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
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*From:*CCP4 bulletin board [[email protected]] on behalf of Keller, Jacob
[[email protected]]
*Sent:* Wednesday, November 30, 2016 5:44 PM
*To:* [email protected] <mailto:[email protected]>
*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:[email protected]]
*Sent:* Wednesday, November 30, 2016 5:19 PM
*To:* Keller, Jacob <[email protected] <mailto:[email protected]>>;
[email protected] <mailto:[email protected]>
*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: [email protected] <mailto:[email protected]>/
/Phone: 972-8-647-2220 Skype: boaz.shaanan /
/Fax: 972-8-647-2992 or 972-8-646-1710 //
//
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*From:*CCP4 bulletin board [[email protected]] on behalf of Keller, Jacob
[[email protected]]
*Sent:* Wednesday, November 30, 2016 11:37 PM
*To:* [email protected] <mailto:[email protected]>
*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: [email protected] <mailto:[email protected]>
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