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

Thomas Goddard goddard at cgl.ucsf.edu
Mon Nov 28 13:27:26 PST 2005

Hi Sabuj,

  Chimera currently has no capability to display standard deviation
values for volume data.  It would be useful if the volume viewer dialog
had an option to use sigma units.

  Could you tell me what crystallographers define "1 sigma" to be for
a density map?  Is it the root mean square density value over the entire

  For now here is a Chimera tool to report mean, root mean square, and
standard deviation values for a volume data set.


This archive contains a directory VolumeStatistics that you put in
your Chimera distribution in


or on the Mac in


Then when you start Chimera you will have a new menu entry

	Tools -> Volume Data -> Volume Statistics

that reports the values for the current volume viewer data set, printing
them in the Chimera reply log (menu entry Favorites / Reply Log).


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