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Chapter 0

Description of the BUSTER manual

Copyright    © 1995-2008 by Global Phasing Limited
 
  All rights reserved.
 
  This software is proprietary to and embodies the confidential technology of Global Phasing Limited (GPhL). Possession, use, duplication or dissemination of the software is authorised only pursuant to a valid written licence from GPhL.
 
Contact buster-develop@GlobalPhasing.com


Contents


Overview

This manual describes how to use BUSTER, a software system for crystallographic structure determination by Bayesian statistical methods. It does not deal with more technical tasks such as installing BUSTER on a computer: for this, please refer to the Installation Guide (for Site Administrators only).

The manual consists of five chapters and four Appendices:

  1. Chapter 1 : Basic notions about BUSTER The purpose of BUSTER and the statistical principles it implements.

  2. Chapter 2 :Present Capabilities of BUSTER This offers a survey of the types of problems BUSTER can currently tackle and, for each problem type, a description of the prerequisite information.

  3. Chapter 3 : The BUSTER Control Panel and environment Explains how to deal with a browser as a Graphical User Interface; explains what CCP4, the MTZ format and the TNT program are; and describes the first interface pages you will have to deal with : the BUSTER Control Panel (to access all the functionalities of BUSTER) and the Preferences page (to tailor certain BUSTER and helper applications parameters to your requirements and tastes).

  4. Chapter 4 : Preparing the BUSTER input The use of the graphical interface is explained. Each field of the input form is described. Parameter choices for typical problems are suggested.

  5. Chapter 5 : Browsing the BUSTER output The use of the graphical interface for examining the results produced by BUSTER is explained. The main categories of results are described step by step.

  6. FAQ : Troubleshooting and FAQ Checks for possible troubles are indicated, together with the actions to be taken.

  7. Appendix A : NCS in TNT A simplified description of TNT Non-Crystallographic Symmetry handling

  8. Appendix B : Real-space distributions in BUSTER A description of BUSTER algorithms for the generation of low-resolution distributions to model missing atoms.

  9. Appendix C : TNT scripts used by BUSTER A description of BUFFET scripts that run TNT programs during partial structure refinement.


Tutorials

Once you have browsed through the textual material contained in these chapters, you are advised to browse the tutorials to learn by example.

Feedback

BUSTER is a rapidly evolving program. Please report all infelicities and bugs to the authors.

About the Authors

The writing of BUSTER was started in 1989 by Gérard Bricogne, with subsequent contributions from John Irwin (1994-1998), Pietro Roversi (1995-2003), Clemens Vonrhein (since 1998), Eric Blanc (1998-2003), Wlodek Paciorek (since 1998), ClAuS Flensburg (since 2000) and Oliver Smart (since 2004). The graphical interface BUFFET was initially written by John Irwin with contributions from all the other people mentioned above, plus Eric de La Fortelle.

Citation

The use of BUSTER should be acknowledged in all publications or reports mentioning results obtained by means of it, and the following references should be cited:

Bricogne, G. (1993). Direct Phase Determination by Entropy Maximisation and Likelihood Ranking: Status Report and Perspectives. Acta Cryst. D49, 37-60.

Bricogne, G. (1997). The Bayesian Statistical Viewpoint on Structure Determination: Basic Concepts and Examples, in Methods in Enzymology, 276A, 361-423. C.W. Carter & R.M. Sweet, eds.

Roversi, P., Blanc, E., Vonrhein, C., Evans, G. and Bricogne, G. (2000). Modelling prior distributions of atoms for Macromolecular Refinement and Completion. Acta Cryst., D56, 1313-1323.

Blanc, E., Roversi, P., Vonrhein, C., Flensburg, C., Lea, S. M. and Bricogne, G. (2004). Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. Acta Cryst., D60, 2210-2221.

Forthcoming publications on BUSTER will be listed here in due course.


Last modification: 21.07.09