[Chimera-users] isosurface and blobs

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 12 09:33:43 PST 2015

Hi Raphael,
Sorry no, there is no command (or even GUI tool, as far as I know) to count the number of blobs at a given contour level.

There is also no command to measure the area and volume of a specific blob.  There is only the “Measure and Color Blobs” GUI, since to specify each blob you have to pick it by mouseclick.  

Commands “measure area” and “measure volume” only measure the whole surface, that is, all of the blobs together. 
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 12, 2015, at 5:54 AM, Raffaele Raucci <raf.raucci at gmail.com> wrote:
> Hi all,
> I imported in chimera a map file with .cube extension.
> I was able to show isosurface after setting specific isovalue.
> Can you tell me if it is possible, by command line, count the number of different blobs displayed as isosurface?
> Is it also possible determine the area and volume of each blob?
> Thanks in advance,
> Raphael

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