Rosetta 3.1 Release Manual

Rosetta User Guide

3.1 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/rosetta3.1_user_guide
  2. Additional support and documentation is available through the Rosetta Commons Tiki user support web site at: http://www.rosettacommons.org/tiki

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

Applications

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
  1. Applications General Information
  2. Application Instructions
    1. Structure Prediction
    2. Loop Modeling
    3. Fixed Backbone Design
    4. Docking
    5. Rosetta RNA
    6. Scoring Application
    7. Relax Application
    8. Ligand Docking Application
    9. Cluster Application
    10. Idealization Application
    11. Backrub Application
    12. Silent File Tools
    13. Dock Design Parser Application
    14. Membrane ab initio Application
    15. Enforcing symmetry
    16. Scenarios - minor applications targeted at specific problems
    17. Enzyme Design
    18. ddG Prediction

Other Useful Application Commands

Application 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
  9. RNA Structual Modeling Options
  10. RNA Backbone Design Options

Advanced Topics

  1. How Things Work In Rosetta
  2. How To Write Your Own Protocols in Rosetta
  3. Simple Protocol Walkthrough
  4. How To Use Condor in Rosetta
  5. How to run unit test in Rosetta
  6. How to create and run scientific tests
  7. How to use the new job distributor
  8. Scoring structures using electron density data

Appendix

  1. Score Types In Rosetta
  2. Locations Of Files In Rosetta
  3. Application Samples

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