[phenixbb] Implementation of French & Wilson data correction?

Keitaro Yamashita yamashita at castor.sci.hokudai.ac.jp
Mon Feb 28 15:54:46 PST 2011

Dear PHENIX developers,

A little off-topic, but will phenix implement MLI (maximum likelihood
intensity target)?

I heard that MLI target gives a good result because MLI handles
negative intensities naturally.


2011/3/1 Nathaniel Echols <nechols at lbl.gov>:
> On Mon, Feb 28, 2011 at 8:34 AM, Ed Pozharski <epozh001 at umaryland.edu> wrote:
>> Also beware that phenix used to ignore input Fo's as long as the
>> intensities are still present (this may have changed though).  So if you
>> want it to use the Fo's that you have supplied, make sure that
>> intensities are deleted from the input mtz-file.
> This hasn't changed - at least not yet.  (I'm not sure what we decided
> to do here.)  The plan is for phenix.refine (and other apps) to
> automatically run the procedure when intensities are used, skipping an
> extra conversion step.  Right now it's optional, pending some changes
> to the output MTZ file, so it needs an extra parameter:
> phenix.refine i_obs.mtz model.pdb french_wilson=True
> (It isn't obvious what to do in the GUI, but I'll fix that today.)
> -Nat
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