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
>>
>>
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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
>
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