Also, don't forget to add ncs.find_automatically=false
I have run many runs with NCS defined with proper syntax, just to be overwritten by NCS derived automatically by phenix, until I realized what was happening. I have always thought that if I define the NCS restraints, phenix should follow it, not try to "improve" upon it. What is the reason for this default behavior?
Thanks very much for the feedback. I'm thinking setting up the NCS restraints really should be part of the "ready-set" stage, done once, as an explicit step, strongly suggesting review of the results before continuing. With the new GUI tools Nat is working on, we will be in a better position to re-organize the functionality in and around phenix.refine, to reduce the potential for confusion in the future. Ralf