Description of the BUSTER manual
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Copyright © 1995-2004 by | Eric Blanc, Pietro Roversi, Clemens
Vonrhein, |
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Gérard Bricogne and the Buster Development Group. |
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All rights reserved.
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Contents
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:
- Chapter 1 : Basic notions about BUSTER The purpose of BUSTER and the statistical principles it
implements.
- 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.
- 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).
- 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.
- 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.
- FAQ : Troubleshooting and FAQ Checks for possible
troubles are indicated, together with the actions to be taken.
- Appendix A : NCS in TNT A
simplified description of TNT
Non-Crystallographic Symmetry handling
- Appendix B : Real-space distributions in BUSTER A description of BUSTER algorithms for the generation of
low-resolution distributions to model missing atoms.
- Appendix C : TNT scripts used by
BUSTER A description of BUFFET scripts that run TNT programs during partial structure refinement.
- Appendix D : Ligand's stereochemistry generation The
script $BDG_home/bin/buster/SmilesGUI is
described here: it is provided for the generation of the
stereochemical restraints in the TNT format, based on a SMILES string.
Once you have browsed through the textual material contained in these
chapters, you are advised to browse the tutorials to learn by example.
BUSTER is a rapidly evolving program. Please
report all infelicities and bugs to the authors.
The writing of BUSTER was started in 1989 by
Gérard Bricogne,
with subsequent contributions from John Irwin (March 1994-September
1998), Pietro Roversi
(since March 1995), Clemens Vonrhein (since
May 1998), Eric Blanc
(June 1998-January 2003), Wlodek Paciorek (since
September 1998), Gwyndaf
Evans (September 1998-December 2003), ClAuS Flensburg (since March
2000), and Richard
Morris (April 2001-October 2002).
The graphical interface BUFFET was initially written by John Irwin, with contributions from
all the other people mentioned above, plus Eric de La Fortelle.
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). Acta Cryst. D49, 37-60. "Direct
Phase Determination by Entropy Maximisation and Likelihood Ranking:
Status Report and Perspectives."
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
Forthcoming publications on BUSTER will be
listed here in due course.
Last modification: 26.01.04