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CCP4BB  July 2017

CCP4BB July 2017

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Subject:

Re: weird diffraction pattern

From:

Gerard Bricogne <[log in to unmask]>

Reply-To:

Gerard Bricogne <[log in to unmask]>

Date:

Thu, 13 Jul 2017 21:36:31 +0100

Content-Type:

text/plain

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text/plain (147 lines)

Dear Gerd,

     I wasn't really giving much attention to the poke between the
ribs ;-) - for me the more serious matter was to see the merits of
pixel detectors over CCDs made light of, as if they didn't really make
much difference.

     If some people get carried away in the way you describe, well, it
doesn't hurt anyone; but if other people have very small, weakly
diffracting crystals and they are told that they will do as well on a
beamline with a CCD as on one with a Pilatus or an Eiger, then that
will hurt someone.

     The original topic was whether certain images presented without
any information about their angular width and recorded on a CCD were
sufficient to diagnose a diffraction quality problem. As they showed
evidene of at least one long axis, distinguishing streakiness from
plain angular overlap caused by too great an image width seemed the
most natural first step.

     The resolution I was talking about was resolving spots within
images and neighbouring images, either thanks to a detector with a
small PSF or thanks to a very fine image width. CCD detectors are poor
in the first option because of their extended PSF, so emphasis has
always been put on the importance of using the second one when pushed.
Pixel array detectors allow both options to be used simultaneously,
which is especially valuable in the investigation of crystals like
Tang's. Hence, again, my advice in the strict context of the initial
thread. 


     With best wishes,
     
          Gerard.

--
On Thu, Jul 13, 2017 at 02:39:58PM -0500, Gerd Rosenbaum wrote:
> 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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