And the instrument makers (e.g., Rigaku and Bruker) currently sell multi-axis goniostats for in-house data collection--and not just for small-molecule purposes.
Diana P.S. Ron, we still call 'em goniometer heads and goniostats at UT Southwestern. > On Jul 14, 2017, at 1:00 PM, "[email protected]" > <[email protected]> wrote: > > I'm not understanding much of this discussion, but I've noticed the use of > words reminiscent of old issues concerning omega-two theta scans on > four-circle goniostats (see Stout and Jensen, pages 168-173, second edition). > > p.s. In my upbringing, crystals were placed on goniometer heads so they > could be placed on goniometers or goniostats. > >> On Fri, 14 Jul 2017, Harry Powell wrote: >> >> 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: [email protected] >> - >> On 14 Jul 2017, at 14:07, CHAVAS Leonard >> <[email protected]> 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: [email protected] >> - >> On 14 Jul 2017, at 07:36, Graeme Winter >> <[email protected]> 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 >> >> <[email protected]<mailto:[email protected]>> >> 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:[email protected]] On >> Behalf Of Gerd Rosenbaum >> Sent: Thursday, July 13, 2017 3:40 PM >> To: >> [email protected]<mailto:[email protected]> >> 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. If you are not the intended >> addressee or >> an authorised recipient of the addressee please >> notify us of >> receipt by returning the e-mail and do not use, copy, >> retain, >> distribute or disclose the information in or attached >> to the >> e-mail. >> Any opinions expressed within this e-mail are those >> of the >> individual and not necessarily of Diamond Light >> Source Ltd. >> Diamond Light Source Ltd. cannot guarantee that this >> e-mail or >> any attachments are free from viruses and we cannot >> accept >> liability for any damage which you may sustain as a >> result of >> software viruses which may be transmitted in or with >> the message. >> Diamond Light Source Limited (company no. 4375679). >> Registered in >> England and Wales with its registered office at >> Diamond House, >> Harwell Science and Innovation Campus, Didcot, >> Oxfordshire, OX11 >> 0DE, United Kingdom >> Harry >> -- >> Dr Harry Powell >> Chairman of International Union of Crystallography Commission on >> Crystallographic Computing >> Chairman of European Crystallographic Association SIG9 (Crystallographic >> Computing) >> ________________________________ UT Southwestern Medical Center The future of medicine, today.
