qp.structure.missing.write_alignment

qp.structure.missing.write_alignment(residues, pdb, path, out)[source]

Write a Modeller alignment file for filling missing residues.

Creates a PIR-format alignment file with two sequences: the template (with gaps for missing residues) and the target (complete sequence).

Parameters:

  • residues (list of list) – Residues separated by chain, as returned by get_residues().

  • pdb (str) – PDB code (used as sequence identifier).

  • path (str) – Path to the template PDB file.

  • out (str) – Path to the output alignment file (.ali).

See also

https

//salilab.org/modeller/10.4/manual/node501.html Modeller alignment file format documentation.

https

//salilab.org/modeller/wiki/Missing_residues Modeller missing residues tutorial.