List of file types in Rosetta

Getting Started

Build Documentation

Rosetta Tutorials

Rosetta Basics

• Running Rosetta

• Units in Rosetta

• How Rosetta works

• File Formats in Rosetta

• Non-protein Residues

• Preparing Structures

• Command line options

Rosetta Applications

Rosetta Scripting Interfaces

Development Documentation

FAQ

Glossary

RosettaEncyclopedia

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.

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

• Rosetta Basics: The Rosetta Basics home page
• Options overview: Overview of Rosetta command line options
• Glossary: Brief definitions of Rosetta terms
• RosettaEncyclopedia: Detailed descriptions of additional concepts in Rosetta.
• Rosetta overview: Overview of major concepts in Rosetta
• Application Documentation: Links to documentation for a variety of Rosetta applications