Scoring Application

This application can (re)score PDBs and silent files. It also can be used to extract PDBs from silent files, and assemble PDBs into silent files. The score application is at mini/src/apps/public/. The name of the application is score.cc.

Input Files

The input files can be regular pdb file or Rosetta silent file.

Command Lines and Options

• Options used by the score application:

  *PDB input:
  ------------
  -in:file:s *.pdb   or                       Name(s) of single PDB file(s) to process. [FileVector]
  -in:file:l  list_of_pdbs
  -no_optH                                    Dont change positions of Hydrogen atoms! (default true, specify false if you want optH)
  
  *Silent input:
  --------------
  -in:file:silent silent.out                  Silent input filesname. [FileVector]
  -in:file:tags                               Specify specific tags to be extracted, if left out all will be taken.[StringVector]
  -in:file:fullatom                           Enable full-atom input of PDB or centroid structures.[Boolean]
  -in:file:silent_optH                        Call optH when reading silent files (useful for HisD/HisE determination). [Boolean]
  
  -score_app:linmin                           Run a quick linmin before scoring. [Boolean]
  
  *Native:
  --------
  -in:file:native                             native PDB (rms, maxsub and gdtm scores will be calculated).[File]
  
  *Scorefunction:
  ---------------
  -score:weights                              Name of weight set or weights file, default is 'standard'. [String]
  -score:patch                                Name of patch file (without extension)" , default="". [String]
  -score:optH_weights                         Name of weights file (without extension .wts) to use during optH
                                              (default standard.wts w/ sc12 patch). [String]
  -score:optH_patch                           Name of weights file (without extension .wts) to use during optH
                                              [String]
  -rescore:verbose                            Full break down of weights, raw scores and weighted scores. [Boolean]
  
  *Output:
  --------
  -out:nooutput                               Don't print PDB structures (default false) [Boolean]
  -out:output                                 Force printing of PDB structures.(default false) [Boolean]
  -out:file:silent                            Write a scorefile to the provided filename.
                                              (default = default.sc) [String]
  -out:file:scorefile                         Write a scorefile to the provided filen (default default.sc)
                                              [String]
  -out:prefix                                 Prefix the output structures with a string.[String]
  

• Sample Command Lines
  Most commands output score file that contains the scores of each structure.(capitalized text between "<" and ">" indicates user input)
  1. Score a protein with the defaults:

     ./score.linuxgccrelease -database <PATH TO ROSETTA 3 DATABASE> -s <PATH TO PDB COORDINATES>
     

  2. Score a protein with the softrep weights and the score12 patch after doing a minimization using the linmem optimization method:

     ./score.linuxgccrelease -database <PATH TO ROSETTA 3 DATABASE> -s <PATH TO PDB COORDINATES>
     -score:weights soft_rep -score:patch score12 -score_app:linmin
     

  3. Score a protein with the defaults and ouput a scored pdb:

     ./score.linuxgccrelease -database <PATH TO ROSETTA 3 DATABASE> -s <PATH TO PDB COORDINATES> -out:output
     

  4. Score a slient file format protein with fullatom

     ./score.linuxgccrelease -in:file:silent <PATH TO SILENT FILES> -score:weights score3 -database <PATH TO ROSETTA 3 DATABASE>
     ./score.linuxgccrelease -in:file:silent <PATH TO SILENT FILES> -in:file:fullatom -database <PATH TO ROSETTA 3 DATABASE>
     

  5. Create a silent file from 2 pdbs:

     ./score.linuxgccrelease -database <PATH TO ROSETTA 3 DATABASE> -s <PATH TO FIRST PDB> -s <PATH TO SECOND PDB>
     -out:file:silent <PATH TO SILIENT FILE>
     

  6. Create a silent file from a list of pdbs:

     ./score.linuxgccrelease -database <PATH TO ROSETTA 3 DATABASE> -l <PATH TO FILE WITH LIST OF PDB FILE PATHS>
     -out:file:silent <PATH TO SILIENT FILE>
     

  7. Extract a pdb(s) file from a silent file:

     ./score.linuxgccrelease -database <PATH TO MINIROSETTA DATABASE> -in:file:silent <PATH TO SILIENT FILE>
     -in::file::fullatom -in:file:silent_optH -out:output
     

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