[Chimera-users] Sum of map values

Tom Goddard goddard at sonic.net
Thu Feb 28 18:44:48 PST 2013


Hi Lothar,

 I added a "measure mapSum" command

	measure mapSum #0 above 0.178 

--> emd_1776.map, level >= 0.178, npoints 33636: sum = 7327.1

It sums map values above a specified threshold.  If no threshold is specified it sums over the whole map.  Will be in tonight's Chimera daily builds.

	Tom


> Hi Tom,
> 
>  thanks, I appreciate your response. I will first try and see how it works in
> chimera. I am tempted to ask you to add the integration feature. Thanks also
> for the link with the code - I looked at it briefly but I fear that it might
> take me a bit too long to figure out how to use it despite the fact that it
> is very well written !
> 
> Thanks,
> 
>    Lothar

On Feb 25, 2013, at 10:46 AM, Tom Goddard  wrote:

> 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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>> 
> 




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