Re: [ccp4bb] anomalous signal of Mn and Ca ions

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CCP4bb <-- 2008 <-- February 2008 <-- 29 February 2008

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Subject: Re: anomalous signal of Mn and Ca ions
From: Stephen Graham stepheng {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-29

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Subject: Re: anomalous signal of Mn and Ca ions
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-02-29

Subject: Re: anomalous signal of Mn and Ca ions
From: Johan Turkenburg jpt {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-02-29

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.

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
>
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Dr. Johan P. Turkenburg X-ray facilities manager
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CCP4bb <-- 2008 <-- February 2008 <-- 29 February 2008

Previous message:
Subject: Re: anomalous signal of Mn and Ca ions
From: Stephen Graham stepheng {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-02-29

Next message:
Subject: Re: anomalous signal of Mn and Ca ions
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-02-29