<html>
Lisa,<br>
<br>
the approach of realigning the camera is absolutely correct. If fringes
are tilted in empty holes, the camera has to be rotated; the image is
just projected upon the CCD chip with an azimuthe offset. And you need
not be concerned, subtracting a blank scan is an absolutely legitimate
approach to cure this problem as long as the camera has not been
aligned.<br>
<br>
BTW, aligning the camera is easy and you could easily do it yourself. The
camera need just be turned on its socket, but probably you would infringe
your warranty.<br>
<br>
So blank scans are OK but if the blank scanning does not work then this
is the actual problem. I think the blank scan option in Beckman software
is unfavorable, because I can not see the effect of the correction and
cannot undo it. As we *always* have to correct for fringe errors (as we
use sapphire windows) we do it another way.<br>
<br>
For each run, we acquire a "blank" scan at the beginning of the
experiment. It has turned out that blank corrections only work if
acquired in the same run. We do blank subtraction only if feasible and
use our own software for it. Often, we restrict b. s. to a range of
interest in order not to introduce errors elsewhere for the benefit of
removing them in one place. Sometimes, it is not possible to acquire a
blank scan due to instantaneous sedimentation. In such cases, we use a
statistical procedure, adding all scans so that the errors, always at the
same position, add up to a signifiant error profile that we
subtract.<br>
<br>
But if your fringes are just tilted, you can have it an easier way. Just
get the derivative of your data. Your tilt shows up as a vertical offset
in all scans. Subtract the average offset from all scans and reintegrate.
You need no integration constant as interference datasets always start
with zero.<br>
<br>
Hope this helps,<br>
Kristian<br>
<br>
At 20:21 16.03.2003 -0700, you wrote:<br>
<blockquote type=cite cite>Hello All,<br>
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. <br>
<br>
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!). <br>
<br>
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?<br>
<br>
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.<br>
<br>
Thanks <br>
<br>
Lisa<br>
<br>
<hr>
<font face="Helvetica, Helvetica" size=4>Lisa
Joss</font><font face="Helvetica, Helvetica">
(801) 585-3919</font><br>
<font face="Helvetica, Helvetica">Postdoctoral
Fellow
email:
<a href="mailto:ljoss@biochem.utah.edu">ljoss@biochem.utah.edu</a><br>
</font><br>
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