The AlignmentFileGeneratorMover is used to generate Alignment Files for the SEWING design protocol and can be accessed via RosettaScripts
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
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...
<AlignmentFileGeneratorMover name="AFG" model_file_name="smotifs_H_1_100_L_1_100_H_1_100.segments" edge_file_name="smotifs_H_1_100_L_1_100_H_1_100.edges" match_segments="1,3" set_segments_from_dssp="true" />