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
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: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html> I hope this helps, Elaine ---------- 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@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
That really helps! thanks a lot! Zhihai 发自我的 iPhone
在 2014年5月14日，0:26，Elaine Meng <meng@cgl.ucsf.edu> 写道：
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: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002651.html>
I hope this helps, Elaine ---------- 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@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
participants (3)
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Elaine Meng -
李智海 -
海Dee