$ gemmi mask -h
Usage:
 gemmi mask [options] INPUT output.msk

Makes a bulk-solvent mask in the CCP4 format.
INPUT is a coordinate file (mmCIF, PDB, etc).
  -h, --help           Print usage and exit.
  -V, --version        Print version and exit.
  -v, --verbose        Verbose output.
  --timing             Print how long individual steps take.
  -s, --spacing=D      Max. sampling for the grid (default: 1A).
  -g, --grid=NX,NY,NZ  Grid sampling.
  -r, --radius=R       Use constant radius of atom spheres.
  --r-probe=Rp         Use VdW radius + Rp (default: 1.0A).
  --r-shrink=Rs        Finally, remove a shell of thickness Rs (default: 1.1A).
  --island-limit=VOL   Remove "islands" up to VOL A^3.
  --hydrogens          Don't ignore hydrogens.
  --any-occupancy      Don't ignore zero-occupancy atoms.
  --set-occupancy      Set values according to occupancy.
  --cctbx-compat       Use vdW, Rprobe, Rshrink radii from cctbx.
  --refmac-compat      Use radii compatible with Refmac.
  -I, --invert         0 for solvent, 1 for molecule.
