Running :command:`prody contacts -h` displays:
usage: prody contacts [-h] [--quiet] [--examples] [-s SELSTR] [-r FLOAT] [-t STR] [-p STR] [-x STR] target ligand [ligand ...] positional arguments: target target PDB identifier or filename ligand ligand PDB identifier(s) or filename(s) optional arguments: -h, --help show this help message and exit --quiet suppress info messages to stderr --examples show usage examples and exit -s SELSTR, --select SELSTR selection string for target -r FLOAT, --radius FLOAT contact radius (default: 4.0) -t STR, --extend STR output same residue, chain, or segment as contacting atoms -p STR, --prefix STR output filename prefix (default: target filename) -x STR, --suffix STR output filename suffix (default: _contacts)
Running :command:`prody contacts --examples` displays:
Identify contacts of a target structure with one or more ligands. Fetch PDB structure 1zz2, save PDB files for individual ligands, and identify contacting residues of the target protein: $ prody select -o B11 "resname B11" 1zz2 $ prody select -o BOG "resname BOG" 1zz2 $ prody contacts -r 4.0 -t residue -s protein 1zz2 B11.pdb BOG.pdb