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