[phenixbb] Whic mtz file to use and parameters for phenix.refine (GUI) to set?

Nathaniel Echols nechols at lbl.gov
Mon Jul 19 06:41:22 PDT 2010

On Mon, Jul 19, 2010 at 6:15 AM, Hermella Woldemdihin <hermifi at yahoo.com>wrote:

> I am new to phenix.refine. I'm using the graphical interface.
> I hav processed my dfiffraction data and used Phaser MR for molecular
> replacement.
> And I goyt a result: a solution pdb file and the associated mtz file.
> 1. So I use the mtz file from this Phaser MR solution or the original file
> from my data
> processing in phenix.refine?

The original file.  I think Phaser outputs anisotropy-corrected data, and it
may be at reduced resolution depending on how you run it.

2. I have set parameters for phenix.refine like this:
> Is there other settings for the parameter which I should do for a better
> result?
> PDB data: my solution from Phaser MR
> XRAY DATA= ????
> Simulated Annealing=1000
> Update waters
> Refine Target weights: Wxc=0.8 Wxu=1.6
> Cycles=5
> Fix rotamers
> Fix bad side chains

Unless you've already run refinement with this dataset and are confident
about the weights, I would not set wxc and wxu initially; automatic weight
optimization is a better place to start.  Otherwise, which refinement
settings are most appropriate depends on the resolution and starting R-free.
 As Frederic points out, rigid-body refinement may be a good idea at this
stage.  (By the way, you list both "Fix rotamers" and "Fix bad side chains",
but these are the same thing - unless I mislabeled something in the GUI...)

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