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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
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>>>
>>
>>
>>
>> -- 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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