[Chimera-users] calculation of volume

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 14 09:19:34 PDT 2008

Hi Navnit,
Sorry, I don't know of a way to calculate the van der Waals volume in  
Chimera.  You can see the VDW volume, of course, by simply displaying  
the atoms in the sphere representation, but that does not give the  
volume value.

In theory, you could get values closer to the VDW volume by  
calculating molecular surface with smaller and smaller probe radius.   
In practice, this tends to increase the number of surface calculation  
failures, and currently the smallest allowed probe radius value is 0.5  
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 14, 2008, at 7:01 AM, Navnit Kumar Mishra wrote:

> Hi Elaine;
> Thank you for so detailed description. I am interested in measuring  
> the compactness of the complex during the simulation, I think the  
> calculation of the ratio of molecular volume to van der waals volume  
> provides the compactness. I have tried the procedure as you  
> suggested to calculate the molecular volume, the value in replylog  
> file is in two digits precision, for these calculation can I get the  
> value in four digits precision. I am using latest chimera version  
> 1.2540. I can calculate the total van der waals volume using the van  
> der Waals radii for each atom excluding the hydrogen atoms. Is there  
> a way in chimera to calcualte the van der waals volume. I would be  
> thankful to you for any suggestions.
> with regards,
> navnit

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