One point which I don't understand is how can someone compare the two
different programs when they don't use the same numbers for
xray:geometry terms? Taking the default settings for a given
resolution might not be enough.. !
On Tue, Mar 4, 2008 at 7:58 PM, Savvas Savvides
<[log in to unmask]> wrote:
> Hi Yang
> how many reflections do you have in your test-set for calculating
> R-free? Too few reflections, typically less than 500, may not
> constitute a statistically robust cross-validation data set, and thus may
> lead to fluctuations in R-free plus a tendency for R-free to increase
> as a function of refinement cycle. Some of the early
> publications from Axel Brunger on crystallographic cross-validation
> address the need for enough reflections (>500) in the test-set. In
> addition, the presence of even a handful of strong but inaccurately
> measured/integrated low-resolution reflections in a limited test-set
> can aggravate abnormal behavior in R-free.
>
> Best wishes
> Savvas
>
>
> toQuoting yang li <[log in to unmask]>:
>
> > Dear All,
> > I have post a similar question about CNS and refmac before, now in
> > another structure I met a similar problem. I have an almost finished
> > structure, the Rfree of which
> > is about 0.28 by refmac. Then I used phenix to refine it, below is the
> > result:
> > REMARK ******************** REFINEMENT SUMMARY: QUICK FACTS
> > *******************
> > REMARK Start: r_work = 0.1970 r_free = 0.2892 bonds = 0.006 angles = 1.213
> > REMARK Final: r_work = 0.1917 r_free = 0.2617 bonds = 0.008 angles = 1.374
> > REMARK
> > ************************************************************************
> > Since the map from phenix couldnot be opened by coot directly--or I
> > donnot know how to--I used refmac to get a mtz map file. But I found that at
> > the first several cycle of
> > refmac the Rfree decreased, then both the R and Rfree values continued
> > increasing and FOM decreasing.
> > The best R/Rfree/FOM during the refinement is
> >
> > -----------------------------------------------------------------------------
> > Overall R factor = 0.1932
> > Free R factor = 0.2513
> > Overall figure of merit = 0.8168
> > -----------------------------------------------------------------------------
> > And after 40 cycles the final result is:
> > -----------------------------------------------------------------------------
> > Overall R factor = 0.2008
> > Free R factor = 0.2772
> > Overall figure of merit = 0.7902
> > -----------------------------------------------------------------------------
> > The values looks like keep going up if increase the cycles. Then which
> > value should I take as the final result? The phenix or the best Refmac
> > result or I have to take a converged
> > value from refmac?
> >
>
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