[Chimera-users] isosurface and blobs

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 12 09:35:52 PST 2015


Pardon me, that should be “Raffaele” not “Raphael” — sorry for the wrong spelling!
Elaine

> On Nov 12, 2015, at 9:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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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