hi folks
Just my two ha'porth - the small molecule crystallographers have been doing
multi-orientation data collections
since they moved from point detectors to area detectors in the early 1990's,
for the very reasons that Gerard
gives (their cusps are huge compared to ours...). Since they were perfectly
used to using multi-axis goniostats*,
this wasn't a big psychological jump for them.
* I prefer calling the thing that the crystals sit on a "goniostat" because a
"goniometer" is correctly something
for measuring angles (however, a "positioning goniometer" appears to be a
specialised kind of goniostat);
wikipedia tells me that crystallographers seem to be the only group of people
who confuse the two (but I didn't
read the article very carefully so IMWBW).
On 14 Jul 2017, at 15:15, Gerard Bricogne wrote:
Dear Leo,
What seems to have happened is that an existing thread where fine
phi (actually: omega!) slicing was discussed, among many other things,
digressed into a discussion of data collection protocols using more
than one instrumental setting (either using a 2-theta motion of the
detector, or a chi reorientation of the crystal). Briefly, my two
cents on that topic: a 2-theta movement may help use different pixels
on the detector, and could be valuable in filling the wide horizontal
gaps on a Pilatus or Eiger, but it will leave the cusp in the same
place and therefore will not fill it. Reorienting the crystal, on the
other hand, can help cure all the known ills of single-sweep datasets
(gaps and cusp in particular).
On the matter of multi-orientation data collection, the idea and
the practice go back (at least, in my memory) to Alan Wonacott, the
co-creator of the Arndt-Wonacott rotation camera in the early 1970's.
It was all done with gonio arcs. As each crystal had to be aligned
manually in order to continue data collection where the previous one
had left off, these arcs were in constant use, and there was always an
extra cusp-filling collection at the end. Nowadays data collection has
speeded up so much, and has become so dominated by automation, that
multi-axis goniometry has been sidestepped because using it properly
would have had to involve non-automated steps that are difficult to
standardise (a notable exception being the protocol with 8 different
values of Chi, using the PRIGo goniometer on the PX-III beamline at
the SLS, that has been "instrumental" in enabling large structures to
be experimentally phased by native SAD at 6keV).
It is great to see that there are many developments underway in
both hardware and software, leading gradually towards a reinstatement
of multi-orientation data collection as an off-the-shelf option for
those who are prepared to spend a bit more time to reliably get much
better data. The Proxima-1 beamline scientists at SOLEIL have always
been among the believers that the time would come when these efforts
would bear fruit, and what my group has been able to do in this area
owes a great deal to them.
With best wishes,
Gerard.
--
On Fri, Jul 14, 2017 at 01:18:35PM +0000, CHAVAS Leonard wrote:
Reading back my email, when I mentioned 'just introduced', it is
not giving justice to
the reality and those who came up with the concept. I should have
mentioned 'just
reminded us', as the concept has been introduced quite a long time
ago and few tens of
communications. It is therefore a reminder that when coming to the
will to collect good,
clean and complete data, things aren't as simple as they would
seem. Automation at our
favourite beamlines do help by providing much more time thinking
properly of the
necessary strategies when coming to these difficult crystals so
important to our hearts.
Sorry again for the confusion. No hurt feelings I hope.
Cheers, leo
-
Leonard Chavas
-
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
-
Phone: +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-
On 14 Jul 2017, at 14:07, CHAVAS Leonard
<leonard.cha...@synchrotron-soleil.fr> wrote:
Just to comment on what Graeme just introduced. We (and I
know we are not the
first ones and not the only ones) are pushing our user
community towards this
procedure as a standard: lowering the transmission (less
juicy, yet...) and
getting few data with various chi. It does help greatly in
getting fully
complete data, with no loss in resolution. Just fantastic!
Cheers, leo
-
Leonard Chavas
-
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
-
Phone: +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-
On 14 Jul 2017, at 07:36, Graeme Winter
<graeme.win...@diamond.ac.uk> wrote:
Jacob
If you have a complete 360 deg data set and your sample
is still
alive, and you have a multi-axis gonio, I would
recommend
rotating the crystal about the beam (ideally by ~
maximum
scattering 2-theta angle) and collecting again. This
would record
your blind region as well as moving the reflections to
different
pixels, and (as a bonus) also will move reflections out
from the
tile join regions into somewhere they can be measured,
which
would not happen for small 2-theta shift.
See http://scripts.iucr.org/cgi-bin/paper?BA0020 Figure
16 as
excellent illustration of this.
Biggest risk with this is getting *moving* shadows on
the data on
the second run, as an effective 45-50 degree chi shift
(say) will
usually be a pretty wide opening angle for a kappa
gonio. XDS and
DIALS both have mechanisms to deal with this, and
automated
processing packages are able to apply these given a
reasonable
understanding of the beamline.
Also saves building 2-theta axes which can handle 92 kg
;o)
Cheers Graeme
On 13 Jul 2017, at 21:00, Keller, Jacob
<kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org>>
wrote:
I thought there was a new paper from the Pilatus people
saying
fine slicing is worth it even beyond the original 1/2
mosaicity
rule?
I would think, actually, more gains would made by doing
light
exposures at, say, 1/3 mosaicity, collecting 360 deg,
then
shifting the detector in 2theta by a degree or two to
shift
uniformly the spots to new pixels, maybe accompanied by
a kappa
change. One would have to remember about the two-theta
when
processing, however!
JPK
-----Original Message-----
From: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Gerd Rosenbaum
Sent: Thursday, July 13, 2017 3:40 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] weird diffraction pattern
Dear Gerard,
my "sound like a sales person" was meant as poking a
little fun -
nothing serious, of course.
I and our users like our not-so-new-anymore Pilatus3
6M. It's a
great detector in many ways. But, there is a lot of
hype that
this detector solves all-problem, for instance fine
slicing that
is claimed to be only possible with a pixel array
detector.
People get carried away and use
0.01 degree slices even as the mosaicity of their
sample is, say,
0.3 degree. Slicing beyond 1/3 of the mosaicity will
gain you
very little - only more frames, more processing time.
This discourse is already drifting away from the
original topic
of the thread so I will comment on the other arguments
you made
like resolution in a private e-mail.
Best regards,
Gerd
On 13.07.2017 14:00, Gerard Bricogne wrote:
Dear Gerd,
I can assure you that I have no shares in Dectris nor
any
commecial connections with them. What I do have is a
lot of still
vivid memories of CCD images, with their wooly
point-spread
function
that was affected by fine-grained spatial variability
as well as
by
irredicible inaccuracies in the geometric corrections
required to
try
and undo the distortions introduced by the fiber-optic
taper. By
comparison the pixel-array detectors have a very regular
structure, so
that slight deviations from exact registering of the
modules can
be
calibrated with high accuracy, making it possible to
get very
small
residuals between calculated and observed spot
positions. That, I
certainly never saw with CCD images.
I do think that asking for the image width was a
highly
pertinent question in this case, that had not been
asked. As a
specialist you might know how to use a CCD to good
effect in
fine-slicing mode, but it is amazing how many people
there are
still
out there who are told to use 0.5 or even 1.0 degree
image
widths.
Compensating the poor PSF of a CCD by fine slicing in
the
angular dimension is a tall order. With a Pilatus at
350mm from
the
crystal, the angular separation between 174-micron
pixels is 0.5
milliradian.
To achieve that separation in the angular (rotation)
dimension,
the
equivalent image width would have to be 0.03 degree.
For an EIGER
the
numbers become 75 microns, hence 0.21 milliradian i.e.
0.012
degree.
Hence my advice, untainted by any commercial agenda
:-) .
With best wishes,
Gerard.
--
On Thu, Jul 13, 2017 at 01:25:08PM -0500, Gerd
Rosenbaum wrote:
Dear Gerard,
you sound like a sales person for Dectris. Fine slicing
is
perfectly
fine with CCD detectors - it takes a bit longer because
of the
step
scan instead of continuous scan. The read noise issue
is often
overstated compared to the sample induced scatter
background. If
for
fine slicing at 0.05 degree or less the diffraction
peaks go too
close to the read noise make a longer exposure - signal
goes up,
ratio signal to sample-induced-BG less, as for any fine
slicing,
same read noise.
It would be helpful to analyze the dense spot packing
along layer
lines if we knew the wavelength and the
sample-to-detector
distance
(assuming this is a 300 mm detector) and the rotation
width - as
you
pointed out. That would help to distinguish between
multiple
crystals
(my guess) and lattice translocation disorder. Fine
slicing is
definitely needed to figure out what the diffraction
pattern at
120
degree could tell you in terms of strong anisotropy .
Best regard.
Gerd
On 13.07.2017 08:20, Gerard Bricogne wrote:
Dear Tang,
I noticed that your diffraction images seem to have
been
recorded on a 3x3 CCD detector. With this type of
detector, fine
slicing is often discouraged (because of the readout
noise), and
yet
with the two long cell axes you have, any form of thick
(or only
semi-fine) slicing would result in spot overlaps.
What, then, was your image width? Would you have
access to a
beamline with a Pilatus detector so that you could
collect
fine-sliced data?
I would tend to agree with Herman that your crystals
might be
cursed with lattice translocation disorder (LTD), but
you might
as
well try and put every chance of surviving this on your
side by
making sure that you collect fine-sliced data. LTD plus
thick
slicing would give you random data along the streaky
direction.
Use
an image width of at most 0.1 degree (0.05 would be
better) on a
Pilatus, and use XDS to process your images.
Good luck!
Gerard
--
On Thu, Jul 13, 2017 at 01:21:02PM +0100, Tang Chenjun
wrote:
Hi David,
Thanks for your comments. Although the spots become
streaky in
certain directions, I have processed the data in
HKL3000 and
imosflm, which suggested the C2221 space group (66.59,
246.95 and
210.17). The Rmerge(0.14), completeness(94.8%),
redundancy(4.6)
are OK. When I tried to run Balbes with the solved
native
structure, the molecular replacement solution was poor.
So I ran
Balbes with the split domains of the native structure.
Although
the solutions were also poor, I found the MR score of
one
solution above 35. On the basis of this solution, I
tried to run
Buccaneer and the Rfree could be 0.46. Unfortunately,
there are
four molecules in the asymmetric unit and it is to hard
for me to
reduce the Rfree further.
All best,
Chenjun Tang
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