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CCP4BB  April 2013

CCP4BB April 2013

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Subject:

Re: Refinement with anomalous signal

From:

Tim Gruene <[log in to unmask]>

Reply-To:

Tim Gruene <[log in to unmask]>

Date:

Fri, 19 Apr 2013 14:06:31 +0200

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-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Dear Kavya,

one reason could be an incorrect script for running refmac, or a bug
in refmac, or, if the distance allows, that the two peaks really are
two different fully occupied atoms with a lesser anomalous signal than
expected.

Best,
Tim

On 04/19/2013 02:02 PM, Kavyashree Manjunath wrote:
> Sir,
> 
> Thank you Sir. I tried this once at the end in order to check the
> refinement statistics, R, Rfree and FOM showed improvement. but I
> encountered one problem. One of the a nomalous scatters which had
> double occupancies (which was confirmed by anomalous peak search)
> after the refinement of occupancy using "SAD data directly" it
> turned out that the sum of the refined occupancies of this atom was
> more than 1. Why is it so? What might have gone wrong here?
> 
> Regards Kavya
> 
>> Hi Kavya,
>> 
>> In my experience, if the SAD data are good, in addition to
>> helping with anomalous scatterer occupancy refinement the R
>> factors can be significantly improved as well. I would give it a
>> try. As far as the other options in refmac such as inclusion of
>> H-L coefficients or phase, FOM, I believe that direct refinement
>> against the SAD data is preferred.
>> 
>> Philip
>> 
>> 
>> On Fri, Apr 19, 2013 at 7:43 AM, Kavyashree Manjunath < 
>> [log in to unmask]> wrote:
>> 
>>> Dear users,
>>> 
>>> The native structure for a protein is available and there is a 
>>> ligand bound data. The crystallisation condition has anomalous 
>>> scattering metal ions (Cd). Both the data are scaled by
>>> separating anomalous pairs. So while refining a ligand bound
>>> data with a solution obtained using Molecular replacement, is
>>> it recommended to refine using "SAD data directly" in refmac so
>>> that the anomalous atoms can be occupancy refined?
>>> 
>>> Thanking you Regards Kavya
>>> 
>>> 
>>> -- This message has been scanned for viruses and dangerous
>>> content by MailScanner, and is believed to be clean.
>>> 
>> 
>> 
>> 
>> -- Philip D. Kiser, Pharm.D., Ph.D. Department of Pharmacology 
>> Case Western Reserve University 10900 Euclid Ave. Wood Building
>> Room 317 Cleveland, OH 44106 (216) 368-8794
>> 
>> -- This message has been scanned for viruses and dangerous
>> content by MailScanner, and is believed to be clean.
>> 
>> 
> 
> 
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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