[phenixbb] Phenix composite omit map

Chen Zhao c.zhao at yale.edu
Mon Apr 21 12:58:48 PDT 2014

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).


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

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