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Phaser is crystallographic software for phasing macromolecular crystal structures with maximum likelihood techniques. It is available through the Phenix and CCP4 software suites, and directly from the authors.

Most people will not need to read this documentation to solve their structure! To solve a structure by molecular replacement go to Automated Molecular Replacement and copy and edit the command script. Similarly, for SAD phasing, go to Automated Experimental Phasing and copy and edit the command script.

Other good sources of information are found in Frequently Asked Questions and Top Tips

Index to Documentation

1. Introduction
2. Molecular Replacement Modes
3. Experimental Phasing Modes
4. General Modes
5. Keyword Input
6. XML Output (for developers)
7. Python Scripting (for developers)
8. Version History
9. References

1. Introduction

1.1 Modes

1.2 Keyword Index

1.3 Tutorials and Example Files

1.4 Bug Reports

2. Molecular Replacement Modes

2.1 Automated Molecular Replacement

2.2 Has Phaser Solved It?

2.3 What to do in difficult cases

2.4 How to Define Data

2.5 How to Define Models

2.5 How to Define Composition

2.6 How to Define Solutions

2.7 How to Control Output

2.8 How to Select Peaks

2.9 Basic Modes for Molecular Replacement

3. Experimental Phasing Modes

3.1 Automated Experimental Phasing

3.2 How to Define Data

3.3 How to Define Atoms

3.4 How to Control Output

3.5. Basic Modes for Experimental Phasing

5. General Modes

5.1 Anisotropy Correction

5.2 Cell Content Analysis

5.3 Normal Mode Analysis

5. Keyword Input

5.1 Preprocessor

5.2 Syntax of Documentation

5.3 Keywords

6. XML Output (for developers)

7. Python Scripting (for developers)

8. Version History

9. References

Citation: Other references:
  1. Read, R.J. (2001). Pushing the boundaries of molecular replacement with maximum likelihood. Acta Cryst. D57, 1373-1382
  2. Storoni, L.C., McCoy, A.J. & Read, R.J. (2004). Likelihood-enhanced fast rotation functions. Acta Cryst D60, 432-438
  3. McCoy, A.J., Grosse-Kunstleve, R.W., Storoni, L.C. & Read, R.J. (2005). Likelihood-enhanced fast translation functions. Acta Cryst D61, 458-464
  4. McCoy, A.J., Storoni, L.C. and Read, R.J. (2004) Simple algorithm for a maximum-likelihood SAD function Acta Cryst. D60, 1220-1228.