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    smlewis’s script is a pseudo code, the PDB variable is undefined.
    You can change your script like this:

    #for example, my pdb files are in /home/SunH/my_decoys/
    foreach PDB ( /home/SunH/my_decoys/* )
    echo “Extract loop residues from $PDB”
    #read loop residues from each pdb file and then write to a new pdb file
    head -1 $PDB | tail -100 > “$PDB”_loop_only