shell script to open each pdb file in a file tree, colour by chain and take a raytraced image

snapshotModel.sh

#!/bin/zsh

# Find all *.pdb files recursively
find . -name "*.pdb" | while read -r file; do
    # Extract the filename without extension
    filename=$(basename "$file" .pdb)
    # Extract the name of the directory
    dirname=$(dirname "$file")
    # Concatenate the directory name and the filename, separated by an underscore
    output="${dirname}_${filename}"

    # Run the pymol command
    pymol -qc "$file" -d "util.cbc; ray 1280, 1024; png ${output}.png; quit"
done