Silent File Applications

There are two applications in this system. One is combine_silent.cc, the other is extract_pdb.cc.

• How to combine pdbs into silent file format.
  You can use combine_silent.cc to combine regular pdbs to be silent files. Here are the avaliable options

  -in:file:database                 Path to rosetta 3 databases. (required)
  -out::file::silent                Output silent-files paths and names, Specifies silent file into which silent-files are combined.
  -in::file::tags                   Silent-files tags. List of tags to be read from input silent-files (optional)
  -out::file::silent_struct_type    Silent file strucutre types. silent-file output format. Default='Protein'
                                    Legally choices: 'rna', 'binary', 'protein', 'pdb'
  -in::file::residue_type_set       ResidueTypeSet used in creating Pose from input silent-files. default='fa_standard'. (optional)
  

• How to extract pdbs from a silent file.
  You can use extract_pdb.cc to retrieve pdb files from a silent file

  -in::file::silent                  Silent-files path and names, specifies list of silent-files to be read in.(required)
  -in::file::tags                    Silent-file tags. List of tags to be extracted from silent-files. (optional)
  -in::file::silent_struct_type      Silent-file strucutre types. silent-file input format. Default='Protein'
                                     Legally choices: 'rna', 'binary', 'protein', 'pdb'.
                                     We recommended using the binary format silent file rather than others here.
  -in::file::residue_type_set        ResidueTypeSet used in creating Pose from input silent-files. default='fa_standard'. (optional)
                                     Legally choices: 'centroid'
  -out::prefix                   	   Prefix that is appended onto extracted PDB files.
  -in::file::rescore                 Governs whether Pose from silent-file is rescored or not. <true/false>
  -score::weights                    Weights file for ScoreFunction, defaults to standard.
  -score::patch                 	   Patch file for ScoreFunction.
  

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