I usually have a shortcut on my windows Desktop that targets C:\Windows\System32\cmd.exe /k <path-to-phenix-build-folder>\setpaths.bat From that command prompt you then have all the phenix command line tools available. Rob On 2014-06-09 19:17, Nathaniel Echols wrote:

On Sat, Jun 7, 2014 at 10:24 PM, 李翔 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-1.9-1692Phenix-1.9-1692_buildsetpaths.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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb