Phaser 2.3.0 (CCP4: Supported Program)

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

This is the documentation for Phaser 2.3. There are some changes between this version and previous versions so input scripts may need editing.

More extensive documentation can be found on the Phaser Wiki site.

Keywords

Phaser can be run using CCP4-style keyword input from a pre-compiled executable

Command Line Arguments

When run from the executable, phaser accepts some command line arguements

Keyword Modes

The different functions that Phaser can perform and the keywords relevant for each mode

Keywords

Detailed descriptions of the keywords

Keyword Example Scripts

Copy and edit to start using Phaser from keyword input

Python

Phaser can be scripted using python.

Python Run-Jobs

How to run Phaser from python and the functions relevant for each Run-Job

Python Functions

Detailed descriptions of the functions

Python Example Scripts

Copy and edit to start using Phaser from python

XML

There is XML output available for developers writing automation scripts.
Please contact us for more information or XML output requests.

XML

References

J. Appl. Cryst. (2007). 40, 658-674. Phaser crystallographic software. A. J. McCoy, R. W. Grosse-Kunstleve, P. D. Adams, M. D. Winn, L.C. Storoni and R.J. Read.

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.