estimaded standard deviation (sigma levels) for electron densities in volume viewer
Hi,
Is it possible to specify the estimated standard deviation (sigma level) for electron densities in the volume viewer? Currently, I have to eyeball the distribution of the volume data and place the bar accordingly.
Thanks, Sabuj Pattanayek
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 map?
For now here is a Chimera tool to report mean, root mean square, and standard deviation values for a volume data set.
http://www.cgl.ucsf.edu/home/goddard/temp/volumestats.tar
This archive contains a directory VolumeStatistics that you put in your Chimera distribution in
chimera/share
or on the Mac in
Chimera.app/Contents/Resources/share
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).
Tom
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.
Tom
participants (2)
-
Pattanayek, Sabuj -
Thomas Goddard