This document was edited 6/20/2016 by Jared Adolf-Bryfogle. This application in Rosetta3 was created and documented by Mike Tyka,et al.

Purpose and Algorithm

This application simply rescores PDBs, silent files, and PDBs within relational databases. It also can be used for conversion - aka convert to/from silent files, PDBs, and relational databases. Use Rosetta's general output options for file type conversions.

The default behavior is to not echo PDBs, so only the scorefile will be output. This can be controlled via cmd-line options.

An introductory tutorial describing scoring in Rosetta can be found here.

Command Line Options

* Sample command:  score_jd2.linuxgccrelease -database db_path -l PDBLIST.txt

Score Application Specific
-score_app:linmin                  Run a quick linmin before scoring
-rescore:verbose                   display score breakdown

Quick Start Options
-in:file:native                    native PDB if CaRMS is required
-score:weights  weights            weight set or weights file
-score:patch  patch                patch set

-out:nooutput                      don't print PDB structures (default now)
-out:output                        force printing of PDB structures

-out:file:score_only               Only output score file (supress all other filetypes)
-out:file:scorefile        Name of scorefile (default
-out:file:silent                   write silent-out file
-out:prefix  myprefix              prefix the output structures with a string
-scorefile_format json             Write the output score file as a JSON file (useful for reading into python)

General Options

Call optH when reading silent files (useful for HisD/HisE determination)


  • If you want to find the lowest energy structure easily, use the sort command. You can sort on a particular column using the -kx option. See this page for more.
    • Sort by total score: sort
    • Sort by energy term: sort -k5, which would sort by the 5th column, or the 4th score term.
    • To get general summaries of the score file, and of specific terms (If output in JSON format): Rosetta/main/source/tools/

See Also