convert-help.txt

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

Allows conversion between PDB, mmCIF, and mmJSON formats.

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

mmCIF output options:
  --style=STYLE           one of: default, pdbx (categories separated with #),
                          aligned (left-aligned columns).
  --all-auth              Write _atom_site.auth_atom_id (same as label_atom_id)
                          and auth_comp_id (same as label_comp_id).
  -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 of each 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.

General 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).
  --shorten-tlc           Change 5-character monomer names to 3-char. aliases.
  --monomer=OLD:NEW       Change monomer name (CCD code) OLD to NEW.
  -s FILE                 Use sequence(s) from FILE in PIR or FASTA format. Each
                          chain is assigned the best matching sequence, if any.
  --sifts-num[=AC,...]    Set sequence ID to SIFTS-mapped UniProt positions, add
                          5000+ to non-mapped seqnums. See docs for details.
  -B MIN[:MAX]            Set isotropic B-factors to a single value or constrain
                          them to a range.
  --scale-biso=MULT       Multiply isotropic B-factors by MULT.
  --anisou=yes|no|heavy   Add or remove ANISOU records.
  --assign-records[=A|H]  Re-assign ATOM/HETATM (w/o argument: auto).

Macromolecular operations:
  --select=SEL            Output only the specified selection.
  --remove=SEL            Remove the specified selection.
  --apply-symop=OP        Apply operation, e.g. '-x,y+1/2,-z' or 'x,y,z+0.1'.
  --reframe               Standardize the coordinate system (frame).
  --expand-ncs=dup|num|x  Expand strict NCS from MTRIXn or _struct_ncs_oper.
                          Argument controls naming of new chains; see docs.
  --assembly=ID           Output bioassembly with specified 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.

FORMAT can be specified as one of: mmcif, mmjson, pdb. chemcomp (read-only).
chemcomp = coordinates of a component from CCD or monomer library (see docs).
When output file is -, write to standard output (default format: pdb).