$ gemmi prep -h
Usage:
 gemmi prep [options] INPUT_FILE OUTPUT_FILE
 gemmi prep --split [options] INPUT_FILE OUTPUT_BASENAME

Prepare intermediate Refmac files.
INPUT_FILE can be in PDB, mmCIF or mmJSON format.

Options:
  -h, --help          Print usage and exit.
  -V, --version       Print version and exit.
  -v, --verbose       Verbose output.
  --split             Split output into two files: crd and rst.
  --monomers=DIR      Monomer library dir (default: $CLIBD_MON).
  --libin=CIF         Custom additions to the monomer library.
  --auto-cis=Y|N      Assign cis/trans ignoring CISPEP record (default: Y).
  --auto-link=Y|N     Find links not included in LINK/SSBOND (default: N).

Hydrogen options (default: remove and add on riding positions):
  -H, --no-hydrogens  Remove (and do not add) hydrogens.
  --keep-hydrogens    Preserve hydrogens from the input file.
