Unfortunately, there isn’t a good way to easily go from a fragments file to PDB format. There is a way to tell the fragment picker to output a silent file instead of a fragments file (-frags::output_silent), but nothing which will convert the fragments file.
You may have to write a script to do this for you. (PyRosetta http://www.pyrosetta.org may be helpful here). I see two options. Either you can read the phi/psi angles from the fragment file and set them in a peptide, or you can read off the source information encoded in the fragment file, and just grab that region from the original PDBs.
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