• 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

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