$ 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: --pdbx-style Similar styling (formatting) as in wwPDB. -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. 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. --anisou=yes|no|heavy Add or remove ANISOU records. Macromolecular operations: --expand-ncs=dup|new Expand strict NCS specified in MTRIXn or equivalent. New chain names are the same or have added numbers. --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.