[Chimera-users] isosurface and blobs
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
sop split #0 model #5
measure volume #5
measure area #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.
> 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.
> 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 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,
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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