Select, (re-)score and extract the low scoring structures
(Re-)score the structures found in fullatom-pool sub-directory within the run directory
$ score_jd2.(macosclang/linuxgcc)release -in:file:silent decoys.out -out:file:silent rescored_decoys.out
Depending on your operating system and the compiler, you can either use macosclangrelease or linuxgccrelease in the above command. Refer here to learn about scoring applications in Rosetta.
Extract 10 lowest-energy structures from the (re-)scored structures
$ extract_decoys rescored_decoys.out -formula 'score' -N 10 -verbose 0 > low_10_rescored.out
This protocol creates a silent file consisting of 10 lowest-energy rescored structures
Pack the 10 lowest energy structures and put them into a pdb file
$ pack_pdbs -silent low_10_rescored.out > low_10_rescored.pdb
Unpack the PDB files from the bundle created previously
cat low_10_rescored.pdb | unpack_pdbs -remark ROSETTA-TAG