[Chimera-users] Work with Volumetric Data

Tom Goddard goddard at sonic.net
Mon Feb 25 10:46:46 PST 2013


Hi Lothar,

  You can measure surface area and enclosed volume using Chimera menu Tools / Volume Data / Measure Volume and Area or the "measure area" and "measure volume" commands.

	http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html

There is not a command to sum the map values inside a surface.  You would think that would be useful but because the scale and shift of the map values is often not calibrated to any standard the sum is often not useful.  Still if you want the sum I could add a "measure mapsum" command that would sum map values above a threshold level (i.e. inside a contour surface).

  The code to compute areas, volumes and sums is trivial.  But the data structures to represent the maps and surfaces are pretty complex. Here is the relevant Chimera code if you are interested.

	http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/_surface
	http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/VolumeData

  Tom


On Feb 25, 2013, at 7:12 AM, wrote:

> Hi,
> 
>  I am using Chimera to render electron density in gaussian cube files and it
> works well. I am wondering though whether it is possible to integrate the
> e-density inside the current volume as defined by the closed surface. If
> there are people with expertise in this field of volumetric data
> (processing), I would be interested in obtaining C or C++ libraries that
> provide functions to calculate volume, surface areas etc.
> 
> Thanks,
> 
>  Lothar
> 
> 
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