[phenixbb] no mtz file

Nathaniel Echols NEchols at lbl.gov
Sun Nov 22 12:09:29 PST 2009

On Nov 22, 2009, at 11:50 AM, Maia Cherney wrote:
> Hi Pavel,
> I just installed the phenix-1.5-2 version and got some problems using my 
> previous .def file (from 1.4-4 version).
> The result of the refinement was a new pdb file, but no mtz file with 
> map coefficients. The error message:
> Sorry: Duplicate mtz_label_amplitudes:FOFCWT
> I guess, I need to remove some lines from my old .def in a new 
> refinement run, but can I get the mtz without rerunning the
> refinement (it takes a very long time to rerun it with tls etc.)

Two methods:

1) Run phenix.create_maps (or click "Create Maps" in the GUI).  Note that by default, this program does not automatically fill missing F(obs) with F(calc) in the standard weighted difference maps, but phenix.refine does.  You'll probably want to turn this on.

2) phenix.model_vs_data coords.pdb data.mtz --map=2mFo-DFc_filled
    phenix.model_vs_data coords.pdb data.mtz --map=mFo-DFc_filled
("_filled" is optional)


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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