[phenixbb] on Phenix refine

[Nathaniel Echols]

On Mon, Nov 21, 2011 at 2:21 PM, Dialing Pretty <hdc123hdc123 at yahoo.com> wrote:
> By rigid body refinement (Phenix) with a searching model (Model A) I got a
> output PDB (Model B) and output mtz file (MTZ FILE) of a diffraction
> dataset. In Coot I modify the Model B and saved it as Model C. I want to
> continue  to optimize Model C by Phenix.refine.
>
> In the GUI interface of Phenix.refine input, of course I need to input the
> MTZ FILE, but for the PDB file, should I only input the PDB of Model C, or
> all of Model A, Model B and Model C? If I input all of Model A, Model B and
> ModeC, then how does Phenix.refine distinguish the function of each PDB
> model?

You only need to input the latest model.  The exception is when you
are working with low-resolution data (worse than about 2.8 Angstrom)
and want to use a higher-resolution structure as a reference model,
but this is completely optional (and sometimes unnecessary).

-Nat