Hi Tim, This sounds like fun - I was not at the ECM so did not hear about this. Would like to hear more 'bout it though if anyone has any pointers :o)
That said, I would also suspect that the statistics would still be "hard" due to the low counts... Cheerio, Graeme On 1 May 2014 09:40, Tim Gruene <[email protected]> wrote: > Dear Graeme, > > at the ECM last year Arwen Pearson suggested an even more sophisticated > method than the sum of runs. It was based on a set of random sums based > on Hadamard-matrices and the subsequent 'deconvolution'. > > It sounded very promising to improve signal-to-noise and to turn your > sentence "you may get better data" into "you will get better data". I > think this would be worth implementing at beamlines - do you know if > anything in this direction is on its way? > > Best, > Tim > > On 05/01/2014 09:25 AM, Graeme Winter wrote: > > Hi All, > > > > A major opportunity with Pilatus detectors is the chance to redistribute > > the dose in reciprocal space i.e. measure a lot more data, with less > dose / > > frame, then decide in hindsight where you probably should have cut off > the > > data set. > > > > It is certainly true that "strategies" such as 0.2 s/0.2 degree (I would > > call this a tactic myself ;oD) seem to work well, and that it often seems > > that you need a reasonable dose to be able to process the data properly > > (see below). I would however agree strongly that unless you are not > > vulnerable to radiation damage the use of a strategy program such as EDNA > > is critical as continuous readout of a fast detector can let you kill > your > > sample really quickly... and it would be a shame to measure the wrong > part > > of reciprocal space. > > > > Also the 0.2s / 0.2 degree rate is very beamline dependent. Here at > Diamond > > it is certainly routine to measure data with 0.05 s / 0.1 degree exposure > > times with Pilatus2 and end up with very good data, and the latest > Pilatus3 > > machines can run with 0.01s exposure times. As Nukri said earlier, once > you > > start running at these very high rates you become much more sensitive to > > beamline and source characteristics, so your mileage may vary and so on. > > It's certainly worth spending some time exploring the capability and what > > works well for *your* samples. I would however strongly agree with the > > recommendations for fine slicing, and avoid e.g. 1 degree images. > > > > In terms of "a reasonable dose to process the data properly" there are > some > > major challenges when dealing with exceedingly weak data in measuring the > > reflections at high resolution well: the statistics start to become > poorly > > behaved with current analysis software. One tactic I have been playing > with > > is to record the same wedge of data (for example from an EDNA strategy) > > with exceedingly low dose perhaps 20 times, then to process this and look > > for signs of radiation damage. After arbitrarily deciding which "pass" > > radiation damage kicked in at then *sum* the *raw images* from each pass > up > > to this point e.g. > > > > pass_1_0001.cbf + pass_2_0001.cbf + .... pass_N_0001.cbf => sum_0001.cbf > > > > Then process these summed images as if this was the original data. > Funnily > > enough you may get better data than processing pass_1 to pass_N > separately > > and then scaling and merging all of the measurements, which leads me to > > pointing the pointy finger of blame at the behaviour of the statistics, > and > > that statistics and things like background subtraction become hard when > you > > have very sparse data. > > > > This summing process may seem like manipulating your raw data (naughty!!) > > but in essence it is really just performing the same process as when you > > recorded multiple exposures / passes on a single CCD image. It also has > the > > happy side effect of averaging out any random / high frequency effects > > induced from source / beamline effects, but will also average in any > > radiation damage effects as well! This by the way is what I was getting > at > > with redistributing your dose in reciprocal space... > > > > Cheerio, Graeme > > > > > > > > > > On 30 April 2014 17:41, Harry Powell <[email protected]> wrote: > > > >> Hi > >> > >> Marcus Mueller (from Dectris, who develop and manufacture the Pilatus) > did > >> some work on this a couple of years ago and determined that an > oscillation > >> angle ~ 0.5x the mosaicity of the crystal (using the XDS value of > >> mosaicity, which is not the same as Mosflm's); the abstract says - > >> > >> The results show that fine ’-slicing can substantially improve scaling > >>> statistics and anomalous signal provided that the rotation angle is > >>> comparable to half the crystal mosaicity. > >>> > >>> > >>> Acta Cryst. (2012). D68, 42-56 [ doi:10.1107/S0907444911049833 ] > >>> Optimal fine > >> > >> > >> -slicing for single-photon-counting pixel detectors > >>> > >>> M. Mueller, M. Wang and C. Schulze-Briese > >>> > >>> > >> My reading of this is that there is still a place for strategy > >> calculations. > >> > >> > >> > >> On 30 Apr 2014, at Wed30 Apr 15:06, Sanishvili, Ruslan wrote: > >> > >> Hi Jacob, > >>> > >>> I'll take a first crack as I am sure many will follow. > >>> It is true that with CCD detectors one has to be careful how small an > >>> oscillation range to use for a frame before read noise starts to eat > into > >>> the data quality. > >>> Pilatus offers two major new features - is fast and is photon counting > as > >>> opposed to integrating detector. > >>> The speed allows to collect data without a shutter and it is very > >>> important as it can dramatically improve data quality. Now there are > fast > >>> CCD detectors as well on the market. > >>> Being a photon counter, Pilatus has no "read" noise which, as you have > >>> pointed out, allows you to collect as thin a frame as you want. > However, it > >>> is if you consider the detector only. In reality, if you go very thin > and > >>> very fast, you may not have enough flux to record the data. Also, even > once > >>> we get rid of the shutter, there are still other sources of > instabilities > >>> and they do affect the fast data collection adversely. One could try > going > >>> (very) thin sliced and somewhat slow but there is another gotcha there. > >>> Most rotation stages used for rotating the sample crystal, do not like > >>> going extremely slow which would be the case with thin frames and long > >>> exposure times. In this case the speed may not remain as constant as we > >>> would like during data collection. > >>> I think there was a publication from Diamond Synchrotron discussing > >>> strategies of data collection with Pilatus. > >>> We've done a little bit of systematic studies as well and while things > >>> may well be sample- and facility-dependent, ~0.2 degree frames with > ~0.2 > >>> sec exposure time seemed to make good compromise between > above-mentioned > >>> issues. Here I would like to emphasize again - there certainly will be > >>> samples which will benefit from somewhat different parameters. > >>> Hope it helps, > >>> Cheers, > >>> N. > >>> > >>> Ruslan Sanishvili (Nukri) > >>> Macromolecular Crystallographer > >>> GM/CA@APS > >>> X-ray Science Division, ANL > >>> 9700 S. Cass Ave. > >>> Lemont, IL 60439 > >>> > >>> Tel: (630)252-0665 > >>> Fax: (630)252-0667 > >>> [email protected] > >>> > >>> > >>> ________________________________________ > >>> From: CCP4 bulletin board [[email protected]] on behalf of Keller, > >>> Jacob [[email protected]] > >>> Sent: Wednesday, April 30, 2014 7:49 AM > >>> To: [email protected] > >>> Subject: [ccp4bb] Pilatus and Strategy wrt Radiation Damage > >>> > >>> Dear Pilatus/Radiation Damage Cognoscenti, > >>> > >>> I read a few years ago, before the advent of Pilatus detectors, that > the > >>> best strategy was a sort of compromise between number of images and > >>> detector readout noise "overhead." I have heard that Pilatus detectors, > >>> however, have essentially no readout noise, so I am wondering whether > >>> strategies have changed in light of this, i.e., is the best practice > now to > >>> collect as many images as possible at lowest exposure possible? > >>> > >>> JPK > >>> > >>> ******************************************* > >>> Jacob Pearson Keller, PhD > >>> Looger Lab/HHMI Janelia Farms Research Campus > >>> 19700 Helix Dr, Ashburn, VA 20147 > >>> email: [email protected] > >>> ******************************************* > >>> > >> > >> Harry > >> -- > >> ** note change of address ** > >> Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick > >> Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH > >> Chairman of European Crystallographic Association SIG9 (Crystallographic > >> Computing) > >> > >> > >> > >> > >> > >> > > > > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > >
