[Chimera-users] ses volume

Thomas Goddard goddard at cgl.ucsf.edu
Tue Mar 21 09:26:58 PST 2006

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


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



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