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 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
