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 lines

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

PDB input:      -in:file:s *.pdb   or
                -in:file:l  list_of_pdbs
                -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
Silent input:   -in:file:silent silent.out                  silent input filesname
                -in:file:tags                               specify specific tags to be extracted, if left out all will be taken
                -in:file:fullatom                           for full atom structures
                -in:file:nonideal_silentfile                for non-ideal structures (such as from looprelax)
                -in:file:silent_optH               ** 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