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

with possible conversions between PDB, mmCIF and mmJSON.
FORMAT can be specified as one of: mmcif, mmjson, pdb, ccd (read-only).
ccd = coordinates of a chemical component from CCD or monomer library.

General options:
  -h, --help              Print usage and exit.
  -V, --version           Print version and exit.
  -v, --verbose           Verbose output.
  --from=FORMAT           Input format (default: from the file extension).
  --to=FORMAT             Output format (default: from the file extension).

CIF output options:
  --style=STYLE           one of: default, pdbx (categories separated with #),
                          aligned (left-aligned columns).
  -b NAME, --block=NAME   Set block name and default _entry.id
  --sort                  Sort tags in alphabetical order.
  --skip-category=CAT     Do not output tags starting with _CAT

PDB input options:
  --segment-as-chain      Append segment id to label_asym_id (chain name).
  --old-pdb               Read only the first 72 characters in line.
  -L, --force-label       Add label_seq_id even if SEQRES is missing

PDB output options:
  --short-ter             Write PDB TER records without numbers (iotbx compat.).
  --linkr                 Write LINKR record (for Refmac) if link_id is known.
  --copy-remarks          (pdb->pdb only) Copy REMARK records.

Any output options:
  --minimal               Write only the most essential records.
  --shorten               Shorten chain names to 1 (if # < 63) or 2 characters.
  --rename-chain=OLD:NEW  Rename chain OLD to NEW (--rename-chain=:A adds
                          missing chain IDs).
  -s FILE                 Use sequence from FILE (PIR or FASTA format), which
                          must contain either one sequence (for all chains) or
                          as many sequences as there are chains.
  --sifts-num             Use SIFTS-mapped position in UniProt sequence as
                          sequence ID.
  -B MIN[:MAX]            Set isotropic B-factors to a single value or change
                          values out of given range to MIN/MAX.
  --anisou=yes|no|heavy   Add or remove ANISOU records.
  --set-cispep            Reset CISPEP records from omega angles.

Macromolecular operations:
  --select=SEL            Output only the selection.
  --remove=SEL            Remove the selection.
  --apply-symop=OP        Apply symmetry operation (e.g. '-x,y+1/2,-z'.
  --expand-ncs=dup|num|x  Expand strict NCS from in MTRIXn or _struct_ncs_oper.
                          New chain names are the same, have added numbers, or
                          the shortest unused names are picked.
  --assembly=ID           Output bioassembly with given ID (1, 2, ...).
  --remove-h              Remove hydrogens.
  --remove-waters         Remove waters.
  --remove-lig-wat        Remove ligands and waters.
  --trim-to-ala           Trim aminoacids to alanine.

When output file is -, write to standard output.
