[phenixbb] Does PHENIX exclude Rfree reflections in maps?

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Sep 30 17:32:13 PDT 2009

Hi Pavel and Joe,

I'm glad you put that option in, Pavel.  However for model-building it is
not so straightforward. Normally we are building into density-modified
maps. Density modification works poorly when a significant set of
reflections is excluded, so this becomes impractical. We could exclude
those reflections in the map only, but they will have been used in density
modification so they are no longer truly free.  I don't have a good
solution for that.

I am guessing that for model-building, the free R is hardly affected,
compared to refinement against the map, though I haven't tested this.

All the best,
Tom T

>> 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
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