This document was edited 6/20/2016 by Jared Adolf-Bryfogle. This application in Rosetta3 was created and documented by Mike Tyka,et al.
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.
* 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.sc Name of scorefile (default score.sc)
-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)
sort command. You can sort on a particular column using the -kx option. See this page for more.
sort my_score_file.sc sort -k5 my_score_file.sc, which would sort by the 5th column, or the 4th score term.Rosetta/main/source/tools/scorefile.py my_score_file.sc