Hi, Jobi, 

I think you may need to change the coot path for Phenix. 

It can be done easily through the GUI, File, preferences, Coot Path: 

Best, 

Zheng


On Thu, Dec 5, 2013 at 3:36 AM, Nathaniel Echols <nechols@lbl.gov> wrote:
On Tue, Dec 3, 2013 at 10:54 PM, Jobichen Chacko <jobichenc@gmail.com> wrote:
I recently upgraded to latest version of coot (version0.7.2). When I
try to do the Real space refine zone option, coot is giving the
following complaint (Refinement setup failure. Failed to find
restraints for PROLYSILE).

But it works fine when I open coot separately from a terminal and read
the pdb and mtz file.

Phenix will instruct Coot to load user-provided CIF files, but I didn't think we interfere with Coot's own restraints otherwise.  Can you please send me the console output of Coot a) when launched from Phenix b) when launched by itself?

-Nat

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