[Chimera-users] Measuring the volume enclosed by a complex

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 10 10:15:03 PST 2010

Hi Andy,
I can't tell whether you are starting with a density map or an atomic structure.  The short answer in either case is to show a surface, then measure the volume enclosed in the surface.  Volume enclosed in the whole surface model is calculated with "Measure Volume and Area" whereas if a single model has multiple blobs and you only want the volume inside one of the blobs, you would use "Measure and Color Blobs."  Those are both under "Tools... Volume Data" in the menu.

If it is an atomic structure, there are a few additional issues. 
(A) whether you want the proteins as separate surfaces or the complex as one big surface.  If one big surface,  it is necessary to put all the proteins in one model (can be done with "copy/combine" function in the Model Panel) and it may also be necessary to specify they should be grouped together using the "surfcat" command

(B) surface calculation parameters, whether you want to allow molecular surfaces to have inside bubbles.
If you do not want to include these bubbles in subsequent surface calculations, use the Preferences (under Favorites menu), New Surface category, turn off "show disjoint surfaces" and click Save.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 9, 2010, at 7:15 PM, Anindito Sen wrote:
> Dear All 
> This question may have been answered before but will be helpful if you can let me know - 
> How can I measure the volume enclosed by a protein complex.
> Thanks
> Andy

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