(Re-)Scoring of Structures

Select, (re-)score and extract the low scoring structures

1.1 (Re-)scoring the 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.

1.2 Extract lowest energy structures

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

1.3 Convert silent structures to a PDB bundle

Pack the 10 lowest energy structures and put them into a pdb file

$ pack_pdbs -silent low_10_rescored.out > low_10_rescored.pdb

1.4 Extract individual PDBs from the bundle

Unpack the PDB files from the bundle created previously

cat low_10_rescored.pdb | unpack_pdbs -remark ROSETTA-TAG