[phenixbb] Does PHENIX exclude Rfree reflections in maps?
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
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.
>> Joe Krahn
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