Dear Nathaniel,

Thank you for your reply.

I am trying to run it with simulated annealing refinement. Because I am a new user I might have made some mistakes, but the error message popped up during the second cycle of twinning refinement at the beginning.

For the R-free, I agree that I could use the data generated by phenix.refine (because I generate the R-free in phenix.refine).

Sincerely,

Chen

On Mon, Apr 21, 2014 at 3:45 PM, Nathaniel Echols <nechols@lbl.gov> wrote:

On Mon, Apr 21, 2014 at 12:39 PM, Chen Zhao <c.zhao@yale.edu> wrote:

But through the GUI, the program can run smoothly with twin refinement.

It's not clear what you mean - the operation of the program should be no different on the command line versus the GUI. �All that matters is what method you use for the omit map preparation. �The default "simple" method ("iterative" might be a better name for it) is apparently incompatible with a twin law. � The "refine" or "anneal" methods will work fine with a twin law, but are far slower even if you have a big cluster. �What exactly are you trying to run?

My only problem with the GUI is that I cannot find the the place to generate R-free flags in the highest symmetry for twinning refinement.

The lattice symmetry option is already enabled by default. �However, if you already have R-free flags defined, it will not generate a new set; for this, you need to use the reflection file editor (GUI->Reflection tools). �However, if you're at the stage of generating a composite omit map, this usually means that you've already done refinement and have R-free flags already - in which case calculating maps or performing further refinement with a different test set is a bad idea. �If you want to change test sets in the middle of the refinement process, you should first do some simulated annealing refinement to un-bias R-free.

-Nat