[Chimera-users] map sigma

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 5 09:46:14 PST 2020

Hi Dieter,
I changed the Subject line to this new subject.  

How to “get" sigma is still the same as discussed in that message: you would either divide by the std dev before or after subtracting the mean, depending on your definition of sigma, and the mean and std dev can be reported with the "Volume Mean, SD, RMS” tool or command “measure mapStats”

However, you can specify threshold directly using either of these definitions with the volume command “rmsLevel” and “sdLevel” options.  That will not change the values shown in the data histogram in Volume Viewer, it will merely do the calculation and set the thresholds accordingly.   Example:

volume #4 sdLevel 1.5

For description of these options, see:

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 4, 2020, at 10:15 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> Dear Elaine, thank you and please forgive me still another question: Was there any followup on this?
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html
> I am wondering how the sigma can be determined correctly from the level value in the Volume Viewer and the outputs from Tools > Volume Mean, SD, RMS and, eventually, from Measure Volume and Area.
> Is there now a way of getting the sigma directly?
> Thank you very much, bw Dieter

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