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<TITLE>Re: [RASMB] "wavy" interference optics residuals</TITLE>
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<BLOCKQUOTE><FONT COLOR="#800000">Greetings Debra<BR>
<BR>
I have noticed a very similar effect. I have a little routine which I use to check up on stochastic noise in final scans, in which I estimate the magnitude of the latter by subtracting 2 final equilibrium scans from each other. That (obviously) eliminates TI noise. Yet resulting residuals have a waveform pattern superimposed on top of the high frequency 'shot noise' stuff. The amplitude (SD around mean) of the latter is of the order of 0.006 fringes, with the mysterious longer frequency waveform being just a little larger than that. And, just like your case, Debra, I find 7 or so wavelengths in this pattern.<BR>
<BR>
I'm not sure that I have any very good ideas as to what the cause is of this phenomenon. I do not think that this bit of waveform noise will have all that much effect of fits - maybe if I can find a moment to do it I ought to simulate addition of a bit of waveform noise, and see what effect this has on SE fits.<BR>
<BR>
Kind regards to you and to all<BR>
<BR>
Arthur<BR>
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</FONT></BLOCKQUOTE><FONT COLOR="#800000">-- <BR>
*************************<BR>
Arthur Rowe<BR>
Lab at Sutton Bonington<BR>
tel: +44 115 951 6156<BR>
fax: +44 115 951 6157<BR>
*************************<BR>
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<BLOCKQUOTE><TT>> <BR>
> Hi All,<BR>
> <BR>
> We have been experiencing a problem with our interference data in which<BR>
> after data fitting, the residuals frequently have a systematic "wavy" look<BR>
> to them where they rise above and below zero multiple times >7 across the<BR>
> fitted data. Subtracting a water blank does not fix the problem, and it has<BR>
> occurred an several different samples. In real time, the fringes also<BR>
> "jump" during centrifugation. Is this an indication of an equipment<BR>
> problem, perhaps that there is something unstable in the centrifuge and/or<BR>
> optical system that is leading to the movement of the fringe pattern<BR>
> detected by the camera? If so, is there a likely culprit? If not, what is<BR>
> likely to cause this?<BR>
> <BR>
> Thanks for the help, <BR>
> <BR>
> Debra M. Eckert, Ph.D.<BR>
> <BR>
> Research Assistant Professor of Biochemistry<BR>
> <BR>
> University of Utah<BR>
> <BR>
> deckert@biochem.utah.edu<BR>
> <BR>
<BR>
Debra,<BR>
<BR>
have you tried to fit the data with time invariant noise subtraction?<BR>
It sounds like you have a time invariant noise contribution to your data that<BR>
can easily be removed. In UltraScan, you would do that during your initial<BR>
fit of the data with the 2-dimensional spectrum analysis. These TI noise<BR>
contributions are common in interference data, especially if you have <BR>
low protein concentration, or if use quartz instead of sapphire windows.<BR>
<BR>
For equilibrium data, you have two options: either collect approach-to-<BR>
equilibrium data and subtract the ti noise calculated from the early<BR>
scans, or collect a baseline scan to get the ti noise contributions.<BR>
The latter process could be a bit tricky if the protein doesn't pellet<BR>
during a high speed run. But for velocity data this works great.<BR>
<BR>
Regards, -Borries<BR>
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