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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 (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-<version>
To install:
% ./install [will install in /usr/local/phenix-<version> by default,
requires root permissions]
% ./install --prefix=<directory> [will make <directory>/phenix-<version> and install there]
Note: <directory> must be a absolute path (i.e. starts with a /). A relative path starting with ../ will not work correctly.
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.
There are 4 different Linux installations available, based on the version of the kernel (2.4 or 2.6) and the CPU type (ix86 or x86_64). If it isn't clear which you need then type this command on the machine in question:
% uname -rm
The first item is the kernel version, the second is the machine hardware. Please download the appropriate installer based on this table:
| Hardware | Kernel | |
| 2.4 | 2.6 | |
| ix86 | intel-linux-2.4 | intel-linux-2.6 |
| x86_64 | intel-linux-2.4-x86_64 | intel-linux-2.6-x86_64 |
Currently, the following other platforms are being ported, and therefore supported for the distribution:
For license information please see LICENSE file.
For source of components see SOURCES.
For the complete PHENIX installation you will need approximately 1.5GB of disk space.
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-<version>/phenix_env [csh/tcsh users]
or
% . /usr/local/phenix-<version>/phenix_env.sh [sh/bash users]
To run jobs remotely, you need to source the phenix_env in the .cshrc (or equivalent) file.
To run PHENIX:
% phenix &
There are also many command line tools (described in the documentation). Examples are:
phenix.refine mmtbx.xtriage iotbx.reflection_statistics textal.build phenix.runWizard
If you use a shell with command completion, you can type the first part of a command, hit the command list key (<ctrl>-D in tcsh) and see a list of the available commands. For example, this is the list of commands that begin with mmtbx:
mmtbx.fest mmtbx.fest_1.24.1b mmtbx.geometry_minimization mmtbx.geometry_minimization_1.24.1b mmtbx.monomer_library.comp_as_motif mmtbx.monomer_library.comp_as_motif_1.24.1b mmtbx.pdb_interpretation mmtbx.pdb_interpretation_1.24.1b mmtbx.python mmtbx.python_1.24.1b mmtbx.show_build_path mmtbx.show_build_path_1.24.1b mmtbx.show_dist_paths mmtbx.show_dist_paths_1.24.1b mmtbx.xtriage mmtbx.xtriage_1.24.1b
Note: all commands have their regular name and name qualified with the version. You can always use the version-qualified name to ensure which version of a command you are using (in case you have multiple versions of PHENIX or related applications installed).
You can also run the solve, resolve and resolve_pattern programs from the command line, for example to run solve:
% phenix.solve [--giant|--huge|--extra_huge] < command-file > log-file
The same syntax applies for phenix.resolve and phenix.resolve_pattern.
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-<version>/doc/index.html
or:
% mozilla $PHENIX/doc/index.html
You can also visit the PHENIX Wiki, which is being regularly updated:
http://www.phenix-online.org/phenix_wiki
For license information please see the LICENSE file.
For the source of the components see SOURCES.