Rosetta Basics

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

Internal Documentation

How to Write Documentation

FAQ

Glossary

RosettaEncyclopedia

Options list

If you are new to Rosetta, start here to understand what you need to run Rosetta. Then check out these introductory tutorials.

If you are trying to find the right protocol to use for your biological application, look here.

Controlling Rosetta Execution

• Running Rosetta
  • Fixing errors
• Running Rosetta Parallel via MPI
• Graphics output and GUIs
  • PyMOL
  • PyRosetta Toolkit GUI
  • Foldit
• Scripting Rosetta
  • RosettaScripts
  • PyRosetta
  • Topology Broker
• Analyzing Results

Common/Useful Rosetta Options

• Input options
• Output options
• Relational Database options
• Run options
• Score options
• Packing options
• Renamed and Deprecated Options

Fundamental Rosetta Concepts

• Brief history of Rosetta
• FAQ
• Glossary of terms
  • Longer form descriptions

• Units in Rosetta

• Scoring

• Scorefunctions and Score types - Description of the default Rosetta Scorefunction and common score types.
  • Lazaridis-Karplus solvation energy
  • Scoring non-canonical molecular entities
  • MM Std Scorefunction
  • Orbitals Scorefunction
  • Additional score types
  • Design-centric guidance terms
  • Hydrogen bonding score term
  • Centroid score terms
• Symmetry
• Minimization - Backbone and/or side chain degrees of freedom
• Comparing Structures

• I want to do _x_. How do I do _x_?

• Advanced Topics

  • Rosetta3 Architecture
  • Rosetta AtomTypes
  • Foldtree Overview
  • AtomTree Overview
  • Loop modeling styles and algorithms

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
• Fragment file - Database of backbone fragment conformations
• Loops file - Which regions of the protein should be rebuilt
• Residue Params file - Residue chemical information
• Symmetry file - Dealing with symmetric proteins.
• FoldTree file - define structure connectivity, both covalent and non-covalent

Protocol-specific file formats

• Matcher (Enzdes) Constraint Files - A constraint file specialized for protein-ligand interactions
• Chemical shift file - NMR chemical shifts
• Bin transition probabilities file - Probabilities of transitioning from one mainchain torsion bin to another, used by some sampling schemes

Preparing structures to be used by Rosetta

• Preparing typical PDB files
• Preparing PDB files for non-peptide polymers
• Preparing ligands

Working with Non-Protein Residues and Molecules

• General Guidance:
  • General Control
  • Preparing PDB files for non-peptide polymers
  • How to turn on residue types that are off by default
  • Non-canonical Scorefunction and Scoreterm Info
  • Controlling the design process with additional guidance terms
• DNA
• RNA
• Ligands
• Water
• Metals
• Carbohydrates
• Mineral Surfaces
• Noncanonical Amino Acids
  • D-Amino Acids
  • Alpha-Amino Acids with Nonstandard Side-Chains
  • Beta-Amino Acids
• Noncanonical backbones

Misc

• Database support - Relational database support in Rosetta.
  • Database input/output - Platform-specific information on Rosetta database support.
  • Sqlite3-interface - More information on the sqlite database interface.
• Full options list - A (mostly) complete list of availible Rosetta options.
• Rosetta Job Distribution Discussion
• Analyzing results

Help

• RosettaCommons Forums
• RosettaCommons Bug Tracker

See Also

• Getting Started: A page for people new to Rosetta. New users start here.
• Introductory Rosetta Tutorials
• FAQ: Frequently Asked Questions
• Glossary: Brief definitions of Rosetta terms
• RosettaEncyclopedia: Detailed descriptions of additional concepts in Rosetta.
• Rosetta overview: Overview of major concepts in Rosetta
• Build Documentation: Information on setting up Rosetta
• Rosetta on different scales: Guidelines for how to scale your Rosetta runs
• TACC: Information for running Rosetta on the TACC/Stampede cluster.
• Solving a Biological Problem: Guide to approaching biological problems using Rosetta
• I want to do x: Guide to making specific structural perturbations using RosettaScripts
• Application Documentation: Links to documentation for a variety of Rosetta applications
• Commands collection: A list of example command lines for running Rosetta executable files
• Rosetta Servers: Web-based servers for Rosetta applications
• Scripting Documentation: Scripting interfaces to Rosetta
• Resources for learning biophysics and computational modeling
• Analyzing Results: Tips for analyzing results generated using Rosetta
• Comparing structures: Essay on comparing structures
• Using the ResourceManager
• Non-protein Residues: Information on running Rosetta with non-protein residues and ligands