[RASMB] XL/I absorbance problem

[John Philo]

Andrew,

I agree with Virgil that the slit assembly should be checked for smooth
motion and absence of dirt, but the fact that the incident data shows spikes
too suggests this may be a lamp (or lamp power supply) problem.

Inside the monochromator there is a partially-reflective surface that
directs about 10% of the light coming from the diffraction grating to the
"incident" detector. That detector measures the intensity of each flash and
is used to normalize each flash. Thus the graph of the incident intensity
tells you how constant your lamp output is from flash to flash. In principle
lamp variation is completely compensated, but I think in practice big
variations do add to the noise.

Since you see this when scanning an empty hole this is not the problem in
your case, but many users are not aware that one thing that can fool the
incident detector and cause extra noise is shiny surfaces on the cell. Those
blackened areas on the window holders and the screw rings really do need to
be black for optimal signal/noise and linearity! Shiny surfaces can
re-direct light back up into the monochromator and onto the incident
detector, causing false readings. So take a permanent black marker and fill
in the chips and scratches on the black anodization.

John

-----Original Message-----
From: rasmb-bounces at rasmb.bbri.org [mailto:rasmb-bounces at rasmb.bbri.org] On
Behalf Of Leech, AP
Sent: Wednesday, June 13, 2007 7:03 AM
To: rasmb at server1.bbri.org
Subject: [RASMB] XL/I absorbance problem


Hello all,

I'm not rally happy with the noise I'm seeing on my XL/I's absorbance scans,
and I have a few queries. I'd be grateful for any comments.

1. Noise seems excessive even on reasonable samples. Scans on an empty hole
at 280 nm give an overall flat profile (in A280) but peak noise is +/-0.05.
More peculiar is that the noise seems to be spikes, randomly distributed
along radius and not in the same place on successive scans. (For comparison
our old XL/A has peak to peak noise +/- 0.015 under the same conditions)

2. Using the request data intensity option, the overall profile has a dip at
r=6.3, but also numerous spikes, mostly upwards of about 600 counts on a
background of 6000. Cleaning if anything has made this worse. (Cf about 3000
for the XL/A which does need
cleaning.)

3. A wavelength intensity profile looks normal though the maxima are not
great (16000 at 230 nm after cleaning, 11000 before).

4. What does the "request data incident" option in the GUI do? For the XL/A
this produces very flat lines with some spikes upward or downward, of
constant size; for the XL/A reasonably flat lines with random noise
superimposed (4000 +/-100). As I don't know what this is measuring, I'm not
sure what to expect.

I'll try and post some graphs later.

Many thanks,

Andrew

-- 
Dr Andrew Leech                   *  Laboratory Manager
Technology Facility               *  Molecular Interactions Laboratory
Department of Biology (Area 15)   *  Tel   : +44 (0)1904 328723
University of York                *  Fax   : +44 (0)1904 328804
PO Box 373,  York  YO10 5YW       *  Email : apl3 at york.ac.uk
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