[phenixbb] Does PHENIX exclude Rfree reflections in maps?

Joe Krahn krahn at niehs.nih.gov
Wed Sep 30 17:03:14 PDT 2009

Normally, 5% for R-free is sufficient. Even though you may not do 
real-space refinement with free reflections, external tools can do that 
with the maps written out. I am sure that many people will use it when 
they find that real-space fitting and refinement tools lower R-free, 
unaware that they are cheating.

With 10% test reflection, I suspect that difference maps used to find 
waters can easily find a few noise peaks with significant R-free 
contributions. Those should probably only use unbiased maps.

IMHO, using test reflections for anything but computing R-free should 
always be avoided unless you are unable to proceed using only the 
non-test. Using test reflections is always cheating to some extent, 
although trivial amounts of bias are probably removed during refinement. 
I just think it is better to be very strict about test reflections and 
avoid the possibility of bias.

Exclusion of test reflections ought to be an option. Ideally, deposited 
PDB files should report whether maps used for model building included 
test reflections.


Pavel Afonine wrote:
> 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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