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

## Subtags

The AlignmentFileGeneratorMover can be given a Ligands subtag.

## Example

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"
/>