Are there parts of Phenix that can run on a Linux cluster in parallel.
Some wizards can take advantage of multiple CPUs: http://phenix-online.org/documentation/running-wizards.htm Search for "parallel". This doesn't speed up individual tasks, but rather tries the same algorithms with different random seeds in parallel.
I understand that a good part of Phenix is written in python, but there are certainly numerically intensive aspects of structure refinement that could be amenable to parallelization.
If you install from sources and you have gcc 4.3 or higher, the core FFT in refinement will use multiple CPUs. However, there are many other serial calculations. The speedup due to parallel FFTs is hardly noticeable. refinement is notoriously difficult to parallelize. Ralf