[RASMB] "wavy" interference optics residuals

[Borries Demeler]

> 
> Hi All,
> 
> We have been experiencing a problem with our interference data in which
> after data fitting, the residuals frequently have a systematic "wavy" look
> to them where they rise above and below zero multiple times >7 across the
> fitted data.  Subtracting a water blank does not fix the problem, and it has
> occurred an several different samples.  In real time, the fringes also
> "jump" during centrifugation.  Is this an indication of an equipment
> problem, perhaps that there is something unstable in the centrifuge and/or
> optical system that is leading to the movement of the fringe pattern
> detected by the camera?  If so, is there a likely culprit?  If not, what is
> likely to cause this?
> 
> Thanks for the help, 
> 
> Debra M. Eckert, Ph.D.
> 
> Research Assistant Professor of Biochemistry
> 
> University of Utah
> 
> deckert at biochem.utah.edu
> 

Debra,

have you tried to fit the data with time invariant noise subtraction?
It sounds like you have a time invariant noise contribution to your data that
can easily be removed. In UltraScan, you would do that during your initial
fit of the data with the 2-dimensional spectrum analysis. These TI noise
contributions are common in interference data, especially if you have 
low protein concentration, or if use quartz instead of sapphire windows.

For equilibrium data, you have two options: either collect approach-to-
equilibrium data and subtract the ti noise calculated from the early
scans, or collect a baseline scan to get the ti noise contributions.
The latter process could be a bit tricky if the protein doesn't pellet
during a high speed run. But for velocity data this works great.

Regards, -Borries