Python-based Hierarchical ENvironment for Integrated Xtallography
Documentation Home

Running PHENIX

Command Line Interface

Different user interfaces are required depending on the needs of a diverse user community. There are currently three different user interfaces, each described below.

Command Line Interface

For a number of applications a command-line interface is most effective. This is particularly the case when rapid results are required, such as data quality assessment and twinning analysis, or substructure solution at the synchrotron beam line. Tools that facilitate the ease of use at the early stages of structure solution, such as data analyses (phenix.xtriage), substructure solution (phenix.hyss) and reflection file manipulations such as the generation of a test set, reindexing and merging of data (phenix.reflection_file_converter) are available via simple command line interfaces. Another major application that is controlled via the command line interface is phenix.refine. To illustrate the command line interface, the command used to run the program that carries out a data quality and twinning analyses is:

phenix.xtriage [options]
Further options can be given on the command line, or can be specified via a parameter file:
phenix.xtriage my_parameters.def
A similar interface is used for macromolecular refinement:
phenix.refine my_model.pdb my_data.mtz

Although SCALEPACK and MTZ formats are indicated in the above example, reflection file formats such as D*TREK, CNS/XPLOR or SHELX can be used, as the format is detected automatically.

Help for all command line applications can be obtained by use of the flag --help :

phenix.refine --help
There are also many other command line tools (described in detail elsewhere in this documentation). 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 start of the list of commands that begin with
phenix.autobuild      phenix.automr         phenix.autosol
phenix.autobuild_1.3  phenix.automr_1.3     phenix.autosol_1.3
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).


To run the PHENIX Graphical Interface:

% phenix &
Please see the other documentation files to get more details about the PHENIX GUI.


The decision-making in strategies is local, with decisions being made at the end of each task to determine the next path in the network. Crystallographers typically make decisions in a very similar way during structure solution; a program is run, the outputs manually inspected and a decision made about the next step in the process. By contrast, a wizard provides a user interface that can make more global decisions, by considering all of the available information at each step in the process. Wizards can be run from both the command line and the PHENIX GUI. Details on wizards can be found in: