[Chimera-users] volume of an ensemble

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 31 12:19:04 PDT 2012

Hi Andy,
Hmmm ... here is one approach that would give at least an estimate:

(a) use "molmap" command to simulate a density map from all of the docked structures collectively.  That would automatically open Volume Viewer and show a histogram with slider for setting contour level on that density map. For example, if the docked structures were all submodels of #1, command could be something like:

molmap #1 2 

(b) move contour level low enough so that all atoms of the original ensemble are enclosed in the isosurface.  Can show as mesh to see atoms inside.

(c) you can use Measure Volume and Area (under Tools... Volume Data) to report the contour surface enclosed volume and surface area.

Or if that makes several separate blobs and you want the measurements of a specific blob rather than all collectively, instead use Measure and Color Blobs (also under Tools... Volume Data).

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 Aug 31, 2012, at 11:57 AM, R. Andrew Byrd wrote:

> Dear Chimera Team,
> Is it possible to get the total volume that encompasses an ensemble of structures?
> For example, if a docking or structure calculation produces an ensemble of structures,
> can one calculate the volume that encompasses all the members of the ensemble?
> A docking calculation may have one component superimposable and the second component
> represent an ensemble, and it is that ensemble that I would I like a measure of the total
> volume.
> Thanks!
> Andy

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