[phenixbb] Reducing R/R-free

George Devaniranjan devaniranjan at gmail.com
Mon Jan 12 13:10:07 PST 2015


I have a related question to this.

I have a PDB structure (not mine I downloaded it from RCSB) and wondered if
I could improve some of the problems in it using Phenix.

The Rw/R-free for the downloaded structure was 0.1279/0.1390

After I improved (or so I think so) the Rw/R-free is 0.1326/0.1440

The structure I have seems better in many aspects including its fit to the
map (COOT/RSCC) + RMS Angles

I am a little confused whether to accept it or think I might have to do
more validation checks as something has gone wrong?

Thank you,
George


On Mon, Jan 12, 2015 at 4:01 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  Hi Tim,
>
> it is a shame that I can't remember that particular paper where I think
> Randy Read or Axel Brunger have demonstrated that phase error and Rfree are
> well correlated. So if you get best Rwork and Rfree chances are you also
> get best map too.
>
> All the best,
> Pavel
>
>
> On 1/12/15 3:54 AM, Tim Gruene wrote:
>
> Dear George,
>
> what are the reasons why are you trying to reduce the R/Rfree instead of
> producing the best possible map?
>
> Best,
> Tim
>
> On 01/11/2015 11:24 PM, George D wrote:
>
>  Hi Phenix users,
>
> I was looking at the phenix-refine manual and it mentions running
>
> optimize_mask=true
>
> optimize_xyz_weight=true
>
> optimize_adp_weight=true
>
>
> I was wondering what else I could try to bring the Rw/Rf down by 1-2%
> if possible, just wondering if there are any other strategies I could
> try.
>
>
> Thank you,
>
> George
>
>
>
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