On Wed, Aug 4, 2010 at 10:43 AM, Joseph Noel
Thanks Pavel! I will wait and see what Ralf says regarding defining the symmetry operator. If I am using the GUI for phenix.refine should I create a new file with the bond definition you mention and include it as one of the starting files or should I edit the Refine_*.eff file that gets created and insert it somewhere there?
Either of these should work, but there is also a third option: open Settings menu, select "Geometry restraints", then "Edit geometry restraints", and define custom bonds there. (FYI, if you're going to edit the .eff file directly, you want to select "Edit parameters and run" when clicking the run button - not sure if that's what you meant, but other methods involving the GUI tend to not work, which has been a source of confusion for some command-line users.) -Nat