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 My molecule disappeared from the GraphEnt EM projection map.

Electron microscopy data quite often have a problem with the estimated standard deviations of the amplitudes. Let me illustrate this with an example. The figure below compares the conventional and GraphEnt maps for a 8Å potential density projection of a large complex.

Figure: Problematic EM projection
Problematic EM run

It looks as if all low resolution information disappeared from the GraphEnt map, and this is more-or-less what has indeed have happened. The reason is shown in the next figure. The two graphs show on the same scale the distribution of log10(F/sigma(F)) versus resolution for the EM data (left graph) and of a typical X-ray crystallographic data set (right graph).

Figure: Distribution of F/sig(F)
F/sig(F) EM data

Whereas the X-ray data have a dynamic range extending approximately over two orders of magnitude, the EM data show a flat distribution with the (strong) low resolution terms having a value of F/sigma(F) not much different from the data in the highest resolution shell. Because I have seen this behaviour with almost all EM data sets that I have come across, I suspect that the problem is with the data processing programs used by the EM community.


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Next: About this document ... Up:  Pathology of GraphEnt calculations, Previous:  My native Patterson function   Contents
NMG, Nov 2002