[phenixbb] Appropriate number of reflections for FreeR
pafonine at lbl.gov
Sat Nov 2 21:01:23 PDT 2013
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..
On 11/2/13 9:19 AM, Nathaniel Echols wrote:
> 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
> <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.
> 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
> set, I could have better data/parameters ratio. But this may
> not make
> much difference.
> Best, and have a great weekend.
> 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
> 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
> 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
> 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
> maybe you simply need to run more cycles of refinement with
> 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
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