[Chimera-users] Volume thresholds in Chimera
goddard at cgl.ucsf.edu
Fri Jun 1 10:35:03 PDT 2007
Huang, Ren-Huai wrote:
> 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,
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).
> 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.
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