>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
Phil Jeffrey
Princeton
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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
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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
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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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