The AlignmentFileGeneratorMover is used to generate Alignment Files for the SEWING design protocol and can be accessed via RosettaScripts

Command-Line Flags

The AlignmentFileGeneratorMover uses the MotifHasher utility designed by Will Scheffler. The command-line flags required for this utility can be found on the AssemblyMover )

  • edge_file_name : Path to the edge file ( See Edge File Generation )
  • recursive_depth : Determines how many nodes away from the starting segment you want to generate alignments for
  • match_segments : Designates which segments in the input structure are allowed to form alignments
  • pose_segment_starts : A comma separated list of the first residue of each segment in the pose
  • pose_segment_ends : A comma separated list of the last residue of each segment in the pose
  • set_segments_from_dssp : Determine segment boundaries based on pose secondary structure - Can be used in place of the pose_segment_starts and pose_segment_ends options
  • required_resnums : The residue numbers of residues in the input structure that must be preserved - Can use a residue selector instead


The AlignmentFileGeneratorMover can be given a Ligands subtag.


Here is an example RosettaScripts tag for a HLH input structure that will be added to on both the N- and C-terminal helices.

Disclaimer: At this time I cannot confirm that this xml script actually works, but it should...


See Also