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Subject:

Re: anomalous signal of Mn and Ca ions

From:

"Nave, C (Colin)" <[log in to unmask]>

Reply-To:

Nave, C (Colin)

Date:

Sat, 1 Mar 2008 10:44:37 -0000

Content-Type:

text/plain

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text/plain (97 lines)

Dear all
If you simply want to see if Ca and Mn are in your sample, you could
also use x-ray fluorescence excited by the x-rays on the beamline used
to collect the diffraction data. It doesn't need the energy set to be at
each absorption edge, it just has to be above the edges. One then sets
the fluorescence detector (used for wavelength setting in MAD
experiments) to MCA mode, giving a spectrum showing the characteristic
lines for each element present. 

I believe the PIXIE technique has certain advantages. However it is not
available on the beamlines used to collect the data.

Of course, I think the question related to whether specific peaks in a
map were Mn or Ca. Then, as stated before, diffraction data collection
on either side of the Mn edge should reveal all, with good data of
sufficient resolution.

The x-ray fluorescence technique was used at the SSRL to reveal details
of the Archimedes Palimsest. This showed there were in fact two geniuses
coming from Greece -  not just Tassos.

Cheers
   Colin



-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Anastassis Perrakis
Sent: 29 February 2008 10:06
To: [log in to unmask]
Subject: Re: [ccp4bb] anomalous signal of Mn and Ca ions

On Feb 29, 2008, at 10:29, Johan Turkenburg wrote:

> Hi,
>
> You need to firstly check that you did the map calculation correctly, 
> see comments below:
>
> Sun Tang wrote:
>> Dear All,
>>  In my structures, I want to assign Mn or Ca ions for some densities.

>> But when I did not have  anomalous density in CCP4i. I am not sure 
>> whether I was correct. The following was what I did:
>>  I processed the data with HKL2000 and select anomalous signal in 
>> scaling. In CCP4i, I selected "Run FFT-Creat Map" in the "Map& Mask 
>> Utilities".
>
> What labels did you assign, and did you select 'anomalous map'?  
> This is crucial, as the protein (model) phase needs to be shifted by 
> 90 degrees, and this is done 'automatically' by FFT when you ask for 
> an anomalous map. Certainly with data of sufficient quality collected 
> on a home source with Cu radiation anomalous maps may well show up 
> such ions.
>

Exactly! Thats the most important bit to get right.

Another comment is that if you want to be sure about the nature of the
ions, you might want to try PIXE.

http://www.ee.surrey.ac.uk/IBC/index.php?target=13:68

I think all other suggestions are of course valid, but, without being
sure, the X-ray suggestions I see, need high resolution data ? PIXE is a
more direct method if it works well for your sample.

	A.


> I select "O format to cover asymmetric unit" and "Plot
>> section on Z axis from 0 to 1 in steps on 10". All others were by  
>> default values. I display in ono10.
>>  I collected the data at the wavelength of 1 A. Do I need to  
>> adjust the wavelength to maximize the anomalous signal from Mn or Ca?
>>  Any ideas and suggestions are greatly appreciated!
>>  Sun Tang
>> ---------------------------------------------------------------------

>> ---
>> Never miss a thing. Make Yahoo your homepage. <http:// 
>> us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs>
>
> -- 
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Dr. Johan P. Turkenburg                     X-ray facilities manager
> York Structural Biology Laboratory	
> University of York                          Phone (+) 44 1904 328251
> York YO10 5DD   UK                          Fax   (+) 44 1904 328266
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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