list index out of range at codes/MSA_embedding.py:60

[JunfengWu163]

We recently discovered your AI-HDX program on GitHub, and it has proven to be extremely valuable for our research. However, while following the instructions in MSA_embedding.md, we encountered an error and hope you and the other authors of AI-HDX can assist us in resolving it.

The error message is as follows: Traceback (most recent call last): File "codes/MSA_embedding.py", line 60, in sequence_matrix[idx].append(str(hhm_val1)) IndexError: list index out of range

The error occurred during the 6th step, as detailed below:

1. Activate the environment: $ conda activate hhblits
2. Enter the folder containing the Fasta files: $ cd ~/AI-HDX-main/Fasta
3. Ensure the hhm_data folder exists. If not, create it in the Fasta folder: $ mkdir hhm_data Then, run HHBlits: for file in ./*.fasta do BASE=$(basename $file | sed 's/.fasta//g') hhblits -i $file -ohhm $BASE.hhm -d /home/lstm/database/UniRef30_2020_06 if [ -f "$BASE.hhm" ]; then mv $BASE.hhm hhm_data/ else echo "Error: $BASE.hhm file not found, skipping." fi done
4. Activate the HDX environment: $ conda activate HDX
5. Generate the dssp.txt file using a command like: $ python codes/accessScore.py P61371 AF-P61371-F1-model_v4.pdb
6. Combine the results: $ python codes/MSA_embedding.py Fasta/hhm_data/rcsb_pdb_4XI2.hhm 4xi2.pdb.dssp.txt

inputs.zip

[JunfengWu163]

the two input files are attached in my previous message.