On Fri, Jun 25, 2010 at 3:42 PM, Subhangi Ghosh <subhangi.g@gmail.com> wrote:
/apps/coot/current/bin/coot-real --version
0.6.2-pre-1 (revision 2981)  [with guile 1.6.8 embedded]

This is the problem: it doesn't have Python.  If you download Coot from Paul Emsley's web page, you usually need one of the packages with "python" in the file name.  If "coot --version" does not print any mention of Python, it won't work with Phenix.

I guess I need to add this to the FAQ list.

-Nat