[Chimera-users] volume of an ensemble

R. Andrew Byrd byrdra at mail.nih.gov
Fri Aug 31 13:50:53 PDT 2012

Thanks Elaine...this is good enough!

At 03:19 PM 8/31/2012, you wrote:
>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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