[phenixbb] can phenix.refine output mtz with structure factors not just coeficients?

Pavel Afonine pafonine at lbl.gov
Thu Sep 2 12:18:44 PDT 2010

  Hi Yarrow,

> I am going to deposit a structurein the pdb but noticed that all of the
> mtz files from phenix.refine only contain coeficients and not reflection
> info.

this is expected.

I'm not sure why you need a separate tool to create a data file for PDB 
deposition if you already have that file... The reflection data file 
that contains your Fobs (or Iobs), as well as free-R flags (and may be 
HL coefficients, if available) and that you used to run the refinement 
is what you should deposit to PDB.

> Is it as simple as running another refinement with write_maps = true
> instead of false?

"write_maps = true " will output CNS/X-plor formatted electron density maps.

> Will this right out an mtz with structure factors
> instead of just coeficients.


> Ideally, I would like to create an mtz with structure factors as well as a
> map for CNS.

Regarding an MTZ with structure factors -- see above. For the maps in 
X-plor/CNS format use "write_maps=true" keyword or whatever is 
equivalent in the GUI.

Let me know if you have questions or need help with this.


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