Dear Gerard, Marina and others.
I agree that using a multi-axis goniostat is one way of separating the spots.
Also that the separation of spots provided by the spatial resolution of the
detector is often much better than the separation you could get from even very
fine-sliced images. However, if both the beam divergence and fine phi slicing
range are small, then the spots should be resolved independently of the
direction of the large unit cell axis. Many beamlines are targeted to small
focal spots to examine small crystals. The downside is often that the beam
divergence is large, at least in the horizontal direction. Reducing the beam
divergence by means of slits will lead to a reduction in flux. However, the
spot to background ratio should be better with the more parallel beam and fine
phi slicing option. Orienting the crystal appropriately with a multi-axis
goniostat will reduce the number of images required but this should not be an
issue with modern detectors.
It would be interesting to find out the relevant parameters in this case.
Detector - pixel size, detector distance
Beam - wavelength, divergence and beam size at crystal (both horizontal and
vertical)
Data collection - rotation range per image, crystal orientation
Crystal - unit cell parameters
Plus of course any which I have forgotten!
Best regards
Colin
-----Original Message-----
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Gerard Bricogne
Sent: 12 March 2021 18:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Can twinning be seen in the diffraction pattern?
Dear Marina,
Mark seems to have hit the nail on the head. The left-hand picture of your
second jpg shows that you have an axis, at about 45 degrees from the horizontal
(and hence from the rotation axis), along which the spots are very close. These
spots seem to be only just separated on that picture, when that direction is
parallel to the detector plane, but for values of the rotation angle away from
that particular one, they are likely to collide or even overlap within the same
diffraction image, especially if your image width is not especially small.
When you have a crystal with such a long axis in real space, and therefore
closely spaced spots in reciprocal space, you need to orient it in such a way
that this axis be essentially aligned with the rotation axis, and to put the
detector far enough that the close spots in that direction be resolved. The
idea is that the angular separation of spots provided by the spatial resolution
of the detector is much better than the separation you could get from even very
fine-sliced images.
To orient your crystals in this way you will benefit from using a beamline
equipped with a multi-axis goniostat. The dataset you will collect with such an
aligned axis will have a "cusp" of missing reflections around that axis, but
that is a better outcome than the alternative of having the zillions of
"angular overlaps" between distinct reflections that would be produced with a
long-axis orientation such as that shown in your pictures.
That random overlap will produce the same effect on intensity statistics as
twinning, but there would not be a consistent twinning fraction among all your
measurements that you could then put into a refinement against them.
Do your unit-cell parameters confirm this scenario?
With best wishes,
Gerard.
--
On Fri, Mar 12, 2021 at 06:29:06PM +0100, Mark J van Raaij wrote:
> Hi Marina,
> The close-together spots in the zoom inset of your figure I think are not
> split spots, but separate reflections. They are close togeter because you
> appear to have a unit cell with one axis much longer than the other two (we
> work on elongated proteins, so we have some experience with that). The same
> short distances are also clearly visible in the picture on the bottom left.
> If you index the image in MOSFLM and it puts boxes around both I'd conclude
> they are separate reflections, but there are perhaps more sophisticated ways
> to verify this.
> So I think its true that in this case the twinning is not (obviously) visible
> in the diffraction pattern - but detected through intensity statistics later.
> Best wishes,
> Mark
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC calle Darwin 3
> E-28049 Madrid, Spain
>
>
>
> > On 12 Mar 2021, at 11:30, Marina Gárdonyi
> > <marina....@pharmazie.uni-marburg.de> wrote:
> >
> >
> > Hello everyone,
> >
> > I am a PhD student at the Philipps-University in Marburg and I am currently
> > writing my thesis.
> >
> > I have problems to understand whether in my case twinning can be seen in
> > the diffraction pattern or not.
> >
> > I know that it depends on the type of twinning wheter you can see it in the
> > diffraction pattern. The crystal had a resolution of 2.2 A. During
> > processing it seemed to have the space group P622, but in the end it was
> > P3(2)21. With phenix Xtriage I found out, that the data set was twinned.
> > The twin law was -h,-k,l. So it should be merohedral twinning.
> > I read in a paper, that in case of merohedral twinning you cannot see it in
> > the diffraction pattern. But in my case that seemed not to be the case
> > because of splitted reflections. Or am I wrong???
> >
> > I would be very happy to hear your opinion on that. Thanks in advance!
> >
> > Best regards,
> > Marina
> >
> > --
> > Marina Gárdonyi
> >
> > PhD Student, Research Group Professor Dr. Klebe
> >
> > Department of Pharmaceutical Chemistry
> >
> > Philipps-University Marburg
> >
> > Marbacher Weg 6, 35032 Marburg, Germany
> >
> > Phone: +49 6421 28 21392
> >
> > E-Mail: marina....@pharmazie.uni-marburg.de
> >
> > http://www.agklebe.de/
> >
> > ####################################################################
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> > <diffraction-pattern.jpg><diffraction-pattern-2.jpg>
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