[Chimera-users] (no subject)

Tom Goddard goddard at cgl.ucsf.edu
Tue Jul 6 11:13:41 PDT 2010

Hi Maria,

   Chimera shows the volume data as an "isosurface" meaning all points 
on the surface are at a specific map value.  That map value is called 
"level" in the volume viewer dialog.  The values in a map (volume data 
file) determined by electron microscopy are often not normalized in any 
way -- useful values could be 10000 or 0.1 depending on the map.  For 
x-ray maps it is common to normalize so that standard deviation over the 
unit cell is 1.0.  In EM there no unit cell so the standard deviation 
would depend on how big a box surrounded the virus density -- so this is 
not as useful a normalization.  There is no standard accepted EM map 
normalization that I know of.  If you knew the expected volume occupied 
by the structure you could set a contour level so that the surface 
encloses that volume.  Here's an explanation of how to do that in Chimera


More often you just visually choose a level that you believe gives a 
surface matching the envelope of the proteins in the structure.  The map 
mean, standard deviation and root mean square value can be calculated 
with menu entry

     Tools / Volume Data / Volume Mean, SD, RMS


> Dear Chimera users,
> I'm using Chimera to inspect my calculated density maps of viruses. In
> order to compare different tree d reconstructions I would like to know
> what the 'Level' value in Volume Viewer dialog means. At present I'm using
> the level value 1 but I'm not sure if this is correct.
> Could you please give me some advice how to define the right contouring
> threshold to present my data in order to inspect it?
> Thank you for your help,
> Maria L.

More information about the Chimera-users mailing list