[[ https://phenix-online.org/ | Phenix Home ]]
====== Installation ======
  * Uncompress the package, enter into the folder and run
<code>
./install --prefix=/home/usr/share
</code>

  * For Ubuntu server, you may need to add en_GB into system ([[https://askubuntu.com/questions/76013/how-do-i-add-locale-to-ubuntu-server | ref]])
<code>
sudo locale-gen en_GB
#sudo update-locale  # this line may not be required
</code>

====== Benchmark ======
  * On rabi; 1UBQ; phenix.fmodel
    * fft: 3.3s (time phenix.fmodel 1UBQ.pdb 1ubq-sf.mtz format=cns algorithm=fft file_name=fft.hkl)
    * direct: 5.1s (time phenix.fmodel 1UBQ.pdb 1ubq-sf.mtz format=cns algorithm=direct file_name=direct.hk)

====== Install additonal python packages for Phenix ======
  * openopt: just link /home/yxue/codelib/pypkg/openopt to /home/usr/share/phenix-1.12-2829/base/lib/python2.7/site-packages
  * scipy (note: build-in numpy is 1.81, higher version of scipy is not recommended)
<code>
cd /home/usr/share/phenix-1.12-2829/base/bin
phenix.python ./pip install scipy==0.14.1
</code>

====== Reference ======
  * [[http://www.phenix-online.org/documentation/glossary.htm | Glossary of X-ray Crystallography]]
  * http://www.ccp4.ac.uk/ccp4bin/viewcvs/cctbx/cctbx_sources/iotbx/iotbx/mtz/Attic/writer.py?rev=1.1.1.1&content-type=text/vnd.viewcvs-markup