[RASMB] IF/vs. intensity scans

[Borries Demeler]

To follow the suggestions given earlier by others on this list, we ran
the empty cells in both intensity and interference mode.

The scans were scaled and plotted in the same plot. A magnification of 
one of the dark spaces between two channels is shown in a plot at:

http://www.biochem.uthscsa.edu/demeler/plot.gif

Several things become pretty clear from looking at this data:

1. Intensity scanning is the best way to determine the boundaries of a channel.

2. either the alignment of the centerpieces is poor or the centerpieces 
   are poorly cut, because there is a noticeable difference between the 
   positions of sample channel (black) and reference channel (red).

3. The extra peaks seen in the absorbance scans are optical artifacts
   presumably resulting from the overlapping of the boundaries of 
   reference and sample channels.

4. a similar effect is visible when looking at interference (shown in the 
   bottom of the plot (URL above). In that case the boundaries for both
   channels seems to be "averaged" out.

I gather that it will be difficult to reproducibly determine the bottom
position of each centerpiece channel - arghhh.  As Tom Laue pointed out,
this position is probably even sensitive to cell housing, which rotor
and which rotor hole is used, although I haven't confirmed this yet.

Any suggestions on how to keep the position constant from run to run 
or how to correct for these errors?

Thanks, -Borries