On Sat, Jun 7, 2014 at 10:24 PM, 李翔 <lixiang1642@gmail.com> wrote:

I currently can only access to PHENIX with my laptop which has a Windows system (GUI). I want to run some commands for generating restraints for my models such as:

iotbx.show_distances MR.1.pdb > contacts.distances, phenix.secondary_structure_restraints model.pdb

Is there a way I can run commands in GUI version or can I run the above commands in the GUI version?

Yes, I think you need to run a command like this:

C:\PHENIX-1.9-1692\Phenix-1.9-1692_build\setpaths.bat

which will add the path to all of the command-line executables. This is only partially supported, however - I can't guarantee that all of the commands will actually work on Windows.

-Nat