[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.  
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html>

Commands “measure area” and “measure volume” only measure the whole surface, that is, all of the blobs together. 
Best,
Elaine
----------
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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