Dear Harry,
I think that sharp ice rings (or, better, a powder pattern from silicon
powder) are only part of the solution to the calibration of beam energy, as
there is an interaction with the detector distance. If I recall what I saw
in my now distant days at LURE, a precise energy calibration would be done
using an absorption edge. I can remember Richard Kahn using a Cu metal foil
to lock precisely onto an energy close to the Ytterbium edge he wanted to
use in a MAD experiment. When the beam energy is precisely established by
this diffraction-free method, then a Si powder allows a precise calibration
of detector distance (and location of beam centre).
With best wishes,
Gerard.
--
On Thu, Jul 16, 2020 at 12:25:55PM +0100, Harry Powell - CCP4BB wrote:
> Hi
>
> Does anyone bother collecting a powder image (e.g. Si powder) these days so
> they actually have a reference that can be used to check both the wavelength
> and the beam centre? Or is this considered just something that old folk do?
>
> Harry
>
> > On 16 Jul 2020, at 12:19, Gerard DVD Kleywegt <ger...@xray.bmc.uu.se> wrote:
> >
> > There was a case a few years ago (not too many though) where a 1.6 Å
> > structure had been solved using an incorrect value for the wavelength (~5%
> > too low, leading to a cell that was slightly too small for its contents to
> > be comfortable). It was later corrected so we could compare their
> > validation statistics. Some interesting observations:
> >
> > - the geometry had been very tightly restrained so that didn't give a clue
> > about the cell error (WhatCheck only suggested a very small change)
> >
> > - somewhat surprisingly (I thought) the Ramachandran plot did not improve in
> > the correct model (0.3% outliers in the wwPDB validation report), and the
> > sidechain rotamer outliers even got worse (from 1.5 to 2.5 %)
> >
> > - the map looked surprisingly good for the incorrect cell
> >
> > - however, RSR-Z told clearly that the map was not good enough for the
> > claimed
> > resolution - the model had 24% outliers! (3% in the corrected model which
> > still only put it at the ~50th percentile)
> >
> > - another good indicator was the clashscore (went from 44 to 7)
> >
> > - the original model did not include an Rfree, but the R-value (>0.3 at 1.6Å
> > resolution) ought to have provided a clue to the crystallographers and
> > reviewers one would think
> >
> > It would be interesting to see what would happen if the wavelength would be
> > set 5% too high.
> >
> > --Gerard
> >
> >
> >
> > On Thu, 16 Jul 2020, Clemens Vonrhein wrote:
> >
> >> Hi Robbie,
> >>
> >> On Wed, Jul 15, 2020 at 07:23:15PM +0000, Robbie Joosten wrote:
> >>> At the same time if you have a a more relaxed approach to restraints
> >>> than you might find systematic deviations in bond lengths. A test
> >>> for that has been in WHAT_CHECK for decades and it actually works
> >>> surprisingly well to detect cell dimension problems.
> >>
> >> Indeed.
> >>
> >>> That said, the problem is uncommon now.
> >>
> >> Not so sure about that: we all rely on an accurate value of the
> >> energy/wavelength from the instrument/beamline - and if that is off
> >> (for whatever reasons) it will result in incorrect cell dimensions and
> >> a systematic deviation from the various restraints.
> >>
> >> This would even affect the best experiment done on the best crystal
> >> ... so fairly easy to spot at the refinement stage, especially if such
> >> an energy/wavelength offset is constant over a long period of time on
> >> a given instrument. To spot this at the data collection stage one
> >> would hope that at some point a crystal with very pronounced ice-rings
> >> will be looked at properly (and the fact these are not where we expect
> >> them to should cause some head-scratching).
> >>
> >> Cheers
> >>
> >> Clemens
> >>
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> >
> >
> > Best wishes,
> >
> > --Gerard
> >
> > ******************************************************************
> > Gerard J. Kleywegt
> >
> > http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
> > ******************************************************************
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> > to actual opinions, living or dead, is purely coincidental.
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