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

xaravich ivan xaravich.ivan at gmail.com
Mon Jul 19 17:07:06 PDT 2010

I thought you initially do not add waters until you have a reasonable
density fit with the protein molecules. Is it ok to update waters right from
the begining starting from an MR solution?

On Mon, Jul 19, 2010 at 6:41 AM, Nathaniel Echols <nechols at lbl.gov> wrote:

> 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...)
> -Nat
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