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 <[email protected]> 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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