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

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.
  --monomers=DIR      Monomer library dir (default: $CLIBD_MON).
  --lib=CIF           User's library with priority over the monomer library. Can
                      be given multiple times. If CIF is '+' reads INPUT_FILE
                      (mmCIF only).
  --low=CIF           Like --lib, but with the lowest priority.
  --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).
  --auto-ligand=Y|N   If ligand has no definition make ad-hoc restraints (N).
  --no-aliases        Ignore _chem_comp_alias.

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.
