[phenixbb] Does PHENIX exclude Rfree reflections in maps?

Pavel Afonine PAfonine at lbl.gov
Wed Sep 30 14:29:00 PDT 2009

Hi Joe, hi Tom,

until recently, all reflections (work and test) were used in map 
calculation. When I added a real-space refinement option to 
phenix.refine I spent a day thinking hard about why Rfree was almost 
always equal to Rwork after real-space refinement, until I realized that 
I have to exclude test reflections from map calculation, and that fixed 
the problem.

I think it depends on the task:

- for things like real-space refinement (where the map is heavily used) 
or automated model building, the test reflections have to be excluded 
from map calculation;

- for catching a tiny detail (looking at weak ligand density = slight 
map use) or fixing a few side chains, all reflections should be used, 
since 10% of data put aside may sometime significantly affect map quality.


On 9/30/09 11:51 AM, Tom Terwilliger wrote:
> Hi Joe,
> In PHENIX R-free reflections are included in your maps.
> All the best,
> Tom T
> On Sep 30, 2009, at 12:47 PM, Joe Krahn wrote:
>> Does PHENIX exclude R-free reflections when computing maps? IMHO, it is
>> bad to use test reflections in maps, or anywhere else other than
>> computing R-free, but opinions vary. If some people still want test
>> reflections in maps, maybe it could be an option.
>> Thanks,
>> Joe Krahn

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