| SHARP/autoSHARP User Manual | previous next |
| Chapter 0 |
| Copyright | © 2001-2006 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. | |
| Documentation | (2001-2006) Clemens Vonrhein |
| (1995-1997) Eric de La Fortelle | |
| Contact | sharp-develop@GlobalPhasing.com |
If you are just learning crystallography, this manual will guide you from the time you obtain your MIR(AS), SIR(AS), SAD or MAD data all the way to an electron density map, from which (hopefully) you will be able to build an atomic model of your molecule. Some new terms and ideas, especially concerning statistics, may sound unfamiliar: the glossary is there to remove some of the mystery.
If you are an experienced crystallographer, you will already be familiar with many of the ideas in SHARP. You should be aware, however, that SHARP differs from classical heavy atom refinement and phasing programs in some fundamental ways. It can be seen as a consolidation of the traditional isomorphous phasing techniques within the single, consistent framework of likelihood testing in Bayesian statistics.
Whatever your background, you do not need to be a computer programmer, and you do not need to know a lot of UNIX to read this manual or to use SHARP or autoSHARP.
This manual will not deal with more technical aspects such as installing SHARP/autoSHARP on a computer. For this, please refer to the "Installation guide" (available on-line at www.globalphasing.com or as part of the distribution locally).
| Chapter 2 : |
What SHARP/autoSHARP can do |
| This offers a survey of all the types of problem SHARP/autoSHARP can be used to tackle. It also describes what SHARP/autoSHARP cannot do (or at least not yet!). For each problem type, the prerequisite information is given. It gives an overview of some of the classical problems of phasing heavy-atom datasets. Of particular interest are MAD, MIR(AS), SIR(AS) and SAD datasets. The emphasis here is on recipes which are general enough to be adapted, yet specific enough so you can see step by step how to proceed. | |
| Chapter 3 : |
The environment of SHARP |
| Gives the basics of how to deal with a browser as a Graphical User Interface, explains what CCP4 and the MTZ format are, and describes the very first interface pages you will have to deal with: the SHARP Control Panel (to access all the functionalities of SHARP) and the Preferences page (to tune SHARP to your needs and taste). | |
| Chapter 4 : |
How to tell SHARP what to do |
| 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 : |
What SHARP is telling you |
| The use of the graphical interface for examining the results produced by SHARP is explained. The results are explained step by step. Recipes for diagnosing the results and modifying the input are described. | |
| Chapter 6 : | When trouble strikes |
| Suggestions for dealing with errors are given. Many problems have straightforward solutions, others are not so easy to diagnose. Strategies for diagnosing problems are proposed. | |
| Appendix One : |
What can I do with results from SHARP? |
| This part is about converting results such as electron density maps, atomic coordinates and other things into formats that can be used by other common crystallographic programs. | |
| Appendix Two : |
How to use SHARP under UNIX |
| If for some reason the graphical user interface is unsuitable or unavailable, this section shows you how to do everything in UNIX. | |
| Appendix Three : |
Detailed description of the Sharp INput file |
| If you want to understand what information is in the SHARP input file, or if you want to use some features not (yet) supported by the interface, a description of the various keywords is given. | |
| References : | Background about SHARP and autoSHARP |
| Glossary : | Some terminology explained |