[Chimera-users] calculation of volume

Tom Goddard goddard at cgl.ucsf.edu
Thu Aug 14 10:13:28 PDT 2008

Hi Navnit,

  Not sure what you mean by "vdw volume".  I guess you mean the volume 
within the vdw surface.  That's not just the sum of the spherical atom 
volumes since those atom spheres overlap, so the calculation is not trivial.

  Perhaps the following will serve as a useful measure of 
"compactness".  Divide the solvent excluded surface enclosed volume by 
the solvent excluded surface area.  This gives a value with units of 
distance, a kind of mean radius quantifying the curvature of the 
surface.  For a given volume a sphere will give the largest value, while 
a shape with many protrusions will give a smaller value.  The larger the 
value the more sphere-like (globular) the shape.


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