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Python-based Hierarchical ENvironment for Integrated Xtallography
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The PHENIX environment

Setting up your environment
Documentation
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Setting up your environment

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 [sh/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 your .cshrc (or equivalent) file. The following environmental variables should now be defined (here with example values):
  • PHENIX=/usr/local/phenix
  • PHENIX_INSTALLER_DATE=080920070957
  • PHENIX_VERSION=1.3
  • PHENIX_RELEASE_TAG=final
  • PHENIX_ENVIRONMENT=1
  • PHENIX_MTYPE=intel-linux-2.6-x86_64
  • PHENIX_MVERSION=linux
  • PHENIX_USE_MTYPE=intel-linux-2.6-x86_64
It is not necessary (or useful) to define environmental variables for SOLVE/RESOLVE for PHENIX. If you have them set in your environment they are ignored by PHENIX.

Documentation

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 because of browser installation issues then you can point a web browser to the correct location in your PHENIX installation (for example):
% firefox /usr/local/phenix-<version>/doc/index.html
or:
% mozilla $PHENIX/doc/index.html
For license information please see the LICENSE file. For the source of the components see SOURCES.

Help

You can join the PHENIX bulletin board and/or view the archives:

http://www.phenix-online.org/mailman/listinfo/phenixbb
Alternatively you can send email to:
bugs@phenix-online.org  (if you think you've found a bug)
help@phenix-online.org  (if you'd like to ask us questions)