Back to Main
PHENIX (Python-based Hierarchical Environment for INtegrated Xtallography) is a new program that provides tools for automated structure solution by X-ray crystallography. It is being developed as part of an international collaboration, funded by the National Institute for General Medical Sciences (NIH). The principal investigators are:
Paul Adams (Lawrence Berkeley Laboratory)
Tom Terwilliger and Li-Wei Hung (Los Alamos National Laboratory)
Randy Read (University of Cambridge, U.K.)
Tom Ioerger and Jim Sacchettini (Texas A&M University)
The PHENIX software provides algorithms to proceed from reduced intensity data to a refined molecular model, and facilitate structure solution for both the novice and expert crystallographer. Further details can be found at the PHENIX website:
http://www.phenix-online.org
A number of publications describing PHENIX can be found at:
http://www.phenix-online.org/papers/
If you use PHENIX to solve a structure please cite this publication:
PHENIX: building new software for automated crystallographic structure determination P.D. Adams, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter and T.C. Terwilliger. Acta Cryst. D58, 1948-1954 (2002)
You should obtain the latest distribution of PHENIX including the binary bundles for your machine architectures. Unpack the tar file:
% tar xvf phenix-installer-<version>-<platform>.tar
Change to the installer directory:
% cd phenix-installer-1.1a
To install:
% ./install [will install in /usr/local by default,
requires root permissions]
% ./install --prefix=<directory> [will install in <directory>]
Installation of the binary version of PHENIX requires no compilation, only the generation of some data files, so you will probably have to wait about 30 minutes for the installation to complete (depending on the performance of your installation platform).
Currently, the following Redhat Linux platforms are tested, and therefore supported for the distribution:
Redhat versions prior to 8.0 are not supported.
PHENIX should install on other Linux platforms such as Mandrake, or SuSe. However, the Linux kernel will need to be 2.4.20-18.8 or later, with glibc 2.2.93-5 or later, for PHENIX to run.
Currently, the following other Unix platforms are tested, and therefore supported for the distribution:
In the future, SGI Irix, Windows and MacOS-X will be supported.
For license information please see LICENSE file.
For source of components see SOURCES.
Once you have successfully installed PHENIX, to set up your environment please source the phenix_env file in the phenix installation directory (for example):
% source /usr/local/phenix-1.1a/phenix_env
To run jobs remotely, you need to source the phenix_env in the .cshrc (or equivalent) file.
You can find documentation in the PHENIX GUI (under the Help menu). Alternatively, you can use a web browser to view the documentation supplied with PHENIX, by typing:
% phenix.doc
If this doesn't work then you can point a web browser to your PHENIX installation (for example):
% mozilla /usr/local/phenix-1.1a/doc/index.html
Back to Main