[phenixbb] Appropriate number of reflections for FreeR

[Pavel Afonine]

Typically, 10% of *randomly* (as opposed to systematically) missing data 
doesn't change maps visibly. Of course there are corner cases where even 
a few missing reflections make difference..
Pavel

On 11/2/13 9:19 AM, Nathaniel Echols wrote:
> What about the effect of missing data on maps used in real-space refinement?
>
> -Nat
>
>
> On Fri, Nov 1, 2013 at 11:29 PM, Pavel Afonine <pafonine at lbl.gov
> <mailto: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>
>         <mailto: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>
>              <mailto: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
>
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>