[sharp-discuss] Combining MAD with native

[Derek Logan]

Dear all,

I would like some advice on how to combine MAD and native in SHARP.  
I've never done this before. I've tried following the instructions in  
the manual, with little success. Two scenarios are described there:

1) Use SeMet in the derivative and S-Met in the native
2) Use (Se-S)Met in the derivative and nothing in the native.

In both cases I use the peak wavelength of the MAD data set as  
reference. I have a set of 11 Se positions from a simple MAD  
refinement. The orthorhombic cell dimensions are 75.47  128.94   
175.98 for SeMet and 74.95  127.25  175.21 for native. The MAD data  
go to 2.8Å and native to 2.3Å. SCALEIT gives an isomorphous R-factor  
of 17%, which is maybe a bit on the high side for Se...

In scenario 1, if I let the occupancies of the S atoms in the native  
vary then they fluctuate wildly, as do the Se occupancies in the  
derivative. If I fix the S occupancies to 1.0 then nothing much  
happens to the Se occupancies, but the NISO_BGLO parameter for native  
goes up to 4.4 and the native contributes nothing to the phasing. Am  
I refining incorrectly or are the data just very non-isomorphous?  
There is after all a 1.7Å difference in the b dimension...

In scenario 2 I have not gotten very far because I have no idea what  
to put in as f' and f'' for a Se-S atom. Any suggestions?

I would like to know generally speaking what is the correct course of  
action for combining native with MAD and what experiences people have  
had in the past.

Thanks
Derek
--
Derek Logan             tel: +46 46 222 1443
Molecular Biophysics    fax: +46 46 222 4692
Lund University
Box 124, Lund, Sweden

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.globalphasing.com/pipermail/sharp-discuss/attachments/20070320/52fdb7b8/attachment.html