Rosetta 3.5
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Commands for the scoring application

Metadata

This document was edited Nov 1st 2008 by Yi Liu. This application in mini was created and documented by Mike Tyka,et al.

Purpose and Algorithm

This application simply rescores PDBs and silent files. It also can be used to extract PDBs from silent files, assemble PDBs into silent files.

Command Line Options

** Sample command:  score.linuxgccrelease @flags > score.log

General:
   -database                                   Path to rosetta_database

General Input:
   -in:file:path                               Base path for input data
   -no_optH                                    Dont change positions of Hydrogen atoms! (default true, specify false if you want optH)
   -score:optH_weights                         Weights file for optH (default standard.wts w/ sc12 patch)
   -score:optH_patch                           Weights patch file for optH
   -ignore_unrecognized_res                    Alternatively, add residue params file to rosetta_database
   -ignore_waters                              Ignore only water molecules

PDB input:
   -in:file:s *.pdb   or                       PDB input file name
   -in:file:l  list_of_pdbs                    File containing list of PDB input file names relative to -in:file:path

Silent input:
   -in:file:silent silent.out                  silent input filesname
   -in:file:tags                               specify specific tags to be extracted, otherwise use all
   -in:file:fullatom                           for full atom structures
   -in:file:silent_struct_type <type>          Specify the input silent-file format e.g. 'binary' for binary silent files
                                                 protein_float, protein, rna, binary, score, binary_dna, pdb
   -in:file:silent_read_through_errors         Try to salvage damaged silent files
   -in:file:silent_renumber                    Renumber residues starting from 1
   -in:file:nonideal_silentfile                for non-ideal structures (such as from looprelax)
   -in:file:silent_optH

General Database:
   -inout:dbms:mode                            Specify database backend. default: 'sqlite3'
   -inout:dbms:database_name                   If sqlite3 the filename for the database
   -inout:dbms:pq_schema                       For PostgreSQL, the schema namespace in the database to use
   -inout:dbms:host                            NOTE to use mysql or postgres as a backend:
   -inout:dbms:user                               compile with 'extras=mysql' or 'extras=postgres' and use
   -inout:dbms:password                           the '-inout:dbms:mode mysql' or
   -inout:dbms:port                               the '-inout:dbms:mode postgres' flag
                                                  Consider using ~/.pgpass or ~/.my.cnf to store connection info

 Database Input:
   -in:use_database                               Indicate that structures should be read from the given database
   -in:select_structures_from_database            An sql query to select which structures should be extracted. e.g.:
                                                  "SELECT tag FROM structures WHERE tag = '7rsa';"

 General Output:
   -out:nooutput                                  Do not output any structures
   -out:no_nstruct_label                          Do not append _#### to tag for output structures
   -out:overwrite                                 Overwrite structures if they already exist
   -out:path:all                                  Path where to write output data
   -out:prefix                                    Prefix for output structures
   -out:suffix                                    Suffix for output structures
   -out:file:fullatom                             Force full-atom output
   -out:file:scoretype <filename>                 Write scorefile (default default.sc)

PDB Output:
   -pdb                                           Output structures in PDB file format
   -pdb_gz                                        Output structures in zipped PDB file format

Silent Output:
  -out:file:silent <filename>                     Output structures to specified silent file (default 'default.out')
  -out:file:silent_gz                             Output structures to specified silent file in zipped format
  -out:file:silent_struct_type <type>             Specify the input silent-file format e.g.
                                                     protein_float, protein, rna, binary, score, binary_rna, pdb
  -out:file:silent_print_all_score_headers        Use if outputing structures for multiple sequences
  -out:file:silent_preserve_H                     Preserve hydrogens in PDB silent-file format

Database Output:
  -out:use_database                           Output structures to database (see General Database Options)


** Sample command:  relax.linuxgccrelease @flags > relax.log
** Options in flag file:
   -database                 Path to minirosetta databases
   -s                        Input file paths and name
   -relax:fast               Invokes a fast mode, which is almost as effective as a normal relax but 5-10 faster(optional)

** Normal IO and Score Function flags also apply         Call optH when reading silent files (useful for HisD/HisE determination)
                -score_app:linmin                           Run a quick linmin before scoring
Native:         -in:file:native                             native PDB if CaRMS is required
Scorefunction:  -score:weights  weights                     weight set or weights file
                -score:patch  patch                         patch set
                -rescore:verbose                            display score breakdown
                -rescore:output_only                        don't rescore
Output:         -nooutput                                   don't print PDB structures (default now)
                -output                                     force printing of PDB structures
                -out:file:silent                            write silent-out file
                -out:prefix  myprefix                       prefix the output structures with a string