[Chimera-users] ses volume

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 21 09:45:54 PST 2006

The Voronoi volume is very different and not what you were asking  
about: it is the volume allotted to each atom when space is  
partitioned into chunks that each only contain one atom. Atoms on the  
surface will get infinite volumes since they don't have neighbors on  
all sides.

As Tom mentioned, the Measure Volume tool can be used to get the  
volume within the molecular surface in Chimera (Richards definition,  
thus the solvent-excluded surface).  It can also be used to calculate  
the volume enclosed by a Grasp surface, which can be a solvent- 
accessible surface, but such a surface must be created by an outside  
program (DelPhi or Grasp; Chimera does not generate these).  My  
understanding is that a Grasp surface might be either an SAS or SES  
depending on the parameters used to run the program.

On Mar 21, 2006, at 9:26 AM, Thomas Goddard wrote:

> Hi Charlie,
>   There are two tool in Chimera that can calculate volume enclosed  
> in a
> surface, menu entries
> 	Tools / Volume Data / Measure Volume
> 	Tools / Surface Binding & Analysis / Surface Area & Volume
> The first one allows you to compute the volume enclosed in the solvent
> excluded surface.  Just open your PDB model.  Use menu entry Actions /
> Surface / show.  That shows the solvent excluded surface.  Then use  
> the
> above Measure Volume tool to get the enclosed volume.
>   I don't know of a way to get the volume within the solvent  
> accessible
> surface (which will be larger) because Chimera does not have a way to
> compute that surface.
>   The second tool above can compute the Voronoi volume by sending  
> the PDB
> model to a web server
> 	http://molbio.info.nih.gov/structbio/basic.html
> I don't know the definition of that volume, but I assume it is neither
> the volume for solvent accessible nor solvent excluded surfaces.  The
> paper that defines it is referenced in the Chimera manual if you are
> interested:
> 	http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ 
> surfvol.html
>   Tom
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Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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