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Compare a set of homologous but structurally heterogeneous PDBs to a template PDB and find structurally highly conserved sites that can serve as stems for splicing segments.
<StemFinder name="(&string)" from_res="(1&int)" to_res="(pose.total_residue()&int)" rmsd="(0.7&float)" stems_on_sse="(false&bool)" stems_are_neighbors="(true&bool)" neighbor_distance="(4.0&float)" neighbor_separation="(10&int)" filenames="(&comma-separated list of pdb file names)"/>