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. Pavel. 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