FoldSeek Score between two protein structures

[JamberFX]

I would like to have the FoldSeek score

No output. It seem to align the structures but never produces output. It says the files are not created.

Steps to Reproduce (for bugs)

Run below script in WSL using /mnt/c/Users/realt/Downloads/3di_aa_align.sh to call the script.

####Script####
#!/bin/bash

Paths to your protein structure files

protein1="/mnt/c/Users/realt/Downloads/AF-M1W266-F1-model_v4.pdb"
protein2="/mnt/c/Users/realt/Downloads/AF-O64637-F1-model_v4.pdb"

Define paths for Foldseek databases and results

protein1_db="/mnt/c/Users/realt/Downloads/protein1_db"
protein2_db="/mnt/c/Users/realt/Downloads/protein2_db"
results_db="/mnt/c/Users/realt/Downloads/results_db"
alignment_results_db="/mnt/c/Users/realt/Downloads/alignment_results_db"
alignment_results_tsv="/mnt/c/Users/realt/Downloads/alignment_results.tsv"

Create Foldseek databases

foldseek createdb "$protein1" "$protein1_db" > foldseek_createdb1_log.txt 2>&1
foldseek createdb "$protein2" "$protein2_db" > foldseek_createdb2_log.txt 2>&1

Run Foldseek search for 3Di+AA alignment and capture all output

foldseek search "$protein1_db" "$protein2_db" "$results_db" "$alignment_results_db" --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits --alignment-type 3d+aa > foldseek_search_log.txt 2>&1

Convert the results to a readable format

foldseek convertalis "$protein1_db" "$protein2_db" "$alignment_results_db" "$alignment_results_tsv" > foldseek_convert_log.txt 2>&1

Print the alignment results

echo "Foldseek createdb1 log:"
cat foldseek_createdb1_log.txt

echo "Foldseek createdb2 log:"
cat foldseek_createdb2_log.txt

echo "Foldseek search log:"
cat foldseek_search_log.txt

echo "Foldseek convert log:"
cat foldseek_convert_log.txt

echo "Alignment results:"
cat "$alignment_results_tsv"

Clean up (optional)

rm -r "$protein1_db" "$protein2_db" "$results_db" "$alignment_results_db"

Foldssek Output (for bugs)

Input /mnt/c/Users/realt/Downloads/alignment_results_db does not exist
Alignment results:
view alignment_results

MMseqs Version: 9.427df8a
Selected entries with key
Database ID mode 0
Index entry type 0
Verbosity 3

rm: cannot remove '/mnt/c/Users/realt/Downloads/results_db': No such file or directory
rm: cannot remove '/mnt/c/Users/realt/Downloads/alignment_results_db': No such file or directory

Context

I need the FoldSeek score to compare to other metrics.

Your Environment

Windows 11 using WSL to execute script in Linux environment. I would prefer to use FoldSeek in Jupyter Notebook in windows but have not been successful in getting that to work.

[Pooryamb]

Try running the search step with "-e inf --exhaustive-search 1" options as well