Dear Jakob,

There is also a paper from people at the SLS and which have
participated in the development of the Pilatus detector.
They tried to identify what is the best data collection
strategy using single photon counting pixel detectors, also
considering the crystal mosaicity. 

Here is the link:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245722/

Best,

Christophe 


----------------------------------------------------------
Christophe Wirth, PhD
Centre for Biological Signalling Studies (bioss)
Institute for Biochemistry and Molecular Biology
University of Freiburg
Stefan-Meier-Str. 17
D-79104 Freiburg, Germany
Tel: +49 (0) 761 203 52 77
----------------------------------------------------------




On Thu, 1 May 2014 08:25:43 +0100
 Graeme Winter <[log in to unmask]> 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
> <[log in to unmask]> 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
> >> [log in to unmask]
> >>
> >>
> >> ________________________________________
> >> From: CCP4 bulletin board [[log in to unmask]] on
> behalf of Keller,
> >> Jacob [[log in to unmask]]
> >> Sent: Wednesday, April 30, 2014 7:49 AM
> >> To: [log in to unmask]
> >> 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: [log in to unmask]
> >> *******************************************
> >>
> >
> > 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)
> >
> >
> >
> >
> >
> >