prody contacts


Running 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
  -p STR, --prefix STR  output filename prefix (default: target filename)
  -x STR, --suffix STR  output filename suffix (default: _contacts)


Running 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