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
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
_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb