$ gemmi align -h
Pairwise sequence alignment with scoring matrix and affine gap penalty.

Usage:

gemmi align [options] FILE[...]
    Aligns sequence from the model to the full sequence (SEQRES).
    Both are from the same FILE - either in the PDB or mmCIF format.
    If the mmCIF format is used, option --check-mmcif can be used.

gemmi align [options] --query=CHAIN1 --target=CHAIN2 FILE1 FILE2
    Aligns CHAIN1 from FILE1 to CHAIN2 from FILE2.
    By default, the sequence of residues in the model is used.
    To use SEQRES prepend '+' to the chain name (e.g. --query=+A).

gemmi align [options] --text-align STRING1 STRING2
    Aligns two ASCII strings (used for testing).

Options:
  -h, --help         Print usage and exit.
  -V, --version      Print version and exit.
  --check-mmcif      checks alignment against _atom_site.label_seq_id
  --query=[+]CHAIN   Align CHAIN from file INPUT1.
  --target=[+]CHAIN  Align CHAIN from file INPUT2.
  --text-align       Align characters in two strings (for testing).

Scoring (absolute values):
  --match=INT        Match score (default: 1).
  --mism=INT         Mismatch penalty (default: -1).
  --gapo=INT         Gap opening penalty (default: -1).
  --gape=INT         Gap extension penalty (default: -1).

Output options:
  -p                 Print formatted alignment with one-letter codes.
  --rmsd             In addition to aligning two CHAINs (--query and --target),
                     superpose structures and print RMSD.
  -v, --verbose      Verbose output.
