It is helpful to have an idea about the directory structure in Phenix so that you can find Phenix tools that you want to use in your programming. This page describes the overall setup.
The top-level Phenix directory is typically located in the directory referred to by the environmental variable
$PHENIX. It contains the following files and folders:
Since all Phenix code is in the
modules directory, the location of a particular file is often referred to relative to this modules directory. For example, as
Within the modules directory are a big set of directories for different modules of Phenix (including cctbx_project, the computational crystallography project):
Several directories are of particular interest:
The phenix module has the following subdirectories:
Often, you will add to existing files or create new files within the existing directory structure. If you start a completely new area of Phenix programming, you would create a new directory structure to hold it. Before creating a new directory structure, it should be discussed among Phenix group members.
The phenix/phenix/ subdirectory is further subdivided into:
There are two special subdirectories in the phenix/phenix directory: