[phenixbb] Reducing R/R-free

Pavel Afonine pafonine at lbl.gov
Mon Jan 12 14:55:42 PST 2015


George,

it's difficult to tell without looking at models before and after 
modifications, and data. Did refinement converge (do you need to run 
more cycles)? Are weights optimal? etc etc...

Pavel


On 1/12/15 1:10 PM, George Devaniranjan wrote:
> 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 
> <mailto: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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>>
>>
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