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$ 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.
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