[phenixbb] Phenix composite omit map

Nathaniel Echols nechols at lbl.gov
Mon Apr 21 12:45:58 PDT 2014

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.

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