Dear Randy,
Might it be these?
https://doi.org/10.1107/S0907444997013875
https://doi.org/10.1107/S0907444999016868
Best wishes,
Gerard
--
On Mon, Jun 23, 2025 at 03:33:36PM +0000, Randy John Read wrote:
> Hi,
>
> I think it was Ian Tickle who worked out the statistical error in R-free that
> arises from taking different random samples, though I can’t track down the
> publication quickly. Anyway, the take-home from this is that you don’t expect
> all free sets to give the same R-free, and you shouldn’t over-interpret small
> differences in R-free.
>
> Does anyone have the citation for this?
>
> Best wishes,
>
> Randy
>
> > On 23 Jun 2025, at 15:55, Oganesyan, Vaheh
> > <[email protected]> wrote:
> >
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> > WordSection1 {size:8.5in 11.0in; margin:1.0in 1.0in 1.0in 1.0in;}
> > div.WordSection1 {page:WordSection1;} --> Hi all,
> > I’ve spent some time going through different flags for free reflections
> > for (somewhat stupid) reason to get lower Rfree. I made sure all different
> > flags were used only for each of sets of refinement. I wanted to satisfy my
> > inner belief that it doesn’t matter which flag is used (between 0 and 19).
> > To be short: I failed.
> > Free reflections have been chosen “randomly”, no suspicion there. However,
> > there was clear difference at the end. The difference was about 2-3%
> > difference in Rfree value. This tells me that the randomness has some sort
> > of rule, which makes “random” choice not so random. Having found this I
> > also tried to see “a rule” that breaks this randomness, like even numbers,
> > odds, etc. I did not. Because this was only on few cases I won’t even try
> > to connect it to # of molecules per AU, or SG. For each structure (I tried
> > this for 2-3 structures about 10 years ago) it was a different flag.
> > I’m not sure if DCC also is looking through different flags, but at the end
> > it finds the best, making these exercises unnecessary.
> > Sorry, cannot present a case. Was too long ago.
> > Vaheh Oganesyan, Ph.D.<image001.png>R&D | Biologics Engineering
> > One Medimmune Way, Gaithersburg, MD 20878
> > T: 301-398-5851
> > [email protected]
> > From: CCP4 bulletin board <[email protected]> On Behalf Of Randy
> > John Read
> > Sent: Monday, June 23, 2025 10:29 AM
> > To: [email protected]
> > Subject: Re: [ccp4bb] free R in shells
> > Hi Ben,
> >
> > I would be very interested if you have a case where it makes a difference
> > to do this. At one point I was convinced that it had been important when we
> > were working on the structure of a Shiga-like toxin bound to trisaccharide
> > (1bos), with four pentamers in the asymmetric unit. However, Pavel Afonine
> > challenged me to show that the free set was less biased when chosen in
> > shells than when chosen randomly, and even in that relatively extreme case
> > I couldn’t see evidence of it. So it’s probably not worth the bother. Also,
> > if you select the free set randomly, it’s distributed over the same
> > resolutions as the working data, which arguably is important when you’re
> > using it to calibrate the sigma(A) estimates for likelihood targets.
> >
> > Best wishes,
> >
> > Randy
> >
> > > On 23 Jun 2025, at 12:35, Ben Bax <[email protected]> wrote:
> > >
> > > Hi,
> > > How do you select R-free in shells with CCP4?
> > > Thanks, Ben Bax
> > >
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> > -----
> > Randy J. Read
> > Department of Haematology, University of Cambridge
> > Cambridge Institute for Medical Research Tel: +44 1223 336500
> > The Keith Peters Building
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> > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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> -----
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> The Keith Peters Building
> Hills Road E-mail:
> [email protected]
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
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