Rosetta Basics
Controlling Rosetta Execution
-
Running Rosetta - Controlling Rosetta with command line options
- Database - The Rosetta database
- Input options
- Output options
- Relational Database options
- Run options
- Score options
- Packing options
- Full options list - A (mostly) complete list of availible Rosetta options.
- Scripting Rosetta
- Graphics output and GUIs
- JD2
Preparing structures to be used by Rosetta
Common File Formats
- Fasta file - Input protein sequences
- Silent file - Rosetta-specific compact output representation
- Resfiles - Which residue sidechains can move and mutate
- Movemap file - Which sidechains and backbones can move
- Constraint file - Add energy restraints to scoring
- Matcher (Enzdes) Constraint Files - A constraint file specialized for protein-ligand interactions
- Fragment file - Database of backbone fragment conformations
- Loops file - Which regions of the protein should be rebuilt
- Chemical shift file - NMR chemical shifts
- Residue Params file - Residue chemical information
- Symmetry file - Dealing with symmetric proteins.
Working with Non-Protein Residues and Molecules
- General Guidance:
- DNA
- RNA
- Ligands
- Water
- Metals
- Carbohydrates
- Mineral Surfaces
- Noncanonical Amino Acids
Fundamental Rosetta Concepts
- Scorefunctions and Score types - Description of the default Rosetta Scorefunction and common score types.
- Symmetry
- Minimization - Backbone and/or side chain degrees of freedom
- Advanced Topics
Misc
-
Database support - Relational database support in Rosetta.
- Sqlite3-interface - More information on the sqlite database interface.
- Full options list - A (mostly) complete list of availible Rosetta options.