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