$ 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 FILE [FILE2]
    Aligns CHAIN1 from FILE to CHAIN2 from FILE2 (if given) or FILE.
    By default, the sequence of residues in the model is used.
    To use SEQRES prepend '+' to the chain name (e.g. --query=+A),
    or, when using mmCIF, prepend '@' to entity name (--query=@1).

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):
  --blosum62           Use BLOSUM62 score matrix.
  --partial=y|n        Use scoring meant to align partially-modelled polymer to
                       its full sequence (default in 1st mode).
  --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.
