Most of these programs are under restrictive licenses which limit their distribution.  (Coot is the big exception, but it's also even messier to build than Phenix.)  If you want an integrated solution, I urge you to look into joining SBGrid, which takes care of all building/installation issues and will automatically push out updates as they become available.  (This is done on a per-lab basis but I have also seen individual laptops set up as SBgrid clients.)  The disadvantages are (1) it costs money, and (2) it may not always update as quickly as you'd like - looks like they haven't switched to CCP4 6.5 yet but I assume this is what happens when you release software right before Christmas.  But I think it is a huge improvement over the old system where random grad students got stuck handling system administration and arcane software.  It has certainly simplified Phenix support, especially where Rosetta integration is concerned.

(In any case, I have modified the script that auto-detects Coot installations so that it will also check for CCP4 installations on Mac - and pick the newest one containing Coot - so you won't have to enter this in the preferences any more.)

Just be glad you're doing crystallography and not next-gen sequencing - programs like Phenix/CCP4/Coot are vastly simpler to install and use, and there's much less fragmentation of developer efforts (especially since everyone has standardized on Coot for interactive model-building).

-Nat