Hi Graeme, I see your point about the blind region and also the tile lines. But 2-theta would have the advantage of also shifting the low-res spots to entirely new pixels, which would be harder through rotation. Also, wouldn't rotating about the beam axis shift the spots to variable degrees across rotation space, with some angles (+/- 90 deg) negligibly shifted?
Further, does it give anyone pause: Graeme makes a subtle implication that most samples die before collecting 360 degrees, which I think may be true. What can be done about this tragic lack of attenuation? One possibility is to model the radiation damage in refinement, but wouldn't it make a lot more sense to have a lot of good attenuators installed by default (or use sealed-tube sources!). JPK -----Original Message----- From: graeme.win...@diamond.ac.uk [mailto:graeme.win...@diamond.ac.uk] Sent: Friday, July 14, 2017 1:37 AM To: Keller, Jacob <kell...@janelia.hhmi.org> Cc: ccp4bb@jiscmail.ac.uk Subject: Re: [ccp4bb] Fine Phi Slicing 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 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. 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