That seems the right procedure.
I presume the two crystals have similar cell, etc?
What is the Riso plot from scaleit look like - if it is 55% + then there
is no isomorphism, but if it is < 30% then the map should be reasonable.
which phase did you use for the map calculation?
Eleanor
intekhab alam wrote:
> Hi Folks
> I have a query regarding the difference map between the two structures
> ligand bound data (2.5A) and native (2.8A).
> I tried to calculate the fourier difference map between two data sets ligand
> bound- native.
> The protocol in CCP4 that i used is as:
> 1.merge the mtz file of native nad ligand bound using cad
> 2. scaling this combine file with scaleit program followed by map generation
> uisng fft.
>
> I got the map but i did not find the fu;ll map of the ligand,i can only see
> small density nera the ligand binding site at 5 sigma level.
> I have calculated omit map that cleraly showed the ligand.
> why is such discrepency in the two cases, is there is something missing from
> the calculation. kindly help me out.
>
> Thanks and regards
> Intekhab alam
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