Rosetta User Guide

3.2.1 release

Rosetta is a library based object-oriented software suite which provides a robust system for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. The library contains the various tools that Rosetta uses, such as Atom, ResidueType, Residue, Conformation, Pose, ScoreFunction, ScoreType, and so forth. These components provide the data and services Rosetta uses to carry out its computations.

The major library is named "core", which contains conformational representations of polymer structures, their constituents, the capability to alter the conformations of those structures, and the ability to score those structures with the Rosetta scoring algorithms. It also contains the command-line options system.

The next most important library is "protocol". It contains higher-level classes and functions needed by Rosetta subprotocols. All the protocols are wrapped by Mover objects, which unifies their interface and integrates them with the job distributor for use on clusters. This Mover interface also allows you to use pre-developed protocols by just calling the corresponding mover, making it easier to create new protocols.

Rosetta also provides a component named "apps". It contains source code for released applications.

Documentation and Support

1. The latest version of this document is available at: http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide
2. Additional support and documentation is available through the Rosetta Commons forums: http://www.rosettacommons.org/forum

Installation

1. Platforms
2. Install SCons
3. Build Rosetta

Things you need to know before running Rosetta

1. Rosetta Database
2. Command Line Options and Flag File

Released Applications

We introduce the official release applications here. These applications have been used and tested by developers and well documented. We will also provide technical support to help you use these applications Before you read the application's manual we suggest that you read the next page: Applications General Information

Structure Prediction

1. Abinitio Modeling
2. Comparative Modeling
3. Relax Application
4. Loop Modeling
   • Loop Modeling
   • Fragments Based Loop Modeling
   • Kinematic Loop Modeling
5. Backrub Application (Localized Backbone Movement)

Docking

1. Docking
2. Ligand Docking
   • Ligand Docking
   • Extract Atomtree Diffs
3. Flexible Peptide Docking

Design

1. Fix Backbone Design
2. Enzyme Design
   • Enzyme Design
   • Match Application
   • Match Enzdes Cstfile
3. RosettaScripts
4. RosettaDNA Application

Symmetry User's Guide.

1. Introduction To Symmetry
2. Symmetric Docking
3. Make Symmdef File
4. Make Symmdef File Denovo

Applications To Specific Problems

1. Membrane Abinitio
2. Scenarios
   • FloppyTail Application
   • CA-to-allatom Application
3. Electron Density
   • Loops-from-Density Application
   • Molecular Replacement Protocols
   • Prepare Template For MR

Bundle

1. Minirosetta (Boinc Application)
2. Fold And Dock

Scoring

1. Score Commands

Other

1. Cluster Application
2. Idealization Application
3. Sequence Tolerance
4. Silent File Tools
5. Extra useful command line samples

Files In Rosetta

1. Using Constraints Files in Rosetta
2. Fragments File
3. Chemical Shift File
4. Sequence (fasta) File
5. Resfile Syntax
6. Loop Files
7. Silent Files

Options System

1. Input Options
2. Output Options
3. Run Options
4. Score Function Options
5. Docking Options
6. Loop Modeling Options
7. Packing Options
8. Structual Refinement Options

Appendix

1. Score Types In Rosetta
2. Locations Of Files In Rosetta

Advanced Topics

Developer Guide

1. A Guide to the Structure of the Rosetta Library
2. An Introduction to Important Rosetta Concepts
3. Simple Protocol Walkthrough
4. A Guide to Developing in Rosetta
5. How To Write Your Own Protocols in Rosetta
6. Tips for writing doxygen documentation
7. Coding Guidelines
   • List of things you should check in your code before committing it in to svn
   • Guidelines on Owning pointers usage
   • Option list with description/range/default values
8. How to make mini 'robust' against badly formatted PDBs
9. How to prepare structures for use in Rosetta
10. How To Use Condor in Rosetta
11. Scoring structures using electron density data

Core Tutorial and Reference

1. kinematics
   • AtomTree overview and concepts
   • FoldTree overview and concepts
2. optimization
   • Minimization overview and concepts
3. pack
   • How to use the PackerTask
   • Resfile syntax and conventions
   • How to write new resfile commands
4. scoring
   • How to add a new scoring term
   • Constraints file formats
   • How to score structures using electron density data
5. util
   • Tracer, tool for debug IO
6. fragment
   • core::fragment::picking User's Guide.
   • core::fragment::picking_old User's Guide.
7. io
   • brief summary of atomtree diff format and silent file extraction

Protocol Tutorial and Reference

1. New job distributor README

Numeric Tutorial and Reference

1. Numeric Library page has a (very) brief introduction to the numeric library

Tests Tutorial and Reference

1. Unit test and Performance test Mini Rosetta Documentation
2. Mover test HOWTO
3. Different way to run unit tests
4. How to create and run scientific tests

Important Namespaces

1. core
   • core::pose
   • core::chemical
2. utility
3. numeric

Important Classes

1. core::pose::Pose
2. core::conformation::Residue
3. core::chemical::ResidueType