It’s best to think of slicing as just sampling the 3D reciprocal space. Then in the absence of errors fine slicing will improve signal/noise by reducing the excess background under the peaks. However [Mueller M, Wang M, Schulze-Briese C. Acta Cryst (2012) D68, 42-56] show that there are diminishing returns from slicing the spot width into more than 4 or 5 slices, and with finer slicing handling more data may be a nuisance. Shutterless data collection with modern pixel array detectors introduces very little noise / image, so this argument holds.
With older systems, there is a compromise with
1. shutter jitter, depending on the speed of data collection compared to the shutter speed
2. goniometer accuracy, to handle the stop/start synchronised with the shutter
3. read-out noise of the detector
4. reducing the background under the spots
1-3 favour thicker slices, 4 favours thinner
Judging the balance with shuttered collection is complicated, but the advantage of shutterless data collection with fast detectors is clear
Phil
> On 1 Dec 2016, at 04:42, Edward A. Berry <[log in to unmask]> wrote:
>
> On 11/30/2016 10:16 PM, Keller, Jacob wrote:
>>> If you fine slice and everything is then a partial, isn't that *more* sensitive to lack of synchronization between the shutter and rotation axis than the wide-frame method where there's a larger proportion of fulls that don't approach the frame edges (in rotation space) ? Especially if you're 3D profile fitting ?
>>
>> That is how the argument seems to go in Pflugrath 1999, but I would think that shutter jitter is a random error, so it would seem better to have several of these random errors for a given spot than just one. Perhaps measuring with high multiplicity would have the same averaging effect.
>>
>>> Is fine slicing more or less beneficial at high resolutions relative to lower ones ?
>>
>> In terms of I/sigI, it seems to be the same proportional improvement across all resolutions. See Fig 4 of the Pflugrath 1999 paper.
>>
>> JPK
>
> I think the problem there is that, if the shutter jitter is random with a constant sigma, it becomes a larger percent of the total exposure for that frame. It would be like taking a 1ml pipetor with an error of 2% of full scale, i.e. 20 ul. Because you want to average this out, you set it to 200 ul and pipet 5 times. The sigma of that measurement would be sqrt(5) * 20 ul, I think, so worse than doing it all in one shot. On the other hand if you take a 200 ul pipet with sigma 2% of full scale or 4 ul, and take 5 times, the error is sqrt(5) * 4 ul which is less than 20 ul.
> Of course this would not apply to reflections that are fully recorded on one frame since they are not reflecting while the shutter is open/closing. Then it would be only variation in background.
>
>>
>> Phil Jeffrey
>>
>> Princeton
>>
>> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>> *From:*CCP4 bulletin board [[log in to unmask]] on behalf of Keller, Jacob [[log in to unmask]]
>> *Sent:* Wednesday, November 30, 2016 5:44 PM
>> *To:* [log in to unmask] <mailto:[log in to unmask]>
>> *Subject:* Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers
>>
>> If the mosaicity is, say, 0.5 deg, and one is measuring 1 deg frames, about half the time is spent measuring non-spot background noise under spots in phi, which is all lumped into the intensity measurement. Fine slicing reduces this. But I am conjecturing that there is also fine-slicing-mediated improvement due to averaging out things like shutter jitter, which would also be averaged out through plain ol’ multiplicity.
>>
>> I guess a third equal-count dataset would be useful as well: one sweep with six-fold finer slicing. So it would be:
>>
>> One sweep, 0.6 deg, 60s
>>
>> Six sweeps, 0.6 deg, 10s
>>
>> One sweep, 0.1 deg, 10s
>>
>> Or something roughly similar. Who will arrange the bets?
>>
>> JPK
>>
>> *From:*Boaz Shaanan [mailto:[log in to unmask]]
>> *Sent:* Wednesday, November 30, 2016 5:19 PM
>> *To:* Keller, Jacob <[log in to unmask] <mailto:[log in to unmask]>>; [log in to unmask] <mailto:[log in to unmask]>
>> *Subject:* RE: Effects of Multiplicity and Fine Phi with Equivalent Count Numbers
>>
>> Hi Jacob,
>>
>> I may have missed completely your point but as far as my memory goes, the main argument in favour of fine slicing has always been reduction of the noise arising from incoherent scattering, which in the old days arose from the capillary, solvent, air, you name it. The noise reduction in fine slicing is achieved by shortening the exposure time per frame. This argument still holds today although the sources of incoherent scattering could be different. Of course, there are other reasons to go for fine slicing such as long axes and others. In any case it's the recommended method these days, and for good reasons, isn't it?
>>
>> Best regards,
>>
>> Boaz
>>
>> /Boaz Shaanan, Ph.D. //
>> /Dept. of Life Sciences /
>> /Ben-Gurion University of the Negev /
>> /Beer-Sheva 84105 /
>> /Israel /
>> //
>> /E-mail: [log in to unmask] <mailto:[log in to unmask]>/
>> /Phone: 972-8-647-2220 Skype: boaz.shaanan /
>> /Fax: 972-8-647-2992 or 972-8-646-1710 //
>>
>> //
>>
>> ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>> *From:*CCP4 bulletin board [[log in to unmask]] on behalf of Keller, Jacob [[log in to unmask]]
>> *Sent:* Wednesday, November 30, 2016 11:37 PM
>> *To:* [log in to unmask] <mailto:[log in to unmask]>
>> *Subject:* [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers
>>
>> Dear Crystallographers,
>>
>> I am curious whether the observed effects of fine phi slicing might in part or in toto be due to simply higher “pseudo-multiplicity.” In other words, under normal experimental conditions, does simply increasing the number of measurements increase the signal and improve precision, even with the same number of total counts in the dataset?
>>
>> As such, I am looking for a paper which, like Pflugrath’s 1999 paper, compares two data sets with equivalent total counts but, in this case, different multiplicities. For example, is a single sweep with 0.5 degree 60s exposures empirically, in real practice, equivalent statistically to six passes with 0.5 degree 10s frames? Better? Worse? Our home source has been donated away to Connecticut, so I can’t do this experiment myself anymore.
>>
>> All the best,
>>
>> Jacob Keller
>>
>> *******************************************
>>
>> Jacob Pearson Keller, PhD
>>
>> Research Scientist
>>
>> HHMI Janelia Research Campus / Looger lab
>>
>> Phone: (571)209-4000 x3159
>>
>> Email: [log in to unmask] <mailto:[log in to unmask]>
>>
>> *******************************************
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