[Chimera-users] threshold level problem

Elaine Meng meng at cgl.ucsf.edu
Tue May 13 09:26:52 PDT 2014

Hi Zhihai Li,
The values on the histogram and the threshold values are the numbers given directly in your density map file.  Sigma is the standard deviation, but exactly how to convert from the values in the map to sigma values depends on how it is defined.

There is a Chimera tool that will give you the mean (average), standard deviation, and RMS of your density map, but then you would need to use those values yourself to convert threshold values to sigma units or vice versa.  See this earlier post for details:

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

On May 13, 2014, at 5:48 AM, 李智海 <21620101152414 at stu.xmu.edu.cn> wrote:

> Hello,
> I am a freshman for Chimera, sorry for a possibly stupid question but i seem to be confused by the difference between threshold level in volume view and the sigma value that is used to contour the density map in some articles.
> please help me out!
> Thank you very much!
> Zhihai Li

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