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Re: [ccp4bb]: A SAD case...
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>
Just to make sure - Could you have different origins for the selenium positions and your model (and the maps calculated therefrom)?
greetings
Gottfried
>
> Dear all,
>
> Perhaps some of you have come across a situation similar to this: I have a fairly complete selenium MAD dataset (10 Se atoms in total), reduced and scaled with excellent statistics in P212121, with a decent anomalous signal. Shake-and-bake finds all 10 peaks, with I/sigma(I) between 15.0-5.0, using the peak wavelength as a SAS dataset. When I refine those peaks with MLPHARE against the entire MAD dataset, the statistics look very good: phasing power of 1.1 and R-Cullis of 0.85 across all resolution bins (for the refinement I am using the strategy outlined by Ian Tickle's tutorial). Only the real occupancies tend to a low value, 0.1, while the anomalous occupancies remain at 0.85. Density modification (solvent content of 50%) seems to improve the matter bringing the figure of merit from 0.36 to 0.55 (both RESOLVE and DM). Even better, the map is fairly interpretable, and RESOLVE can trace almost 500f the protein as a polyalanine model. But, when I inspect the fom-weigh!
te!
> d maps, all of the Se's are in the solvent!
>
> So, the question is: How is it possible this lack of density around the peaks if the figure of merit is 0.55, the phasing power 1.0-1.1 and the R-Cullis 0.85? Have I got to discard the Se positions calculated by Shake-and-Bake? Where could the error be? (As for the scripts I use to produce maps, they are pretty simple and had always worked, so it cannot be just that.)
>
> Any help would be highly appreciated!
>
> I have done the following patches:
> No
> Please send replies to the bulletin board.
--
Dr. Gottfried Palm
Ernst-Moritz-Arndt-Universität
Inst. f. Chemie und Biochemie
Abt. Biochemie I
Soldmannstr. 16
17489 Greifswald
Germany
Tel. +49(03834)-515241,515242 Fax. +49(03834)-864373
email palm@uni-greifswald.de