[phenixbb] Appropriate number of reflections for FreeR

Nathaniel Echols nechols at lbl.gov
Sat Nov 2 09:19:39 PDT 2013

What about the effect of missing data on maps used in real-space refinement?


On Fri, Nov 1, 2013 at 11:29 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Rongjin,
> it's not really waste: test reflections are used not only in Rfree
> calculations, but in ML refinement target parameters estimations, so more
> test reflections you use better these estimations are, and so better
> refinement target is. I still believe that 10% is a good number, and any
> capping the amount of test reflections is NOT necessary: it's not about
> getting a statistically meaningful amount of them overall, but rather it's
> about getting the right spread of them across the whole resolution range,
> and the right amount across all of the thin slices of resolution. I imagine
> by capping them at a particular number you may end up having a couple of
> test reflections per certain bin, which isn't great.
> Pavel
> On 11/1/13 9:18 PM, Rongjin Guan wrote:
>> Thank you, Nat and Pavel. I just came back and saw replies from both of
>> you. Thanks a lot.
>> I have an impression that free_R set has max 2000 reflections, and more
>> importantly, each resolution shell has at least
>> 50 reflections, so I feel >4500 in the free_R set / 150 each shell kind
>> of luxury ("waste"), and if I have more reflections in the refinement
>> set, I could have better data/parameters ratio.  But this may not make
>> much difference.
>> Best, and have a great weekend.
>> Rongjin
>> On Fri, Nov 1, 2013 at 3:18 PM, Nathaniel Echols <nechols at lbl.gov
>> <mailto:nechols at lbl.gov>> wrote:
>>     On Fri, Nov 1, 2013 at 12:13 PM, rjguan <rjguan at gmail.com
>>     <mailto:rjguan at gmail.com>> wrote:
>>      > I solved a structure with 2.7 A Se-Met data set,  with 10%
>>     reflections in free_R set.
>>      > Now I have 2.0 A native data set, and extended free_R to 2.0A.
>>     Now I have >4500 reflections
>>      > in free_R set, each resolution shell has >150 reflections. Kind
>>     of too much, right?
>>     I don't think it's necessarily too much, but it is probably more
>>     than you need.
>>      > What is the best way to reduce the number of reflections in the
>>     free_R set, say, to 5%?
>>      > I already built and refined model at 2.7 A, but do not want to
>>     redo autobuild.
>>     Use the reflection file editor in the GUI - click "More options" in
>>     the section for R-free flags, and check the box "Adjust test set
>>     size to specified fraction".
>>      > Another question: now I have 2.0A data set, shall I use phases
>>     from 2.7 A data in refinement?
>>      > I compared, without using the phases I got lower R/R_free (about
>>     1% lower).
>>      > is this because the 2.0 A data is more accurate than the 2.7 A
>>     phases, and I should continue
>>      > to refine at 2.0A without the phases from 2.7 A data?
>>     It's difficult to reach a conclusion by comparing R-factors alone;
>>     maybe you simply need to run more cycles of refinement with phases
>>     to get the same result.  Alternately, if the crystals aren't truly
>>     isomorphous, the phases may be inappropriate for the native
>>     structure.  But I think with 2.0Å data and a complete model, it is
>>     perfectly valid to use the amplitudes-only ML refinement target.
>>     -Nat
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