[Chimera-users] isosurface and blobs

Tom Goddard goddard at sonic.net
Thu Nov 12 11:44:23 PST 2015


You can convert a map surface to one where each connected blob is a separate surface piece, then measure their area and volume using the following commands

open emdbID:1080
sop split #0 model #5
measure volume #5
measure area #5
close #5

with output to the Reply Log (in Favorites menu) that looks like:

emd_1080.map split ? 1:  volume = 2389
emd_1080.map split ? 3:  volume = 73628
emd_1080.map split ? 2:  volume = 2425.3
emd_1080.map split ? 9:  volume = 4.008
emd_1080.map split ? 4:  volume = 2417.6
…
emd_1080.map split ? 1:  area = 1403.7
emd_1080.map split ? 3:  area = 43120
emd_1080.map split ? 2:  area = 1431.9
emd_1080.map split ? 9:  area = 16.329
emd_1080.map split ? 4:  area = 1463.1

The blobs are number (82 in this example), but it seems they aren’t printed out in order — but you can count the lines when you process this data to see how many blobs there are.  Volume and area are in Angstrom^3 and Angstrom^2 if the grid spacing of the map is given in Angstroms.

	Tom


> On Nov 12, 2015, at 9:33 AM, Elaine Meng  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 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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