Graeme and Bob, Wow... It's great to learn from actual experiences.
Thanks much for this write up. If this were stackoverflow, +1. F On May 8, 2013, at 12:32 AM, Graeme Winter <graeme.win...@gmail.com> wrote: > A couple of extra comments on top of Bob's rather comprehensive > recommendations, based purely on actually looking at Pilatus data (I > mean *looking*) > > When you are inspecting the images looking at them at 100% size is > important: spots are small relative to pixels and the point spread is > essentially zero. I also find it helpful to look at white spots on a > black background rather than the reverse. > > The DECTRIS folks have an image viewer named ALBULA which works well, > however ADXV also works fine (IMHO) if you tweak the settings as > above. It is remarkable how big a difference it makes. > > The other big difference in terms of viewing the images is that (if > you have low counts) you are actually at the mercy of real Poisson > statistics. For example, if you have a "spot" (pixel) with 8 counts in > against a background of 0 - 3 counts (say) it looks nice and clear - > certainly based on experience of CCD images. And the spot is say four > times the background so it must be good right? > > However the variance on a spot with 8 counts is 8, the variance from > background subtraction may be about 3 so your spot has a maximum > I/sigma of ~ 8 / sqrt(11) so about 2 and a bit. On the flip side, data > from a decent crystal taken with a low dose can look almost blank at > first glance (esp. with black spots on white; zoomed out) but process > very nicely. Take some time to get used to the instrument. > > A couple of final comments: > > The machine has no read-out noise so fine phi slicing (and dose > slicing) can only help - recording twice as many degrees with half as > much dose increases the chance of getting a complete and relatively > undamaged data set. All it does is take up lots of disk space. There > is really no risk in doing this, unlike with a CCD where you are at > war with the read-out noise. > > The machine also behaves completely differently to a CCD: this takes > some getting used to. Take narrow oscillations as this will give > better measurements of strong reflections (which I think is detailed > in the papers Bob recommended.) Also *take your time* - one of the > great things about these detectors is that they allow you to do > continuous exposures, which can essentially double the throughput or > more of data collection. Take back some of that time to use a lower > dose rate and spread your photons out more evenly across reciprocal > space. You can always measure more data if your sample is undamaged. > > Best wishes, > > Graeme > > On 7 May 2013 02:00, Robert Sweet <rsw...@bnl.gov> wrote: >> The seminal paper on actually how to collect data from detectors like this >> and others with negligible read-out time is this one, which I strongly >> recommend: >> >> Optimal Fine phi-slicing for Single-Photon-Counting Pixel Detectors Marcus >> Mueller, Meitian Wang, and Clemens Schulze-Briese, Acta Cryst.(2012) D68, >> 42-56 >> >> And you can pick up a copy of the paper from the RapiData web site: >> http://www.px.nsls.bnl.gov/courses/papers/Mueller_ACD68_2012.pdf >> >> >> The classic paper on data-collection strategies is this: >> >> Data-Collection Stragegies, Dauter, Z. Acta Cryst. (1999). D55, 1703-1717. >> >> Also available from the RapiData site: >> >> http://www.px.nsls.bnl.gov/courses/papers/dauter_strategy.pdf >> >> >> Then there are multiple papers on damage and its impact on your data. I >> suggest this one: >> >> Radiation damage in macromolecular crystallography: what is it and why >> should we care?, E.Garman, Acta Cryst. D66, 339-351(2010). >> >> which you can find here: >> >> http://www.px.nsls.bnl.gov/courses/papers/actad-garman-2010.pdf >> >> With this under your belt you'll be able to decide how to collect your >> phasing data. The bottom line is probably that you should go for SAD data. >> Employ multiple crystals and average them together in a judicious way, >> keeping only the sweeps from barely damaged x-tals. >> >> Good luck, >> >> Bob Sweet >> >> ========================================================================= >> Robert M. Sweet E-Dress: sw...@bnl.gov >> Group Leader, PXRR: Macromolecular ^ (that's L >> Crystallography Research Resource at NSLS not 1) >> http://px.nsls.bnl.gov/ >> Photon Sciences and Biosciences Dept >> Office and mail, Bldg 745, a.k.a. LOB-5 >> Brookhaven Nat'l Lab. Phones: >> Upton, NY 11973 631 344 3401 (Office) >> U.S.A. 631 344 2741 (Facsimile) >> ========================================================================= >> >> >> On Mon, 6 May 2013, Theresa Hsu wrote: >> >>> Dear crystallographers >>> >>> Is there a good source/review/software to obtain tips for good data >>> collection strategy using PILATUS detectors at synchrotron? Do we need to >>> collect sweeps of high and low resolution data separately? For anomalous >>> phasing (MAD), does the order of wavelengths used affect structure solution >>> or limit radiation damage? >>> >>> Thank you. >>> >>> Theresa >>> >>
