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Options list

  • Flags files: File used to specify multiple options on the command line using the syntax @flags_file.

Protein structure input/output formats

  • PDB file: Standard file format for input/output of single protein structures. See information on PDB file requirements here.
  • Silent file: Useful for input/output of large numbers of structures.

Commonly used input files

  • Fasta files: File to provide sequence information.
  • Fragment files: Commonly used in structure prediction.
  • Resfiles: File to specify residues allowed to design and repack.
  • Movemap files: File (supported by some protocols, see page for details) to specify which torsion angles and rigid body degrees of freedom will be allowed to change.
  • Residue params files: Stores chemical and geometric information for a residue or ligand. Useful when running Rosetta with non-protein residues.
  • Loops files: Specifies loop definitions used in loop modeling.
  • Symmetry file: Dealing with symmetric proteins.
  • Constraint file: Provide information about constraints (restraints) for use in a Rosetta protocol
  • FoldTree file: Allows external definition of pose connectivity

Protocol-specific input files

  • "Grishin" alignment format: A protein sequence alignment format used by comparative modeling.
  • Match constraint files: File specifying geometric constraints for the match application.
  • Chemical shift files: NMR chemical shift information used with CS-Rosetta.
  • Bin transition probabilities files: Probabilities of transitioning from one mainchain torsion bin to another, used by some sampling schemes.
  • SEWING-specific files:
    • Model files: Specify substructures (nodes) to be used when generating structures
    • Edge files: Specify edges to be used when generating structures
    • Rot files: Store information about native residue identities in SEWING assemblies. Used with the AssemblyConstraintsMover. <!--- BEGIN_INTERNAL -->
    • Alignment files: Store pre-calculated alignments near a given starting node. Optional for use with AppendAssemblyMover.

Database input/output

Rosetta supports input/output of databases in SQLite3, MySQL, and PostgreSQL. More information on input/output with these formats can be found here. A tutorial on how to output information to a database in Rosetta can be found here. Specific information on interfacing with SQLite3 can be found here, and advanced details on Rosetta's interface with databases is found here.

See Also