Thanks to Nigel and Nat for their help. The link description did the trick. 

Mario Sanches

On Mon, Apr 2, 2012 at 12:49 PM, Nathaniel Echols <nechols@lbl.gov> wrote:
On Mon, Apr 2, 2012 at 9:09 AM, Mario Sanches <mariosan@gmail.com> wrote:
> "phenix.ligand_linking"  is not an option with my current installation
> (PHENIX version dev-1021). I have "phenix.ligand_identification"  and "
> phenix.ligandfit" .

It's not shown by default.  Open the Preferences, go to the "General"
section, and check "Enable alpha-test programs and features", then
close and restart the GUI.  The ligand linking program will be listed
in the Refinement category.

-Nat
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--
Mario Sanches
Postdoctoral Researcher
Samuel Lunenfeld Research Institute
Mount Sinai Hospital
600 University Ave
Toronto - Ontario
Canada
M5G 1X5
http://ca.linkedin.com/in/mariosanches