[Chimera-users] estimaded standard deviation (sigma levels) for electron densities in volume viewer

Thomas Goddard goddard at cgl.ucsf.edu
Mon Nov 28 15:09:14 PST 2005

Hi Sabuj,

  When setting volume data threshold levels based on the appearance of
the volume viewer histogram it is important to know that the heights
of the histogram bars are the logarithm of the number grid points in
the density range (bin) represented by that histogram bar.  So if one
histogram bin contains 10 volume grid points and another contains
1000, then the larger one will be 3 times higher than the smaller (not
100 times higher).  So the bars for high density values appear much
taller than if they directly represented the number of density values.
It is done this way so useful information can be seen in the histogram
outside of the noise density range.


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