in pairwise_constraint_types: ---> 96 if preds[pred_i][i, j].argmax().item() >= len( 97 constraint_bin_value_dict[constraint_type]): 98 continue

IndexError: index 235 is out of bounds for dimension 0 with size 235

[aaaniich]

H QVQLKESGPGLVAPSQSLSITGTDNYIEVSGDYGVSWIRQPPGKGMVSGSGLTDGGSTYYNSALKSRLSI SKDNSKSQVFLKMNSLDASADAMYYCAKHTYGGPGDSWGQGTSVTVSS L DIVMSQSPSSLAVSAGEKVTMSCRSSQSLVHSNGNTYLYRKNYLAWYQQKPGQYDATKLDSASTRESGVP DRFTGSGSGTDFTQQSGSYPLTDLAVYYCKQSYDLPTFGAGTKLELK

It's my sequence

[jeffreyruffolo]

Hello, this may be a result of Colab updating to python3.8 in the last couple days. I am working on a fix for this currently.

[aaaniich]

Hello, this may be a result of Colab updating to python3.8 in the last couple days. I am working on a fix for this currently.

Sorry to bother you again! Some of my sequences still end up with an error. Can you tell me what I'm doing wrong?

H QVQLKESGPGLVAPSQSLSITGTSGSSLSKGYYGDYGVSWIRQPPGKGAISSGGGTAGGGSTYYNSALKS RLSISKDNSKSQVFLKMNSLDDDDSAMYYCAKHTYGGPGDSWGQGTSVTVSS L DIVMSQSPSSLAVSAGEKVTMSCTAESQTSHVNRKNYLAWYQQKPGQRDGSSLSGASTRESGVPDRFTGS GSGTDFTSQSKEVPLTDLAVYYCKQSYDLPTFGAGTKLELK

[aaaniich]

Hello, this may be a result of Colab updating to python3.8 in the last couple days. I am working on a fix for this currently.

I have this error every time, when I try to start step "Predict antibody structure with DeepAb" IndexError: index 233 is out of bounds for dimension 0 with size 233