Silent file is a compact format file which stores information from multiple structures. Silent files can be generated by many Rosetta simulations. Such as Abintio and Ligand Docking. You also can use silent file tools to combine regular pdb files to be binary format silent file to save computer storage spaces. We will briefly introduce silent file format here.

Protein Silent Struct is usually seen in the Abinitio outputs.

  • Header

    SEQUENCE                      Structure sequences presented by one letter amino acid code
    SCORE                         Rosetta score terms
  • Body

    Colunms 1-4                   Residue sequence number
    Colunms 5-7                   Seconary structure one letter code
    Colunms 8-17                  Phi angle
    Colunms 18-26                 Psi angle
    Colunms 27-35                 Omega angle
    Colunms 36-44                 CA atom coordinates x
    Colunms 45-53                 CA atom coordinates y
    Colunms 55-62                 CA atom coordinates z
    Colunms 64-98                 Chi angle real data if possible

Binary Silent Struct File is very useful to compress multiple pdbs and save computer spaces.

  • Header

    SEQUENCE                      Structure sequences presented by one letter amino acid code
    SCORE                         Rosetta score terms
  • Body

    Binary contents

Silent files can be converted into PDB files using the extract_pdbs application. Information about the options can be found in the integration test folder /Rosetta/main/tests/integration/tests/extract_pdbs/.

See Also