[RASMB] Looking for help with the XL-A optics

Mon Nov 28 11:32:33 PST 2011

Osman,

I agree with Bo and Andrew that a damaged monochromator could cause both
symptoms, and that is a serious problem. However if perhaps you instead have
two different problems things might not be quite so serious.

The radial intensity variation could easily be explained by a dirty face on
the photomultiplier tube, with more dirt at lower radii. That is especially
true since those scans you sent were at 230 nm, where the absorbance of any
contaminant will likely be higher. You could for example get deposition of
diffusion pump oil on the PMT if the vacuum was released before the
diffusion pump had cooled.

That however would clearly not explain the wavelength calibration issue. If
that is a separate problem from the other, one possible cause would be that
the monochromator was not seated properly (red screw ring not tightened
sufficiently, or it is binding due to cross-threading or some dirt in the
threads). Another would be that you have somehow lost the wavelength
calibration information that was stored on the hard drive of the data
acquisition computer. This would happen, for example, if you swapped
computers or had to restore the hard drive to its original condition. If
this latter hypothesis were true then you have also lost the radial
calibration so any data acquired would likely be useless.

Also FYI for diagnostic purposes it is better to scan an empty HOLE in the
rotor rather than an empty CELL. For a 4-hole rotor put a cell in hole 2 to
keep the rotor balanced, but leave holes 1 and 3 empty and scan one of those
empty holes. At low rotor speeds the unbalanced stress due to the empty
holes is not a problem.

John

-----Original Message-----
From: rasmb-bounces at rasmb.bbri.org [mailto:rasmb-bounces at rasmb.bbri.org] On
Behalf Of Leech, AP
Sent: Monday, November 28, 2011 3:05 AM
To: Osman Bakr
Cc: rasmb at server1.bbri.org
Subject: Re: [RASMB] Looking for help with the XL-A optics

Hello Osman,

I would also suspect the monochromator. Could it have been dropped or
accidentally damaged?

You may have done this already, but if not I would get someone to shine a
torch into the exit slit of the monochromator assembly, while you push the
actuator rod in the plug part (use a small plastic stick or similar). You
should be able to see the diffracted light coming through and tell if there
is any obstruction or if the actuator is not moving smoothly. You can also
see if the 400 nm filter is out of position.

I hope this is helpful,

Best regards,

Andrew

On 28/11/2011 00:41, Borries Demeler wrote:
> Dear Osman,
>
> I agree that the radial intensity variation is much greater than it 
> should be. Also, the maximum emission intensity should be at 230 nm (+/-
1-2 nm).
>
> There are a couple of issues you should look at:
>
> 1. I would ask Beckman to send you a different monochromator that has 
> been verified to work well in a different instrument. There may be a 
> flaw with yours that causes the wrong wavelength to be set.
>
> 2. check other components in your optical path that may be obstructing 
> the light path. They include the slit assembly. Be very careful when 
> you clean the slit not to damage the film. Also clean the lens in the slit
assembly.
>
> You should be able to get this to work by yourself, but let me know if 
> you need help with instructions to clean the slit assembly. We can 
> probably guide you over skype how to do this.
>
> Regards, -borries
>
>>
>> Dear RASMB subscribers,
>>
>> We recently noticed that the intensity scans taken by our XL-A show 
>> extreme radial dependence. Furthermore, we discovered that our lamp 
>> was exhibiting intensity peaks significantly shifted from their supposed
wavelengths.
>>
>> Below are radial scans taken for empty holes and the counterbalance, 
>> and also a wavelength-intensity scan taken at 6.5 cm:
>>
>> http://dl.dropbox.com/u/10119274/reanalyticalultracentrifugexla.zip
>>
>>
>> We tried cleaning the lamp and adjusting its alignment, but that did 
>> not help.
>>
>> We are located in Saudi Arabia, and the local distributor does not 
>> have the expertise to deal with an AUC. We contacted Beckman in 
>> Europe for help, but they are being much slower in their response  
>> than I had hoped.  Having the AUC up and running again is of critical 
>> importance to the users at my university (KAUST), since it is currently
the only AUC in Saudi Arabia.
>> Therefore, the university's priority is to get it fixed in the 
>> shortest time frame possible.
>>
>> If you or someone you know can resolve this problem, we'll be more 
>> than happy to: a) pay a consulting fee (if the problem can be 
>> resolved by remotely directing us); or b) pay for a round trip plane 
>> ticket, plus lodging and a consulting fee, if the problem can only be 
>> resolved by on-site service.
>>
>>
>> Please send your inquiries or suggestions directly to me at 
>> osman.bakr at kaust.edu.sa
>>
>>
>>
>> Regards.
>>
>>
>> -Osman
>>
>>
>>
>>
>>
>>
>>
>> --
>> Osman Bakr
>> Assistant Professor
>> Materials Science and Engineering
>> King Abdullah University of Science and Technology (KAUST) Building 
>> 3, Room # 3236 Thuwal 23955-6900 Saudi Arabia
>> Tel: +96628084439
>> http://www.kaust.edu.sa/academics/faculty/bakr.html<http://www.kaust.
>> edu.sa/academics/faculty/bakr.html>
>>
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-- 
Dr Andrew Leech                   *  Laboratory Head
Technology Facility               *  Molecular Interactions Laboratory
Department of Biology (Area 15)   *  Tel   : +44 (0)1904 328723
University of York                *  Fax   : +44 (0)1904 328804
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