[Chimera-users] Volume thresholds in Chimera

[Tom Goddard]

Huang, Ren-Huai wrote:
> Hi, 
>
> Thanks for your help before. 
>
> Chimera runs smoothly in my Linux computer. It generates very nice images for
> EM reconstruction map. 
> Could you explain the concepts of thresholds of contour used in Volume
> histogram? What is the value mean? 
> Thanks very much in advance,
>
> Ren-Huai
>   
Thomas Goddard wrote:
> Hi Ren-Huai,
>
>   The map values shown in the Chimera volume viewer dialog are the 
> values that come from the file.  Typically the map files do not have 
> any meaningful normalization.  There is currently no facility for 
> instead showing values in standard deviation units.  Chimera also does 
> not report the mean.  These capabilities are on our requested features 
> list (entry #88).
    http://www.cgl.ucsf.edu/chimera/plans.html
>
>   The histogram shows the distribution of map data values.  The height 
> is the logarithm of the number of grid points with values in a small 
> value range.
>
>     Tom
>