[RASMB] Interference Optics - HELP!

[Lisa Joss]

Hello All,
We have recently purchased an XLI and I have some questions regarding 
the interference optics that I am hoping some of you can help me with. 
My problem is basically non-linearity of the scans, and correction of 
that non-linearity using a blank scan correction.

Firstly, when scanning an empty rotor hole the slope of the best fit 
line to the resulting data is about 0.2 finges/cm (well outside 
Beckman's specs of 0.04 fringes/cm). Scan's of an empty cell are 
comparable.  Beckman is not terribly concerned about this and will have 
a service rep align the camera to try and improve, they suggest that if 
I just do the appropriate blank scan subtraction everything will be OK 
(confidence that I do not share!).

Which brings me to my next, more troubling, concern - blank scan 
subtractions. Subtraction of a blank scan taken of the same empty rotor 
hole, empty cell or water cell does not always give me a flat baseline, 
particularly when I use the option of subtracting a previously saved 
scan. When dealing with only one cell the result is fine, however when I 
do several cells in one scan only the one whose baseline was scanned 
last is flat, all the rest have a significant deviation from zero. I 
think what's happening is that even though all cells have a blank file 
(blank.ipx) all the subtractions are using the last file scanned. We 
have version 4.5 of the data acquisition software and it doesn't have an 
option to select an actual scan so I'm assuming that it should just use 
whatever the last blank.ipx is for the relevant cell. I have tried 
deleting some of these blank files and the software is looking for them 
- apparently just not using them. Can anyone shed any light on this?

While I agree that I need not worry about this non-linearity for our 
g*(s) analysis, I am trying to get good equilibrium data for a system 
that we have to use interference for (buffer contains nucleotide) and I 
am sure this is causing a problem. Any suggestions or information would 
be appreciated.

Thanks

Lisa

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Lisa Joss                                                           
 (801) 585-3919
Postdoctoral Fellow                                           email: 
ljoss at biochem.utah.edu

UNIVERSITY OF UTAH
BIOCHEMISTRY
20 N 1900 E RM 211
SALT LAKE CITY UT 84132-3201


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