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Set raw alignment

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set_raw_alignment is an API-only function to create an alignment object from lists of atom indices.

New in PyMOL 2.3


  • name = str: alignment object name
  • raw = list: list of lists (columns) with (model, index) tuples
  • guide = str: name of guide object {default: first in list}
  • state = int: object state {default: 1}


cmd.align('1t46', '1oky', object='aln')
raw = cmd.get_raw_alignment('aln')
cmd.set_raw_alignment('alnnew', raw)

See Also